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1,973 results for “dendrite”
Fig. 17 in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
Fig. 17. Abeliella riccioides Mägdefrau, 1937. A–B. Early illustrations of this trace fossil by Rose (1855) and Kölliker (1860) based on observations of Cretaceous fish scales (reproduced from Rose 1855: pl. I, fig. 5 and Kölliker 1860: pl. XVI, fig. 14). C. Lectotype sample showing numerous specimens in a transparent Oligocene fish scale. D. Close-up of lectotype (arrow) and several paralectotypes, illustrating near-perfect bilateral symmetry of the traces. E. Surface SEM of a Cretaceous echodont tooth, showing the avoidance of tunnels as opposed to true anastomosis (reproduced from Underwood 1999: fig. 2a). F–H. Overview and close-ups of an unidentified Cretaceous fish tooth from the lower Campanian of Höver, Germany, illustrating typical increase in abundance towards the base.
Fig. 18 in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
Fig. 18. Abeliella procera Mägdefrau, 1937. A. Two specimens in the lectotype sample, a transparent Oligocene fish scale. B. Close-up of lectotype illustrating details of the dichotomous bifurcation pattern in the central part of the larger (upper) specimen in A. Note the spherical aggregates (fossil spores?) filling part of the empty tunnels. C. Large specimen, together with a small A. riccioides to the right, in a Hexanthus sp. fish tooth from the lower Maastrichtian of Rügen, Germany.
Fig. 15 in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
Fig. 15. Dictyoporus nodosus Mägdefrau, 1937. A–B. Overview and close-up of the holotype in an Upper Cretaceous belemnite from Misburg, Germany. C. Specimen with lower degree of anastomosis, but better defined centre; same belemnite as holotype of Calcideletrix flexuosa Mägdefrau, 1937. D. Large specimen in a shell of the bivalve Inoceramus Sowerby, 1814 from the upper Campanian of Kronsmoor, Germany, showing a combination of open channels and endolithic tunnels. E–F. Incipient and transmission light micrographs of a pyritised specimen in an aptychus from the lower Campanian of Höver, Germany, showing surficial channels, a deeper tier of endolithic tunnels and variability in tunnel diameter. G. Holotype of junior synonym Cliona fenestralis Elias, 1957, preserved as natural cast in a Late Mississippian brachiopod (currently lost; reproduced from Elias 1967: pl. 40, fig. 2; scale bar derived from original description). H. Holotype of junior synonym Cicatricula retiformis Palmer & Palmer, 1977 on a slab of Ordovician hardground, displaying readily anastomosing channels with a decrease in mesh size towards the periphery. I. Holotype of junior synonym Dictyoporus garsonensis Elias, 1980, preserved in an Upper Ordovician rugose coral.
Fig. 9 in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
Fig. 9. Clionolithes alcicornis (Vogel, Golubic & Brett, 1987) comb. nov. A–B. SEM planar and oblique views of the holotype epoxy cast (together with bryozoan borings) recorded in a Devonian brachiopod shell from New York State, USA. C. SEM of the holotype of junior synonym C. bullahirsuta Plewes, 1996 from the Lower Jurassic of Yorkshire, UK (reproduced from Plewes 1996: pl. 28, fig. 1). D. Close-up of C, illustrating the characteristic cuspate microtexture (reproduced from Plewes 1996: pl. 28, fig. 3). E. SEM close-up of another specimen showing additional hairy filaments (reproduced from Plewes 1996: pl. 28, fig. 7).
Fig. 8 in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
Fig. 8. Clionolithes cervicornis (Vogel, Golubic & Brett, 1987). A. SEM of pyritised and epoxycast holotype in a Devonian brachiopod shell from New York State, USA. B–C. SEM overview and close-up of another specimen from the original material of Vogel et al., recorded in a coral substrate. D–E. Overview and close-up of several natural casts that are part of the suite of paratypes of Olkenbachia hirsuta Solle, 1938 (junior synonym of Clionolithes radicans Clarke, 1908), from the Devonian near Koblenz, Germany (compare with Solle 1938: fig. 5). F. Holotype of nomen nudum "Chondrites" symmetricus (Solle 1938), a morphologically similar (cf.) but unusually large specimen from the Devonian near Koblenz, Germany.
Fig. 11 in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
Fig. 11. Calcideletrix flexuosa Mägdefrau, 1937. A–C. Holotype in an Upper Cretaceous belemnite rostrum from Misburg, Germany. Close-up in B illustrates anastomosis and two potential points of initial entry (arrows). Close-up in C shows peripheral ramification. D–F. Respective SEM views of an epoxy casts of the holotype of junior synonym D. brachiopodicola Hofmann, 1996, illustrating the very close morphological resemblance of the trace in a belemnite vs a brachiopod substrate. G. Natural casts in a Devonian brachiopod with several C. flexuosa (original of Clarke 1908: pl. 10; damaged since original publication). H. Another silicified cast in a Devonian brachiopod shell (reproduced from Clarke 1908: pl. 11, fig. 2).
Fig. 12 in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
Fig. 12. Calcideletrix breviramosa Mägdefrau, 1937. A–C. Holotype covering several square centimetres of an Upper Cretaceous belemnite from Misburg, Germany. Close-up in B shows main tunnels with lateral secondary galleries and close-up in C illustrates connections to the substrate surface at the end of the secondary branches (arrows).
Fig. 4. Dendrina lacerata Hofmann, 1996. A in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
Fig. 4. Dendrina lacerata Hofmann, 1996. A. SEM of holotype in an epoxy cast of an upper Campanian belemnite from Misburg, Germany. B. Paratype on the same cast as the holotype. C. Several paratypes in the periphery of a Calcideletrix anomala from the type locality. D. Oblique view of a specimen in a belemnite from the upper Campanian of Kronsmoor, Germany, illustrating a tubular inlet tunnel on the left and peripheral connections to the substrate surface on the right. E. Surface view of a solitary specimen with inlet canal in a belemnite from the upper Campanian of Misburg, Germany.
Fig. 7 in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
Fig. 7. Clionolithes pannosus (Solle, 1938) comb. nov. A. Holotype preserved as natural cast in a Devonian brachiopod shell from the Mosel Valley near Münstermaifeld, Germany. B–C. SEM overview and close-up of the holotype. D–F. SEM planar view, oblique view and close-up of pyritised and resinembedded holotype of junior synonym Platydendrina platycentrum Vogel et al., 1987 in a shell of Mediospirifer Bublichenko, 1959 from the Middle Devonian of New York State, USA.
Fig. 3 in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
Fig. 3. Dendrina belemniticola Mägdefrau, 1937. A. Original illustration of belemnite with various traces including D. belemniticola (arrow; reproduced from Quenstedt 1849: pl. 30, fig. 36); provenance unresolved. B. Original amalgam, including D. belemniticola (arrow; reproduced from Quenstedt 1885: pl. 38, fig. 39). C. Re-illustration of original Quenstedt Dendrina (reproduced from Plewes 1996: pl. 22, fig. 3); inlet tunnel roughly at 11h in this and the following four sub-figures. D. Lectotype of D. belemniticola in an upper Senonian belemnite from Rosenthal near Peine, Germany (compare to Mägdefrau 1937: pl. IV, fig. 1). E. Holotype of junior synonym D. orbiculata Hofmann, 1996. SEM of epoxy cast of an upper Campanian belemnite from Lüneburg, Germany. F. Paratype of junior synonym D. constans Hofmann, 1996. SEM of epoxy cast of a lower Maastrichtian belemnite from Lüneburg, Germany. G. Holotype of junior synonym D. constans. SEM of epoxy cast of a lower Maastrichtian belemnite from Lüneburg, Germany. E–G illustrate the morphological range of D. belemniticola from almost completely fused radiating galleries, to partially fused galleries forming anastomoses, to rarely fused radiating galleries. H. Detail of partly obscured inlet tunnel connecting to centre of a paratype of junior synonym D. orbiculata. SEM of epoxy cast of an Upper Cretaceous belemnite from Lüneburg, Germany. I. Rarely observed overlap of D. belemniticola in a lower Maastrichtian belemnite from Rügen, Germany. J. Specimen of D. belemniticola (left) next to a D. dendrina (right) at the very tip of a lower Campanian belemnite from Höver, Germany.
Fig. 13 in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
Fig. 13. Calcideletrix anomala (Mägdefrau, 1937) comb. nov. A. Original glass negative of the lost holotype from an Upper Cretaceous belemnite from Misburg, Germany. B–C. Overview and closeup of the neotype from the same type locality and horizon; the centre of the colony is partly obscured by a deeper tier of Dendrina ispp. D. A large specimen in a belemnite from the upper Campanian of Kronsmoor, Germany. E–F. SEM planar and oblique views of an epoxy cast of the same specimen.
Fig. 10 in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
Fig. 10. Clionolithes convexus (Hofmann, 1996) comb. nov. A–C. SEM of the lectotype in planar view, oblique view and a detail, preserved in an epoxy cast from an Upper Cretaceous Ostrea shell from the Swedish island Ivö. Note the prominent initial tunnel with a slightly hairy texture leading to the main trunk of the trace.
Fig. 6. Clionolithes palmatus Clarke, 1908. A in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
Fig. 6. Clionolithes palmatus Clarke, 1908. A. Original drawing of the lectotype, a natural cast in a shell of Loxopteria dispar Sandberger & Sandberger, 1857 from the Upper Devonian of New York State, USA (reproduced from Clarke 1908: pl. 12, fig. 1). B. The lectotype in its present state, either slightly damaged or originally idealised. C. Original drawing of the paralectotype, a natural cast in a Loxonema danai Clarke, 1904 from the type locality (reproduced from Clarke 1908: pl. 12, fig. 2). D. Significantly damaged paralectotype. E–F. A number of natural casts in a shell of Leptostrophia Hall & Clarke, 1892 from the Devonian of Victoria, Australia, including the holotype (close-up in F) and several paratypes of junior synonym Clionolithes sollei Talent, 1963 (compare with Talent 1963: pl. 9, figs 3–8). G. SEM of a specimen cast in epoxy resin by Plewes (1996) from the Devonian of Iowa, USA, illustrating the morphological range within one trace, comprising sheet-like fans and galleries terminating in fine ramifications (reproduced from Plewes 1996: pl. 1, fig. 1).
Fig. 14 in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
Fig. 14. Calcideletrix fastigata (Radtke, 1991) comb. nov. A–C. SEM of the lectotype (together with fungal trace Saccomorpha clava Radtke, 1991) in an epoxy cast of an Oligocene Pecten bivalve shell from the Niederrheinische Bucht, Germany. Close-up in B illustrates the fine rhizoidal connections to the substrate surface. Close-up in C shows framboidal pyrite spheres (fossil fungal spores?) embedded within the resin. D–F. Large paralectotype in a cast of an Oligocene Ostrea bivalve shell from the same locality. Close-up in E exhibits the alternating bifurcation pattern of very fine peripheral galleries. Closeup in F shows the centre of the trace with further framboidal pyrite aggregates; epoxy resin was hindered in penetrating the cavity due to calcite spar (now dissolved).
Fig. 5. Clionolithes radicans Clarke, 1908. A in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
Fig. 5. Clionolithes radicans Clarke, 1908. A. Original illustration of the lectotype from the Devonian of Mansfield, Pennsylvania, USA (reproduced from Clarke 1908: pl. 11, fig. 1). B–C. Overview and close-up of a shell of the brachiopod Atrypa bearing the lectotype and a number of further specimens. D. Holotype of junior synonym Olkenbachia hirsuta Solle, 1938 from the Devonian near Koblenz, Germany, reproduced from Solle (1938: fig. 2). E–F. Overview and SEM close-up of one of the paratypes of junior synonym Olkenbachia hirsuta (compare with Solle 1938: fig. 4).
Fig. 1 in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
Fig. 1 (page 7). Morphological characters of dendrinid microborings with respect to overall shape and symmetry of the trace, its vertical profile, openings to the substrate surface, orientation of entrance tunnel (where present), branching pattern and surface texture (in order of decreasing relevance as ichnotaxobase).
Dataset of article: Synthesis of Dendritic ZSM‑5 Zeolite through Micellar Templating Controlled by the Amphiphilic Organosilane Chain Length
<p>Data used for preparation of the article : Synthesis of Dendritic ZSM‑5 Zeolite through Micellar Templating Controlled by the Amphiphilic Organosilane Chain Length</p> <p> Abstract of article: </p> <p>The synthesis of ZSM-5 zeolites by hydrothermal crystallization of protozeolitic nanounits functionalized with amphiphilic organosilanes of different chain length (Cn-N(CH3)2-(CH2)3-Si- (OCH3)3, n = 10, 14, 18 and 22) has been investigated. Well developed dendritic nanoarchitectures were achieved when using C14 and C18 organosilanes, exhibiting a radial and branched pattern of zeolitic nanounits aggregates. In contrast, although C10 and C22 organosilanes led to materials with hierarchical porosity, they lack of dendritic features. These differences have been linked to the formation of an amorphous mesophase at the gel preparation stage for the C14 and C18 samples, in which the surfactant micelles are covalently connected with the protozeolitic nanounits through siloxane bonds. The presence of the dendritic nanostructure positively impacts both the textural and catalytic properties of ZSM-5 zeolite. Thus, ZSM-5 (C14) and ZSM-5 (C18) samples exhibit the largest contribution of mesoporosity in terms of both surface area and pore volume. On the other hand, when tested as catalysts in the aldol condensation of furfural with cyclopentanone, which is an interesting reaction for the production of sustainable jet fuels, the highest catalytic activity is attained over the dendritic ZSM-5 materials due to their remarkable accessibility and balanced Brønsted/Lewis acidity.</p>
Native MS dataset for: "Caldendrin and myosin V regulate synaptic spine apparatus localization via ER stabilization in dendritic spines."
<p>Native mass spectrometry dataset used in: <strong>Caldendrin and myosin V regulate synaptic spine apparatus localization via ER stabilization in dendritic spines.</strong> Anja Konietzny, Jasper Grendel, Alan Kadek, Michael Bucher, Yuhao Han, Nathalie Hertrich, Dick H. W. Dekkers, Jeroen A. A. Demmers, Kay Grünewald, Charlotte Uetrecht and Marina Mikhaylova. <i>The EMBO Journal</i> (2021) e106523. doi:<a href="https://doi.org/10.15252/embj.2020106523">10.15252/embj.2020106523</a></p><p> </p><p><strong>Description:</strong></p><p>Native mass spectrometry (MS) analysis of the stoichiometry and ion occupancy of recombinant human calmodulin (CaM) and recombinant rat caldendrin (CaD) complex with synthetic mouse myosinV IQ1 (myoIQ) motif in the presence / absence of excess Ca2+ and Mg2+ ions.</p><p><strong>Sample processing:</strong></p><p>Full-length CaD and CaM as well as the synthetic myoVa peptide were buffer exchanged into 150 mM aqueous ammonium acetate solution (pH 7.4). CaM was twice passed through a Bio-Spin P-6 gel filtration spin column (6 kDa cut-off, <i>Bio-Rad</i>), CaD and the myoVa peptide were buffer exchanged through five cycles of tenfold dilution and re-concentration using centrifugal concentrators Vivaspin 500 (10 kDa cut-off, <i>Sartorius</i>) or Amicon Ultra 0.5mL (3 kDa cut-off, <i>Merck/Millipore</i>), respectively. Desalted proteins were introduced into an Orbitrap Q Exactive UHMR mass spectrometer (<i>Thermo Scientific</i>) via static nanoelectrospray ionization from in-house prepared gold-coated borosilicate glass capillaries Kwik-Fil 1B120F-4 (<i>World Precision Instruments</i>). Proteins were sprayed and analysed at 8.5 µM concentration in ammonium acetate alone or supplemented with 200 µM calcium acetate and 100 µM magnesium acetate (both for trace metal analysis, <i>Sigma-Aldrich</i>). For interaction analysis, CaM and/or caldendrin were mixed with myoVa peptide which had final concentration of 8.5 µM (low concentration) or 34 µM (high concentration). The mass spectrometer was tuned for best signal quality and intensity, keeping ion activation and unfolding minimal. Namely, electrospray voltage was kept at 1.3 kV, source desolvation temperature 250°C, in-source desolvation -50 V, ion transfer profile "high m/z", analyzer profile "low m/z", analyzer target resolution 12500 acquiring in mass range 500 – 9000 m/z. Nitrogen was used as collision gas in HCD cell at relative gas pressure setting 7.0 with gentle collisional activation by 10 V HCD voltage gradient.</p><p><strong>Data processing:</strong></p><p>Raw spectra were averaged over at least 50 scans for mass deconvolution and peak assignment in UniDec 4.4.1 package (<i>Marty et al., 2015</i>). The averaged spectra were exported for ZENODO deposition using <i>Thermo Scientific</i> FreeStyle 1.5.93.34 as single-scan Thermo .raw files (including instrumental parameters metadata) as well as in plain m/z vs intensity .txt files.</p>
Associated code and data for "Multi-level computational modeling of anti-cancer dendritic cell vaccination utilized to select molecular targets for therapy optimization (doi: 10.3389/fcell.2021.74635)"
<p>This deposit contains the data, code, and analysis to reproduce the results in the manuscript - Lai X, Keller C, Santos-Rosales G, Schaft N, Dörrie J, Vera J. Multi-level computational modeling of anti-cancer dendritic cell vaccination utilized to select molecular targets for therapy optimization. Frontiers in Cell and Developmental Biolology. 2022; 9:746359; <a href="https://www.researchgate.net/publication/358461035_Multi-Level_Computational_Modeling_of_Anti-Cancer_Dendritic_Cell_Vaccination_Utilized_to_Select_Molecular_Targets_for_Therapy_Optimization">doi:10.3389/fcell.2021.746359</a>.</p> <p>If you have used the code for your research, please cite the original publication. Thank you very much.</p> <p> </p>
Harnessing single cell RNA sequencing to identify dendritic cell types, characterize their biological states and infer their activation trajectory
<p><strong>Summary: </strong>Dendritic cells (DCs) orchestrate innate and adaptive immunity, by translating the sensing of distinct danger signals into the induction of different effector lymphocyte responses, to induce different defense mechanisms suited to face distinct types of threats. Hence, DCs are very plastic, which results from two key characteristics. First, DCs encompass distinct cell types specialized in different functions. Second, each DC type can undergo different activation states, fine-tuning its functions depending on its tissue microenvironment and the pathophysiological context, by adapting the output signals it delivers to the input signals it receives. Hence, to better understand DC biology and harness it in the clinic, we must determine which combinations of DC types and activation states mediate which functions, and how.<br> To decipher the nature, functions and regulation of DC types and their physiological activation states, one of the methods that can be harnessed most successfully is ex vivo single cell RNA sequencing (scRNAseq). However, for new users of this approach, determining which analytics strategy and computational tools to choose can be quite challenging, considering the rapid evolution and broad burgeoning of the field. In addition, awareness must be raised on the need for specific, robust and tractable strategies to annotate cells for cell type identity and activation states. It is also important to emphasize the necessity of examining whether similar cell activation trajectories are inferred by using different, complementary methods. In this chapter, we take these issues into account for providing a pipeline for scRNAseq analysis and illustrating it with a tutorial reanalyzing a public dataset of mononuclear phagocytes isolated from the lungs of naïve or tumor-bearing mice. We describe this pipeline step-by-step, including data quality controls, dimensionality reduction, cell clustering, cell cluster annotation, inference of the cell activation trajectories and investigation of the underpinning molecular regulation. It is accompanied with a more complete tutorial on Github. We anticipate that this method will be helpful for both wet lab and bioinformatics researchers interested in harnessing scRNAseq data for deciphering the biology of DCs or other cell types, and that it will contribute to establishing high standards in the field.</p> <p> </p> <p><strong>Data:</strong></p> <p>1. negative_cDC1_relative_signatures.csv : Negative signatures for performing Connectivity Map (cMAP) Analysis</p> <p>2. positive_cDC1_relative_signatures.csv : Positive signatures for performing Connectivity Map (cMAP) Analysis</p>
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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.
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DANDI Archive for NWB datasets
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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.
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