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Fig. 4 in Globicephaline whales from the Mio-Pliocene Purisima Formation of central California, USA
Fig. 4. Reconstruction of Globicephalinae gen. et sp. indet. 1, in dorsal view. Gray denotes the preserved portion of the cranium.
Fig. 2 in Palaeobiology of orthothecide hyoliths from the Cambrian Manto Formation of Hebei Province, North China
Fig. 2. Scanning electron micrographs of shell and shale fabrics as well as mineral elemental analyses of matrix from the Manto Formation (Cambrian Stage 4/5) in the Zuojiawu section of Tangshan, China. A. NIGPAS 166334, fine grained clay minerals and hematite crystals in the matrix (A1). Tabular crystals of hematite forming rosette-shaped aggregations in the matrix (A2, A3); the cross in A2 shows the location of elemental analysis (A4). B. NIGPAS 166339a, skeleton coated with hematite. C. NIGPAS 166337, halite pseudomorphs distributed on the surface of undetermined fossil (C1), calcite imprints in the matrix (C2). Scale bars: A1, A2, C2, 2 μm; A3, 1 μm; B, 10 μm; C1, 50 μm.
Fig. 3 in Palaeobiology of orthothecide hyoliths from the Cambrian Manto Formation of Hebei Province, North China
Fig. 3. Novitatid hyolith Decoritheca cyrene (Walcott, 1905) from the Manto Formation (Cambrian Stage 4/5) in the Zuojiawu section of Tangshan, China. A. NIGPAS 166338 in dorsal view. B. NIGPAS 166335 in ventral (B1) and ventro-lateral (B3) views; detail showing transverse lines on the external surface of venter (B2). C. NIGPAS 166337 in dorsal view, conch of Decoritheca cyrene with operculum of Cupitheca convexa sp. nov. in apertural region (C1); rows of tubercles (C2), inset shows enlarged individual tubercle with nearly flat top. D. NIGPAS 166329 in ventral view. E. NIGPAS 166341b, aperture with reniform cross section. F. NIGPAS 166331 in ventral view; F1, incomplete shell showing well developed median concavity and adjacent ridges; F2, nearly complete shell with broken aperture and adapically shallowing median concavity. G. NIGPAS 166330, both shells display partial venter and partial dorsum from dorsal view. H. NIGPAS 166333 in ventral view. I. NIGPAS 166332 in dorsal view, white arrows indicate algae. Scale bars: A, D, B3, F–I, 2 mm; B1, C1, 1 mm; B2, 100 μm; C2, 20 μm; E, 200 μm.
Fig. 3 in ATP accumulation in early resting cyst formation towards cryptobiosis in Colpoda cucullus
Fig. 3. Measurement of the relative amount of ATP per 10,000 cells in vegetative cells and cells at 12 h after the onset of encystment induction. The columns and attached bars represent the means and standard errors of 9 identical replicates, respectively. Double asterisks represent significant differences at p <0.01.
Fig. 2 in ATP accumulation in early resting cyst formation towards cryptobiosis in Colpoda cucullus
Fig. 2. Relative gene expression of ATP synthase beta chain by real time PCR analysis. The columns and attached bars represent the means and standard errors of 4 identical replicates, respectively. Double asterisks represent significant differences at p <0.01.
Fig. 1 in ATP accumulation in early resting cyst formation towards cryptobiosis in Colpoda cucullus
Fig. 1. Visualization of the mitochondrial membrane potential of Colpoda vegetative cells using a Mito PT assay kit; the results from cells at 0 h and cells at 1–24 h after the onset of encystment induction are shown. Differential interference microscopic observation (A) and fluorescence microscopic observation (B). Cells that contain mitochondria with polarized inner membranes show orange fluorescence, whereas those with depolarized mitochondria show green fluorescence. The bar represents 100 μm.
Fig. 6 in New fossil remains from the Pliocene Koetoi Formation of northern Japan provide insights into growth rates and the vertebral evolution of porpoises
Fig. 6. Comparisons of the vertebral column of living and extinct phocoenids in lateral view. A. Pterophocaena nishinoi Murakami, Shimada, Hikida, and Hirano, 2012a, late Miocene of Hokkaido, Japan, NMV-7. B. Numataphocoena yamashitai Ichishima and Kimura, 2000, early Pliocene of Hokkaido, Japan, NFL 7. C. Piscolithax aenigmaticus Pilleri and Siber, 1989, late Miocene of Aguada de Lomas of Peru, SMNK-PAL 6660. D. Piscolithax longirostris Muizon, 1983, late Miocene of Sud-Sacaco, → Peru, MNHN SAS 934. E. Neophocaena phocaenoides Cuvier, 1829, Holocene of Japan?, NMNS M 24659. F. Phocoena sinus Norris and McFarland, 1958, Holocene of Baja California, Mexico, LACM 28259. G. Phocoena spinipinnis Burmeister, 1865, Holocene of Peru, USNM 550782. H. Phocoena dioptrica Lahille, 1912, Holocene of Tierra del Fuego, Argentina, LACM 86042. I. Phocoena phocoena Linnaeus, 1758, Holocene of Hokkaido, Japan, NMNS M 27393. J. Phocoenoides dalli True, 1885, Holocene of Iwate, Japan, NMNS M 21382. Not to scale.
(U)SAXS data (ID02 beamline, ESRF): Effects of pH on the fibrous structure formation of plant proteins during high-moisture extrusion
<p>Due to health and environmental factors, the food industry is looking for ways to introduce meat replacers made from plant-based proteins to consumer markets. The presence of structural anisotropy in the form of fibre is a prerequisite for meat analogues. Structure formation ability depends on the protein ingredients used, which leads to plant protein products with varying texture hardness and extent of fibre alignment. In the current study, we will test if it is possible to tune these properties based on the hypothesis that plant proteins have different structure formation abilities under varying pH conditions.</p>
Table 1 in A new fossil Euspira? (Mollusca: Gastropoda: Naticidae) from the Gubik Formation on the North Slope of Arctic Alaska
<p><b>Table 1.</b> Correction of Pliocene and Pleistocene marine transgressions of western and northern Alaska (after Marincovich and Powell, 1991).</p><table><tbody><tr><th><b>Age</b> (Hopkins 1965, 1967, Carter et al. 1986)</th><th><b>Bering Sea</b> (Kaufman et al. 1989, Hopkins, written common., 1990 in Marincovich and Powell 1991)</th><th><b>Western and northern Alaska</b> (Brouwers et al. 1984)</th><th><b>Skull Cliff (northwest Alaskan coast)</b> (Brigham 1985, these units are all informal)</th><th><b>Arctic Coastal Plain</b> (Carter et al. 1986)</th></tr></tbody><tbody><tr><th><b><4 ka</b></th><td>Krusensternian</td><td>Flandrian</td><td>—</td><td>Flandrian</td></tr><tr><th><b>circa. 25 ka</b></th><td>—</td><td>—</td><td>—</td><td>Middle Wisconsin</td></tr><tr><th><b>90–105 ka</b></th><td>—</td><td>Flaxsman Fm.</td><td>—</td><td>Simpsonian</td></tr><tr><th><b>120–130 ka</b></th><td>Pelukian</td><td>Pelukian</td><td>Walakpa beds</td><td>Pelukian</td></tr><tr><th><b>circa. 500 ka</b></th><td>Anvilian</td><td>Kotzebuan</td><td>Karmuk beds</td><td>Wainwrightian</td></tr><tr><th><b>>1.5 Ma, <2.4 Ma</b></th><td>Beringian III</td><td>Fishcreekian</td><td>Tuapaktushak beds</td><td>Fishcreekian</td></tr><tr><th><b>>2.4 Ma</b></th><td>Beringian II</td><td>Anvilian</td><td>Killi Creek beds</td><td>Bigbendian</td></tr><tr><th><b><3.5 Ma</b></th><td>Beringian I</td><td>Beringian</td><td>Nulavik beds</td><td>Colvillian</td></tr></tbody></table>
Silva taxonomic training data formatted for DADA2 (Silva version 138.2)
<p>These DADA2-formatted training fasta files were derived from the Silva Project's version 138.2 release: https://www.arb-silva.de/</p> <p>These fastas were generated by the following commands (using the dada2 R package version 1.35.4):</p> <blockquote> <p>path <- "~/tax/Silva/v138_2"<br>fn.out.slv <- "~/Desktop/silva_nr99_v138.2_toGenus_trainset.fa.gz"<br>dada2:::makeTaxonomyFasta_SilvaNR(file.path(path, "SILVA_138.2_SSURef_NR99_tax_silva.fasta.gz"), <br> file.path(path, "tax_slv_ssu_138.2.txt"), <br> fn.out.slv)<br> <br>fn.out.spc.slv <- "~/Desktop/silva_nr99_v138.2_toSpecies_trainset.fa.gz"<br>dada2:::makeTaxonomyFasta_SilvaNR(file.path(path, "SILVA_138.2_SSURef_NR99_tax_silva.fasta.gz"), <br> file.path(path, "tax_slv_ssu_138.2.txt"), <br> fn.out.spc.slv, include.species=TRUE)</p> <p>fn.out.aS.slv <- "~/Desktop/silva_v138.2_assignSpecies.fa.gz"<br>dada2:::makeSpeciesFasta_Silva("~/tax/silva/v138_2/SILVA_138.2_SSURef_tax_silva.fasta.gz", <br> fn.out.aS.slv)</p> </blockquote>
Greengenes2 training data formatted for DADA2 (Greengenes2 release version 2024.09)
<p>These DADA2-formatted training fasta files were derived from the Greengenes2 version 2024.09 release. https://ftp.microbio.me/greengenes_release/2024.09/</p> <p>These fastas were generated by the following commands (using the dada2 R package version 1.35.4):</p> <blockquote> <p>path <- "~/tax/GG2/2024_09"<br>fn <- file.path(path, "5b42d9b6-2f24-4f01-b989-9b4dafca7d5e/data/dna-sequences.fasta")<br>txfn <- file.path(path, "b7c3e691-ea51-4547-94dd-f79f49e41a36/data/taxonomy.tsv")</p> <p>fn.out.gg <- "~/Desktop/gg2_2024_09_toGenus_trainset.fa.gz"<br>dada2:::makeTaxonomyFasta_GG2(fn, txfn, fn.out.gg, include.species=FALSE, compress=TRUE)</p> <p>fn.out.spc.gg <- "~/Desktop/gg2_2024_09_toSpecies_trainset.fa.gz"<br>dada2:::makeTaxonomyFasta_GG2(fn, txfn, fn.out.spc.gg, include.species=TRUE, compress=TRUE)</p> </blockquote>
RDP taxonomic training data formatted for DADA2 (RDP release 19 - update 2023-08-23)
<p>These DADA2-formatted training fasta files were derived from the Ribosomal Database Project's Training Set 19 and the 2023-08-23 release of the RDP database. https://sourceforge.net/projects/rdp-classifier/files/RDP_Classifier_TrainingData/</p> <p>These fastas were generated by the following commands using the dada2 R package version 1.35.4:</p> <blockquote> <p>## RDP data: https://sourceforge.net/projects/rdp-classifier/files/RDP_Classifier_TrainingData/</p> <p>path <- "~/tax/rdp/v19"<br>fn.out.rdp <- "~/Desktop/rdp_19_toGenus_trainset.fa.gz"<br>dada2:::makeTaxonomyFasta_RDP(file.path(path, "trainset19_072023_speciesrank.fa"), <br> file.path(path, "trainset19_db_taxid.txt"), <br> fn.out.rdp, include.species=FALSE,<br> compress=TRUE)</p> <p>fn.out.spc.rdp <- "~/Desktop/rdp_19_toSpecies_trainset.fa.gz"<br>dada2:::makeTaxonomyFasta_RDP(file.path(path, "trainset19_072023_speciesrank.fa"), <br> file.path(path, "trainset19_db_taxid.txt"), <br> fn.out.spc.rdp, include.species=TRUE,<br> compress=TRUE)</p> </blockquote>
Figure 14 in A methane seep from the deep-marine, late Eocene Keasey Formation, Rock Creek, Columbia County, Oregon
Figure 14. Detail of chimney at the Second Seep Site, where the location of a solemyid bivalve in figure 12A is situated at periphery of seep limestone .
Figure 4 in A methane seep from the deep-marine, late Eocene Keasey Formation, Rock Creek, Columbia County, Oregon
Figure 4. Sketch of the Main Seep Site in east-west cross-sectional view. The sketch shows some representative positions of primary seep-related bivalves. Note relative positions of massive limestone in relation to areas dominated by nodules and carbonate blebs. Dashed symbol represents Keasey mudstone. A meter or more of black mudstone immediately subjacent to the limestone yield seep-related mollusks.
Figure 13 in A methane seep from the deep-marine, late Eocene Keasey Formation, Rock Creek, Columbia County, Oregon
Figure 13. Early diagenetic infilling of botryoidal aragonite in shell interior of the epitonid gastropod Boreoscala condoni (Dall, 1908). Note different size bubbles in successive layers. Scale bar = 1 cm.
Figure 3 in A methane seep from the deep-marine, late Eocene Keasey Formation, Rock Creek, Columbia County, Oregon
Figure 3. The Main Seep Site, east side, looking west. The numbers denote the top (1) and base (2) of the seep limestone body, respectively. The limestone is covered at top by approx. 1.8 m of Keasey mudstone, typical of middle member lithology..
Figure 12 in A methane seep from the deep-marine, late Eocene Keasey Formation, Rock Creek, Columbia County, Oregon
Figure 12. Solemyid bivalve preservation in the seep mudstone facies. A. Chalky remnant shell material on an articulated internal mold collected in life orientation. B. Fragments of chalky articulated internal molds and extremely thin shell fragments that exfoliated during collection. Scale bars = 1 cm.
Figure 8 in A methane seep from the deep-marine, late Eocene Keasey Formation, Rock Creek, Columbia County, Oregon
Figure 8. Select carbonate rock hand samples from the Main Seep Site, with some showing taphonomy of macrofossil occurrences. A. Articulated specimens of Conchocele taylori Hickman, 2015 on weathered (orange-brown stained) outer surface of medium gray colored microcrystalline carbonate; sample RC9(2). B. Articulated specimen of C. taylori with partial recrystallized shell, found in stratigraphic up position, and infilled with medium gray microcrystalline carbonate sample RC10B. C. Dark gray, homogeneous to slightly mottled microcrystalline carbonate with scattered, thin-shelled bivalve fragments; sample RC9. D. Irregular, coalesced nodular, medium to dark gray microcrystalline carbonate with scattered, straight bivalve shell fragments; sample RC10A. E. Irregularly nodular and mottled microcrystalline carbonate to cemented breccia of medium to dark gray microcrystalline carbonate with scattered, relatively thick, single curved valves of C. taylori shells; sample RC11. F. microcrystalline carbonate cemented, friable calcareous sandstone with nacreous molluscan shell fragments; sample RC21.
Figure 6 in A methane seep from the deep-marine, late Eocene Keasey Formation, Rock Creek, Columbia County, Oregon
Figure 6. Photographs of exposures. A. Upper turbidite bed with meter-stick for scale. Note sharp base of bed. B. Closeup of the base of the upper turbidite bed showing scour channel filled with medium sand. C. Rockfall in predominantly medium- to thick-bedded mudstones 1-3 meters below lower turbidite bed. Blocks in background are pieces of turbidite bed fallen from the bank. D. Lower turbidite bed at a point where it descends to near river level. E. Medium-bedded mudstones at base of stratigraphic section. Upper part of bank exposure is composed of Pleistocene fluvial gravels.
Figure 5 in A methane seep from the deep-marine, late Eocene Keasey Formation, Rock Creek, Columbia County, Oregon
Figure 5. Stratigraphic sections of the Main Seep Site in relation to Second and Third sites and stratigraphic position of UCMP localities. The Main Seep Site (Fig. 4) consists of a thick limestone lithosome including immediately subjacent black mudstone. The Second Seep Site about 70m west of the main seep, consists of a large conduit about 0.5 m wide by 3 meters high and a complex association of concretions. This site occurs at the east end of the exposure shown in Fig. 7. The Third Seep Site includes a localized concentration of small blebby concretions.
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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.