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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).
Data and analysis scripts for the OSDI 2018 paper "Taming Performance Variability"
<p>This repository contains our raw datasets and notebooks for analyzing performance results of benchmarks executed on CloudLab machines.</p> <p>File organization:</p> <ul> <li><code>notebooks/</code> - Various Jupyter notebooks containing our analysis. Contains analysis on our main dataset as well as some analysis on one-off collections. <ul> <li><code>bench-lib/common.py</code> - Common python utilities that are shared by the notebooks.</li> <li><code>disk-process.ipynb</code> - Main notebook for analysis of disk performance (both HDDs and SSDs).</li> <li><code>e-vs-cov.ipynb</code> - Analysis of E vs CoV for selected configurations.</li> <li><code>env-test.ipynb</code> - Version information for Python and installed packages.</li> <li><code>kernel-testing-Nd.ipynb</code> - Analysis of data using kernel two-sample testing in one and multiple dimensions..</li> <li><code>mem-process.ipynb</code> - Main notebook for analysis of memory performance.</li> <li><code>network-process.ipynb</code> - Main notebook for analysis of network performance.</li> <li><code>normality.ipynb</code> - Notebook for the high-level analysis of normality (or lack of it) in the collected data.</li> <li><code>quantile-regression.ipynb</code> - Notebook for Quantile Regression analysis for both disk and memory data.</li> <li><code>temporal-analysis.ipynb</code> - Notebook to search for/analyze any temporal aspects to our dataset.</li> <li><code>testbed-coverage.ipynb</code> - Analysis of the extent to which we were able to cover all of the test hardware.</li> <li><code>variability.ipynb</code> - Notebook for the high-level analysis of variability.</li> <li><code>wisc-disktests.ipynb</code> - <strong>ONE-OFF RUN</strong>: Analyzing variation in fio results on Wisconsin SSDs over repeated runs.</li> <li><code>wisc-memtests.ipynb</code> - <strong>ONE-OFF RUN</strong>: Analysis of benchmark order for various Wisconsin hardware/memory configurations.</li> </ul> </li> <li><code>data/</code>. Contains a dump of the dataset (as of 04/04/2018). This dataset is generated by running the code contained in the <a href="https://gitlab.flux.utah.edu/emulab/cloudlab-orchestration">https://gitlab.flux.utah.edu/emulab/cloudlab-orchestration</a> repository. Some additional one-off collections are contained here as well. <ul> <li><code>CoV-Summary/</code> - Data derived from our raw dataset for use by <code>notebooks/e-vs-cov.ipynb</code>.</li> <li><code>nodes/</code> - Simple list of all nodeids for each hardware type for use in <code>notebooks/testbed-coverage.ipynb</code>.</li> <li><code>raw-data/</code> - Raw .sql (and .csv files made from it) file containing a dump of our primary dataset through April 4th, 2018, used for the majority of the notebooks. Filtering is done in our notebooks to exclude data past April 1st, 2018 (as well as remove runs that appear to contain impossible execution conditions).</li> <li><code>wisc-disktests/</code> - <strong>ONE-OFF RUN</strong>: Results from successive runs of fio on Wisconsin SSDs. Used in <code>notebooks/wisc-disktests.ipynb</code>.</li> <li><code>wisc-memtests/</code> - <strong>ONE-OFF RUN</strong>: Results from memory benchmarks run with specific orderings on various Wisconsin machines. Used in <code>notebooks/wisc-memtests.ipynb</code>.</li> <li><code>wisc-pagemaps/</code> - <strong>ONE-OFF RUN</strong>: Virtual-to-Physical memory address mappings for tests run in <code>wisc-memtests/</code>. Used in <code>notebooks/wisc-memtests.ipynb</code>.</li> </ul> </li> </ul>
Table 1 in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
<p><b>Table 1.</b> Studied material, listed by original ichnotaxon nomen and in order of publication date, with specification of collection, inventory number and investigation methods. Present type assignments: H = holotype, P = paratype, L = lectotype, PL = paralectotype(s), S = syntype(s), N = neotype. Inventory numbers from the Institut für Geowissenschaften, Goethe-Universität, Frankfurt include the sample code on the stub in brackets. Continued on next page.</p><table><thead><tr><th><b>Publication</b></th><th><b>Ichnotaxon</b></th><th><b>Inventory numbers</b></th><th><b>Collection</b></th><th><b>Comments</b></th></tr></thead><tbody><tr><th>von Hagenow</th><td><i>Talpina ramosa</i></td><td>MB.Po 2128.1 (L)</td><td>Museum für Naturkunde, Berlin,</td><td>loaned for</td></tr><tr><th>(1840)</th><td>T. solitaria Talpina ramosa</td><td>MB.W. 0864 (L+PL) MMG: MvK 530 (PL)</td><td>Germany Senckenberg Naturhistorische</td><td><i>macrophotography and microscopy</i></td></tr><tr><th></th><td><i>T. solitaria</i></td><td>MMG: MvK 532 (PL)</td><td>Sammlungen, Dresden, Germany</td><td></td></tr><tr><th>von Hagenow</th><td><i>Talpina foliacea</i></td><td>MB.Po 2130.1–3 (S)</td><td>Museum für Naturkunde, Berlin,</td><td>loaned for</td></tr><tr><th>(unpubl.)</th><td>T. sentiformis Talpina foliacea</td><td>MB.W. 0866 (S) MMG: MvK 529 (S)</td><td>Germany Senckenberg Naturhistorische</td><td><i>macrophotography and microscopy</i></td></tr><tr><th></th><td><i>T. sentiformis</i></td><td>MMG: MvK 530 (S)</td><td>Sammlungen, Dresden, Germany</td><td></td></tr><tr><th>Morris (1851)</th><td><i>Talpina dendrina</i></td><td>PI A 559 (L+PL)</td><td>Natural History Museum,</td><td>loaned for</td></tr><tr><th></th><td></td><td></td><td>London, UK</td><td>macrophotography, microscopy and μCT</td></tr><tr><th>Clarke (1908)</th><td><i>Clionolithes radicans</i></td><td>6702 (L+PL) 6700 (PL) 6701</td><td>New York State Museum, New York, USA</td><td>series of images provided by collection manager</td></tr><tr><th></th><td><i>C. palmatus</i></td><td>6697 (L)</td><td></td><td></td></tr><tr><th></th><td></td><td>6698 (PL)</td><td></td><td></td></tr><tr><th>Thomas (1911)</th><td><i>Clionolithes hackberryensis</i></td><td>2807, 2808, 2809, 2810 (S)</td><td>Palaeontology depository, University of Iowa, Iowa City, USA</td><td>loaned for microscopy</td></tr><tr><th>Lees & Thomas (1918)</th><td><i>Clionolithes lizardensis</i></td><td>2811, 2812, 2813 (S)</td><td>Palaeontology depository, University of Iowa, Iowa City, USA</td><td>loaned for microscopy</td></tr><tr><th>Ruedemann (1925)</th><td><i>Clionolithes quaerens</i></td><td>6699 (H)</td><td>New York State Museum, Albany, USA</td><td>series of images provided by collection manager</td></tr><tr><th>Fenton & Fenton</th><td><i>Clionolithes fossiger</i></td><td>4811 (H)</td><td>Carnegie Museum of Natural</td><td>series of images</td></tr><tr><th>(1932)</th><td><i>C. hackberryensis</i></td><td>4810, 4812 (P) 4804, 4805, 4806, 4807, 4808, 4809</td><td>History, Pittsburgh, USA</td><td>provided by collection manager</td></tr><tr><th></th><td><i>Clionolithes irregularis</i></td><td>PAL 84693 (H)</td><td>Smithsonian Institution, National Museum of Natural History, Washington DC, USA</td><td>loaned for microscopy</td></tr><tr><th>Mägdefrau</th><td><i>Dendrina belemniticola</i></td><td>MLU.Mäg1937.IV.1 (L)</td><td>Institut für Geowissenschaften</td><td>loaned for</td></tr><tr><th>(1937)</th><td></td><td>MLU.Mäg1937.IV.6 MLU.Mäg1937.IV.8</td><td>und Geographie, Halle, Germany</td><td>macrophotography, microscopy and scans of glass negatives</td></tr><tr><th></th><td><i>D. anomala</i></td><td>MLU.Mäg1937.IV. 5 (H) (glass negative only)</td><td></td><td></td></tr><tr><th></th><td></td><td>MLU.Mäg1937.IV.10 (N)</td><td></td><td></td></tr><tr><th></th><td><i>D. incomposita</i></td><td>MLU.Mäg1937.IV.2 (L+PL)</td><td></td><td></td></tr><tr><th></th><td><i>D. minor</i></td><td>MLU.Mäg1937.IV.3 (S)</td><td></td><td></td></tr><tr><th></th><td><i>Calcideletrix flexuosa</i></td><td>MLU.Mäg1937.IV.4 (H)</td><td></td><td></td></tr><tr><th></th><td><i>C. breviramosa</i></td><td>MLU.Mäg1937.IV.9 (H)</td><td></td><td></td></tr><tr><th></th><td><i>Dictyoporus nodosus</i></td><td>MLU.Mäg1937.IV.10 (H)</td><td></td><td></td></tr><tr><th></th><td><i>Abeliella riccioides</i></td><td>MLU.Mäg1937.V.1 (L+PL)</td><td></td><td></td></tr><tr><th></th><td><i>A. procera</i></td><td>MLU.Mäg1937.V.2 (L+PL)</td><td></td><td></td></tr><tr><th>Solle (1938)</th><td><i>Olkenbachia hirsuta</i></td><td>XXVI 165 a, d, e, f, i (3x), n (4x), s (3x) (P)</td><td>Senckenberg, Frankfurt, Germany</td><td>photographed at collection and/or loaned</td></tr><tr><th></th><td>O. pannosa O. simplex</td><td>XXVI 166a (H) XXVI 167a (H)</td><td></td><td><i>for microscopy and SEM</i></td></tr><tr><th></th><td><i>" Chondrites " symmetricus</i></td><td>XXX 415a (H)</td><td></td><td></td></tr><tr><th></th><td></td><td>XXX 415b (P)</td><td></td><td></td></tr><tr><th></th><td><i>"C." multifilum</i></td><td>XXX 414b (P)</td><td></td><td></td></tr><tr><th>Talent (1963)</th><td><i>Clionolithes sollei</i></td><td>P60575 (H+P)</td><td>Museum Victoria, Melbourne, Australia</td><td>series of images provided by collection manager</td></tr></tbody></table>
Table 4 in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
<p><b>Table 4.</b> Compilation of informally named records of dendrinid microborings (in order of publication), together with the identifications based on the revised dendrinid ichnotaxonomy.? = uncertain; p = partim. Continued on next page.</p><table><thead><tr><th><b>Informal name</b></th><th><b>Publication</b></th><th><b>Identification</b></th></tr></thead><tbody><tr><th>Spinate Microborings</th><td>Edwards & Perkins (1974)</td><td>? <i>Rhopalondendrina contra</i> isp. nov.</td></tr><tr><th>Spinate boring form</th><td>Zeff & Perkins (1979)</td><td>? <i>Rhopalondendrina acanthina</i> isp. nov.</td></tr><tr><th>Algal form B</th><td>Budd & Perkins (1980)</td><td>? <i>Calcideletrix fastigata</i> comb. nov.</td></tr><tr><th>Sponge form B</th><td>Budd & Perkins (1980)</td><td>? <i>Rhopalondendrina acanthina</i> isp. nov.</td></tr><tr><th>Morfotipo B2</th><td>Mayoral (1988)</td><td>? <i>Calcideletrix fastigata</i> comb. nov.</td></tr><tr><th>Morfotipo B3</th><td>Mayoral (1988)</td><td>? <i>Calcideletrix fastigata</i> comb. nov.</td></tr><tr><th>Morfotipo B4</th><td>Mayoral (1988)</td><td>? <i>Pyrodendrina villosa</i> isp. nov.</td></tr><tr><th>Morfotipo B5</th><td>Mayoral (1988)</td><td><i>= Nododendrina europaea</i> comb. nov.</td></tr><tr><th>J-Form C-1</th><td>Glaub (1988)</td><td><i>= Nododendrina europaea</i> comb. nov.</td></tr><tr><th>J-Form C-2</th><td>Glaub (1988)</td><td>? <i>Entobia</i> isp.</td></tr><tr><th>J-Form F-4</th><td>Glaub (1988)</td><td><i>= Rhopalondendrina avis</i> isp. nov.</td></tr><tr><th>Sponge, Form 1</th><td>Günther (1990)</td><td>= <i>Rhopalondendrina tigris</i> isp. nov.</td></tr><tr><th>Rosetten-Form B</th><td>Hofmann & Vogel (1992)</td><td>= <i>Calcideletrix anomala</i> comb. nov.</td></tr><tr><th>Rosetten-Form D</th><td>Hofmann & Vogel (1992)</td><td>= <i>Dendrina belemniticola</i></td></tr><tr><th>Rosetten-Form E</th><td>Hofmann & Vogel (1992)</td><td>= <i>Dendrina belemniticola</i></td></tr><tr><th>Rosetten-Form G</th><td>Hofmann & Vogel (1992)</td><td>= <i>Calcideletrix flexuosa</i></td></tr><tr><th>Dendroid-Form I</th><td>Schmidt (1992)</td><td>? <i>Entobia</i> isp.</td></tr><tr><th>Dendroid-Form II</th><td>Schmidt (1992)</td><td>? <i>Clionolithes radicans</i></td></tr><tr><th>Dendroid-Form III</th><td>Schmidt (1992)</td><td>? <i>Rhopalondendrina acanthina</i> isp. nov.</td></tr><tr><th>Echinoid form</th><td>Radtke (1993)</td><td>= <i>Rhopalondendrina tigris</i> isp. nov.</td></tr><tr><th><i>Cliona</i> sp. 1</th><td>Schmidt & Freiwald (1993)</td><td><i>= Nododendrina europaea</i> comb. nov.</td></tr><tr><th>Semidendrina-Form</th><td>Glaub (1994)</td><td><i>= Nododendrina europaea</i> comb. nov.</td></tr><tr><th>Fastigatdendrina-Form</th><td>Glaub (1994)</td><td>?</td></tr><tr><th>Rhopalondendrina-Form</th><td>Glaub (1994)</td><td>= <i>Rhopalondendrina avis</i> isp. nov.</td></tr><tr><th><i>Entobia</i> -Form 2</th><td>Glaub (1994)</td><td>?</td></tr><tr><th>J-Form C-2</th><td>Glaub & Schmidt (1994)</td><td>? <i>Entobia</i> isp.</td></tr><tr><th>Dendroid-Form II</th><td>Glaub & Schmidt (1994)</td><td>? <i>Clionolithes radicans</i></td></tr><tr><th>Dendroid-Form III</th><td>Glaub & Schmidt (1994)</td><td>? <i>Rhopalondendrina acanthina</i> isp. nov.</td></tr><tr><th>Rosetten-Form</th><td>Glaub & Schmidt (1994)</td><td>?</td></tr><tr><th>Rosetten-Form A</th><td>Hofmann (1996)</td><td>? (p) <i>Dendrina dendrina</i></td></tr><tr><th>Fastigatdendrina-Form</th><td>Bundschuh (2000)</td><td>?</td></tr><tr><th>Dendroid-Form A</th><td>Bundschuh (2000)</td><td>= <i>Dictyoporus nodosus</i></td></tr><tr><th>Dendroid-Form B</th><td>Bundschuh (2000)</td><td>? <i>Clionolithes radicans</i></td></tr><tr><th>Dendroid-Form C</th><td>Bundschuh (2000)</td><td>= <i>Dictyoporus nodosus</i></td></tr><tr><th>Dendroid-Form D</th><td>Bundschuh (2000)</td><td>?</td></tr><tr><th>Piatella-Form</th><td>Bundschuh (2000)</td><td>? <i>Dendrina lacerata</i></td></tr><tr><th>Rhopalodendrina form</th><td>Vogel & Marincovich (2004)</td><td>? <i>Rhopalondendrina avis</i> isp. nov.</td></tr><tr><th>Echinoid Form</th><td>Glaub (2004)</td><td>= <i>Rhopalondendrina tigris</i> isp. nov.</td></tr><tr><th><i>Semidendrina</i> Form</th><td>Beuck & Freiwald (2005)</td><td><i>= Nododendrina europaea</i> comb. nov.</td></tr><tr><th>Foraminiferan trace</th><td>Försterra <i>et al.</i> (2005)</td><td><i>= Pyrodendrina villosa</i> isp. nov.</td></tr><tr><th>Rosette A</th><td>Tapanila (2005)</td><td><i>= Pyrodendrina cupra</i></td></tr><tr><th><i>Semidendrina</i> -form</th><td>Bromley (2005)</td><td><i>= Nododendrina europaea</i> comb. nov.</td></tr><tr><th>Non-camerate radiating form</th><td>Bromley (2005)</td><td>= <i>Pyrodendrina villosa</i> isp. nov.</td></tr><tr><th>Hirsute camerate form</th><td>Bromley (2005)</td><td>? <i>Pyrodendrina villosa</i> isp. nov.</td></tr><tr><th><i>Semidendrina</i> Form</th><td>Wisshak <i>et al.</i> (2005a)</td><td>= <i>Pyrodendrina villosa</i> isp. nov.</td></tr><tr><th><i>Semidendrina</i> -form</th><td>Wisshak <i>et al.</i> (2005b)</td><td><i>= Nododendrina europaea</i> comb. nov.</td></tr><tr><th>Sponge form II</th><td>Wisshak <i>et al.</i> (2005a)</td><td>= <i>Pyrodendrina villosa</i> isp. nov.</td></tr><tr><th>Sponge form VI</th><td>Wisshak <i>et al.</i> (2005a)</td><td>? <i>Pyrodendrina arctica</i> isp. nov.</td></tr><tr><th>Rosette-shaped borings</th><td>Botquelen & Mayoral (2005)</td><td>? Clionolithes radicans</td></tr><tr><th><i>Semidendrina</i> -form</th><td>Wisshak (2006)</td><td><i>=</i> (p) <i>Nododendrina europaea</i> comb. nov.</td></tr><tr><th>Microsponge-form 2</th><td>Wisshak (2006)</td><td>= <i>Pyrodendrina villosa</i> isp. nov.</td></tr><tr><th>Microsponge-form 6</th><td>Wisshak (2006)</td><td>? <i>Pyrodendrina arctica</i> isp. nov.</td></tr><tr><th><i>Semidendrina</i> -form</th><td>Wisshak & Rüggeberg (2006)</td><td><i>= Nododendrina europaea</i> comb. nov.</td></tr><tr><th><i>Semidendrina</i> -form</th><td>Santos & Mayoral (2008)</td><td><i>= Nododendrina europaea</i> comb. nov.</td></tr><tr><th><i>Semidendrina</i> -form</th><td>Pereira <i>et al.</i> (2009)</td><td>? <i>Nododendrina europaea</i> comb. nov.</td></tr><tr><th>Dendroid Form 1</th><td>Vogel & Brett (2009)</td><td>? <i>Clionolithes cervicornis</i></td></tr><tr><th>Dendroid Form 2</th><td>Vogel & Brett (2009)</td><td>?</td></tr><tr><th>Mini-Meander Form</th><td>Vogel & Brett (2009)</td><td>?</td></tr><tr><th>Foraminiferan Form</th><td>Beuck <i>et al.</i> (2010)</td><td>= (p) <i>Pyrodendrina villosa</i> isp. nov.</td></tr><tr><th>Bunched whips form</th><td>Wisshak <i>et al.</i> (2011)</td><td>?</td></tr><tr><th>Dendroid form 1</th><td>Wisshak <i>et al.</i> (2011)</td><td>?</td></tr><tr><th>Dendroid form 2</th><td>Wisshak <i>et al.</i> (2011)</td><td>= <i>Rhopalondendrina acanthina</i> isp. nov.</td></tr><tr><th>Morphotype 4</th><td>Seuss <i>et al.</i> (2015)</td><td>?</td></tr></tbody></table>
Table 3 in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
<p><b>Table 3.</b> Revised suite of ichnotaxa (in order of original ichnogenus and ichnospecies establishment; type ichnospecies marked by asterisk) comprised within the ichnofamily Dendrinidae, and the most relevant diagnostic ichnogeneric feature(s).</p><table><thead><tr><th><b>Ichnotaxon</b></th><th><b>Most relevant diagnostic features</b></th></tr></thead><tbody><tr><th><i>Dendrina</i> Quenstedt, 1849</th><td>Thin inlet tunnel leads to substrate parallel, circumradial, rosetted cavity</td></tr><tr><th><i>D. dendrina</i> (Morris, 1851) comb. nov. *</th><td></td></tr><tr><th><i>D. belemniticola</i> Mägdefrau, 1937</th><td></td></tr><tr><th><i>D. lacerata</i> Hofmann, 1996</th><td></td></tr><tr><th><i>Clionolithes</i> Clarke, 1908</th><td>Tapering, ramified galleries radiating from dome-shaped central cavity</td></tr><tr><th><i>C. radicans</i> Clarke, 1908 *</th><td></td></tr><tr><th><i>C. palmatus</i> Clarke, 1908</th><td></td></tr><tr><th><i>C. pannosus</i> (Solle, 1938) comb. nov.</th><td></td></tr><tr><th><i>C. cervicornis</i> (Vogel <i>et al.</i>, 1987)</th><td></td></tr><tr><th><i>C. alcicornis</i> (Vogel <i>et al.</i>, 1987) comb. nov.</th><td></td></tr><tr><th><i>C. convexus</i> (Hofmann, 1996) comb. nov.</th><td></td></tr><tr><th><i>Calcideletrix</i> Mägdefrau, 1937</th><td>Strongly ramified with prostrate, tapering, rarely anastomosing galleries</td></tr><tr><th><i>C. flexuosa</i> Mägdefrau, 1937 *</th><td></td></tr><tr><th><i>C. breviramosa</i> Mägdefrau, 1937</th><td></td></tr><tr><th><i>C. anomala</i> (Mägdefrau, 1937) comb. nov.</th><td></td></tr><tr><th><i>C. fastigata</i> (Radtke, 1991) comb. nov.</th><td></td></tr><tr><th><i>Dictyoporus</i> Mägdefrau, 1937</th><td>Reticulate channel or tunnel network with high degree of anastomosis</td></tr><tr><th><i>D. nodosus</i> Mägdefrau, 1937 *</th><td></td></tr><tr><th><i>D. balani</i> (Tavernier <i>et al.</i>, 1992) comb. nov.</th><td></td></tr><tr><th><i>Abeliella</i> Mägdefrau, 1937</th><td>Strictly dichotomously ramifying prostrate trace in osteic substrates</td></tr><tr><th colspan="2"><i>A. riccioides</i> Mägdefrau, 1937 *</th></tr><tr><th><i>A. procera</i> Mägdefrau, 1937</th><td></td></tr><tr><th><i>Nododendrina</i> Vogel <i>et al.</i>, 1987</th><td>Vertical node with one or several anastomosing and prostrate plexuses</td></tr><tr><th><i>N. europaea</i> (Fischer, 1875) comb. nov.</th><td></td></tr><tr><th><i>N. incomposita</i> (Mägdefrau, 1937) comb. nov.</th><td></td></tr><tr><th><i>N. paleodendrica</i> (Elias, 1957) comb. nov.</th><td></td></tr><tr><th><i>N. nodosa</i> Vogel <i>et al.</i>, 1987 *</th><td></td></tr><tr><th><i>Pyrodendrina</i> Tapanila, 2008</th><td>Vertically tapering galleries emerging from a prostrate, ramifying cavity</td></tr><tr><th><i>P. cupra</i> Tapanila, 2008 *</th><td></td></tr><tr><th><i>P. arctica</i> isp. nov.</th><td></td></tr><tr><th><i>P. belua</i> isp. nov.</th><td></td></tr><tr><th><i>P. villosa</i> isp. nov.</th><td></td></tr><tr><th><i>Rhopalondendrina</i> igen. nov.</th><td>Oblique–arcuate inlet tunnel leading to semi-circular, prostrate plexus</td></tr><tr><th><i>R. avis</i> isp. nov. *</th><td></td></tr><tr><th><i>R. acanthina</i> isp. nov.</th><td></td></tr><tr><th><i>P. contra</i> isp. nov.</th><td></td></tr><tr><th><i>P. tigris</i> isp. nov.</th><td></td></tr><tr><th><i>Antodendrina</i> igen. nov.</th><td>Distinctly widening lobes radiating from a central cavity or depression</td></tr><tr><th colspan="2"><i>A. ligula</i> isp. nov. *</th></tr></tbody></table>
Taming Dragon Lohan 降龙罗汉 木雕
**Taming Dragon Lohan 降龙罗汉** 木雕 Wood Carving 中国工艺美术大师梁铁球2015年作品 现收藏于中国衡阳南岳梁丰助工艺美术馆 高 90.5公分 宽26.6公分 Hight 90.5CM Width 26.6CM In the hands are the spiritual pearl and the holy bowl, Endowed with power that knows no bounds. Full of valour, vigour and awe-inspiring dignity, To succeed in vanquishing the ferocious dragon. Source: Objaverse 1.0 / Sketchfab
"Transarterial Microembolization (TAME) in Inflammatory Knee Pathology"
ClinicalTrials.gov study NCT07140367. IPD Sharing: NO. Countries: 1. Publications: 3.
TAME Health: Testing Activity Monitors' Effect on Health
ClinicalTrials.gov study NCT02554435. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Data from: Taming the wild: resolving the gene pools of non-model Arabidopsis lineages
Background: Wild relatives in the genus Arabidopsis are recognized as useful model systems to study traits and evolutionary processes in outcrossing species, which are often difficult or even impossible to investigate in the selfing and annual Arabidopsis thaliana. However, Arabidopsis as a genus is littered with sub-species and ecotypes which make realizing the potential of these non-model Arabidopsis lineages problematic. There are relatively few evolutionary studies which comprehensively characterize the gene pools across all of the Arabidopsis supra-groups and hypothesized evolutionary lineages and none include sampling at a world-wide scale. Here we explore the gene pools of these various taxa using various molecular markers and cytological analyses. Results: Based on ITS, microsatellite, chloroplast and nuclear DNA content data we demonstrate the presence of three major evolutionary groups broadly characterized as A. lyrata group, A. halleri group and A. arenosa group. All are composed of further species and sub-species forming larger aggregates. Depending on the resolution of the marker, a few closely related taxa such as A. pedemontana, A. cebennensis and A. croatica are also clearly distinct evolutionary lineages. ITS sequences and a population-based screen based on microsatellites were highly concordant. The major gene pools identified by ITS sequences were also significantly differentiated by their homoploid nuclear DNA content estimated by flow cytometry. The chloroplast genome provided less resolution than the nuclear data, and it remains unclear whether the extensive haplotype sharing apparent between taxa results from gene flow or incomplete lineage sorting in this relatively young group of species with Pleistocene origins. Conclusions: Our study provides a comprehensive overview of the genetic variation within and among the various taxa of the genus Arabidopsis. The resolved gene pools and evolutionary lineages will set the framework for future comparative studies on genetic diversity. Extensive population-based phylogeographic studies will also be required, however, in particular for A. arenosa and their affiliated taxa and cytotypes.
Taming the beast: a revised classification of Cortinariaceae based on genomic data
<p>Family <i>Cortinariaceae</i> currently includes only one genus, <i>Cortinarius</i>, which is the largest <i>Agaricales</i> genus, with thousands of species worldwide. The species are important ectomycorrhizal fungi and form associations with many vascular plant genera from tropicals to arctic regions. Genus <i>Cortinarius</i> contains a lot of morphological variation, and its complexity has led many taxonomists to specialize in particular on infrageneric groups. The previous attempts to divide <i>Cortinarius</i> have been shown to be unnatural and the phylogenetic studies done to date have not been able to resolve the higher-level classification of the group above section level. Genomic approaches have revolutionized our view on fungal relationships and provide a way to tackle difficult groups. We used both targeted capture sequencing and shallow whole genome sequencing (WGS) to produce data and to perform phylogenomic analyses of 75 single-copy genes from 19 species. In addition, a wider 5-locus analysis of 245 species, from the Northern and Southern Hemispheres, was also done. Based on our results, a classification of the family <i>Cortinariaceae</i> into ten genera—<i>Cortinarius, Phlegmacium, Thaxterogaster, Calonarius, Aureonarius, Cystinarius, Volvanarius, Hygronarius, Mystinarius, </i>and<i> Austrocortinarius</i>—is proposed. Seven genera, 10 subgenera, and four sections are described as new to science and five subgenera are introduced as new combinations in a new rank. In addition, 41 section names and 514 species names are combined in new genera and four lecto- and epitypes designated. The position of <i>Stephanopus</i> in suborder <i>Agaricineae</i> remains to be studied. Targeted capture sequencing is used for the first time in fungal taxonomy in Basidiomycetes. It provides a cost-efficient way to produce -omics data in species-rich groups. The -omics data was produced from fungarium specimens up to 21 years old, demonstrating the value of museum specimens in the study of the fungal tree of life. This study is the first family revision in Agaricales based on genomics data and hopefully many others will soon follow.</p>
On taming the effect of transcript level intra-condition count variation during differential expression analysis: a story of dogs, foxes and wolves: Bowtie2 counts and kallisto abundances
<p>Intra [1] and inter [2-5] study RNA-seq read datasets representing the varying brain compartments of foxes (n=24), as well as dogs (n=14) and wolves (n=6), as described in Lobo <em>et al.</em>, (2022) (under review), were mapped to the dog reference transcriptome [6], which contained 26,107 annotated transcripts (Ensembl CanFam3.1, release 92) [7], using Bowtie2 v.2.3.4.1 [8] and using kallisto v0.46.1 [9]. Count data obtained following each mapping approach for each dataset had high correlations (Lobo <em>et al.</em>, Figure S2). Bowtie2 counts were subsequently used in multiple differential analysis experiments in order to explore the effects of intra-condition count variation on the detection of differentially expressed transcripts. The individual count and abundance datasets for each corresponding RNA-seq dataset are available here.</p> <p> </p> <p>A preprint of Lobo et al., 2022, currently under review for PLOS ONE, is available [10]. The preprint however does not contain reviewer requested information on simulations as this, along with other additions including an additional author RL, has been subsequently added during the review process. These additions will be made available following review via a link to the final paper. </p> <p> </p> <p>Related software to this project are:<br> 1. <a href="http://sourceforge.net/projects/cstone/">CStone</a> <br> 2. <a href="http://sourceforge.net/projects/csreadgen/">CSReadGen</a><br> 3. <a href="https://sourceforge.net/projects/cview/">CView</a> <br> 4. <a href="https://sourceforge.net/projects/chimsim/">ChimSim</a><br> 5. <a href="https://sourceforge.net/projects/tvscript/">TVScript</a> <</p> <p> </p> <p>General details of the projects involved are available: <a href="https://cibio.up.pt/en/projects/is-hybridization-between-wolves-and-dogs-shaping-the-evolutionary-trajectory-of-wolf-populations-in-human-dominated-landscapes/">dog-wolf</a> and <a href="https://cibio.up.pt/en/projects/de-novo-based-sequence-assembly-of-next-generation-sequence-data-without-chimeras-improved-annotation-gene-expression-profiles-and-haplotype-br-reconstruction/">chimerism</a>.</p> <p> </p> <p><strong>References</strong></p> <p>1. Wang X, Pipes L, Trut L, Herbeck Y, Vladimirova A, Gulevich R, et al. Genomic responses to selection for tame/aggressive behaviors in the silver fox (Vulpes vulpes). Proc Natl Acad Sci. 2018;115: 10398–10403. doi:10.1073/pnas.1800889115</p> <p> </p> <p>2. Roy M, Kim N, Kim K, Chung WH, Achawanantakun R, Sun Y, et al. Analysis of the canine brain transcriptome with an emphasis on the hypothalamus and cerebral cortex. Mamm Genome. 2013;24: 484–499. doi:10.1007/s00335-013-9480-0</p> <p> </p> <p>3. Fushan AA, Turanov AA, Lee SG, Kim EB, Lobanov A V, Yim SH, et al. Gene expression defines natural changes in mammalian lifespan. Aging Cell. 2015;14: 352–365. doi:10.1111/acel.12283</p> <p> </p> <p>4. Hoeppner MP, Lundquist A, Pirun M, Meadows JRS, Zamani N, Johnson J, et al. An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts. PLoS One. 2014;9(3):91172. doi:10.1371/journal.pone.0091172</p> <p> </p> <p>5. Albert FW, Somel M, Carneiro M, Aximu-Petri A, Halbwax M, Thalmann O, et al. A Comparison of Brain Gene Expression Levels in Domesticated and Wild Animals. Akey JM, editor. PLoS Genet. 2012;8:e1002962. doi:10.1371/journal.pgen.1002962</p> <p> </p> <p>6. Hoeppner MP, Lundquist A, Pirun M, Meadows JRS, Zamani N, Johnson J, et al. An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts. PLoS One. 2014;9(3):91172. doi:10.1371/journal.pone.0091172</p> <p> </p> <p>7. Yates AD, Achuthan P, Akanni W, Allen J, Allen J, Alvarez-Jarreta J, et al. Ensembl 2020. Nucleic Acids Res. 2020;48: D682–D688. doi:10.1093/NAR/GKZ966</p> <p> </p> <p>8. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012. doi:10.1038/nmeth.1923</p> <p> </p> <p>9. Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol 2016 345. 2016;34: 525–527. doi:10.1038/nbt.3519</p> <p> </p> <p>10. Lobo D, Godinho R, Archer JP. On taming the effect of transcript level intra-condition count variation during differential expression analysis: a story of dogs, foxes and wolves. bioRxiv. 2022; 2022.01.24.477470. doi:10.1101/2022.01.24.477470</p>
Dataset for: Tameness selection pressure affects gut virome diversity in mice
<p>This dataset comprises a non-redundant set of wild hetrogenouse stock mice virome (WHS-MV) cataleogue of 6,078 vOTUs. All 80 raw shotgun metagenomic sequencing datasets (150 bp reads) used to generate WHS-MV catalogues are available in the NCBI under BioProject PRJDB15857 with BioSample accession numbers from SAMD00614304 to SAMD00614383 and SRA accession numbers from DRR480456 to DRR480535. Raw shotgun metagenomic sequencing datasets of four samples (250 bp reads) are available under BioProject PRJDB18588, with BioSample accession numbers SAMD00805331 to SAMD00805334 and SRA accession numbers DRR585793 to DRR585796.</p>
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