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Text-fig. 14. Photomicrographs of thin sections of specimen BP/16/1732 Palmoxylon dutoitii from Mhengere Hill, Gorongosa, Mozambique. a: transverse section (TS) with four fibre vascular bundles (fvb) and poorly preserved parenchyma between; b: diagram of one of the fvbs in (a) of the reniform type (f – fibres, mx – metaxylum, p – phloem, px – protoxylum); c: close up of the vascular part of a fvb with 2 metaxylem elements and the collapsed cells to the lower left represents the phloem; d: fvb with 2 metaxylem elements, fibrous part to the left and parencymarous ground tissue to the right; e: lower magnification of fvb in (c); f: fvb with three metaxylem elements and phloem patch below; g: longitudinal section (LS) showing the vascular sections alternating with the fibrous sections; h: LS showing the horizontal thickening on the walls of the metaxylem vessels and a patch of parenchyma to the right (darker cells); i: spheroid echinate phytoliths that are typical of Hyphaene and Borassus. in Stratigraphy, Chronology And Palaeontology Of The Tertiary Rocks Of The Cheringoma Plateau, Mozambique
Text-fig. 14. Photomicrographs of thin sections of specimen BP/16/1732 Palmoxylon dutoitii from Mhengere Hill, Gorongosa, Mozambique. a: transverse section (TS) with four fibre vascular bundles (fvb) and poorly preserved parenchyma between; b: diagram of one of the fvbs in (a) of the reniform type (f – fibres, mx – metaxylum, p – phloem, px – protoxylum); c: close up of the vascular part of a fvb with 2 metaxylem elements and the collapsed cells to the lower left represents the phloem; d: fvb with 2 metaxylem elements, fibrous part to the left and parencymarous ground tissue to the right; e: lower magnification of fvb in (c); f: fvb with three metaxylem elements and phloem patch below; g: longitudinal section (LS) showing the vascular sections alternating with the fibrous sections; h: LS showing the horizontal thickening on the walls of the metaxylem vessels and a patch of parenchyma to the right (darker cells); i: spheroid echinate phytoliths that are typical of Hyphaene and Borassus.
Text-fig. 7. Exbeckettia mastixioides (E.REID et M.CHANDLER) comb. nov. Details of anatomy in transverse section on cut surfaces from bilocular fruit shown in Text-fig. 6i, V. 23013(3). a: Details of seed (S), locule (L), distinct endocarp planes of separation (arrows). b: Detail of endocarp adjacent to the locule, and surrounding mesocarp. Blue lines indicate thickness of sclerenchyma lining the locule. Note layer of horizontally oriented periclinal fibres a few cells thick, lining the locule (arrow). c: Enlargement showing parenchyma cells of the mesocarp decreasing in diameter toward the periphery. d: Enlargement showing fibres and sclereids of the endocarp. e: Sharp contact between endocarp and mesocarp. f, g: Detailed anatomy of endocarp including locule lining, and contact with mesocarp. Scale bars 2 mm in (a), (b), 1 mm in (c–g). in Mastixioid Fruits (Cornales) From The Early Eocene London Clay Flora: Morphology, Anatomy And Nomenclatural Revision
Text-fig. 7. Exbeckettia mastixioides (E.REID et M.CHANDLER) comb. nov. Details of anatomy in transverse section on cut surfaces from bilocular fruit shown in Text-fig. 6i, V. 23013(3). a: Details of seed (S), locule (L), distinct endocarp planes of separation (arrows). b: Detail of endocarp adjacent to the locule, and surrounding mesocarp. Blue lines indicate thickness of sclerenchyma lining the locule. Note layer of horizontally oriented periclinal fibres a few cells thick, lining the locule (arrow). c: Enlargement showing parenchyma cells of the mesocarp decreasing in diameter toward the periphery. d: Enlargement showing fibres and sclereids of the endocarp. e: Sharp contact between endocarp and mesocarp. f, g: Detailed anatomy of endocarp including locule lining, and contact with mesocarp. Scale bars 2 mm in (a), (b), 1 mm in (c–g).
Text-fig. 5. Mastixiopsis nyssoides KIRCHH. a, b, g–n: Organic preservation. a, b: Lignitic, unpermineralized, early Eocene Dorset Pipe clays at Arne, V. 40762. a: Ventral view (original illustration from pl. 18, fig. 1 of Chandler 1962). b: Transverse fracture, somewhat distorted by compression. c–f: Pyrite permineralization. c: Ventral view, V. 22963(1) from Sheppey, originally listed as Mastixia cantiensis. d: Lateral view, V. 22969 from Sheppey (identified as Mastixia grandis by Reid and Chandler 1933: pl. 25, fig. 8). e: Equatorial transverse physical section from (c). f: Equatorial transverse physical section from (d). g: Detail of pericarp from (e), showing endocarp formed of dense fibrous tissue, surrounded by mesocarp of anticlinally oriented larger cells. h: Detail of pericarp from (f). i–n: Type material from Eocene of Riestadt, Germany, MNB. i: Ventral view. j, k: Ventral and apical views of holotype. l: View of the transversely fractured surface from (j) showing horseshoe shaped locule. m: Equatorial transverse physical cut of the specimen in (i); note yellow resin cavity (arrow). n: Scanning electron microscopy of pericarp from (l) with locule lining at lower edge of image. Note dense endocarp tissue composed of small cells (fibres and sclereids), extending about 3/5 of distance to periphery, surrounded by mesocarp of larger, anticlinally oriented cells. Scale bars 1 cm in (a–f), (i–k), 1 mm in (g), 2 mm in (h), 3 mm in (l), m, 250 Μm in (n). Bar in (d) applies also to (c). Bar in (l) also applies to (m). Bar in (i) also applies to (j) and (k). in Mastixioid Fruits (Cornales) From The Early Eocene London Clay Flora: Morphology, Anatomy And Nomenclatural Revision
Text-fig. 5. Mastixiopsis nyssoides KIRCHH. a, b, g–n: Organic preservation. a, b: Lignitic, unpermineralized, early Eocene Dorset Pipe clays at Arne, V. 40762. a: Ventral view (original illustration from pl. 18, fig. 1 of Chandler 1962). b: Transverse fracture, somewhat distorted by compression. c–f: Pyrite permineralization. c: Ventral view, V. 22963(1) from Sheppey, originally listed as Mastixia cantiensis. d: Lateral view, V. 22969 from Sheppey (identified as Mastixia grandis by Reid and Chandler 1933: pl. 25, fig. 8). e: Equatorial transverse physical section from (c). f: Equatorial transverse physical section from (d). g: Detail of pericarp from (e), showing endocarp formed of dense fibrous tissue, surrounded by mesocarp of anticlinally oriented larger cells. h: Detail of pericarp from (f). i–n: Type material from Eocene of Riestadt, Germany, MNB. i: Ventral view. j, k: Ventral and apical views of holotype. l: View of the transversely fractured surface from (j) showing horseshoe shaped locule. m: Equatorial transverse physical cut of the specimen in (i); note yellow resin cavity (arrow). n: Scanning electron microscopy of pericarp from (l) with locule lining at lower edge of image. Note dense endocarp tissue composed of small cells (fibres and sclereids), extending about 3/5 of distance to periphery, surrounded by mesocarp of larger, anticlinally oriented cells. Scale bars 1 cm in (a–f), (i–k), 1 mm in (g), 2 mm in (h), 3 mm in (l), m, 250 Μm in (n). Bar in (d) applies also to (c). Bar in (l) also applies to (m). Bar in (i) also applies to (j) and (k).
Text-fig. 4. Charred grass from diatomite of Saint-Bauzile. a: Overview of diatomite slab with one larger specimen of charred grass (left) and several smaller, lath-shaped charcoal fragments; SM.B 22260; scale bar = 1 cm. b: Detail of vein exhibited on split grass blade, with stomata oriented parallel to vein. c: Stomata oriented in rows and bands parallel to veins exposed on split grass blade. d: Surface of grass leaf with rectangular, elongated cells with strongly undulating margins in an intercostal area. in Evidence For Wildfires During Deposition Of The Late Miocene Diatomites Of The Konservat-Lagerstätte Lake Saint-Bauzile (Ardèche, France) - Preliminary Results
Text-fig. 4. Charred grass from diatomite of Saint-Bauzile. a: Overview of diatomite slab with one larger specimen of charred grass (left) and several smaller, lath-shaped charcoal fragments; SM.B 22260; scale bar = 1 cm. b: Detail of vein exhibited on split grass blade, with stomata oriented parallel to vein. c: Stomata oriented in rows and bands parallel to veins exposed on split grass blade. d: Surface of grass leaf with rectangular, elongated cells with strongly undulating margins in an intercostal area.
Text-fig. 5. Plant fragments from Govone with evidence of preserved cuticle. a: Decussate pair of leaves of "Thuja" saviana (C.T.GAUDIN) C.T.GAUDIN with a window (arrow) opened in the brownish cuticle, showing the yellowish mesophyll cells and some possible resin canals (dark), MGPT-PU141094. b: Angiosperm leaf fragment (from sample MGPT-PU141017) under the stereomicroscope, showing the blackish compressed mesophyll on the right and patches of cleaned, yellowish cuticle at the top (arrow). Scale bar 1 mm. in Remains Of A Subtropical Humid Forest In A Messinian Evaporitebearing Succession At Govone, Northwestern Italy - Preliminary Results
Text-fig. 5. Plant fragments from Govone with evidence of preserved cuticle. a: Decussate pair of leaves of "Thuja" saviana (C.T.GAUDIN) C.T.GAUDIN with a window (arrow) opened in the brownish cuticle, showing the yellowish mesophyll cells and some possible resin canals (dark), MGPT-PU141094. b: Angiosperm leaf fragment (from sample MGPT-PU141017) under the stereomicroscope, showing the blackish compressed mesophyll on the right and patches of cleaned, yellowish cuticle at the top (arrow). Scale bar 1 mm.
Text-fig. 6. Transmitted light microphotographs of permineralized wood from Govone. a, b: cf. Cupressinoxylon sp., radial section, MGPT-PU141105, a – nodular end of ray parenchyma (arrow), b – thick and pitted horizontal walls of ray parenchyma (arrow). c–f: Pinaceae gen. et sp. indet., MGPT-PU141107, c – abnormal discoloration due to ecological disruptions (radial section), d – rays up to 10 cells high, uniseriate, partly biseriate (black arrow), intercellular spaces observed (white arrows) (tangential section), e – large, thick-walled axial resin canal with more than 9 epithelial cells observed, axial resin canal diameter>60 Μm (transverse section), f – spiral thickenings due to compression (white arrow) (radial section). in Remains Of A Subtropical Humid Forest In A Messinian Evaporitebearing Succession At Govone, Northwestern Italy - Preliminary Results
Text-fig. 6. Transmitted light microphotographs of permineralized wood from Govone. a, b: cf. Cupressinoxylon sp., radial section, MGPT-PU141105, a – nodular end of ray parenchyma (arrow), b – thick and pitted horizontal walls of ray parenchyma (arrow). c–f: Pinaceae gen. et sp. indet., MGPT-PU141107, c – abnormal discoloration due to ecological disruptions (radial section), d – rays up to 10 cells high, uniseriate, partly biseriate (black arrow), intercellular spaces observed (white arrows) (tangential section), e – large, thick-walled axial resin canal with more than 9 epithelial cells observed, axial resin canal diameter>60 Μm (transverse section), f – spiral thickenings due to compression (white arrow) (radial section).
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.
Raw and processed cell lines (melanomaC818/melanomaMUM-2B/SK-MEL-28) data for detecting DMKN's mutations in melanoma cancer
<p>Raw and processed cell lines (melanomaC818/melanomaMUM-2B/SK-MEL-28) data for detecting DMKN's mutations in melanoma cancer. This research was concluded that DMKN is a trigger of epithelial-mesenchymal transition-driven melanoma.</p>
3D reconstruction of an NIH/3T3 mouse fibroblast cell imaged by the SXT-100.
<p>This dataset (*.mrc file) is a reconstructed 3D volume obtained by soft X-ray tomography on NIH/3T3 cells. The cells were grown on a 200 mesh 3.05 mm EM finder grid with a Quantifoil Holey Carbon support. The sample was vitrified by plunge-freezing in liquid ethane. The tomogram was collected with a pixel size of 28.85 nm over the tilt range from -53 to 53.5 degrees with 1.5 deg step size and 116 s exposure per tilt.</p>
High-resolution hard X-ray tomography and histology of a rat jaw for stem cell-mediated distraction osteogenesis
<p>Histology and microtomography of a rat jaw after distraction. These datasets appear in "<em>Combining high-resolution hard X-ray tomography and histology for stem cell-mediated distraction osteogenesis</em>" Applied Sciences 12(12) (2022) 6268.</p> <p>Micromography (hdr/img files) has pixel size of 10.0228 µm. Histology (.tif file) has pixel size of 0.243094 µm.</p> <p>Slice to volume registration scripts can be found at https://github.com/grodgers1/SliceToVolume.</p>
Raw data accompanying the manuscript "Cost-effective high-speed, three-dimensional live-cell imaging of HIV-1 transfer at the T cell virological synapse"
<p>These are the raw datasets used to generate the figures for the manuscript entitled "Cost-effective high-speed, three-dimensional live-cell imaging of HIV-1 transfer at the T cell virological synapse". The data files are 3D image stacks of a custom-built wide field deconvolution fluorescence microscope (.tif) and super-resolution structured illumination microscopy data (.dv) of Jurkat T cells transferring HIV-1 virus particles to previously uninfected primary T cells.</p>
Computationally profiling peptide:MHC recognition by T-cell receptors and T-cell receptor-mimetic antibodies
<p>Supporting datasets for preprint version of "Computationally profiling peptide:MHC recognition by T-cell receptors and T-cell receptor-mimetic antibodies".</p>
Dataset for: Phenotyping single-cell motility in microfluidic confinement
<p>Associated dataset and simulation codes for the publication "Phenotyping single-cell motility in microfluidic confinement" (2022), by Samuel A. Bentley, Hannah Laeverenz-Schlogelhofer, Vasileios Anagnostidis, Jan Cammann, Marco G. Mazza, Fabrice Gielen, Kirsty Y. Wan. </p>
Phertilizer: growing a clonal tree from single-cell DNA sequencing data of tumors
<p>The is the supplementary data repository for the simulation input data for Phertilizer: growing a clonal tree from single-cell DNA sequencing data of tumors.</p>
Species-specific effects and the ecological role of Programmed cell Death in the microalgae Ankistrodesmus (Sphaeropleales, Selenastraceae)
<p>Reports of programmed cell death (PCD) in phytoplankton raise questions about the ecological evolutionary role of cell death in these organisms. We induced PCD by nitrogen deprivation and unregulated cell death (non-PCD) in one strain of the green microalga <em>Ankistrodesmus densus</em> and investigated the effects of the cell death supernatants on phylogenetically related co-occurring organisms using growth rates and maximum biomass as proxies of fitness. PCD-released materials from <em>A. densus</em> CCMA-UFSCar-3 significantly increased growth rates of two conspecific strains compared to healthy culture (HC) supernatants and improved the maximum biomass of all <em>A. densus</em> strains compared to related species. Although growth rates of non-<em>A. densus</em> with PCD supernatants were not statistically different from HC treatment, biomass gain was significantly reduced. Thus, the organic substances released by PCD, possibly nitrogenous compounds, could promote conspecific growth. These results support the argument that PCD may differentiate species or subtypes and increases inclusive fitness in this model unicellular chlorophyte. Further research, however, is needed to identify the responsible molecules and how they interact with cells to provide the PCD benefits.</p>
Dataset for "Applicability of Control Materials To Support Gene Promoter Characterization and Expression in Engineered Cells Using Digital PCR"
<p>This dataset constitutes the pre-processed data contained in the publication 'Applicability of Control Materials To Support Gene Promoter Characterization and Expression in Engineered Cells Using Digital PCR' Analytical Chemistry (2022) 94(14):5566-5574 (DOI: 10.1021/acs.analchem.1c05134).</p>
Data from: Single cell transcriptomics shows dose-dependent disruption of hepatic zonation by TCDD in mice
<p>2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) dose-dependently induces the development of hepatic fat accumulation and inflammation with fibrosis in mice initially in the portal region. Conversely, differential gene and protein expression is first detected in the central region. To further investigate cell-specific and spatially resolved dose-dependent changes in gene expression elicited by TCDD, single-nuclei RNA sequencing and spatial transcriptomics were used for livers of male mice gavaged with TCDD every 4 days for 28 days. The proportion of 11 cell (sub)types across 131,613 nuclei dose-dependently changed with 68% of all portal and central hepatocyte nuclei in control mice being overtaken by macrophages following TCDD treatment. We identified 368 (portal fibroblasts) to 1,339 (macrophages) differentially expressed genes. Spatial analyses revealed initial loss of portal identity that eventually spanned the entire liver lobule with increasing dose. Induction of R-spondin 3 (<em>Rspo3</em>) and pericentral <em>Apc</em>, suggested dysregulation of the Wnt/β-catenin signaling cascade in zonally resolved steatosis. Collectively, the integrated results suggest disruption of zonation contributes to the pattern of TCDD-elicited NAFLD pathologies.</p>
Supplementary Tables for "Immune cell-specific smoking-related expression characteristics are revealed by re-analysis of transcriptomes from the CEDAR cohort"
<p>Supplementary Tables from "Immune cell-specific smoking-related expression characteristics are revealed by re-analysis of transcriptomes from the CEDAR cohort".</p>
Relief from nitrogen starvation triggers a transient destabilization of glycolytic mRNAs in Saccharomyces cerevisiae cells
<p>Dataset supporting "Relief from nitrogen starvation triggers a transient destabilization of glycolytic mRNAs in Saccharomyces cerevisiae cells" (2018) Molecular Biology of the Cell 29:377-522. DOI: 10.1091/mbc.E17-01-0061</p>
Figure 3: The microscopy images fo neuronal cells generated by SWCNT (a) and MWCNT (b)-COMPARATIVE STUDY OF SINGLE- AND MULTI-WALL CARBON NANOTUBES WITH APPLICATION IN CEREBRAL ANEURYSM
<p>Carbon nanotubes (CNTs) are nanometer-scale cylindrical graphitic struc-<br> tures that exhibit extraordinary physical properties as determined by their<br> structure [6]. Developing neural implants and the process of neuron regener-<br> ation are extremely di±cult. Nerve cells require the right environment and<br> the right growth factors at the right time to grow and proliferate. The elec-<br> trical conductive properties of these nanotubes o®er the possibility of using<br> it as a replacement to transmit and receive signals. The resulting 'hair like'<br> conductive wires that incorporate the properties of electrodes, permeable mi-<br> cro°uidic conduits and the porosity of the CNTs was found to promote cell<br> growth, migration and proliferation. The bridging consists either of an axon<br> or bundles of axons and dendrites. In some cases the bridge is covered with<br> clusters of cells [7]. These bridges form very e±ciently over quartz surfaces<br> which are apparently very poor surfaces for cell attachment. Fig. 2 shows the<br> evolution of a network generated by SWCNT and MWCNT. The data show<br> that cells ¯rst aggregate at the NT islands. As they complete this step axons<br> and dendrites begin to form and to build connections.<br> Also, has been observed for MWCNT higher connections than for SWCNT,<br> Figure 3.</p>
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.