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Probing the Extent of Vertical Mixing in Brown Dwarf Atmospheres with Disequilibrium Chemistry
<p><strong>OVERVIEW</strong></p> <p>The substellar atmospheric models described in <a href="https://ui.adsabs.harvard.edu/abs/2022arXiv220814317M/abstract">Mukherjee et al. (2022)</a> are presented here. The grid of these 1D radiative-convective atmospheric models was computed using the newly released open-source climate code PICASO 3.0 (<a href="https://ui.adsabs.harvard.edu/abs/2022arXiv220807836M/abstract">Mukherjee et al. (2022)</a>, <a href="https://ui.adsabs.harvard.edu/abs/2019ApJ...878...70B/abstract">Batalha et al. (2019)</a>). The grid consists of four parameters – the effective temperature (T<sub>eff</sub>), gravity (log(g)), K<sub>zz</sub> in the radiative zones, and mixing length in the convective zones. Models with T<sub>eff </sub> between 400-1000 K with an increment of 25 K are included. log(g) has been varied from 4.5 to 5.5 with an increment of 0.25 dex. The K<sub>zz</sub> in the radiative zone has been varied between 1x, 0.01x, and 100x the parametrization presented in <a href="https://ui.adsabs.harvard.edu/abs/2022ExA....53..279M/abstract">Moses et al. (2021)</a>, whereas the convective mixing length has been between the atmospheric pressure scale height and 0.1x the scale height.</p> <p>There are three types of files released here – atmospheric composition files (TP_chemistry), thermal emission spectra files (spectra), and atmospheric Kzz profile files (TP_kz). </p> <p><strong>ATMOSPHERIC COMPOSITION</strong></p> <p>The atmospheric composition files are located in the folder TP_chemistry. These files have the temperature structure of the atmosphere as a function of pressure accompanied by the volume mixing ratio of 37 gases as a function of pressure. </p> <p>The TP_chemistry files are named following the format “profile_sc_qt_rz_[factor1]_cz_[factor2]_[Teff]_grav_[gravity]_mh_+0.0_sm_NA.dat", where [factor1] denotes the multiplier used for the radiative zone Kzz and can vary between ‘x0pt01’, ‘x1’, and ‘x100’. [factor2] denotes the multiplier for the mixing length and can vary between ‘1’ and ‘0pt1’. [Teff] and [gravity] denote the Teff and gravity of the models used. A simple code snippet to read and plot these files is presented below.</p> <p><strong>SPECTRA</strong></p> <p>The spectra files are located in the folder "spectra_highres_1", "spectra_highres_2", "spectra_highres_3", and "spectra_highres_4". These files have the thermal emission spectra between 0.3-30 microns calculated using the computed models. The native spectral resolution of these calculations is at an R = 500,000, but <strong>please be aware that these spectra should always be binned down to a resolution of R = 50,000 or less before usage</strong>. This means that these spectra should only be used to interpret datasets with a spectral resolution of 50,000 or less. Please contact the authors if higher resolution spectra are needed. The spectra have been uploaded in three different folders to make the file sizes manageable for transfer.</p> <p>The spectra files are also similarly named using the format “spectra_sc_qt_rz_[factor1]_cz_[factor2]_[Teff]_grav_[gravity]_mh_+0.0_sm_NA.tar.gz". These files can be directly read into a Python pandas dataframe using </p> <pre><code class="language-python">pd.read_csv(filename, compression='gzip')</code></pre> <p> The first column of the file is wavenumbers in cm<sup>-1, </sup>which can be converted to wavelength in microns by wavelength [microns] =10000/wavenumbers[cm<sup>-1</sup>]. The second column of the file is flux in erg/s/cm<sup>2</sup>/cm. Note that these fluxes need to be multiplied with R<sup>2</sup>/D<sup>2</sup> before comparing them with the typically observed flux of brown dwarfs/exoplanets. R is the radius of the object, and D is the distance here. A tutorial to convert these fluxes to other units is present in <a href="https://natashabatalha.github.io/picaso/notebooks/6_BrownDwarfs.html#Convert-to-F_\nu-Units-and-Regrid">this link</a>. A binned-down version (R=15,000) of these high-resolution spectra can also be found in the "spectra_lowres" folder. These can be used for datasets that have a maximum spectral resolution of 15,000.</p> <p><strong>K<sub>zz</sub> PROFILE</strong></p> <p>The K<sub>zz </sub>as a function of pressure for each model is presented in these files. The K<sub>zz</sub> is reported in cm<sup>2</sup>/s. These files are also similarly named using the format “kz_sc_qt_rz_[factor1]_cz_[factor2]_[Teff]_grav_[gravity]_mh_+0.0_sm_NA.dat". The columns of the files are pressure in bars, the temperature in K, and Kzz in cm<sup>2</sup>/s.</p> <p> </p> <p><strong>EXAMPLE PYTHON CODE TO READ AND PLOT COMPOSITION FILES</strong></p> <pre><code class="language-python">import numpy as np import pandas as pd import matplotlib.pyplot as plt grav = np.array([316,562,1000,1780,3160]) Teff=np.array([400,425,450,475,500,525,550,575,600,625,650,675,700,725,750,775,800,825,850,875,900,925,950,975,1000]) factor1 = np.array(['x0pt01','x1','x100']) factor2 = np.array(['1','0pt1']) file ="profile_sc_qt_rz_"+factor1[0]+"_cz_"+factor2[0]+"_"+str(Teff[14])+"_grav_"+str(grav[14])+"_mh_+0.0_sm_NA.dat" df = pd.read_csv(file, sep="\t") # Plot T(P) profile plt.ylim(100,1e-4) plt.semilogy(df['temperature'],df['pressure']) plt.show() # Plot H2O mixing ratio profile plt.ylim(100,1e-4) plt.loglog(df['H2O'],df['pressure']) plt.show()</code></pre> <p><strong>CREDITS</strong></p> <p>If you use these tables, please cite <a href="https://ui.adsabs.harvard.edu/abs/2022arXiv220814317M/abstract">Mukherjee et al. (2022, Astrophysical Journal, in press.)</a></p> <p> </p>
Dataset of "Vertical-Wind-Induced Cloud Opacity Variation in Low Latitudes Simulated by a Venus GCM"
<p>This dataset contains the GrADS data of Venus GCM results used for figures in the paper "Vertical-Wind-Induced Cloud Opacity Variation in Low Latitudes Simulated by a Venus GCM" by H. Karyu et al. (2022). </p> <p>The file 'dataset_day1' contains the three-dimensional (X: longitude, Y: latitude, Z:altitude (km)) data of temperature (unit: K), zonal wind velocity (unit: m/s), meridional wind velocity (unit: m/s), vertical wind velocity (unit: m/s), geopotential height (unit: m), cloud mass mixing ratio of mode 1, 2, 2', 3 particles, mass mixing ratio of sulfuric acid, air density (unit: kg/m<sup>3</sup>), cloud mass mixing ratio changing rate of mode 1, 2, 2', 3 particles (unit: 1/s), in snapshots of every 3 hours for the periods of the first Venusian days (117 Earth days). The file 'dataset_day2' contains the same for the second Venusian days.</p> <p>The file 'cloudtau-wc' contains three-dimensional (X: longitude, Y: latitude, Z:altitude (km)) data of column-integrated optical depth (COD) of mode 1, 2, 2' 3 particles and column mass abundance of mode 1, 2, 2' 3 particles (unit: kg/m<sup>2</sup>), in snapshots of every 3 hours for the periods of 2 Venusian days (234 Earth days). The COD at each altitude corresponds to the integrated value from the top of the atmosphere, and the column mass abundance of each altitude corresponds to the integrated value from the bottom of the atmosphere. The COD is calculated with the cloud mass mixing ratio stored in the file ‘dataset’ and extinction efficiency shown in the paper.</p> <p>The file 'stf-wc' contains two-dimensional (Y: latitude, Z:altitude (km)) data of mass stream function (unit: kg/s) and residual mass stream function (unit: kg/s), in snapshots of every 3 hours for the periods of 2 Venusian days (234 Earth days). One should refer to Holton (2004) for the definition of the (residual) mass stream function.</p> <p>The files 'dataset_comp' and 'taudataset_comp' are composite mean data of 'dataset' and 'cloudtau-wc', respectively, in snapshots of every 3 hours for the period of 30 days starting from day 86 of the simulation (Earth day). The composite mean is calculated by averaging atmospheric parameters with respect to the frame moving at the rotation period of 7.1-day.</p> <p>The file ‘scripts’ contains FORTRAN scripts and some additional files to derive the atmospheric parameters stored in 'cloudtau-wc’, 'stf-wc’, 'dataset_comp' and ‘taudataset_comp' from the GCM output file ‘dataset’. Please refer to the ‘README.txt’ contained in ‘scripts’ for how to use FORTRAN scripts, required input files and their output.</p> <p>The .tar.xz files can be extracted in Linux with 'tar Jxvf' command, and .grd and .ctl files with the same stem are generated.</p> <p> </p>
Text-fig. 5. Lithocarpoxylon ashwillii sp. nov., UF 279-24544. a, b: Semi-ring porous wood, exclusively solitary vessels in a radial/ diagonal arrangement, diffuse axial parenchyma, TS. c: Homocellular rays composed of procumbent cells; vasicentric tracheids; vessel elements with simple perforation plates (PP), TLS. d: Vessel-ray parenchyma pits (VRP) with reduced borders, vertical, RLS. e: Crystalliferous axial parenchyma strand (C) with a single crystal per chamber; ray with procumbent cells, RLS. f: Aggregate ray (right) composed of loosely associated 1–2-seriate rays, TLS. g: Uniseriate rays, thin-walled tyloses in vessels, vasicentric tracheids (VT). Lithocarpoxylon sp., UF 279-84864. h, i: Semi-ring porous wood, exclusively solitary vessels in radial arrangement. j: Aggregate ray and uniseriate rays. k: Scalariform perforation plate with fewer than 10 bars. l: Vessel-ray parenchyma pits with reduced borders to simple, vertical. Scale bars: 200 µm in a, b, f, h, j; 100 µm in c, i; 50 µm in d. e; 20 µm in k, l. in A Diverse Assemblage Of Late Eocene Woods From Oregon, Western Usa
Text-fig. 5. Lithocarpoxylon ashwillii sp. nov., UF 279-24544. a, b: Semi-ring porous wood, exclusively solitary vessels in a radial/ diagonal arrangement, diffuse axial parenchyma, TS. c: Homocellular rays composed of procumbent cells; vasicentric tracheids; vessel elements with simple perforation plates (PP), TLS. d: Vessel-ray parenchyma pits (VRP) with reduced borders, vertical, RLS. e: Crystalliferous axial parenchyma strand (C) with a single crystal per chamber; ray with procumbent cells, RLS. f: Aggregate ray (right) composed of loosely associated 1–2-seriate rays, TLS. g: Uniseriate rays, thin-walled tyloses in vessels, vasicentric tracheids (VT). Lithocarpoxylon sp., UF 279-84864. h, i: Semi-ring porous wood, exclusively solitary vessels in radial arrangement. j: Aggregate ray and uniseriate rays. k: Scalariform perforation plate with fewer than 10 bars. l: Vessel-ray parenchyma pits with reduced borders to simple, vertical. Scale bars: 200 µm in a, b, f, h, j; 100 µm in c, i; 50 µm in d. e; 20 µm in k, l.
Text-fig. 13. Enamel ultrastructure of I1, Equus hydruntinus (Kabazi 2). a: vertical sections, scale bar = 100 Μm; b: horizontal and vertical arrangement of prisms in the HSB structure, scale bar = 10 Μm; c: unstructured PLEX enamel at the end of the root, scale bar = 100 Μm. in The Ultrastructure Of The Tooth Enamel Of Small Equus Of The "Tarpan" Group And Their Possible Phylogenetic Connections
Text-fig. 13. Enamel ultrastructure of I1, Equus hydruntinus (Kabazi 2). a: vertical sections, scale bar = 100 Μm; b: horizontal and vertical arrangement of prisms in the HSB structure, scale bar = 10 Μm; c: unstructured PLEX enamel at the end of the root, scale bar = 100 Μm.
Text-fig. 12. HSB of first and second upper incisors of Equus przewalskii (Chornobyl Exclusion Zone). a, b: vertical section, scale bar = 100 Μm; c: horizontal cross-section, scale bar = 50 Μm. in The Ultrastructure Of The Tooth Enamel Of Small Equus Of The "Tarpan" Group And Their Possible Phylogenetic Connections
Text-fig. 12. HSB of first and second upper incisors of Equus przewalskii (Chornobyl Exclusion Zone). a, b: vertical section, scale bar = 100 Μm; c: horizontal cross-section, scale bar = 50 Μm.
Text-fig. 10. Enamel ultrastructure of I1 (a) and I2 (b, c), Equus gmelini, tarpan (Myrne). a: vertical section; b, c: horizontal cross-section, scale bar = 250 and 100 Μm respectively. in The Ultrastructure Of The Tooth Enamel Of Small Equus Of The "Tarpan" Group And Their Possible Phylogenetic Connections
Text-fig. 10. Enamel ultrastructure of I1 (a) and I2 (b, c), Equus gmelini, tarpan (Myrne). a: vertical section; b, c: horizontal cross-section, scale bar = 250 and 100 Μm respectively.
Text-fig. 11. Enamel ultrastructure of first (a) and second (b, c) lower incisors, Equus caballus (konik polski), vertical sections. a: enamel row, scale bar = 100 Μm; b: arranging the prisms in the HSB structure, scale bar = 20 Μm; c: arranging the prisms in PI structure, scale bar = 20 Μm. in The Ultrastructure Of The Tooth Enamel Of Small Equus Of The "Tarpan" Group And Their Possible Phylogenetic Connections
Text-fig. 11. Enamel ultrastructure of first (a) and second (b, c) lower incisors, Equus caballus (konik polski), vertical sections. a: enamel row, scale bar = 100 Μm; b: arranging the prisms in the HSB structure, scale bar = 20 Μm; c: arranging the prisms in PI structure, scale bar = 20 Μm.
Text-fig. 11. a–d: Palaeophycus tubularis HALL, 1847, full relief, mostly flattened, a – field photo, Layer No. 23, b – field photo, Layer No. 10, c – field photo, Layer No. 23, d – field photo, Layer No. 23; e: Phycosiphon isp., concave epirelief of spreite, field photo, Layer No. 12; f: Polykladichnus isp., full relief on a vertical rock section, BK 11, Layer No. 13; g: Protovirgularia isp., epirelief, field photo, Layer No. 12; h: Scolicia isp., BK 30, Layer No. 6; i: Spirocircus isp., field photo, Layer No. 1. Scale bar = 1 cm. in Early Complex Tiering Pattern: Upper Ordovician, Barrandian Area, The Czech Republic
Text-fig. 11. a–d: Palaeophycus tubularis HALL, 1847, full relief, mostly flattened, a – field photo, Layer No. 23, b – field photo, Layer No. 10, c – field photo, Layer No. 23, d – field photo, Layer No. 23; e: Phycosiphon isp., concave epirelief of spreite, field photo, Layer No. 12; f: Polykladichnus isp., full relief on a vertical rock section, BK 11, Layer No. 13; g: Protovirgularia isp., epirelief, field photo, Layer No. 12; h: Scolicia isp., BK 30, Layer No. 6; i: Spirocircus isp., field photo, Layer No. 1. Scale bar = 1 cm.
Text-fig. 7. Vertical polished sections of samples from selected layers. a: Layer No. 2, completely bioturbated, collection of the Czech Geological Survey (abbr. BK), BK 7; b: Layer No. 3, low: nearly completely bioturbated, upper: cross- to ripple bedding, weakly bioturbated, BK 6; c: Layer No. 7, incompletely bioturbated siltstone/mudstone, BK 5; d: Layer No. 8, low: totally bioturbated background with Zoophycos ichnofabric, upper: spotted, completely bioturbated siltstone, BK 4; e: Layer No. 8, low: in Early Complex Tiering Pattern: Upper Ordovician, Barrandian Area, The Czech Republic
Text-fig. 7. Vertical polished sections of samples from selected layers. a: Layer No. 2, completely bioturbated, collection of the Czech Geological Survey (abbr. BK), BK 7; b: Layer No. 3, low: nearly completely bioturbated, upper: cross- to ripple bedding, weakly bioturbated, BK 6; c: Layer No. 7, incompletely bioturbated siltstone/mudstone, BK 5; d: Layer No. 8, low: totally bioturbated background with Zoophycos ichnofabric, upper: spotted, completely bioturbated siltstone, BK 4; e: Layer No. 8, low:
Text-fig. 8. a, b: Bifungites isp. with fragments of vertical shafts, a – concave hyporelief BK 20, Layer No. 26, b – full relief BK 33, Layer No. 23; c–e: Palaeophycus sulcatus (MILLER et DYER, 1878), c – BK 29, Layer No. 22, d – BK 18, Layer No. 16, e – BK 31, Layer No. 6; f: Palaeophycus cf. tubularis HALL, 1847, BK 25, Layer No. 22; g: Megagrapton isp., concave hyporelief, BK 32, Layer No. 16; h: Teichichnus isp. (bottom) crossing Zoophycos isp. (centre to right bottom), BK 16, Layer No. 22. Scale bar = 1 cm. in Early Complex Tiering Pattern: Upper Ordovician, Barrandian Area, The Czech Republic
Text-fig. 8. a, b: Bifungites isp. with fragments of vertical shafts, a – concave hyporelief BK 20, Layer No. 26, b – full relief BK 33, Layer No. 23; c–e: Palaeophycus sulcatus (MILLER et DYER, 1878), c – BK 29, Layer No. 22, d – BK 18, Layer No. 16, e – BK 31, Layer No. 6; f: Palaeophycus cf. tubularis HALL, 1847, BK 25, Layer No. 22; g: Megagrapton isp., concave hyporelief, BK 32, Layer No. 16; h: Teichichnus isp. (bottom) crossing Zoophycos isp. (centre to right bottom), BK 16, Layer No. 22. Scale bar = 1 cm.
Text-fig. 11. Permian ichthyofaunas from the French Massif Central. Preliminary comparisons based on total accounts of individuals (see text for explanations). Sharks in green, Acanthodes sp. in yellow, Actinopterygians in blue, Dipnoi in white (not visible but present at Autun; see Tab. 1 for details). Each circle is proportional to the total number of specimens recovered. Permian outcrops in black. Hercynian basement indicated by vertical lines. Map modified from Gand and Durand (2006). in New Actinopterygians From The Permian Of The Brive Basin, And The Ichthyofaunas Of The French Massif Central
Text-fig. 11. Permian ichthyofaunas from the French Massif Central. Preliminary comparisons based on total accounts of individuals (see text for explanations). Sharks in green, Acanthodes sp. in yellow, Actinopterygians in blue, Dipnoi in white (not visible but present at Autun; see Tab. 1 for details). Each circle is proportional to the total number of specimens recovered. Permian outcrops in black. Hercynian basement indicated by vertical lines. Map modified from Gand and Durand (2006).
Text-fig. 2. E-W cross section of the Urema Graben from Gorongosa to Inhaminga adapted from Flores (1973: fig. 5). Note that in this schema the Mazamba Sandstone directly overlies the Cheringoma Limestone. I.P.CO No. 5 is a bore hole. Vertical exaggeration ×10. in Stratigraphy, Chronology And Palaeontology Of The Tertiary Rocks Of The Cheringoma Plateau, Mozambique
Text-fig. 2. E-W cross section of the Urema Graben from Gorongosa to Inhaminga adapted from Flores (1973: fig. 5). Note that in this schema the Mazamba Sandstone directly overlies the Cheringoma Limestone. I.P.CO No. 5 is a bore hole. Vertical exaggeration ×10.
Text-fig. 2. Salicaceae (a–g), Cannabaceae (h–n), cf. Betulaceae (o–r). a–g: Saxifragispermum, USNM PAL 772341. Scale bar = 5 mm except as indicated. a–b: Lateral, c: apical, and d: basal views of fruit, reflected light, palladium coated; apex at top of (a, b). e: Equatorial transverse section reflected light; arrows indicate presumed seeds, scale bar = 2 mm. f: Detail of locule contents extracted from (e), transmitted light, scale bar = 200 Μm. g: Interwoven trichomes or fibers from locule, transmitted light, scale bar = 5 Μm. h–j: Celtis. h, i: USNM PAL 772342, reflected light, palladium coated, scale bar = 5 mm. h: Lateral view parallel with plane of dehiscence. i: Lateral view perpendicular to plane of dehiscence. j: DMNH EPI.47809, Celtis in lateral view; showing reticulate sculpture and the vertically-oriented, plane of dehiscence (arrow), scale bar = 5 mm. k–m: Aphananthe. USNM PAL 772344, reflected light, palladium coated, scale bar = 5 mm. k: Apical view, note triangular cross section and apical plug (arrow). l: Lateral view, apex up. m: Lateral view at 90° to (l). n: Detail of cellular pattern at surface of endocarp, scale bar = 0.5 mm. o–r: in The Early Middle Eocene Wagon Bed Carpoflora Of Central Wyoming, U.S.A.
Text-fig. 2. Salicaceae (a–g), Cannabaceae (h–n), cf. Betulaceae (o–r). a–g: Saxifragispermum, USNM PAL 772341. Scale bar = 5 mm except as indicated. a–b: Lateral, c: apical, and d: basal views of fruit, reflected light, palladium coated; apex at top of (a, b). e: Equatorial transverse section reflected light; arrows indicate presumed seeds, scale bar = 2 mm. f: Detail of locule contents extracted from (e), transmitted light, scale bar = 200 Μm. g: Interwoven trichomes or fibers from locule, transmitted light, scale bar = 5 Μm. h–j: Celtis. h, i: USNM PAL 772342, reflected light, palladium coated, scale bar = 5 mm. h: Lateral view parallel with plane of dehiscence. i: Lateral view perpendicular to plane of dehiscence. j: DMNH EPI.47809, Celtis in lateral view; showing reticulate sculpture and the vertically-oriented, plane of dehiscence (arrow), scale bar = 5 mm. k–m: Aphananthe. USNM PAL 772344, reflected light, palladium coated, scale bar = 5 mm. k: Apical view, note triangular cross section and apical plug (arrow). l: Lateral view, apex up. m: Lateral view at 90° to (l). n: Detail of cellular pattern at surface of endocarp, scale bar = 0.5 mm. o–r:
Text-fig. 8. Carpolithes (a–t). a–e: Carpolithes sp. 1. USNM PAL 772366. Scale bar = 1 cm. a: Lateral view of endocarp, note two longitudinal ridges. b: Lateral view of endocarp rotated 90° from (a), note single lateral ridge in center, a, b reflected light, palladium coated. c: Lateral view, Micro-CT scan surface rendering. d: View of rounded end of the endocarp, reflected light, palladium coated. e: View of the opposite (pointed) end of the endocarp, note split; reflected light, palladium coated. f–j: Carpolithes sp. 2. USNM PAL 772367. Scale bar = 5 mm. f: Lateral view, base down; note raphe-like structure (arrow), reflected light, palladium coated. g: Lateral view, the raphe-like structure extending vertically from the base. h: Lateral view, rotated 90° from (g). i: Lateral view, the opposite face to that in (h). j: Basal view, raphe-like structure running from the center to the right of the image. g–j: CT scan surface renderings. k–o: Carpolithes sp. 3 USNM PAL 772368. Scale bar = 5 mm. k: Ventral view of the specimen, note flared apical extension, reflected light, uncoated. l: Dorsal view illustrating the flared apical extension, rotated 180o from (k). m: Lateral view rotated 90° from that in (l). n: Apical view, the apical extension with central pore (arrow) and a clear lineation running down the side to the top of the image. o: Basal view. l–o: Micro-CT scan surface renderings. p–t: Carpolithes sp. 4. USNM PAL 772369. Scale bar = 3 mm. p: Basal view illustrating the concentric rings of radiating possible cells surrounding a central depression. q: Lateral view, base down, note possible cellular pattern. r: Lateral view, rotated 180° from (q), base down; p–r: reflected light, palladium coated. s, t: Basal and lateral views, micro-CT scan surface renderings. in The Early Middle Eocene Wagon Bed Carpoflora Of Central Wyoming, U.S.A.
Text-fig. 8. Carpolithes (a–t). a–e: Carpolithes sp. 1. USNM PAL 772366. Scale bar = 1 cm. a: Lateral view of endocarp, note two longitudinal ridges. b: Lateral view of endocarp rotated 90° from (a), note single lateral ridge in center, a, b reflected light, palladium coated. c: Lateral view, Micro-CT scan surface rendering. d: View of rounded end of the endocarp, reflected light, palladium coated. e: View of the opposite (pointed) end of the endocarp, note split; reflected light, palladium coated. f–j: Carpolithes sp. 2. USNM PAL 772367. Scale bar = 5 mm. f: Lateral view, base down; note raphe-like structure (arrow), reflected light, palladium coated. g: Lateral view, the raphe-like structure extending vertically from the base. h: Lateral view, rotated 90° from (g). i: Lateral view, the opposite face to that in (h). j: Basal view, raphe-like structure running from the center to the right of the image. g–j: CT scan surface renderings. k–o: Carpolithes sp. 3 USNM PAL 772368. Scale bar = 5 mm. k: Ventral view of the specimen, note flared apical extension, reflected light, uncoated. l: Dorsal view illustrating the flared apical extension, rotated 180o from (k). m: Lateral view rotated 90° from that in (l). n: Apical view, the apical extension with central pore (arrow) and a clear lineation running down the side to the top of the image. o: Basal view. l–o: Micro-CT scan surface renderings. p–t: Carpolithes sp. 4. USNM PAL 772369. Scale bar = 3 mm. p: Basal view illustrating the concentric rings of radiating possible cells surrounding a central depression. q: Lateral view, base down, note possible cellular pattern. r: Lateral view, rotated 180° from (q), base down; p–r: reflected light, palladium coated. s, t: Basal and lateral views, micro-CT scan surface renderings.
Text-fig. 9. Carpolithes (a–r). a–d: Carpolithes sp. 5. USNM PAL 772370. Scale bar = 5 mm, reflected light, palladium coated. a: Lateral view of seed, apex up, possible raphe descending from apex toward viewer. b: Lateral view of seed, apex up, possible raphe on right. c: Lateral view, opposite side, apex up, possible raphe on left. d: Apical view, note central pit with raphe descending towards bottom margin. e–h: Carpolithes sp. 6. USNM PAL 772371. Scale bar = 5 mm. e: Basal view illustrating depression and keel in plane of bisymmetry, reflected light, palladium coated. f–h: Micro-CT scan surface rendering. f: Lateral view showing relatively smooth rounded surface. g: Specimen rotated 180° from (f), surface partially eroded. h: Longitudinal view, showing median keel. i–m: Carpolithes sp. 7 USNM PAL 772372. Scale bar = 5 mm. i: View of intact face of globose fruit, possible apical constriction at top. j: Lateral view, intact surface to right, possible apical constriction at top, both micro-CT scan surface renderings. k: Apical view. l: Face view illustrating the mineral filling and the fine, radiating structure of the fruit wall on the left and right margins, both reflected light, palladium coated. m: Closeup of the cellular layer on the left of (l), micro-CT scan surface rendering. n–p: Carpolithes sp. 8. USNM PAL 772373. Scale bar = 3 mm, reflected light, palladium coated. n: Lateral view of pyrene-like structure, one ridge running vertically in the center of view, the other two forming the left and right margins. o: Lateral view of pyrene-like structure, ridge in (n) on the left. p: End-on view illustrating one convex, one concave, and one relatively flat to very slightly concave face. q, r: Carpolithes sp. 9 USNM PAL 772374. Scale bar = 5 mm, reflected light, palladium coated. q: Exterior of the smooth broken half-sphere. r: Interior of the broken half-sphere. in The Early Middle Eocene Wagon Bed Carpoflora Of Central Wyoming, U.S.A.
Text-fig. 9. Carpolithes (a–r). a–d: Carpolithes sp. 5. USNM PAL 772370. Scale bar = 5 mm, reflected light, palladium coated. a: Lateral view of seed, apex up, possible raphe descending from apex toward viewer. b: Lateral view of seed, apex up, possible raphe on right. c: Lateral view, opposite side, apex up, possible raphe on left. d: Apical view, note central pit with raphe descending towards bottom margin. e–h: Carpolithes sp. 6. USNM PAL 772371. Scale bar = 5 mm. e: Basal view illustrating depression and keel in plane of bisymmetry, reflected light, palladium coated. f–h: Micro-CT scan surface rendering. f: Lateral view showing relatively smooth rounded surface. g: Specimen rotated 180° from (f), surface partially eroded. h: Longitudinal view, showing median keel. i–m: Carpolithes sp. 7 USNM PAL 772372. Scale bar = 5 mm. i: View of intact face of globose fruit, possible apical constriction at top. j: Lateral view, intact surface to right, possible apical constriction at top, both micro-CT scan surface renderings. k: Apical view. l: Face view illustrating the mineral filling and the fine, radiating structure of the fruit wall on the left and right margins, both reflected light, palladium coated. m: Closeup of the cellular layer on the left of (l), micro-CT scan surface rendering. n–p: Carpolithes sp. 8. USNM PAL 772373. Scale bar = 3 mm, reflected light, palladium coated. n: Lateral view of pyrene-like structure, one ridge running vertically in the center of view, the other two forming the left and right margins. o: Lateral view of pyrene-like structure, ridge in (n) on the left. p: End-on view illustrating one convex, one concave, and one relatively flat to very slightly concave face. q, r: Carpolithes sp. 9 USNM PAL 772374. Scale bar = 5 mm, reflected light, palladium coated. q: Exterior of the smooth broken half-sphere. r: Interior of the broken half-sphere.
Data from: Sedimentary organic carbon and nitrogen sequestration across a vertical gradient on a temperate wetland seascape including salt marshes, seagrass meadows and rhizophytic macroalgae beds
<p>Dataset </p> <p> </p> <p>Coastal wetlands are key in regulating coastal carbon and nitrogen dynamics and contribute significantly to climate change mitigation and anthropogenic nutrient reduction. We investigated organic carbon (OC) and total nitrogen (TN) stocks and burial rates at four adjacent vegetated coastal habitats across the seascape elevation gradient of Cádiz Bay (South Spain), including one species of salt marsh, two of seagrasses, and a macroalgae. OC and TN stocks in the upper 1 m sediment layer were higher at the subtidal seagrass <em>Cymodocea nodosa</em> (72.3 Mg OC ha<sup>-1</sup>, 8.6 Mg TN ha<sup>-1</sup>) followed by the upper intertidal salt marsh <em>Sporobolus maritimus</em> (66.5 Mg OC ha<sup>-1</sup>, 5.9 Mg TN ha<sup>-1</sup>), the subtidal rhizophytic macroalgae <em>Caulerpa prolifera</em> (62.2 Mg OC ha<sup>-1</sup>, 7.2 Mg TN ha<sup>-1</sup>), and the lower intertidal seagrass <em>Zostera noltei</em> (52.8 Mg OC ha<sup>-1</sup>, 5.2 Mg TN ha<sup>-1</sup>). The sedimentation rates increased from lower to higher elevation, from the intertidal salt marsh (0.24 g cm<sup>-2</sup> yr<sup>-1</sup>) to the subtidal macroalgae (0.12 g cm<sup>-2</sup> yr<sup>-1</sup>). The organic carbon burial rate was highest at the intertidal salt marsh<em> </em>(91 ± 31 g OC m<sup>-2</sup> yr<sup>-1</sup>), followed by the intertidal seagrass, (44 ± 15 g OC m<sup>-2</sup> yr<sup>-1</sup>), the subtidal seagrass (39 ± 6 g OC m<sup>-2</sup> yr<sup>-1</sup>), and the subtidal macroalgae (28 ± 4 g OC m<sup>-2</sup> yr<sup>-1</sup>). Total nitrogen burial rates were similar among the three lower vegetation types, ranging from 5 ± 2 to 3 ± 1 g TN m<sup>-2</sup> yr<sup>-1</sup>, and peaked at <em>S. maritimus </em>salt marsh with 7 ± 1 g TN m<sup>-2</sup> yr<sup>-1</sup>. The contribution of allochthonous sources to the sedimentary organic matter also decreased with elevation, from 72% in <em>C. prolifera</em> to 33% at <em>S. maritimus</em>. Our results highlight the need of using habitat-specific OC and TN stocks and burial rates to improve our ability to predict OC and TN sequestration capacity of vegetated coastal habitats at the seascape level. We also demonstrated that the stocks and burial rates in <em>C. prolifera </em>habitats were within the range of well-accepted blue carbon ecosystems such as seagrass meadows and salt marshes.</p>
Simulation data used for publication "Seeding of equatorial plasma bubbles by vertical neutral wind" by Yokoyama et al.
<p>The dataset includes two-dimensional simulation output used in the paper.</p> <p>"altitude.dat" and "zonal.dat" contains grid information.</p> <p>"read_n_phi_2D.pro" is an IDL file to read the dataset, with detailed description of each data.</p> <p>The original three-dimensional simulation output is too large to publish at the repository. Author (TY) is willing to share the original data.</p>
Figure 5 in Evaluation of vertical and horizontal changes in community structure of zooplankton in a deep dam lake
Figure 5. Tree diagram resulting from average linkage clustering using UPGMA method on the zooplankton community data reported during study period.
Figure 6 in Vertical distribution and migration of planktonic polychaete larvae in Onagawa Bay, north-eastern Japan
Figure 6. Box plots of vertical distribution of two spionid larvae: a, Pseudopolydora achaeta and b, Prionospio spp. The central line in the box represents the median, the upper and lower boundaries of the box represent the quartiles, and the vertical bar represents the 95% range of larval distribution (left axes). The dashed wavy lines and dark shaded areas represent the tidal level (right axes) and night-time, respectively.
Figure 5 in Vertical distribution and migration of planktonic polychaete larvae in Onagawa Bay, north-eastern Japan
Figure 5. Diel changes in vertical distribution of planktonic spionid larvae at St. 1 in Onagawa Bay from 8:00 a.m. on 20 August to 5:00 a.m. on 21 August 2012.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.