Biodiversity of Mineral Nutrient and Trace Element Accumulation in Arabidopsis thaliana
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{"title"=>"Biodiversity of mineral nutrient and trace element accumulation in Arabidopsis thaliana", "type"=>"journal", "authors"=>[{"first_name"=>"Ivan", "last_name"=>"Baxter", "scopus_author_id"=>"15756855100"}, {"first_name"=>"Christian", "last_name"=>"Hermans", "scopus_author_id"=>"57039671700"}, {"first_name"=>"Brett", "last_name"=>"Lahner", "scopus_author_id"=>"12764166000"}, {"first_name"=>"Elena", "last_name"=>"Yakubova", "scopus_author_id"=>"15758451900"}, {"first_name"=>"Marina", "last_name"=>"Tikhonova", "scopus_author_id"=>"55353005600"}, {"first_name"=>"Nathalie", "last_name"=>"Verbruggen", "scopus_author_id"=>"6603790537"}, {"first_name"=>"Dai yin", "last_name"=>"Chao", "scopus_author_id"=>"8889884700"}, {"first_name"=>"David E.", "last_name"=>"Salt", "scopus_author_id"=>"7005540935"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84860484224", "scopus"=>"2-s2.0-84860484224", "doi"=>"10.1371/journal.pone.0035121", "pui"=>"364720847", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"22558123"}, "id"=>"4ca1d2b8-25f0-302a-b4f9-f4a537068492", "abstract"=>"In order to grow on soils that vary widely in chemical composition, plants have evolved mechanisms for regulating the elemental composition of their tissues to balance the mineral nutrient and trace element bioavailability in the soil with the requirements of the plant for growth and development. The biodiversity that exists within a species can be utilized to investigate how regulatory mechanisms of individual elements interact and to identify genes important for these processes. We analyzed the elemental composition (ionome) of a set of 96 wild accessions of the genetic model plant Arabidopsis thaliana grown in hydroponic culture and soil using inductively coupled plasma mass spectrometry (ICP-MS). The concentrations of 17-19 elements were analyzed in roots and leaves from plants grown hydroponically, and leaves and seeds from plants grown in artificial soil. Significant genetic effects were detected for almost every element analyzed. We observed very few correlations between the elemental composition of the leaves and either the roots or seeds. There were many pairs of elements that were significantly correlated with each other within a tissue, but almost none of these pairs were consistently correlated across tissues and growth conditions, a phenomenon observed in several previous studies. These results suggest that the ionome of a plant tissue is variable, yet tightly controlled by genes and gene × environment interactions. The dataset provides a valuable resource for mapping studies to identify genes regulating elemental accumulation. All of the ionomic data is available at www.ionomicshub.org.", "link"=>"http://www.mendeley.com/research/biodiversity-mineral-nutrient-trace-element-accumulation-arabidopsis-thaliana", "reader_count"=>81, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>6, "Researcher"=>24, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>30, "Student > Postgraduate"=>3, "Other"=>4, "Student > Master"=>2, "Student > Bachelor"=>5, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>6, "Researcher"=>24, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>30, "Student > Postgraduate"=>3, "Other"=>4, "Student > Master"=>2, "Student > Bachelor"=>5, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Engineering"=>1, "Environmental Science"=>4, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>64, "Medicine and Dentistry"=>1, "Arts and Humanities"=>1, "Chemistry"=>3, "Computer Science"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>3}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>64}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>4}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Argentina"=>1, "United States"=>3, "Mexico"=>1, "Slovenia"=>1, "France"=>1, "Spain"=>1, "French Polynesia"=>1}, "group_count"=>4}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/646100"], "description"=>"<p>Z-scores ([Line average – Control Average]/Control S.D.) compared to Col-0 in each tray for all instances where Wa-1 K (black triangle) or Fab-2 Zn (blue squares) were measured. Grey lines denote zscores of −2, 0, and 2.</p>", "links"=>[], "tags"=>["wa-1", "fab-2", "zn"], "article_id"=>316589, "categories"=>["Ecology", "Chemistry", "Genetics", "Plant Biology"], "users"=>["Ivan Baxter", "Christian Hermans", "Brett Lahner", "Elena Yakubova", "Marina Tikhonova", "Nathalie Verbruggen", "Dai-Yin Chao", "David E. Salt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035121.g006", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Z_score_values_of_Wa_1_for_K_and_Fab_2_for_Zn_across_the_ionomicshub_org_database_/316589", "title"=>"Z-score values of Wa-1 for K and Fab-2 for Zn across the ionomicshub.org database.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-27 01:49:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/645895"], "description"=>"<p>A–B are taken from Ghandilyan 2009, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035121#pone.0035121-Ghandilyan1\" target=\"_blank\">[26]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035121#pone-0035121-g005\" target=\"_blank\">Figure 5</a>. C is taken from Ghandilyan 2009, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035121#pone.0035121-Ghandilyan2\" target=\"_blank\">[27]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035121#pone-0035121-t002\" target=\"_blank\">Table 2</a>. D–H taken from Buescher et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035121#pone.0035121-Buescher1\" target=\"_blank\">[24] </a><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035121#pone-0035121-g001\" target=\"_blank\">Figure 1</a>. Only significant correlations (p<0.001 and R<sup>2</sup>>0.32) are displayed on each wheel. Positive correlations are denoted by solid lines, negative correlations are denoted by dashed lines. Thick lines indicate R<sup>2</sup>>0.5, thin lines indicate 0.322<0.5. Ions not measured in a given experiment are colored in grey.</p>", "links"=>[], "tags"=>["wheels", "correlations", "elements"], "article_id"=>316382, "categories"=>["Ecology", "Chemistry", "Genetics", "Plant Biology"], "users"=>["Ivan Baxter", "Christian Hermans", "Brett Lahner", "Elena Yakubova", "Marina Tikhonova", "Nathalie Verbruggen", "Dai-Yin Chao", "David E. Salt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035121.g004", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlations_wheels_showing_significant_correlations_between_elements_within_an_experiment_/316382", "title"=>"Correlations wheels showing significant correlations between elements within an experiment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-27 01:46:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/646275"], "description"=>"<p>Minimum (Min), maximum (Max), Max/Min (Ratio), mean and standard deviation (SD) values are calculated off the outlier removed, normalized line averages. Italics: The line factor was not significant in an ANOVA of a linear model for that element. Elements not measured in a given experiment are noted with an ‘NA’.</p>", "links"=>[], "tags"=>["hydroponic"], "article_id"=>316762, "categories"=>["Ecology", "Chemistry", "Genetics", "Plant Biology"], "users"=>["Ivan Baxter", "Christian Hermans", "Brett Lahner", "Elena Yakubova", "Marina Tikhonova", "Nathalie Verbruggen", "Dai-Yin Chao", "David E. Salt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035121.t001", "stats"=>{"downloads"=>3, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_Root_Hydroponic_and_Leaf_Hydroponic_Experiments_/316762", "title"=>"Summary of Root Hydroponic and Leaf Hydroponic Experiments.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-27 01:52:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/645785"], "description"=>"<p>A–F are from Prinzenberg et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035121#pone.0035121-Prinzenberg1\" target=\"_blank\">[17]</a>, with correlations calculated from the original data. G–J are taken from Ghandilyan 2009, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035121#pone.0035121-Ghandilyan2\" target=\"_blank\">[27]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035121#pone-0035121-t003\" target=\"_blank\">Table 3</a>. Only significant correlations (p<0.001 and R<sup>2</sup>>0.32) are displayed on each wheel. Positive correlations are denoted by solid lines, negative correlations are denoted by dashed lines. Thick lines indicate R<sup>2</sup>>0.5, thin lines indicate 0.322<0.5. Ions not measured in a given experiment are colored in grey.</p>", "links"=>[], "tags"=>["wheels", "correlations", "elements"], "article_id"=>316272, "categories"=>["Ecology", "Chemistry", "Genetics", "Plant Biology"], "users"=>["Ivan Baxter", "Christian Hermans", "Brett Lahner", "Elena Yakubova", "Marina Tikhonova", "Nathalie Verbruggen", "Dai-Yin Chao", "David E. Salt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035121.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlations_wheels_showing_significant_correlations_between_elements_within_an_experiment_/316272", "title"=>"Correlations wheels showing significant correlations between elements within an experiment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-27 01:44:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/645656"], "description"=>"<p>Correlations were calculated from line averages and only significant correlations (p<0.001 and R<sup>2</sup>>0.32) are displayed on each wheel. Positive correlations are denoted by solid lines, negative correlations are denoted by dashed lines. Thick lines indicate R<sup>2</sup>>0.5, thin lines indicate 0.322<0.5. Ions not measured in a given experiment are colored in grey.</p>", "links"=>[], "tags"=>["wheels", "correlations", "elements"], "article_id"=>316143, "categories"=>["Ecology", "Chemistry", "Genetics", "Plant Biology"], "users"=>["Ivan Baxter", "Christian Hermans", "Brett Lahner", "Elena Yakubova", "Marina Tikhonova", "Nathalie Verbruggen", "Dai-Yin Chao", "David E. Salt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035121.g002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlations_wheels_showing_significant_correlations_between_elements_within_an_experiment_/316143", "title"=>"Correlations wheels showing significant correlations between elements within an experiment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-27 01:42:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/332729", "https://ndownloader.figshare.com/files/332751", "https://ndownloader.figshare.com/files/332772", "https://ndownloader.figshare.com/files/332980", "https://ndownloader.figshare.com/files/333142", "https://ndownloader.figshare.com/files/333333", "https://ndownloader.figshare.com/files/333506", "https://ndownloader.figshare.com/files/333690", "https://ndownloader.figshare.com/files/333910"], "description"=>"<div><p>In order to grow on soils that vary widely in chemical composition, plants have evolved mechanisms for regulating the elemental composition of their tissues to balance the mineral nutrient and trace element bioavailability in the soil with the requirements of the plant for growth and development. The biodiversity that exists within a species can be utilized to investigate how regulatory mechanisms of individual elements interact and to identify genes important for these processes. We analyzed the elemental composition (ionome) of a set of 96 wild accessions of the genetic model plant <em>Arabidopsis thaliana</em> grown in hydroponic culture and soil using inductively coupled plasma mass spectrometry (ICP-MS). The concentrations of 17–19 elements were analyzed in roots and leaves from plants grown hydroponically, and leaves and seeds from plants grown in artificial soil. Significant genetic effects were detected for almost every element analyzed. We observed very few correlations between the elemental composition of the leaves and either the roots or seeds. There were many pairs of elements that were significantly correlated with each other within a tissue, but almost none of these pairs were consistently correlated across tissues and growth conditions, a phenomenon observed in several previous studies. These results suggest that the ionome of a plant tissue is variable, yet tightly controlled by genes and gene×environment interactions. The dataset provides a valuable resource for mapping studies to identify genes regulating elemental accumulation. All of the ionomic data is available at <a href=\"http://www.ionomicshub.org\">www.ionomicshub.org</a>.</p> </div>", "links"=>[], "tags"=>["biodiversity", "accumulation"], "article_id"=>125712, "categories"=>["Ecology", "Chemistry", "Genetics", "Cell Biology"], "users"=>["Ivan Baxter", "Christian Hermans", "Brett Lahner", "Elena Yakubova", "Marina Tikhonova", "Nathalie Verbruggen", "Dai-Yin Chao", "David E. Salt"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0035121.s001", "https://dx.doi.org/10.1371/journal.pone.0035121.s002", "https://dx.doi.org/10.1371/journal.pone.0035121.s003", "https://dx.doi.org/10.1371/journal.pone.0035121.s004", "https://dx.doi.org/10.1371/journal.pone.0035121.s005", "https://dx.doi.org/10.1371/journal.pone.0035121.s006", "https://dx.doi.org/10.1371/journal.pone.0035121.s007", "https://dx.doi.org/10.1371/journal.pone.0035121.s008", "https://dx.doi.org/10.1371/journal.pone.0035121.s009"], "stats"=>{"downloads"=>8, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Biodiversity_of_Mineral_Nutrient_and_Trace_Element_Accumulation_in_Arabidopsis_thaliana_/125712", "title"=>"Biodiversity of Mineral Nutrient and Trace Element Accumulation in <em>Arabidopsis thaliana</em>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-04-27 01:35:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/646200"], "description"=>"<p>Minimum (Min), maximum (Max), Max/Min (Ratio), mean and standard deviation (SD) values are calculated off the outlier removed, normalized line averages. Italics: The line factor was not significant in an ANOVA of a linear model for that element. Elements not measured in a given experiment are noted with an ‘NA’.</p>", "links"=>[], "tags"=>["genetics and genomics", "chemistry", "plant biology", "ecology"], "article_id"=>316686, "categories"=>["Ecology", "Chemistry", "Genetics", "Plant Biology"], "users"=>["Ivan Baxter", "Christian Hermans", "Brett Lahner", "Elena Yakubova", "Marina Tikhonova", "Nathalie Verbruggen", "Dai-Yin Chao", "David E. Salt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035121.t002", "stats"=>{"downloads"=>4, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_Soil_Leaf_1_and_Soil_Leaf_2_Experiments_/316686", "title"=>"Summary of Soil Leaf 1 and Soil Leaf 2 Experiments.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-27 01:51:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/646006"], "description"=>"<p>A–D from Sankaran et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035121#pone.0035121-Sankaran1\" target=\"_blank\">[30] </a><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035121#pone-0035121-t001\" target=\"_blank\">Tables 1</a> & <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035121#pone-0035121-t002\" target=\"_blank\">2</a> for the <i>Medicago Truncatula</i> Jemalong-6×DZA315.16 population. E–H from Klein et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035121#pone.0035121-Klein1\" target=\"_blank\">[28] </a><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035121#pone-0035121-t002\" target=\"_blank\">Table 2</a>. For the <i>Lotus Japonicus</i> Miyakojima MG-20×Gifu B-129 population. I–L from Ding et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035121#pone.0035121-Ding1\" target=\"_blank\">[25] </a><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035121#pone-0035121-t002\" target=\"_blank\">Table 2</a> for the <i>Brassica Napus</i> B104-2Eyou Changjia population. Mn from Liu et al. 29 table 2 for the Brassica Napus TapidorNingyou 7 population. Only significant correlations (p<0.001 and R<sup>2</sup>>0.32) are displayed on each wheel. Positive correlations are denoted by solid lines, negative correlations are denoted by dashed lines. Thick lines indicate R<sup>2</sup>>0.5, thin lines indicate 0.322<0.5. Ions not measured in a given experiment are colored in grey.</p>", "links"=>[], "tags"=>["wheels", "correlations", "elements"], "article_id"=>316491, "categories"=>["Ecology", "Chemistry", "Genetics", "Plant Biology"], "users"=>["Ivan Baxter", "Christian Hermans", "Brett Lahner", "Elena Yakubova", "Marina Tikhonova", "Nathalie Verbruggen", "Dai-Yin Chao", "David E. Salt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035121.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlations_wheels_showing_significant_correlations_between_elements_within_an_experiment_/316491", "title"=>"Correlations wheels showing significant correlations between elements within an experiment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-27 01:48:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/645575"], "description"=>"<p>BaySha Large, BaySha Small, CviLer and ColLer are RIL populations analyzed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035121#pone.0035121-Buescher1\" target=\"_blank\">[24]</a>.</p>", "links"=>[], "tags"=>["genetics and genomics", "chemistry", "plant biology", "ecology"], "article_id"=>316055, "categories"=>["Ecology", "Chemistry", "Genetics", "Plant Biology"], "users"=>["Ivan Baxter", "Christian Hermans", "Brett Lahner", "Elena Yakubova", "Marina Tikhonova", "Nathalie Verbruggen", "Dai-Yin Chao", "David E. Salt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035121.g001", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Coefficiant_of_variation_C_V_standard_deviation_line_averages_mean_line_averages_/316055", "title"=>"Coefficiant of variation (C.V., standard deviation(line averages)/mean( line averages)).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-27 01:40:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/646152"], "description"=>"<p>nm- not measured ns- non-significant.</p><p>HR to HL- Hydroponic Root to Hydroponic Leaf, HL to SL1- Hydroponic Leaf to Soil Leaf, HL to SL2- Hydroponic Leaf to Soil Leaf 2, SL1 to SL2- Soil Leaf 1 to Soil Leaf 2, SL1 to SS- Soil Leaf 1 to Soil Seed, SL2 to SS- Soil Leaf 2 to Soil Seed.</p>", "links"=>[], "tags"=>["correlations", "tissues"], "article_id"=>316641, "categories"=>["Ecology", "Chemistry", "Genetics", "Plant Biology"], "users"=>["Ivan Baxter", "Christian Hermans", "Brett Lahner", "Elena Yakubova", "Marina Tikhonova", "Nathalie Verbruggen", "Dai-Yin Chao", "David E. Salt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035121.t004", "stats"=>{"downloads"=>2, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Significant_p_lt_0_001_Correlations_between_Tissues_for_each_Element_/316641", "title"=>"Significant (p<0.001) Correlations between Tissues for each Element.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-27 01:50:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/646232"], "description"=>"<p>Minimum (Min), maximum (Max), Max/Min (Ratio), mean and standard deviation (SD) values are calculated off the outlier removed, normalized line averages. Italics: The line factor was not significant in an ANOVA of a linear model for that element. Elements not measured in a given experiment are noted with an ‘NA’.</p>", "links"=>[], "tags"=>["genetics and genomics", "chemistry", "plant biology", "ecology"], "article_id"=>316722, "categories"=>["Ecology", "Chemistry", "Genetics", "Plant Biology"], "users"=>["Ivan Baxter", "Christian Hermans", "Brett Lahner", "Elena Yakubova", "Marina Tikhonova", "Nathalie Verbruggen", "Dai-Yin Chao", "David E. Salt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035121.t003", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_Soil_Seed_Experiment_/316722", "title"=>"Summary of Soil Seed Experiment.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-27 01:52:02"}

PMC Usage Stats | Further Information

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Relative Metric

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