Trace Elemental Imaging of Rare Earth Elements Discriminates Tissues at Microscale in Flat Fossils
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{"title"=>"Trace elemental imaging of rare earth elements discriminates tissues at microscale in flat fossils", "type"=>"journal", "authors"=>[{"first_name"=>"Pierre", "last_name"=>"Gueriau", "scopus_author_id"=>"55325152200"}, {"first_name"=>"Cristian", "last_name"=>"Mocuta", "scopus_author_id"=>"6602114997"}, {"first_name"=>"Didier B.", "last_name"=>"Dutheil", "scopus_author_id"=>"6602537517"}, {"first_name"=>"Serge X.", "last_name"=>"Cohen", "scopus_author_id"=>"56302680400"}, {"first_name"=>"Dominique", "last_name"=>"Thiaudière", "scopus_author_id"=>"6603814242"}, {"first_name"=>"Sylvain", "last_name"=>"Charbonnier", "scopus_author_id"=>"13409819100"}, {"first_name"=>"Gaël", "last_name"=>"Clément", "scopus_author_id"=>"7102259794"}, {"first_name"=>"Loïc", "last_name"=>"Bertrand", "scopus_author_id"=>"23003351100"}, {"first_name"=>"Nour Eddine", "last_name"=>"Jalil", "scopus_author_id"=>"55903034300"}, {"first_name"=>"Abdelilah", "last_name"=>"Tourani", "scopus_author_id"=>"35610469000"}, {"first_name"=>"Fatima", "last_name"=>"Khaldoune", "scopus_author_id"=>"36520967300"}, {"first_name"=>"Paulo M.", "last_name"=>"Brito", "scopus_author_id"=>"7004032258"}, {"first_name"=>"Bouziane", "last_name"=>"Khalloufi", "scopus_author_id"=>"35756091100"}, {"first_name"=>"Hélène", "last_name"=>"Bourget", "scopus_author_id"=>"42761012900"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84900435302", "doi"=>"10.1371/journal.pone.0086946", "sgr"=>"84900435302", "pmid"=>"24489809", "issn"=>"19326203", "pui"=>"373070626"}, "id"=>"2c1ee5af-4e32-38e1-9e13-f4f657ee02e7", "abstract"=>"The interpretation of flattened fossils remains a major challenge due to compression of their complex anatomies during fossilization, making critical anatomical features invisible or hardly discernible. Key features are often hidden under greatly preserved decay prone tissues, or an unpreparable sedimentary matrix. A method offering access to such anatomical features is of paramount interest to resolve taxonomic affinities and to study fossils after a least possible invasive preparation. Unfortunately, the widely-used X-ray micro-computed tomography, for visualizing hidden or internal structures of a broad range of fossils, is generally inapplicable to flattened specimens, due to the very high differential absorbance in distinct directions. Here we show that synchrotron X-ray fluorescence spectral raster-scanning coupled to spectral decomposition or a much faster Kullback-Leibler divergence based statistical analysis provides microscale visualization of tissues. We imaged exceptionally well-preserved fossils from the Late Cretaceous without needing any prior delicate preparation. The contrasting elemental distributions greatly improved the discrimination of skeletal elements material from both the sedimentary matrix and fossilized soft tissues. Aside content in alkaline earth elements and phosphorus, a critical parameter for tissue discrimination is the distinct amounts of rare earth elements. Local quantification of rare earths may open new avenues for fossil description but also in paleoenvironmental and taphonomical studies.", "link"=>"http://www.mendeley.com/research/trace-elemental-imaging-rare-earth-elements-discriminates-tissues-microscale-flat-fossils", "reader_count"=>23, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Student > Doctoral Student"=>2, "Researcher"=>7, "Student > Ph. D. Student"=>3, "Student > Postgraduate"=>1, "Student > Master"=>2, "Other"=>1, "Student > Bachelor"=>2, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Student > Doctoral Student"=>2, "Researcher"=>7, "Student > Ph. D. Student"=>3, "Student > Postgraduate"=>1, "Student > Master"=>2, "Other"=>1, "Student > Bachelor"=>2, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Engineering"=>1, "Materials Science"=>3, "Agricultural and Biological Sciences"=>5, "Physics and Astronomy"=>1, "Chemistry"=>1, "Earth and Planetary Sciences"=>11}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Materials Science"=>{"Materials Science"=>3}, "Chemistry"=>{"Chemistry"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>11}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>5}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Italy"=>1, "France"=>1, "Switzerland"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1365717"], "description"=>"<p>(<i>A</i>) Optical photograph of a cross-section through the fourth somite of the shrimp. (<i>B</i>) Close-up from the pleuron located by the black square in <i>A</i>. (<i>C</i> and <i>D</i>) False color overlays of neodymium (red), yttrium (green) and iron (blue) distributions through a full spectral decomposition from <i>A</i> (scan step: 100×100 µm<sup>2</sup>, 13,578 pixels) and <i>B</i> (scan step: 5×5 µm<sup>2</sup>, 13,231 pixels) respectively. The black arrows in <i>A</i> and <i>C</i> localize the digestive tract. The unique scale bar represents 500 µm in <i>A</i> and <i>C</i>, 100 µm in <i>B</i> and <i>D</i>.</p>", "links"=>[], "tags"=>["Paleontology", "Invertebrate paleontology", "paleobiology", "paleoecology", "taphonomy", "Vertebrate paleontology", "Materials characterization", "microstructure", "statistics", "Statistical methods", "Electromagnetic radiation", "x-rays", "fossil", "tissues", "mhnm-kk-ot"], "article_id"=>917474, "categories"=>["Physics", "Mathematics", "Medicine"], "users"=>["Pierre Gueriau", "Cristian Mocuta", "Didier B. Dutheil", "Serge X. Cohen", "Dominique Thiaudière", "Sylvain Charbonnier", "Gaël Clément", "Loïc Bertrand"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0086946.g003", "stats"=>{"downloads"=>2, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Discrimination_among_fossil_tissues_within_the_shrimp_Cretapenaeus_berberus_MHNM_KK_OT_01a_/917474", "title"=>"Discrimination among fossil tissues within the shrimp <i>Cretapenaeus berberus</i> MHNM-KK-OT 01a.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-29 03:07:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1365721"], "description"=>"<p>(<i>A</i> and <i>B</i>) Images from the integration of counts in regions of interest corresponding to the energy domains of neodymium (<i>A</i>) and gadolinium (<i>B</i>). (<i>C</i> and <i>D</i>) Distributions of neodymium (<i>C</i>) and gadolinium (<i>D</i>) after spectral decomposition of their respective contribution to the full spectra. (<i>E</i>) Mean XRF spectrum (black line) and fit line (red) between 5 and 8 keV from the 9×9 pixels white square area in <i>A</i>, and contributions from iron K lines (orange), neodymium L lines (blue) and gadolinium L lines (green). Total mean XRF spectrum and fit line are given in <i>SI Appendix</i>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086946#pone.0086946.s003\" target=\"_blank\">Fig. S3</a>. The scale bar represents 5 mm.</p>", "links"=>[], "tags"=>["Paleontology", "Invertebrate paleontology", "paleobiology", "paleoecology", "taphonomy", "Vertebrate paleontology", "Materials characterization", "microstructure", "statistics", "Statistical methods", "Electromagnetic radiation", "x-rays", "images", "produced", "counts", "regions", "spectral", "decomposition", "spectra", "teleost", "mhnm-kk-ot"], "article_id"=>917478, "categories"=>["Physics", "Mathematics", "Medicine"], "users"=>["Pierre Gueriau", "Cristian Mocuta", "Didier B. Dutheil", "Serge X. Cohen", "Dominique Thiaudière", "Sylvain Charbonnier", "Gaël Clément", "Loïc Bertrand"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0086946.g004", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_images_produced_by_integration_of_counts_in_regions_of_interest_and_spectral_decomposition_of_the_full_spectra_from_the_new_teleost_fish_MHNM_KK_OT_03a_/917478", "title"=>"Comparison of images produced by integration of counts in regions of interest and spectral decomposition of the full spectra from the new teleost fish MHNM-KK-OT 03a.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-29 03:07:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1365722"], "description"=>"<p>(<i>A</i>–<i>D</i>) False color representations of the Kullback-Leibler divergence of spectral densities of each pixel from that of the pixel located at the center of the white circle, respectively characteristic of bone (<i>A</i>), muscle (<i>B</i>), rest of the body (<i>C</i>) and sedimentary matrix (<i>D</i>). The color scale goes from blue (for high similarity to the selected pixel) to red (high divergence) going through yellow. (<i>E</i>–<i>H</i>) Weighting maps for each of the selected pixels. White correspond to pixels that were ignored, grey to black are increasing weights from 0.8 to 1. (<i>I</i>) Measured spectral density (grey) and its denoised estimation (red) for the pixel characteristic of bone (<i>A</i> and <i>E</i>). (<i>J</i>–<i>L</i>) Pairwise comparisons of denoised estimates of the spectral densities for the pixels indicated on each figure: superposition of the estimated spectral densities (top) and log-ratio of the spectral densities (bottom, amplitude being the absolute log ratio, color at a given energy corresponding to the higher spectral density for this energy). Dots correspond respectively, going from low to high energy, to the L of erbium (7.811 keV), the L of ytterbium (8.402 keV) and K emission lines of strontium (14.165 keV). The scale bar represents 5 mm.</p>", "links"=>[], "tags"=>["Paleontology", "Invertebrate paleontology", "paleobiology", "paleoecology", "taphonomy", "Vertebrate paleontology", "Materials characterization", "microstructure", "statistics", "Statistical methods", "Electromagnetic radiation", "x-rays", "synchrotron", "xrf", "tissues", "teleost", "mhnm-kk-ot"], "article_id"=>917479, "categories"=>["Physics", "Mathematics", "Medicine"], "users"=>["Pierre Gueriau", "Cristian Mocuta", "Didier B. Dutheil", "Serge X. Cohen", "Dominique Thiaudière", "Sylvain Charbonnier", "Gaël Clément", "Loïc Bertrand"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0086946.g005", "stats"=>{"downloads"=>3, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Statistical_discrimination_of_synchrotron_XRF_data_from_distinct_tissues_in_the_characteristic_teleost_fish_MHNM_KK_OT_02_/917479", "title"=>"Statistical discrimination of synchrotron XRF data from distinct tissues in the characteristic teleost fish MHNM-KK-OT 02.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-29 03:07:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1365711"], "description"=>"<p>(<i>A</i>–<i>C</i>) Optical photographs of the specimen of the shrimp <i>Cretapenaeus berberus</i> MHNM-KK-OT 01a (<i>A</i>), the usual teleost fish MHNM-KK-OT 02 (<i>B</i>) and the newly identified teleost fish MHNM-KK-OT 03a (<i>C</i>). (<i>D</i>–<i>F</i>) False color overlays of elemental distributions reconstructed from a full spectral decomposition of the synchrotron raster-scanning data. (<i>D</i>) False color overlay of neodymium (red), yttrium (green) and iron (blue) distributions from the shrimp (scan step: 100×100 µm<sup>2</sup>, 26,751 pixels). (<i>E</i>) False color overlay of neodymium (red), strontium (green) and iron (blue) distributions from the characteristic teleost fish (scan step: 125×123 µm<sup>2</sup>, 21,120 pixels). (<i>F</i>) False color overlay of neodymium (red), yttrium (green) and iron (blue) distributions from the newly identified teleost fish (scan step: 100×100 µm<sup>2</sup>, 50,851 pixels). Images demonstrate the strong elemental contrast between fossil skeletal and soft tissues. The yellow and red squares in <i>C</i> indicate the two areas that were mapped at higher spatial resolution in Fig. 2. The scale bar is 5 mm and applies to all panels.</p>", "links"=>[], "tags"=>["Paleontology", "Invertebrate paleontology", "paleobiology", "paleoecology", "taphonomy", "Vertebrate paleontology", "Materials characterization", "microstructure", "statistics", "Statistical methods", "Electromagnetic radiation", "x-rays", "x-ray", "fluorescence", "major-to-trace", "elements", "fossils", "ot1"], "article_id"=>917468, "categories"=>["Physics", "Mathematics", "Medicine"], "users"=>["Pierre Gueriau", "Cristian Mocuta", "Didier B. Dutheil", "Serge X. Cohen", "Dominique Thiaudière", "Sylvain Charbonnier", "Gaël Clément", "Loïc Bertrand"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0086946.g001", "stats"=>{"downloads"=>3, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Synchrotron_X_ray_fluorescence_mapping_of_major_to_trace_elements_in_fossils_from_the_OT1_Lagerst_228_tte_/917468", "title"=>"Synchrotron X-ray fluorescence mapping of major-to-trace elements in fossils from the OT1 Lagerstätte.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-29 03:07:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1365713"], "description"=>"<p>(<i>A</i>) Close-up of its jaws from the red square in Fig. 1<i>B</i>. (<i>B</i>) Close-up on the area from the yellow square in Fig. 1<i>B</i>. (<i>C</i>–<i>D</i>) False color overlays of elemental distributions reconstructed from a full spectral decomposition of the synchrotron data. (<i>C</i>) False color overlay of phosphorous (red), yttrium (green) and potassium (blue) distributions from the jaws area <i>A</i>, allowing the visualization of hidden teeth (scan step: 10×10 µm<sup>2</sup>, 28,650 pixels). (<i>D</i>) False color overlay of neodymium (red), yttrium (green) and iron (blue) distributions from the area <i>B</i>, showing hidden fin rays back to the cleithrum (scan step: 5×5 µm<sup>2</sup>, 32,361 pixels). The unique scale bar represents 500 µm in <i>A</i> and <i>C</i>, 50 µm in <i>B</i> and <i>D</i>.</p>", "links"=>[], "tags"=>["Paleontology", "Invertebrate paleontology", "paleobiology", "paleoecology", "taphonomy", "Vertebrate paleontology", "Materials characterization", "microstructure", "statistics", "Statistical methods", "Electromagnetic radiation", "x-rays", "visualization", "indiscernible", "anatomical", "details", "teleost", "mhnm-kk-ot", "03a", "synchrotron", "xrf"], "article_id"=>917470, "categories"=>["Physics", "Mathematics", "Medicine"], "users"=>["Pierre Gueriau", "Cristian Mocuta", "Didier B. Dutheil", "Serge X. Cohen", "Dominique Thiaudière", "Sylvain Charbonnier", "Gaël Clément", "Loïc Bertrand"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0086946.g002", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Microscale_visualization_of_previously_indiscernible_anatomical_details_from_the_new_teleost_fish_MHNM_KK_OT_03a_using_synchrotron_XRF_mapping_/917470", "title"=>"Microscale visualization of previously indiscernible anatomical details from the new teleost fish MHNM-KK-OT 03a using synchrotron XRF mapping.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-29 03:07:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1365731", "https://ndownloader.figshare.com/files/1365732", "https://ndownloader.figshare.com/files/1365733", "https://ndownloader.figshare.com/files/1365734"], "description"=>"<div><p>The interpretation of flattened fossils remains a major challenge due to compression of their complex anatomies during fossilization, making critical anatomical features invisible or hardly discernible. Key features are often hidden under greatly preserved decay prone tissues, or an unpreparable sedimentary matrix. A method offering access to such anatomical features is of paramount interest to resolve taxonomic affinities and to study fossils after a least possible invasive preparation. Unfortunately, the widely-used X-ray micro-computed tomography, for visualizing hidden or internal structures of a broad range of fossils, is generally inapplicable to flattened specimens, due to the very high differential absorbance in distinct directions. Here we show that synchrotron X-ray fluorescence spectral raster-scanning coupled to spectral decomposition or a much faster Kullback-Leibler divergence based statistical analysis provides microscale visualization of tissues. We imaged exceptionally well-preserved fossils from the Late Cretaceous without needing any prior delicate preparation. The contrasting elemental distributions greatly improved the discrimination of skeletal elements material from both the sedimentary matrix and fossilized soft tissues. Aside content in alkaline earth elements and phosphorus, a critical parameter for tissue discrimination is the distinct amounts of rare earth elements. Local quantification of rare earths may open new avenues for fossil description but also in paleoenvironmental and taphonomical studies.</p></div>", "links"=>[], "tags"=>["Paleontology", "Invertebrate paleontology", "paleobiology", "paleoecology", "taphonomy", "Vertebrate paleontology", "Materials characterization", "microstructure", "statistics", "Statistical methods", "Electromagnetic radiation", "x-rays", "elemental", "imaging", "elements", "discriminates", "tissues", "microscale"], "article_id"=>917487, "categories"=>["Physics", "Mathematics", "Medicine"], "users"=>["Pierre Gueriau", "Cristian Mocuta", "Didier B. Dutheil", "Serge X. Cohen", "Dominique Thiaudière", "Sylvain Charbonnier", "Gaël Clément", "Loïc Bertrand"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0086946.s001", "https://dx.doi.org/10.1371/journal.pone.0086946.s002", "https://dx.doi.org/10.1371/journal.pone.0086946.s003", "https://dx.doi.org/10.1371/journal.pone.0086946.s004"], "stats"=>{"downloads"=>2, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Trace_Elemental_Imaging_of_Rare_Earth_Elements_Discriminates_Tissues_at_Microscale_in_Flat_Fossils_/917487", "title"=>"Trace Elemental Imaging of Rare Earth Elements Discriminates Tissues at Microscale in Flat Fossils", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-01-29 03:07:45"}

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