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FIGURE 1 in Virtual palaeontology: the effects of mineral composition and texture of fossil shell and hosting rock on the quality of X-ray microtomography (XMT) outcomes using Palaeozoic brachiopods
FIGURE 1. Thin section and cathodoluminescence (CL) photomicrographs: Timaniella harkeri (GSC26406) (1-4), Spiriferina sp. (BS-1) (5-8), Stenoscisma timorense (BS-2) (9-12), Cleiothyridina baracoodensis (ML32) (13-16) and Tylothyris transversa (TeP) (17-20). 1-2, transmitted light (TL) (1) and corresponding CL images (2) of nonluminescent shell and infilling sediment composed of fine sand grains. 3-4, TL (3) and CL (4) images of nonluminescent associated with partially luminescent shell in the cardinal area of dorsal valve. 5-8, TL (5, 7) and CL (6, 8) images of nonluminescent associated with partially luminescent shell and luminescent infilling cement. 9-12, TL (9, 11) and CL (10, 12) images of luminescent shell with thin silicified layers and recrystallization along inner wall of brachiopod shell. 13, plane-polarized light (PPL) image of the original infilling sediment composed of calcareous sands. 14, PPL image showing the section of infilling cement. 15-16, TL (15) and CL (16) images of slightly luminescent shell. 17, PPL image of infilling comprising lime mud, calcite cement and relatively large, radially arranged, siliceous crystals. 18-19, TL (18) and CL (19) images of nonluminescent associated with partially luminescent shell. 20, CL image showing the section of nonluminescent internal shell structure (spiralia) preserved within infilling (This structure is hardly recognized in the TL image). Abbreviations: bs, brachiopod shell; im, infilling material; sl, silicified layer; cc, calcite crystal; NL, nonluminescent; SL, slightly luminescent; L, luminescent.
Fig. 2 in Effect of tenthredinid leaf miner invasions on growth of Alaska white birch in Anchorage, Alaska, USA, and the interaction with biological control of amber-marked birch leaf miner
Fig. 2. Time series analysis of mean radial growth increments (mm) of Alaska white birch (Betula neoalaskana) in Anchorage, Alaska (n = 99) from 1984 to 2018: (1) pre-amber-marked birch leaf miner (Profenusa thomsoni) outbreak control period (1984–1995) (black dots); (2) amber-marked birch leaf miner outbreak period (1996–2007) (red dots); and (3) the amber-marked birch leaf miner suppression period due to biological control (2008–2018) (green dots). Time Series Mean = 1.7938, Std = 0.3843, N = 35, Zero Mean ADF (Augmented Dickey Fuller test) = −0.9887, Single ADF = −2.8315, Trend ADF = −4.8800.
Fig. 1 in Effect of tenthredinid leaf miner invasions on growth of Alaska white birch in Anchorage, Alaska, USA, and the interaction with biological control of amber-marked birch leaf miner
Fig. 1. Percentage of Alaska white birch (Betula neoalaskana) leaves in Anchorage mined by the amber-marked birch leaf miner (AMBLM on graph) (Profenusa thomsoni) or the late birch leaf edge miner (LEM on graph) (Heterarthrus nemoratus) from 1990 to 2019, from the initial invasion of amber-marked birch leaf miner (around 1991) through its suppression by classical biocontrol (2004– 2015) and the invasion of a second species of leaf miner (H. nemoratus) (around 2008). Data on percentage of birch leaves mined by each species were taken from multiple sources: (1) P. thomsoni: 2006–2011 (Soper et al. 2015); 2015 and 2018 (Wenninger unpublished 2018); and 2019 (Andersen et al. 2021); and (2) H. nemoratus: 2008–2010 (Lundquist et al. 2012); 2011 (Mulvey &Lamb 2012, p. 15); 2015 and 2018 (Wenninger unpublished 2018); and 2019 (Andersen et al. 2021).
Fig. 3 in Effect of tenthredinid leaf miner invasions on growth of Alaska white birch in Anchorage, Alaska, USA, and the interaction with biological control of amber-marked birch leaf miner
Fig. 3. Trends in annual radial growth increment (mm) from Alaska white birch (Betula neoalaskana) in Anchorage, Alaska (n = 99 cores) during each of 3 periods: (A) the pre-amber-marked birch leaf miner (Profenusa thomsoni) outbreak period (1984–1995, (B) the amber-marked birch leaf miner outbreak period (1996– 2007), and (C) the biological control amber-marked birch leaf miner suppression period (2008–2018).
Figure 1 in Influence of Mycorrhizae and Irrigation on Growth and Mineral Uptake by Corn (Zea mays L.) Seedlings in a Calcareous Soil
Figure 1. Average of shoot and root biomass (g/plant), leaf width (cm), and chlorophyll SPAD reading of corn seedlings grown in Guam cobbly clay soil, either inoculated (■) or not inoculated (♦) with Glomus aggregatum, and provided one of four volumes of water: W1=7200 mL, W2=3600 mL, W3=1800 mL, and W4=900 mL during a 3-week experiment. Crossbars represent standard deviations of means with four replications.
Fluid-rock interaction of metamorphic fluids caused base metal mineralization in the Moldanubian domain, Bohemian Massif, Czech Republic – a fluid inclusion study - Supplementary data + measuring conditions
Open the record for dataset details and reuse information.
STXM-NEXAFS Analysis of Mineral-Organic Carbon Associations and OC Composition in North Atlantic Sediments
<p>Scanning transmission X-ray microscopy coupled with near edge X-ray absorption spectroscopy (STXM-NEXAFS) data collected on beamline 11.0.2 at the Advanced Light Source (ALS, Lawrence Berkeley National Laboratory) on sediment samples from the North Atlantic gyre collected during piston coring cruise KN223 on the R/V Knorr in 2014. Data include (a) sample geochemistry and lithology (metadata, "STXMNEXAFS_Sample_Geochem.xlsx"), (b) transmission microscopy images with overlaid element masks (organic and inorganic carbon, Al, Fe, Mn, K, and Ca, "mask images.zip") and marked regions ("region images.zip") that carbon NEXAFS spectra were extracted from, (c) NEXAFS spectra extracted from element masks and marked regions ("STXMNEXAFS_mask_reg_spectra_data.xlsx"), and (d) pixel intensity maps of mineral-forming elements used to make element correlation plots ("pixel correlation maps.zip"). The use of the Advanced Light Source is supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences under contract<br>no. DE-AC02-05CH11231. </p>
Research data of "Distribution, characteristics, and importance of particulate and mineral-associated organic carbon in China forest"
<p>We used the Web of Science (https://www.webofscience.com), Google Scholar (https://scholar. google.com), and China National Knowledge Infrastructure (CNKI, http://www.cnki.net) to compile a list of all peer-reviewed articles that investigated the soil organic carbon components in forest ecosystem of China.</p> <p><span>Apart from the SOC and SOC components, forest types, forest age, sampling depth, climatic properties (MAT and MAP), vegetation (</span>microbial biomass carbon<span>, litter biomass, living fin root biomass, above-ground biomass carbon) and edaphic properties (</span>soil pH, total organic carbon, total nitrogen, total phosphorus, soil type<span>, dissolved organic carbon, bulk density and </span>Silt+Clay%<span>) in sites for each study were extracted from material and method section, tables or supporting information in each study.</span></p> <p>After multiple screening of articles, we totally collected 540 observational data from 59 independent studies, which covers major forest ecosystems of China.</p>
Data from: Brine driven destruction of clay minerals in Gale crater, Mars
<p><span><span><span><span><span><span><span><span><span><span><span>This repository contains files and non-commercial software associated with the journal article "Brine Driven Destruction of Clay Minerals in Gale Crater, Mars.<strong>" </strong></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>The article presents mineralogical, geochemical, and sedimentological observations made by the Mars Science Laboratory rover <em>Curiosity </em>in an area called Glen Torridon, Gale crater, Mars. Rocks exposed in Glen Torridon were deposited in a lake that occupied the floor of Gale crater about 3.5 billion years ago and are stratigraphic and depositional equivalents of rocks exposed ~ 400m away on Vera Rubin ridge. The mineralogy of rocks in these two areas are different despite forming in the same lake at the same time. Glen Torridon rocks contain about 30 wt % clay minerals and 2 wt % or less of the mineral hematite (an iron oxide). In contrast, Vera Rubin ridge rocks contain 5 to 13 wt % clay minerals, with larger quantities (between 9 and 16 wt %) of iron oxide and oxyhydroxide minerals. The observed differences in mineralogy are attributed to preferential post-depositional alteration of Vera Rubin ridge rocks by silica-poor brines. These brines are thought to have formed during the deposition of sedimentary strata of the 'sulfate-bearing unit' that overlie Glen Torridon and Vera Rubin ridge rocks. Orbital spacecraft have detected magnesium sulfates in the sulfate-bearing unit. The presence of these highly soluable salts imply that changing climate and/or hydrological conditions in Gale crater resulted in the formation of dense brines during deposition of the sulfate-bearing unit. It is hypothesized that brines infiltrated older clay-bearing sediments, converting iron-rich clay minerals to iron oxides and oxyhydroxides. Glen Torridon rocks also contain a mineral phase not previously identified on the mission. This mineral gives rise to a distinctive x-ray diffraction peak represents a interplanar spacing of 9.22 angstroms. This phase is identified as a mixed-layer serpentine-talc and is thought to have been transported into the crater floor by rivers.</span></span></span></span></span></span></span></span></span></span></span></p> <p>This repository contains:</p> <p>- Files needed to perform mineral search and Rietveld refinement of measured x-ray diffraction data using <span><span><span><span><span><span><span><span><span><span><span>BGMN and MDI Jade software.</span></span></span></span></span></span></span></span></span></span></span> </p> <p>- A non-commerical Excel-based program called FULLPAT, used for mineral and x-ray amorphous quantification of x-ray diffraction patterns collected by the CheMin instrument aboard <em>Curiosity. </em></p> <p><em>- </em>Python code that was used to identify the 9.22 angstrom phase through automated search the American Mineralogist Crystal Structure Database.</p> <p>- Collection times of Alpha Particle X-ray Spectrometer analyses of bulk rock geochemical presented in the article that can be used to retrieve raw data from NASA's Planetary Data system (<span><span><span><span><span><span><span><span><span><span><span>https://pds-geosciences.wustl.edu/msl/msl-m-apxs-4_5-rdr-v1/mslapx_1xxx/extras/)</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>- A compilation of Li abundances across Vera Rubin ridge and Glen Torridon measured by the ChemCam that were presented in the article and used as a proxy for rock clay mineral content.</span></span></span></span></span></span></span></span></span></span></span></p>
N application rates from mineral fertiliser and manure
<p>Historical N application rates from mineral fertiliser and manure. Prepared for Gridded Global Crop Model Intercomparison (GGCMI) project phase 3. </p> <p>Gridded time series of fertiliser application rates are based on national and sub-national estimates for 141 individual crops for the year 2000 from Mueller et al. (2012) and national time series for five different crop groups from LUH2v2 (Hurtt et al., 2020). Gridded time series of manure application rates on cropland are based on total applied manure per grid cell from Zhang et al. (2017) and cropland extent from LUH2v2 (Hurtt et al., 2020).</p> <p>This update (v.1.1) corrects an error in the manure application rates, which was caused by a misalignment of manure data and cropland extent. Files for fertiser application rates are identical to the previous version.</p> <p> </p> <p><strong>Reference</strong></p> <p>Hurtt, G. C., Chini, L., Sahajpal, R., Frolking, S., Bodirsky, B. L., Calvin, K., Doelman, J. C., Fisk, J., Fujimori, S., Klein Goldewijk, K., Hasegawa, T., Havlik, P., Heinimann, A., Humpenöder, F., Jungclaus, J., Kaplan, J. O., Kennedy, J., Krisztin, T., Lawrence, D., … Zhang, X. (2020). Harmonization of global land use change and management for the period 850–2100 (LUH2) for CMIP6. <em>Geoscientific Model Development</em>, <em>13</em>(11), 5425–5464. https://doi.org/10.5194/gmd-13-5425-2020</p> <p>Mueller, N. D., Gerber, J. S., Johnston, M., Ray, D. K., Ramankutty, N., & Foley, J. a. (2012). Closing yield gaps through nutrient and water management. <em>Nature</em>, <em>490</em>(7419), 254–257. https://doi.org/10.1038/nature11420</p> <p>Zhang, B., Tian, H., Lu, C., Dangal, S. R. S., Yang, J., & Pan, S. (2017). Global manure nitrogen production and application in cropland during 1860–2014: a 5 arcmin gridded global dataset for Earth system modeling. <em>Earth System Science Data</em>, <em>9</em>(2), 667–678. https://doi.org/10.5194/essd-9-667-2017</p>
Figure 8 in Ultrastructure and mineral composition of serpulid tubes (Polychaeta, Annelida)
Figure 8. Pomatoceros triqueter, polished section of the tabula, fine crystal homogeneous structure, treated with 1% acetic acid for 2 min. Abbreviations: cryst, crystals; orgm, organic matrix.
Figure 7. A–B in Ultrastructure and mineral composition of serpulid tubes (Polychaeta, Annelida)
Figure 7. A–B, Serpula crenata, inner tube layer. A, cross section, fresh fracture surface, showing the crystals of irregularly oriented prismatic structure completely embedded into the organic matrix. B, polished cross section, treated with GA solution for 5 min; note that the organic matrix is partially decomposed. C, Marifugia cavatica, longitudinal section, fresh fracture surface, inner mineral irregulary oriented prismatic structure, and inner organic tube layer. D, Spirobranchus giganteus, tube lumen, inner organic layer; note the mesh-like composition of the layer. E, Hydroides dianthus, polished longitudinal section, treated with 1% acetic acid for 2 min, showing transition between irregularly oriented prismatic and lamello-fibrillar structure. F, Laminatubus alvini, polished cross section, treated with 1% acetic acid for 2 min, showing transition between inner irregularly oriented prismatic and outer homogeneous angular crystal structure. Abbreviations: cryst, crystals; exter, exterior; HAC, homogeneous angular crystal structure; IOP, irregularly oriented prismatic structure; LF, lamello-fibrillar structure; orgm, organic matrix; orgl, inner organic layer of the tube.
Figure 5. A–B in Ultrastructure and mineral composition of serpulid tubes (Polychaeta, Annelida)
Figure 5. A–B, Vitreotubus digeronimoi, simple prismatic structure, polished, and treated with GA solution for 5 min. A, cross section. B, longitudinal section. C–D, Pomatoceros triqueter, lamello-fibrillar structure. C, cross section. D, longitudinal section. E–F, Floriprotis sabiuraensis, spherulitic lamello-fibrillar structure, inner tube layer. E, cross section. F, longitudinal section. Samples (C–F) were treated with 1% acetic acid for 2 min. Abbreviations: exter, exterior; ginc, growth increments.
Figure 4. A–B in Ultrastructure and mineral composition of serpulid tubes (Polychaeta, Annelida)
Figure 4. A–B, Protula diomedeae, semi-ordered irregularly oriented prismatic structure. A, cross section. B, longitudinal section. C–D, Pyrgopolon ctenactis, semi-ordered spherulitic irregularly oriented prismatic structure, outer tube layer. C, cross section. D, longitudinal section. E–F, Crucigera websteri, contact of inner tube layer with spherulitic prismatic structure, and third tube layer from outside with lamello-fibrillar structure. E, cross section. F, longitudinal section. All samples were polished and treated with 1% acetic acid for 2 min. Abbreviations: exter, exterior; ginc, growth increments; LF, lamello-fibrillar structure; osh, organic sheet; SPHP, spherulitic prismatic structure.
Figure 3. A–B in Ultrastructure and mineral composition of serpulid tubes (Polychaeta, Annelida)
Figure 3. A–B, Neovermilia falcigera, irregularly oriented platy structure, outer tube layer. A, cross section. B, longitudinal section. C–D, Bathyvermilia langerhansi, homogeneous angular crystal structure, outer tube layer. C, cross section. D, longitudinal section. E–F, Pomatostegus stellatus, homogeneous rounded crystal structure. E, cross section. F, longitudinal section. All samples were polished and treated with 1% acetic acid for 2 min. Abbreviations: exter, exterior.
Figure 2. A–B in Ultrastructure and mineral composition of serpulid tubes (Polychaeta, Annelida)
Figure 2. A–B, Pseudovermilia madracicola, spherulitic irregularly oriented prismatic structure. A, cross section. B, longitudinal section. C–E, Crucigera zygophora. C, transition between irregularly oriented prismatic and spherulitic irregularly oriented prismatic structure in cross section. D, spherulitic irregularly oriented prismatic structure, cross section. E, spherulitic irregularly oriented prismatic structure, longitudinal section. F, Spiraserpula caribensis, spherulitic irregularly oriented prismatic structure. All sections were polished and treated with 1% acetic acid for 2 min. Abbreviations: IOP, irregularly oriented prismatic structure; SIOP, spherulitic irregularly oriented prismatic structure.
Figure 1. A–B in Ultrastructure and mineral composition of serpulid tubes (Polychaeta, Annelida)
Figure 1. A–B, Apomatus globifer, irregularly oriented prismatic structure, polished and treated with GA (see Material & Methods) solution for 5 min. A, cross section. B, longitudinal section. C–E, Marifugia cavatica, polished, and treated with 1% acetic acid for 2 min. C, cross section, two-layered tube with irregularly oriented prismatic structure. D, longitudinal section, outer tube layer, with a low content of homogeneous carbonate cement. E, longitudinal section, inner tube layer, with a high content of homogeneous carbonate cement. F, Semivermilia crenata, irregularly oriented prismatic structure with a high content of homogeneous carbonate cement, polished cross section, treated with GA solution for 5 min. Abbreviations: cryst, crystals; exter, exterior; hc, homogeneous carbonate cement.
Figure 6. A–D in Ultrastructure and mineral composition of serpulid tubes (Polychaeta, Annelida)
Figure 6. A–D, Spirobranchus giganteus, polished, and treated with GA solution for 5 min. A, outer tube layer with oriented fibrillar structure, cross section. B, outer tube layer, oriented fibrillar structure, longitudinal section. C, detail of (B), showing the close-up of the organic sheet. D, outer layer with spherulitic irregularly oriented prismatic structure; note the epitaxial growth of prisms through several organic sheets. E, Ficopomatus enigmaticus, polished longitudinal section, spherulites in irregularly oriented prismatic structure, treated with 1% acetic acid for 2 min. F, Placostegus tridentatus, calcitic spherulite, longitudinal section of the tube with simple prismatic structure. Abbreviations: exter, exterior; ginc, growth increments; osh, organic sheet; pr, prismatic crystals; SPH, spherulite.
Figure 10 in Ultrastructure and mineral composition of serpulid tubes (Polychaeta, Annelida)
Figure 10. Evolution of serpulid tube ultrastructures. Phylogenetic relationships of serpulid genera derived from Kupriyanova et al. (2006), Bayesian majority consensus phylogram of the combined molecular and morphological data set. Numbers denote the presence of the ultrastructures in a particular genus: 1, unoriented structures; 2, semi-oriented structures; 3, oriented prismatic structures; 4, oriented complex structures.
Niobium speciation in minerals revealed by L2,3-edges XANES spectroscopy
<p>This metadata file gathers crystal-chemical, crystallographic and spectroscopic raw data supporting the manuscript entitled “Niobium speciation in minerals revealed by L<sub>2,3</sub>-edges XANES spectroscopy“ submitted to <em>American Mineralogist</em>. </p> <p><strong>EMP_natural_references:</strong> spreadsheet compiling crystal-chemical data of the Nb geological references (columbite, fluorcalciopyrochlore, hydropyrochlore, latrappite, niocalite) obtained from electron microprobe analysis (EMP_crystal_chemistry_references.xls). </p> <p><em>Analyses were conducted on a CAMECA SX Five electron at the CAMPARIS facility (Sorbonne Universite, Paris). Two to seven spots were probed for each sample at 15 kV and 40 nA for the major elements and at 15 kV and 299 nA for minor and : trace elements. WDS analyses were performed using the following standards: albite for Na, diopside for Mg, Si and Ca, orthoclase for Al and K, MnTiO<sub>3</sub> for Mn and Ti, hematite for Fe, BaSO<sub>4</sub> for Ba; topaze for F, LiNbO<sub>3</sub> for Nb, metallic Ta for Ta, SrSi for Sr, zircon for Zr, galena for Pb, monazite for Th, uraninite for U, and REE-bearing silicates for for Y, La, Ce, Nd.</em></p> <p><strong>XANES_spectra: </strong>raw X-ray absorption data files (.dat). There are either one or two files per sample (_01/_02). Amounts of Nb in Ti oxide samples are mentionned in file titles (Nb1pc/Nb5pc/Nb10pc). </p> <p><em>Niobium L<sub>2,3-</sub>edges XANES spectra were recorded on the LUCIA beamline of the SOLEIL synchrotron radiation facility (Gif-sur-Yvette, France) operating with a storage ring current of 450 mA and energy of 2.75 GeV. A double crystal Si(111) monochromator crystal was used with an energy resolution of 0.25 eV at 2400 eV and calibrated at this energy using Nb<sub>2</sub>O<sub>5</sub>.</em></p> <p><strong>XRD_geological_references:</strong> spreadsheet compiling crystal-cell parameters obtained from the reduction of single-crystal XRD data (geological_samples_crystal_cell_data.xls). The number of reflections indexed and teta range of measurement are specified.</p> <p><em>An Agilent Diffraction Xcalibur-S diffractometer equipped with a Sapphire CCD-detector with Mo K-α<sub>1</sub> radiation (λ = 0.71073 Å, graphite monochromator) was used at room temperature. Data reduction, cell refinement and space group determination were performed using CrysAlisPro software. </em></p> <p><strong>XRD_synthetic_samples:</strong> XRD data obtained for the synthetic samples (.csv/.xrdml). Amounts of Nb in Ti oxide samples are mentionned in file titles (Nb1pc/Nb5pc/Nb10pc). </p> <p><em>X-ray diffraction was performed with a PANALYTICAL X’pert Pro MPD diffractometer. Measurements were carried out in Bragg-Brentano geometry using a Co K-α anode in order to minimize the X-ray absorption of Fe in iron oxide synthetic compounds. Data were recorded with an X’Celerator detector between 3 ° 2θ and 90 ° 2θ with 0.017 ° steps. Incident beam mask was fixed at 20 mm and soller slits at 0.04 rad.</em></p>
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
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