A Streamlined DNA Tool for Global Identification of Heavily Exploited Coastal Shark Species (Genus Rhizoprionodon)
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{"title"=>"A streamlined dna tool for global identification of heavily exploited coastal shark species (genus rhizoprionodon)", "type"=>"journal", "authors"=>[{"first_name"=>"Danillo", "last_name"=>"Pinhal", "scopus_author_id"=>"12759866300"}, {"first_name"=>"Mahmood S.", "last_name"=>"Shivji", "scopus_author_id"=>"7003555559"}, {"first_name"=>"Pedro G.", "last_name"=>"Nachtigall", "scopus_author_id"=>"55178585300"}, {"first_name"=>"Demian D.", "last_name"=>"Chapman", "scopus_author_id"=>"7402278564"}, {"first_name"=>"Cesar", "last_name"=>"Martins", "scopus_author_id"=>"7201722502"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"22496864", "sgr"=>"84859514656", "doi"=>"10.1371/journal.pone.0034797", "scopus"=>"2-s2.0-84859514656", "pui"=>"364591239", "isbn"=>"19326203 (ISSN)", "issn"=>"19326203"}, "id"=>"92c06ee6-ee96-3681-8dc6-2b819610b85a", "abstract"=>"Obtaining accurate species-specific landings data is an essential step toward achieving sustainable shark fisheries. Globally distributed sharpnose sharks (genus Rhizoprionodon) exhibit life-history characteristics (rapid growth, early maturity, annual reproduction) that suggests that they could be fished in a sustainable manner assuming an investment in monitoring, assessment and careful management. However, obtaining species-specific landings data for sharpnose sharks is problematic because they are morphologically very similar to one another. Moreover, sharpnose sharks may also be confused with other small sharks (either small species or juveniles of large species) once they are processed (i.e., the head and fins are removed). Here we present a highly streamlined molecular genetics approach based on seven species-specific PCR primers in a multiplex format that can simultaneously discriminate body parts from the seven described sharpnose shark species commonly occurring in coastal fisheries worldwide. The species-specific primers are based on nucleotide sequence differences among species in the nuclear ribosomal internal transcribed spacer 2 locus (ITS2). This approach also distinguishes sharpnose sharks from a wide range of other sharks (52 species) and can therefore assist in the regulation of coastal shark fisheries around the world.", "link"=>"http://www.mendeley.com/research/streamlined-dna-tool-global-identification-heavily-exploited-coastal-shark-species-genus-rhizopriono", "reader_count"=>53, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>5, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>13, "Student > Postgraduate"=>4, "Student > Master"=>12, "Other"=>1, "Student > Bachelor"=>7, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>5, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>13, "Student > Postgraduate"=>4, "Student > Master"=>12, "Other"=>1, "Student > Bachelor"=>7, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>45, "Medicine and Dentistry"=>2, "Psychology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Psychology"=>{"Psychology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>45}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Colombia"=>1, "Canada"=>1, "Puerto Rico"=>1, "Sri Lanka"=>1, "Brazil"=>1, "United Arab Emirates"=>1}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/656400"], "description"=>"<p>Rlal: <i>Rhizoprionodon lalandei</i>; Rtay: <i>R. taylori</i>; Rolig: <i>R. oligolinx</i>; Rter: <i>R. terranovae</i>; Rlong: <i>R. longurio</i>; Rpor: <i>R. porosus</i>; Racut: <i>R. acutus</i>.</p>", "links"=>[], "tags"=>["primers", "designed", "sequences", "amplicon", "sizes"], "article_id"=>326883, "categories"=>["Biochemistry", "Inorganic Chemistry", "Genetics", "Ecology"], "users"=>["Danillo Pinhal", "Mahmood S. Shivji", "Pedro G. Nachtigall", "Demian D. Chapman", "Cesar Martins"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034797.t004", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Species_specific_primers_designed_along_with_their_sequences_and_expected_amplicon_sizes_for_each_species_/326883", "title"=>"Species-specific primers designed along with their sequences and expected amplicon sizes for each species.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-09 01:54:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/656310"], "description"=>"<p>Size of ITS2 locus of sharpnose sharks excluding 5.8S and 28S rRNA gene flanking regions.</p>", "links"=>[], "tags"=>["its2", "locus", "sharpnose", "sharks", "excluding", "28s", "rrna", "flanking"], "article_id"=>326789, "categories"=>["Biochemistry", "Inorganic Chemistry", "Genetics", "Ecology"], "users"=>["Danillo Pinhal", "Mahmood S. Shivji", "Pedro G. Nachtigall", "Demian D. Chapman", "Cesar Martins"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034797.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Size_of_ITS2_locus_of_sharpnose_sharks_excluding_5_8S_and_28S_rRNA_gene_flanking_regions_/326789", "title"=>"Size of ITS2 locus of sharpnose sharks excluding 5.8S and 28S rRNA gene flanking regions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-09 01:53:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/655922"], "description"=>"<p>Species geographical ranges were based on data available at Florida Museum of Natural History (<a href=\"http://www.flmnh.ufl.edu/fish/\" target=\"_blank\">http://www.flmnh.ufl.edu/fish/</a>) and Fishbase (<a href=\"http://www.fishbase.org/\" target=\"_blank\">http://www.fishbase.org/</a>) websites. World map in raw version was taken from wikipedia.</p>", "links"=>[], "tags"=>["oceanic", "sharpnose"], "article_id"=>326409, "categories"=>["Biochemistry", "Inorganic Chemistry", "Genetics", "Ecology"], "users"=>["Danillo Pinhal", "Mahmood S. Shivji", "Pedro G. Nachtigall", "Demian D. Chapman", "Cesar Martins"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034797.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Global_oceanic_distribution_of_sharpnose_sharks_/326409", "title"=>"Global oceanic distribution of sharpnose sharks.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-09 01:46:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/656112"], "description"=>"<p>Results of amplification reactions utilizing the triplex primer combination of two shark ITS2 universal primers and the <i>R. lalandei</i> species-specific primer Rlal293F (Lanes 1 to 7). Lane 1 shows the target species-specific (arrow) and positive control (arrowhead) amplicons. Lanes 2–7 show amplification products from non-target <i>Rhizoprionodon</i> species tested for Rlal293F primer cross-amplification: 2, <i>R. porosus</i>; 3, <i>R. terranovae</i>; 4, <i>R. acutus</i>; 5, <i>R. longurio</i>; 6, <i>R. oligolinx</i>; 7, <i>R. taylori</i>; 8, Negative control (no shark DNA in the PCR). Lanes labeled M contain the molecular size-standard 1 kb plus.</p>", "links"=>[], "tags"=>["primer", "amplication", "gel"], "article_id"=>326603, "categories"=>["Biochemistry", "Inorganic Chemistry", "Genetics", "Ecology"], "users"=>["Danillo Pinhal", "Mahmood S. Shivji", "Pedro G. Nachtigall", "Demian D. Chapman", "Cesar Martins"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034797.g004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Triplex_primer_amplication_gel_profile_/326603", "title"=>"Triplex primer amplication gel profile.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-09 01:50:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/656182"], "description"=>"<p>Results of amplification reactions utilizing the nine-primer nonaplex: two shark universal primers and all the seven species-specific primers. Lanes 1–7 show nonaplex-PCR amplification products of target <i>Rhizoprionodon</i> samples: 1- <i>R. acutus</i>; 2- <i>R. porosus</i>; 3- <i>R. longurio</i>; 4- <i>R. terranovae</i>; 5- <i>R. oligolinx</i>; 6- <i>R. taylori</i>; 7- <i>R. lalandei</i>. Lanes 8–17 show nonaplex-PCR amplification products from non-target species: 8- <i>Galeocerdo cuvier</i>; 9- <i>Negaprion acutidens</i>; 10- <i>Carcharhinus porosus</i>; 11- <i>Prionace glauca</i>; 12- <i>Isurus paucus</i>; 13- <i>Alopias superciliosus</i>; 14- <i>Squalus acantias</i>; 15- <i>Nebrius ferrugineus</i>; 16- <i>Squatina californica</i>; 17- <i>Hexanchus griseus</i>. Lines 8–11, Carcharhiniformes; Line 12, Orectolobiformes; Line 13, Squaliformes; Lines 14–15, Lamniformes; Line 16, Squatiformes; Line 17, Hexanchiformes; Line 18 is the negative control. Lanes labeled “M” contain the molecular size-standard 1kb plus. Faint non-specific bands likely correspond to pseudogenes or uncommon variant copies of ribosomal genes rarely amplified by universal and species-specific primers.</p>", "links"=>[], "tags"=>["primer", "amplification", "gel"], "article_id"=>326675, "categories"=>["Biochemistry", "Inorganic Chemistry", "Genetics", "Ecology"], "users"=>["Danillo Pinhal", "Mahmood S. Shivji", "Pedro G. Nachtigall", "Demian D. Chapman", "Cesar Martins"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034797.g005", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nonaplex_primer_amplification_gel_profile_/326675", "title"=>"Nonaplex primer amplification gel profile.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-09 01:51:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/656356"], "description"=>"<p>N/C: intra-specific genetic distances not calculated since only one animal sequenced.</p>", "links"=>[], "tags"=>["distances", "sharpnose", "sharks", "calculated", "pairwise", "tamura-nei", "its2"], "article_id"=>326837, "categories"=>["Biochemistry", "Inorganic Chemistry", "Genetics", "Ecology"], "users"=>["Danillo Pinhal", "Mahmood S. Shivji", "Pedro G. Nachtigall", "Demian D. Chapman", "Cesar Martins"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034797.t003", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_distances_within_and_between_sharpnose_sharks_calculated_as_pairwise_Tamura_Nei_for_the_nuclear_ITS2_locus_/326837", "title"=>"Genetic distances within and between sharpnose sharks calculated as pairwise Tamura-Nei for the nuclear ITS2 locus.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-09 01:53:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/656258"], "description"=>"<p>Inventory of sharpnose sharks showing the number of individuals investigated by species and their geographic ocean basin origins.</p>", "links"=>[], "tags"=>["sharpnose", "sharks", "individuals", "investigated", "geographic", "basin"], "article_id"=>326742, "categories"=>["Biochemistry", "Inorganic Chemistry", "Genetics", "Ecology"], "users"=>["Danillo Pinhal", "Mahmood S. Shivji", "Pedro G. Nachtigall", "Demian D. Chapman", "Cesar Martins"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034797.t001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Inventory_of_sharpnose_sharks_showing_the_number_of_individuals_investigated_by_species_and_their_geographic_ocean_basin_origins_/326742", "title"=>"Inventory of sharpnose sharks showing the number of individuals investigated by species and their geographic ocean basin origins.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-09 01:52:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/338560"], "description"=>"<div><p>Obtaining accurate species-specific landings data is an essential step toward achieving sustainable shark fisheries. Globally distributed sharpnose sharks (genus <em>Rhizoprionodon</em>) exhibit life-history characteristics (rapid growth, early maturity, annual reproduction) that suggests that they could be fished in a sustainable manner assuming an investment in monitoring, assessment and careful management. However, obtaining species-specific landings data for sharpnose sharks is problematic because they are morphologically very similar to one another. Moreover, sharpnose sharks may also be confused with other small sharks (either small species or juveniles of large species) once they are processed (i.e., the head and fins are removed). Here we present a highly streamlined molecular genetics approach based on seven species-specific PCR primers in a multiplex format that can simultaneously discriminate body parts from the seven described sharpnose shark species commonly occurring in coastal fisheries worldwide. The species-specific primers are based on nucleotide sequence differences among species in the nuclear ribosomal internal transcribed spacer 2 locus (ITS2). This approach also distinguishes sharpnose sharks from a wide range of other sharks (52 species) and can therefore assist in the regulation of coastal shark fisheries around the world.</p> </div>", "links"=>[], "tags"=>["streamlined", "dna", "exploited"], "article_id"=>126904, "categories"=>["Biochemistry", "Inorganic Chemistry", "Genetics", "Ecology"], "users"=>["Danillo Pinhal", "Mahmood S. Shivji", "Pedro G. Nachtigall", "Demian D. Chapman", "Cesar Martins"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034797", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Streamlined_DNA_Tool_for_Global_Identification_of_Heavily_Exploited_Coastal_Shark_Species_Genus_Rhizoprionodon_/126904", "title"=>"A Streamlined DNA Tool for Global Identification of Heavily Exploited Coastal Shark Species (Genus <em>Rhizoprionodon</em>)", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-09 01:55:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/656002"], "description"=>"<p>Representation of the shark nuclear 5.8S and 28S ribosomal RNA genes and ITS2 locus showing relative annealing sites and orientation of the shark universal ITS2 primers (Fish 5.8SF and 28SR indicated by gray irregular pentagons). The Brazilian sharpnose (<i>R. lalandei</i>) Rlal293F primer is an example of a species-specific primer used in this study and is shown as a dark gray irregular pentagon. Also represented are the positive control and species-specific amplicons expected to be produced using this combination of three primers when tested against the target species, <i>R.lalandei</i>, DNA (Figure adapted from Shivji et al. 2002).</p>", "links"=>[], "tags"=>["its2", "species-diagnostic"], "article_id"=>326489, "categories"=>["Biochemistry", "Inorganic Chemistry", "Genetics", "Ecology"], "users"=>["Danillo Pinhal", "Mahmood S. Shivji", "Pedro G. Nachtigall", "Demian D. Chapman", "Cesar Martins"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034797.g002", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Triplex_scheme_of_ITS2_species_diagnostic_primers_/326489", "title"=>"Triplex scheme of ITS2 species-diagnostic primers.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-09 01:48:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/656065"], "description"=>"<p>Representation of the shark nuclear 5.8S and 28S ribosomal RNA genes and ITS2 locus showing relative annealing sites and orientation of primers used in the nonaplex-PCR assay. Shark universal primers (Fish 5.8SF and Fish 28SR) are shown as gray irregular pentagons, while the seven sharpnose species-specific primers are shown by dark gray irregular pentagons. Rlal: <i>Rhizoprionodon lalandei</i>; Rtay: <i>R. taylori</i>; Rolig: <i>R. oligolinx</i>; Rter: <i>R. terranovae</i>; Rlong: <i>R. longurio</i>; Rpor: <i>R. porosus</i>; Racut: <i>R. acutus</i>.</p>", "links"=>[], "tags"=>["its2", "species-diagnostic"], "article_id"=>326554, "categories"=>["Biochemistry", "Inorganic Chemistry", "Genetics", "Ecology"], "users"=>["Danillo Pinhal", "Mahmood S. Shivji", "Pedro G. Nachtigall", "Demian D. Chapman", "Cesar Martins"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034797.g003", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nonaplex_scheme_of_ITS2_species_diagnostic_primers_/326554", "title"=>"Nonaplex scheme of ITS2 species-diagnostic primers.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-09 01:49:14"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2013", "month"=>"10"}
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  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"5"}
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  • {"unique-ip"=>"3", "full-text"=>"6", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"3"}
  • {"unique-ip"=>"3", "full-text"=>"5", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"2"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"8"}
  • {"unique-ip"=>"8", "full-text"=>"8", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"9"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"10"}
  • {"unique-ip"=>"5", "full-text"=>"2", "pdf"=>"7", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"7"}
  • {"unique-ip"=>"8", "full-text"=>"6", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"8"}
  • {"unique-ip"=>"8", "full-text"=>"4", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2014", "month"=>"9"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"10"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"2"}
  • {"unique-ip"=>"11", "full-text"=>"10", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"11"}
  • {"unique-ip"=>"2", "full-text"=>"0", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"12"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"1"}
  • {"unique-ip"=>"10", "full-text"=>"6", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"1", "year"=>"2015", "month"=>"11"}
  • {"unique-ip"=>"6", "full-text"=>"7", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"12"}
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Relative Metric

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