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1,170 results for “Compression”
Compressed COBS indexes (XZ) - Full 661k - Part 1
<p><strong>Compressed COBS indexes (XZ) - Full 661k - v0.0.2</strong> – <a href="https://doi.org/10.5281/zenodo.7313926">part1</a>, <a href="https://doi.org/10.5281/zenodo.7313942">part2</a>, <a href="https://doi.org/10.5281/zenodo.7315499">part3</a></p> <p>Part 1 of the compressed COBS indexes built from all assemblies of the 661k dataset. More information can be found on <a href="https://brinda.eu/mof/">https://brinda.eu/mof/</a>.</p> <p><strong>Citation:</strong></p> <blockquote> <p>K. Břinda, L. Lima, S. Pignotti, N. Quinones-Olvera, K. Salikhov, R. Chikhi, G. Kucherov, Z. Iqbal, and M. Baym, <a href="https://doi.org/10.1101/2023.04.15.536996"><strong>Efficient and robust search of microbial genomes via phylogenetic compression</strong></a>, <em>bioRxiv</em> 2023.04.15.536996, 2023. <strong><a href="https://doi.org/10.1101/2023.04.15.536996">https://doi.org/10.1101/2023.04.15.536996</a></strong></p> </blockquote>
Compressed COBS indexes (XZ) - Full 661k - Part 3
<p><strong>Compressed COBS indexes (XZ) - Full 661k - v0.0.2</strong> – <a href="https://doi.org/10.5281/zenodo.7313926">part1</a>, <a href="https://doi.org/10.5281/zenodo.7313942">part2</a>, <a href="https://doi.org/10.5281/zenodo.7315499">part3</a></p> <p>Part 3 of the compressed COBS indexes built from all assemblies of the 661k dataset. More information can be found on <a href="https://brinda.eu/mof/">https://brinda.eu/mof/</a>.</p> <p><strong>Citation:</strong></p> <blockquote> <p>K. Břinda, L. Lima, S. Pignotti, N. Quinones-Olvera, K. Salikhov, R. Chikhi, G. Kucherov, Z. Iqbal, and M. Baym, <a href="https://doi.org/10.1101/2023.04.15.536996"><strong>Efficient and robust search of microbial genomes via phylogenetic compression</strong></a>, <em>bioRxiv</em> 2023.04.15.536996, 2023. <strong><a href="https://doi.org/10.1101/2023.04.15.536996">https://doi.org/10.1101/2023.04.15.536996</a></strong></p> </blockquote>
Compressed Database of Klebsiella pneumoniae for WhatsGNU
<p>WhatsGNU_Kp_Ortholog.zip: <em>Klebsiella pneumoniae</em> Version-04/28/2020 (compressed 46,072,343 proteins in 8752 genomes to 1,466,934 protein variants). Updated File to fix issue with download.</p>
Interlocked thin-ply reinforcements for improved fracture toughness and compression after impact - 0 degree tabs
<p>This dataset contains data showing the effect of thin-ply reinforcement units, interlocked with a tab-and-slit geometry, on the fracture toughness of CFRP laminates. This dataset forms an addition to the dataset previously published here: https://doi.org/10.5281/zenodo.1476886. The previous dataset contains toughness data for reinforcements with tabs at 45 degrees. This dataset contains toughness data for reinforcements with tabs at 0 degrees.</p> <p>The reinforcement concept was first presented at the 18th European Conference on Composite Materials (2018, Athens, Greece). More information on the concept can be found at: http://wwwf.imperial.ac.uk/aeronautics/research/pinholab/interlock-tabs/. Links to publications connected to this data will be added to the Zenoto meta-data as they are published.</p> <p>For the reinforcement concept, both mode I and mode II fracture toughnesses were measured. The mode I data was acquired using DCB specimens, and the mode II data was obtained from 4-point end notch flexure (4ENF) tests. Force, displacement, crack length, and strain energy release rate during the test are provided for all specimens.</p>
PHASTA compressible test case for two processes
<p>Input files and execution instructions for a PHASTA compressible flow case using two processes. The expected results are included in the included README.md.</p>
Using coupled micropillar compression and micro-Laue diffraction to investigate deformation mechanisms in a complex metallic alloy Al13Co4
<p>In this investigation, we have used <em>in-situ</em> micro-Laue diffraction combined with micropillar compression of focused ion beam milled Al<sub>13</sub>Co<sub>4</sub> complex metallic alloy to study the evolution of deformation in Al<sub>13</sub>Co<sub>4</sub>. Streaking of the Laue spots showed that the onset of plastic flow occured at stresses as low as 0.8 GPa, although macroscopic yield only becomes apparent at 2 GPa. The measured misorientations, obtained from peak splitting, enabled the geometrically necessary dislocation density to be estimated as 1.1 x 10<sup>13</sup> m<sup>-2</sup>.</p>
Example data map compressed with ISO29500-2 with 3 entry point for ArcGIS, MiraMon and OWS context file.
<p>A simple map consisting of a 1:1 000 000 country boundaries vector file, produced by the FAO (United Nations – FAOStat; geodata.grid.unep.ch/options.php?selectedID=2135) on top of a 5’ digital elevation model raster file (produced by the NOAA and NGDC; geodata.grid.unep.ch/options.php?selectedID=1414). Data has been obtained from the UNEP EDE Data Portal (UNEP 2013). Vector file is a Shapefile (a de facto standard) (ESRI 1998), while the raster file consists of either a raw signed 16-bit data or a long known TIFF file (Adobe 1992, Perkins 1995). Metadata and symbolization files are included. OPC specifies how to explicitly relate different parts using .rels files. These files are XML files with the same name as that of its respective source part, adding “.rels” and placed in a “rels” folder. Each of these files lists the target parts related to its source and the semantics of this relation.</p> <p>OPC can define entry points to the data by listing them in a “.rels” part in the root “rels” folder. In this file, three map files: for the ESRI software a world.mxd map, for the MiraMon software a world.mmm map, and a world.xml map in the form of an atom file following the new Web Service common standard (OGC OWS) context document. A geospatial application reading the package will determine which entry part it better supports to start recovering the data.</p>
Data for analysis in "Towards optimal cosmological parameter recovery from compressed bispectrum statistics"
<p>Measures of the three point function extracted from a suite of simulations using 4 different estimators: namely, the bispectrum, modal estimator, integrated bispectrum, line correlation function. Also supplied are power spectrum measures across the same simulations. <br> <br> The measures are done across 200 fiducial and 60 non-fiducial cosmology simulations, at 3 redshifts. Further details on what was done can be attained by reading the document, Overview.md/Overview.pdf, attached to the bundle. Even more details can be acquired by reading the paper this data was prepared for at https://arxiv.org/abs/1705.04392! </p>
Source files and reconstructions for "Simple 3D compressed sensing scheme for faster and less phototoxic fluorescence microscopy imaging"
<p>Source files and reconstructions for "Simple 3D compressed sensing scheme for faster and less phototoxic fluorescence microscopy imaging"</p> <p>The source files are to be used with the code on https://github.com/MaximeMaW/CompressedSensingMicroscopy3D (also archived in https://zenodo.org/record/439690)</p> <ol> <li>The files prefixed with "VIZ" are high resolution TIF visualizations.</li> <li>The files come from three experiments on two different setups: <ol> <li>A lattice light sheet microscope (LLSM): beads sample (filed termed "<strong>lattice-beads</strong>" and actin-labelled mESCs (files termed "<strong>lattice-phalloidin</strong>")</li> <li>An epifluorescence microscope: beads sample (files termed "<strong>epifluorescence</strong>")</li> </ol> </li> <li>The acquisitions were either performed using an identity measurement matrix (mimicking the plane-by-plane acquisition mode of a traditional z-stack): files termes "<strong>reference</strong>" or with a Fourier measurement matrix (described in the code mentioned above) with a compression ratio of 2 (files termed "<strong>compressed</strong>".</li> <li>The reconstructions were performed as described in the paper with the code mentioned above. Several reconstructions were computed from the same compressed images by simulating increasing compression ratios. To do so, reconstructions were performed by selecting a subset of the acquired planes (number indicated as "<strong>**frames</strong>")</li> <li>Reconstructions were sparsified using a 2D PSF model computed for our epifliuorescence setup and the LLSM (files termed "<strong>PSF_model</strong>"). These are provided as numpy arrays.</li> </ol> <p> </p>
Compressed EAMv1 simulation output for evaluating two aerosol process coupling schemes
<p>EAMv1 is version 1 of the atmosphere component of the Energy Exascale Earth System Model (E3SM, <a href="https://github.com/E3SM-Project/E3SM">https://github.com/E3SM-Project/E3SM</a>). This upload contains processed output from transient simulations conducted using the F20TRC5-CMIP6 compset. The EAMv1 source code used in the simulations can be found in <a href="https://doi.org/10.5281/zenodo.7995850">Zenodo record 7995850</a>. Scripts used to conduct and analyze the simulations can be found in <a href="https://doi.org/10.5281/zenodo.10371316">Zenodo record 10371316</a>. </p> <p>The following tarballs contain annually averaged simulation output:</p> <ul> <li>cflx_1_L30_F20TRC5-CMIP6.tar.gz</li> <li>cflx_1_L72_F20TRC5-CMIP6.tar.gz</li> <li>cflx_2_L30_F20TRC5-CMIP6.tar.gz</li> <li>cflx_2_L72_F20TRC5-CMIP6.tar.gz</li> </ul> <p>The following split archives contain 6-hourly simulation output:</p> <ul> <li>cflx_1_L30_F20TRC5-CMIP6_6h.tar.gz.*</li> <li>cflx_2_L72_F20TRC5-CMIP6_6h.tar.gz.*</li> </ul> <p>The split archives can be recombined and untarred using, e.g., the following commands: </p> <pre><code>${casename}="cflx_1_L30_F20TRC5-CMIP6_6h" cat ${casename}.tar.gz.* | tar xzvf -</code></pre> <p>A copy of the uncompressed and unsplit files can be found through <a href="https://portal.nersc.gov/project/m4359/huiwan/cflx/EAMv1_output_202311_for_Zenodo/">NERSC's web portal</a>.</p>
Data Supplement for "Phase diagram of compressible and paired states in the quarter-filled Landau level"
<p><strong>Description:</strong> This dataset provides supplemental data for the paper <em>Arxiv 2408.08354</em>, specifically the Density Correlation Function (DCF) and Harmonic Coefficients <span><span>GkG_k</span><span><span><span><span>G</span><span><span><span><span><span><span>k</span></span></span><span></span></span></span></span></span></span></span></span> (Pol) for various fractional quantum Hall wave functions, as outlined in the paper.</p> <h3>Contents:</h3> <ul> <li><strong>Density Correlation Function (DCF)</strong>: Corresponds to Eq. (4) in the paper, capturing correlation behavior in fractional quantum Hall systems.</li> <li><strong>Harmonic Coefficients <span><span>Gk</span></span> (Pol)</strong>: Corresponds to Eq. (5), representing harmonics relevant to polarization effects.</li> </ul> <h3>File Structure:</h3> <p>The data files follow the structure:</p> <ul> <li><strong>DCF[WF_name, Ne, Nc]</strong> and <strong>Pol[WF_name, Ne, Nc]</strong>: <ul> <li><code>WF_name</code>: Identifier for the wave function (details below).</li> <li><code>Ne</code>: Number of particles.</li> <li><code>Nc</code>: Lowest Landau level projection cutoff used in Eq. (C5), if projection is needed.</li> </ul> </li> </ul> <h3>Data Format:</h3> <p>The data is formatted for Mathematica, with each entry stored as a comma-separated list enclosed in curly braces <code>{}</code>. Each function entry is structured as:</p> <ul> <li><strong>DCF[WF_name, Ne, Nc] = {value, ...}</strong> and <strong>Pol[WF_name, Ne, Nc] = {value, ...}</strong></li> </ul> <h3>Error Estimation:</h3> <p>For error assessment, each wave function's data is divided into 20 batches. Each batch is averaged separately:</p> <ul> <li><strong>DCFbatch[WF_name, Ne, Nc, id]</strong> and <strong>Polbatch[WF_name, Ne, Nc, id]</strong>: <ul> <li><code>id</code>: Batch number ranging from 1 to 20.</li> </ul> </li> </ul> <h3>Wave Function Naming Conventions:</h3> <p>The naming convention used in <strong>WF_name</strong> designates the state as follows:</p> <ul> <li> <p><strong>First Letter</strong>: Filling factor</p> <ul> <li><code>H</code>: Half-filled</li> <li><code>Q</code>: Quarter-filled</li> </ul> </li> <li> <p><strong>Second and Third Letters</strong>: Pairing channel (shift)</p> <ul> <li><code>AP</code>: Anti-Pfaffian (<span><span>l=−3</span></span>)</li> <li><code>PH</code>: PH-Pfaffian (<span><span>l=−1</span></span>)</li> <li><code>MR</code>: Moore-Read (<span><span>l=1</span></span>)</li> <li><code>FW</code>: f-wave (<span><span>l=3</span></span>)</li> <li><code>Q0</code>: CFL only (<span><span>l=0</span></span>)</li> </ul> </li> <li> <p><strong>Ending Type</strong>: Wave function type</p> <ul> <li><code>S</code>: Paired state with single-particle projection.</li> <li><code>CFL</code>: Composite Fermi liquid.</li> <li><code>E</code>: Exact wave function for Moore-Read.</li> </ul> </li> </ul> <p><strong>Examples:</strong></p> <ul> <li><strong>QAPS</strong>: Quarter-filled Anti-Pfaffian wave function.</li> <li><strong>HPHCFL</strong>: Half-filled Composite Fermi liquid at PH-Pfaffian shift.</li> <li><strong>QMRE</strong>: Quarter-filled Moore-Read exact wave function without expansion of pairing function.</li> </ul> <h3>Naming Exceptions:</h3> <ul> <li><code>La</code>: Laughlin state at <span><span>ν=1/3.</span></span></li> <li><code>QSU2</code>: SU(2)<span><span>2_2</span><span><span><span><span><span><span><span></span></span></span></span></span></span></span></span> wave function, Eq. (20) with + sign at <span><span>ν=1/4</span></span> (p=2).</li> <li><code>HASU2</code> and <code>QASU2</code>: SU(2)<span><span>2_</span><span><span><span><span><span><span><span><span><span>2</span></span></span><span></span></span></span></span></span></span></span></span> wave function, Eq. (20) with - sign at <span><span>ν=1/2</span></span> and <span><span>ν=1/4</span></span> (p=1 and 2).</li> </ul>
High Temperature Compression Studies of a 6082.50 Aluminium Alloy using Deformation Dilatometer
<p>Data recorded in uniaxial compression for a 6082.50 aluminium alloy deformed at temperatures of 490C, 520C and 560C, at strain rates of 10, 1, and 0.1 s-1, to 50% height reduction, using TA Instruments DIL 805 A/D/T Quenching and Deformation Dilatometer. The cylindrical samples measured 5 mm diameter and 10 mm height. The 6082.50 aluminium specimens were machined from an as-cast billet. Two homogenisation have been performed on this material, one at 590C for 8h and one at 520C for 2h. These are identified as homogenisation 1 and homogenisation 2 in the data. Al2O3 platens were used for all tests, with Mo discs superglued at both ends of the sample to maximise thermal contact. Tests were conducted in an inert He gas atmosphere under a vacuum of 1e-5 mbar. The temperature was controlled using an K-Type thermocouple spot-welded to the centre of the samples with another K-Type thermocouple welded halfway between the centre and end to measure the thermal gradient. Not all of these second thermocouples provided data due to breakages. </p> <p>Data recorded at high acquisition frequency during deformation is stored in the 'data_deformation' folder and saved with the format: ' test number (002 to 038)_Compression_Daniel_Al_(homogenisation treatment - see above)_SHT_540C_Deform_(Deformation temperature)_(deformation strain rate)_QuenchHeGas__1. Here SHT_540C refers to the solutionising treatment and QuenchHeGas__1 refers to the method of cooling after deformation. This dataset does not include readings from the off-centre thermocouple. Data in the 'data_basic' folder is recorded at a lower acquisition frequency but includes a recording of the entire thermomechanical cycle, including both heating and cooling stages, as well as deformation. The 'method' folder includes contains the temperature and deformation profiles used. 'pictures' includes images taken of the samples and set up during the experiment. </p>
SLAC/MEC LJ55 experiment on hcp-Fe plasticity under shock compression
<p>Raw data for experiment LJ55 at SLAC/MEC on hcp-Fe strength and plasticity: X-ray diffraction data and X-ray beam energies.</p> <p>Corresponding publication is published in <em>Physical Review Letters</em>: S. Merkel, S. Hok, C. Bolme, D. Rittman, K. J. Ramos, B. Morrow, H. J. Lee, B. Nagler, E. Galtier, E. Granados, A. Hashim, W. L. Mao, and A. E. Gleason, Femtosecond Visualization of hcp-Iron Strength and Plasticity under Shock Compression, <em>Physical Review Letters</em>, 127, 205501 (2021), [doi: <a href="http://dx.doi.org/10.1103/PhysRevLett.127.205501">10.1103/PhysRevLett.127.205501</a>]</p>
Global and tropical band averages for a selection of CMIP5 and CMIP6 models: piControl and abrupt-4xCO2 experiments (compressed)
<p>This dataset provides post-processed spatial averages for a selection of 55 CMIP5 and CMIP6 models. The experiments contained in this dataset are only the pre-industrial controls (piControl) and the experiments with a four-fold increase in the atmospheric CO$_{2}$ concentration in relation to the pre-industrial level (abrupt-4xCO2). The spatial averages are global and tropical bands from x°S to x°N, where the x value is between 5 and 40 in increments of 5°. This dataset was created to study climate sensitivity in general and the effect of stratospheric circulation changes on the tropical equilibrium climate sensitivity. It contains the following variables:</p> <ul> <li>incoming (d) short-wave (SW, s) radiative flux (RF, r) at the top of the atmosphere (TOA, t): rsdt</li> <li>outgoing (u) SW RF at TOA: rsut</li> <li>outgoing long-wave (LW, l) RF at TOA: rlut</li> <li>net (n) RF at TOA: rnt*</li> <li>incoming SW RF at the surface (s): rsds</li> <li>outgoing SW RF at the surface: rsus</li> <li>incoming LW RF at the surface: rlds</li> <li>outgoing LW RF at the surface: rlus</li> <li>net RF at the surface: rns*</li> <li>sensible heat flux (hfs) at the surface: hfss</li> <li>latent heat flux (hfl) at the surface: hfls</li> <li>surface temperature (t): ts</li> <li>atmospheric temperature: ta</li> <li>specific humidity: hus</li> <li>zonal component of wind: ua</li> <li>meridional component of wind: va</li> <li>lagrangian tendency of pressure (vertical component of wind in pressure per time dimensions): wap</li> <li>surface pressure: ps</li> <li>geopotential height: zg</li> </ul> <p>*rnt and rns were calculated for the creation of this dataset using the model output rlut rsut, rsds, rsus, rlds, rlus.</p> <p>This version updates the previous version by providing the dataset in a compressed tarball. Use `tar -xzvf CMIP_data.tar.gz` to extract and decompress.</p>
F-actin Imaging of Mechanically Compressed Pseudostratified Human Bronchial Epithelial Cells
<p><strong>Overview</strong></p> <p>This dataset includes immunofluorescence microscopy of pseudostratified airway epithelial cells stained for F-actin. Each field of view consists of 3 images visualizing the apical cell boundaries, basal cell boundaries, and basal cell stress fibers.</p> <p><strong>Cell Culture and Treatment</strong></p> <p>Primary human bronchial epithelial cells (from a single donor) were grown on transwells in air-liquid interface culture for 14 days to model a well-differentiated, pseudostratified airway epithelium. Cells were then exposed to mechanical compression (30 cmH2O for 3 hours) mimicking asthmatic bronchoconstriction. Cells were fixed (4% PFA for 30 minutes) at 24, 48, or 72 hours after mechanical compression. Two transwells were collected per condition and timepoint.</p> <p><strong>Immunofluorescence Imaging</strong></p> <p>Fixed transwells were stained for F-actin (Alexa fluor 488-Phalloidin, ThermoFisher Scientific, diluted 1:40, 30 minutes). Transwell membranes were cut from the plastic support and mounted on glass slides. Slides were imaged using a Zeiss Axio Observer Z1 with an apotome module controlled using Zen Blue 2.0 software. Five random fields of view were imaged from each transwell membrane in a z-stack from substrate to apical cell surface. To visualize various planes through the pseudostratified epithelial layer (apical cell boundaries, basal cell boundaries, and basal cell stress fibers), maximum intensity projections were generated from regions of interest through the z-stack.</p> <p><strong>Dataset</strong></p> <p>Each image file contains</p> <ul> <li>Timepoint: <strong>24</strong>, <strong>48</strong>, or <strong>72 </strong>hours after treatment</li> <li>Condition & Well: control <strong>(C) </strong>or mechanical compression<strong> (P) </strong>followed by a number indicating the well (1 or 2)</li> <li>Unique Z-stack ID: <strong><em>3-digit number</em></strong></li> <li><em>Miscellaneous note: MIP or MIP_ROI</em></li> <li>Region of Interest: apical cell boundaries (<strong>ACB</strong>), basal cell boundaries (<strong>BCB</strong>), or basal stress fibers (<strong>SF</strong>)</li> </ul> <p>For example, these 3 maximum intensity projection images came from the<em> same z-stack/field of view. </em>They are from the 72 hour timepoint, mechanical compression, well #2, z-stack #147:</p> <ul> <li>72hr_P2_147_MIP_ACB.tif: <em>apical cell boundaries</em></li> <li>72hr_P2_147_MIP_ROI_BCB.tif: <em>basal cell boundaries</em></li> <li>72hr_P2_147_MIP_ROI_SF.tif: <em>basal stress fiber</em></li> </ul>
Phase Contrast Time-Lapse and F-actin Imaging of Mechanically Compressed or Irradiated Pseudostratified Human Bronchial Epithelial Cells
<p><strong>Overview</strong></p> <p>This dataset includes phase contrast time-lapse imaging of <em>in vitro</em> pseudostratified airway epithelial cells to visualize their collective cellular migration after exposure to mechanical compression (mimicking bronchoconstriction) or irradiation. Additionally, the cells were fixed and stained for F-actin to visualize the apical cell boundaries, basal cell boundaries, and basal cell stress fibers.</p> <p><strong>Cell Culture and Treatment</strong></p> <p>Primary human bronchial epithelial cells (from a single donor) were grown on transwells in air-liquid interface (ALI) culture for 14 days to model a well-differentiated, pseudostratified airway epithelium. Cells were then exposed to either mechanical compression (30 cmH2O for 3 hours) mimicking asthmatic bronchoconstriction or irradiation (1Gy of ionizing radiation using a RS 2000 Biological Research Irradiator (RadSource) on ALI days 7, 10, and 14).</p> <p><strong>Phase Contrast Time-Lapse Imaging</strong></p> <p>At 24 or 72 hours after final treatment, cells were imaged to visualize collective cellular migration. For each independent experimental replicate (2 transwells per treatment per timepoint), six fields of view per well were imaged every 6 minutes over 1.5 hours. The imaging chamber was supplied with 37°C, 5% CO2, humidified air on a Zeiss Axio Observer Z1 to collect phase contrast images. <em>The image resolution is 0.586 µm/pixel.</em></p> <p><strong>Immunofluorescence Imaging</strong></p> <p>Cells were fixed (4% PFA for 30 minutes) at 24 or 72 hours after final treatment (and after phase contrast time-lapse imaging). Fixed transwells were stained for F-actin (Alexa fluor 488-Phalloidin, ThermoFisher Scientific, diluted 1:40, 30 minutes). Transwell membranes were cut from the plastic support and mounted on glass slides. Slides were imaged using a Zeiss Axio Observer Z1 with an apotome module controlled using Zen Blue 2.0 software. Five random fields of view were imaged from each transwell membrane in a z-stack from substrate to apical cell surface. To visualize various planes through the pseudostratified epithelial layer (apical cell boundaries, basal cell boundaries, and basal cell stress fibers), maximum intensity projections were generated from regions of interest through the z-stack. <em>The image resolution is 0.293 µm/pixel.</em></p> <p><strong>Dataset</strong></p> <p>Phase contrast time-lapse movies are provided as *.avi files. Immunofluorescence images are provided as *.tif files. For an individual transwell, the imaging dataset includes:</p> <ul> <li>6 phase contrast time-lapse movies</li> <li>5 immunofluorescence images of apical cell boundaries</li> <li>5 immunofluorescence images of basal cell boundaries</li> <li>5 immunofluorescence images of basal cell stress fibers</li> </ul> <p>Phase contrast time-lapse filenames contain</p> <ul> <li>Donor: U13</li> <li>Timepoint: 24 or 72 hours</li> <li>Treatment & Well: control (C), mechanical compression (P), or irradiation (R); well 1 or 2</li> <li>Field of View: (1) – (6)</li> </ul> <p>Immunofluorescence image filenames contain:</p> <ul> <li>Donor: <strong>U13</strong></li> <li>Timepoint: <strong>24</strong> or <strong>72</strong> hours</li> <li>Treatment & Well: control (<strong>C</strong>), mechanical compression (<strong>P</strong>), or irradiation (<strong>R</strong>); well <strong>1</strong> or <strong>2</strong></li> <li>Field of View: <strong>1-5</strong></li> <li>Region of Interest: apical cell boundaries (<strong>ACB</strong>), basal cell boundaries (<strong>BCB</strong>), or basal stress fibers (<strong>SF</strong>)</li> </ul> <p>Phase contrast time-lapse and immunofluorescence from the same transwell will all start with the same “Donor_Timepoint_Treatment/Well...” (i.e. U13_24_C1…). <strong>Note that the images from phase contrast and immunofluorescence are not necessarily from matched locations within the transwell and are at different spatial scales.</strong></p> <p>Immunofluorescence images from the same z-stack field of view will start with the same “Donor_Timepoint_Treatment/Well_FieldofView…” (i.e. U13_24_C1_1…).</p>
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. 1. Diplopanax cacaoides (ZENKER) comb. nov. a–d: [Holotype of Mastixia cantia E.REID et M.CHANDLER, V.22953]. a: Lateral view of longitudinally broken specimen, reflected light. b–d: Surface renderings from micro-CT data. b: Lateral view of longitudinal fracture surface. c: Same specimen rotated to show external surface. d: Enlargement of lower half from (a, b), reflected light. e, f: Specimen figured originally as a paratype of M. cantia, V.22954 (Reid and Chandler 1933: pl. 25, fig. 3), reflected light. e: Ventral view with much of the endocarp wall fallen away exposing smooth convex ventral surface of locule cast. f: Transversely fractured surface, showing thick wall of the endocarp, and dehiscence plane leading to the left limb of the locule. g: Transversely sectioned, laterally compressed specimen from Miocene of Wiesa, Germany for comparison, Senckenberg Museum, SM.B. 21034/I. h–j: Digital transverse sections from micro-CT data of the Holotype V.22953. h: Transverse fracture surface from (b), showing curved locule and zone of weakness defining the germination valve (arrow), reflected light. i: Same orientation with clear demarcation of the separation plane of the germination valve (arrow), digital section from micro-CT scan. j: Enlargement from (h). Scale bars 5 mm. in Mastixioid Fruits (Cornales) From The Early Eocene London Clay Flora: Morphology, Anatomy And Nomenclatural Revision
Text-fig. 1. Diplopanax cacaoides (ZENKER) comb. nov. a–d: [Holotype of Mastixia cantia E.REID et M.CHANDLER, V.22953]. a: Lateral view of longitudinally broken specimen, reflected light. b–d: Surface renderings from micro-CT data. b: Lateral view of longitudinal fracture surface. c: Same specimen rotated to show external surface. d: Enlargement of lower half from (a, b), reflected light. e, f: Specimen figured originally as a paratype of M. cantia, V.22954 (Reid and Chandler 1933: pl. 25, fig. 3), reflected light. e: Ventral view with much of the endocarp wall fallen away exposing smooth convex ventral surface of locule cast. f: Transversely fractured surface, showing thick wall of the endocarp, and dehiscence plane leading to the left limb of the locule. g: Transversely sectioned, laterally compressed specimen from Miocene of Wiesa, Germany for comparison, Senckenberg Museum, SM.B. 21034/I. h–j: Digital transverse sections from micro-CT data of the Holotype V.22953. h: Transverse fracture surface from (b), showing curved locule and zone of weakness defining the germination valve (arrow), reflected light. i: Same orientation with clear demarcation of the separation plane of the germination valve (arrow), digital section from micro-CT scan. j: Enlargement from (h). Scale bars 5 mm.
Text-fig. 3. Examples of plant macrofossil assemblages from post-evaporitic sections. a: bedding plane from Ciabòt Cagna covered by impressions of plant parts, with dominance of leaves of cf. Oleinites liguricus M.SACHSE, MCEA-P05038. b: waterloggedcompressed seeds of Toddalia latisiliquata (R.LUDW.) H.-J.GREGOR sieved out of a bulk sediment sample from Pollenzo, MGPTPU141033. c: millimeter-sized, waterlogged-compressed seeds of Sambucus pulchella C.REID et E.REID with abundant cracks, probably formed during both diagenesis and extraction of the fossils (bulk sediment sample from Ciabòt Cagna), MGPT- in Late Messinian Flora From The Post-Evaporitic Deposits Of The Piedmont Basin (Northwest Italy)
Text-fig. 3. Examples of plant macrofossil assemblages from post-evaporitic sections. a: bedding plane from Ciabòt Cagna covered by impressions of plant parts, with dominance of leaves of cf. Oleinites liguricus M.SACHSE, MCEA-P05038. b: waterloggedcompressed seeds of Toddalia latisiliquata (R.LUDW.) H.-J.GREGOR sieved out of a bulk sediment sample from Pollenzo, MGPTPU141033. c: millimeter-sized, waterlogged-compressed seeds of Sambucus pulchella C.REID et E.REID with abundant cracks, probably formed during both diagenesis and extraction of the fossils (bulk sediment sample from Ciabòt Cagna), MGPT-
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.
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Allen Brain Atlas
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