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1,773 results for “Supplementary data,”
Supplementary data for analysing distributed temperature sensing (DTS) measurements from Helsinki, Finland
<p>Supplementary data used in the analysis of distributed temperature sensing (DTS) measurements from Helsinki, Finland, as described in a journal article manuscript "Quantifying coastal urban surface layer structure using distributed temperature sensing in Helsinki, Finland".</p> <p>Eddy covariance, radiation and precipitation data is provided from the SMEAR III station by the Institute for Atmospheric and Earth System Research at the University of Helsinki under Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/). The data can also be accessed programmatically via https://smear.avaa.csc.fi/. All SMEAR III data is time referenced to UTC+2.</p> <p>The 2-metre temperature data is provided by the Finnish Meteorological Institute under Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/). All Finnish Meteorological Institute data is referenced to UTC.</p>
Supplementary data: Accurate large-scale simulations of siliceous zeolites by neural network potentials
<p><strong>Content</strong></p> <p><em>1. Zeolite databases</em></p> <ul> <li>Deem database containing 331170 hypothetical zeolite frameworks [Deem09, Pophale11] geometrically optimized at the NNPscan level (note, the first row of the database is alpha-quartz): "DEEM_NNPscan.db"</li> <li>Database of 236 exiting zeolite frameworks of the <a href="http://www.iza-structure.org/databases/">International Zeolite Association (IZA) </a>optimized at the NNPscan level: "IZA_NNPscan.db"</li> <li>Both databases are <a href="https://wiki.fysik.dtu.dk/ase/ase/db/db.html">ASE SQLite database files</a> of the <a href="https://wiki.fysik.dtu.dk/ase/index.html">Atomic Simulation Environment</a> containing the ASE <a href="https://wiki.fysik.dtu.dk/ase/ase/atoms.html">Atoms objects</a> with energies and forces (NNPscan level); readable with ASE's <a href="https://wiki.fysik.dtu.dk/ase/ase/io/io.html">I/O module</a></li> <li>Additionally, relevant quantities can be extracted with, e.g., the following queries (further information: ase db --help):</li> </ul> <pre><code class="language-bash">ase db DEEM_NNPscan.db -c id,formula,natoms,volume,mass,density,energy_per_tsite,n_tsites,relative_energy # Output id|formula|natoms| volume| mass|density|energy_per_tsite|n_tsites|relative_energy 1|O6Si3 | 9|111.161|180.249| 26.988| -31.796| 3| 0.000 2|O16Si8 | 24|433.858|480.664| 18.439| -31.638| 8| 15.265 3|O16Si8 | 24|421.114|480.664| 18.997| -31.596| 8| 19.359 4|O16Si8 | 24|426.557|480.664| 18.755| -31.614| 8| 17.613 5|O16Si8 | 24|412.410|480.664| 19.398| -31.613| 8| 17.677 6|O16Si8 | 24|393.544|480.664| 20.328| -31.594| 8| 19.546 7|O16Si8 | 24|422.400|480.664| 18.939| -31.657| 8| 13.476 8|O16Si8 | 24|394.405|480.664| 20.284| -31.581| 8| 20.797 9|O12Si6 | 18|265.201|360.498| 22.624| -31.611| 6| 17.868 10|O16Si8 | 24|357.047|480.664| 22.406| -31.581| 8| 20.785 11|O16Si8 | 24|434.894|480.664| 18.395| -31.621| 8| 16.911 12|O16Si8 | 24|384.158|480.664| 20.825| -31.657| 8| 13.448 13|O12Si6 | 18|258.977|360.498| 23.168| -31.679| 6| 11.278 14|O16Si8 | 24|466.429|480.664| 17.152| -31.593| 8| 19.588 15|O16Si8 | 24|423.469|480.664| 18.892| -31.639| 8| 15.179 16|O16Si8 | 24|450.716|480.664| 17.750| -31.628| 8| 16.219 17|O16Si8 | 24|331.528|480.664| 24.131| -31.642| 8| 14.857 18|O16Si8 | 24|458.573|480.664| 17.445| -31.635| 8| 15.572 19|O16Si8 | 24|359.298|480.664| 22.266| -31.655| 8| 13.636 20|O16Si8 | 24|464.264|480.664| 17.232| -31.612| 8| 17.750 Rows: 331171 (showing first 20) Keys: density, energy_per_tsite, n_tsites, relative_energy ase db IZA_NNPscan.db -c id,formula,natoms,volume,mass,density,energy_per_tsite,n_tsites,relative_energy,iza_code # Output id|formula |natoms| volume| mass|density|energy_per_tsite|n_tsites|relative_energy|iza_code 1|O16Si8 | 24| 435.488| 480.664| 18.370| -31.676| 8| 11.594|ABW 2|O32Si16 | 48| 961.419| 961.328| 16.642| -31.645| 16| 14.612|ACO 3|O96Si48 | 144|3154.579|2883.984| 15.216| -31.664| 48| 12.810|AEI 4|O80Si40 | 120|2102.921|2403.320| 19.021| -31.703| 40| 9.021|AEL 5|O96Si48 | 144|2417.286|2883.984| 19.857| -31.666| 48| 12.586|AEN 6|O144Si72| 216|4075.300|4325.976| 17.667| -31.674| 72| 11.831|AET 7|O96Si48 | 144|2786.810|2883.984| 17.224| -31.675| 48| 11.716|AFG 8|O48Si24 | 72|1400.247|1441.992| 17.140| -31.690| 24| 10.268|AFI 9|O64Si32 | 96|1764.823|1922.656| 18.132| -31.653| 32| 13.809|AFN 10|O80Si40 | 120|2080.330|2403.320| 19.228| -31.707| 40| 8.632|AFO 11|O64Si32 | 96|2097.384|1922.656| 15.257| -31.655| 32| 13.622|AFR 12|O112Si56| 168|3820.116|3364.648| 14.659| -31.650| 56| 14.150|AFS 13|O144Si72| 216|4732.720|4325.976| 15.213| -31.664| 72| 12.793|AFT 14|O60Si30 | 90|1897.074|1802.490| 15.814| -31.659| 30| 13.268|AFV 15|O96Si48 | 144|3154.885|2883.984| 15.214| -31.664| 48| 12.776|AFX 16|O32Si16 | 48|1137.335| 961.328| 14.068| -31.591| 16| 19.790|AFY 17|O48Si24 | 72|1283.812|1441.992| 18.694| -31.620| 24| 17.034|AHT 18|O96Si48 | 144|2479.287|2883.984| 19.360| -31.681| 48| 11.155|ANA 19|O64Si32 | 96|1797.086|1922.656| 17.807| -31.662| 32| 12.924|APC 20|O64Si32 | 96|1751.393|1922.656| 18.271| -31.678| 32| 11.422|APD Rows: 236 (showing first 20) Keys: density, energy_per_tsite, iza_code, n_tsites, relative_energy # Filtering of the database, e.g., for structures with relative energies < 10 kJ/(mol Si) ase db IZA_NNPscan.db relative_energy\<10 -c density,energy_per_tsite,n_tsites,relative_energy,iza_code # Output density|energy_per_tsite|n_tsites|relative_energy|iza_code 19.021| -31.703| 40| 9.021|AEL 19.228| -31.707| 40| 8.632|AFO 19.385| -31.695| 24| 9.802|ATV 18.778| -31.702| 34| 9.061|DOH 19.570| -31.693| 24| 9.959|EWO 18.401| -31.698| 32| 9.451|GON 18.551| -31.695| 112| 9.807|IHW 17.778| -31.693| 288| 9.972|IMF 19.154| -31.695| 6| 9.762|JBW 18.187| -31.695| 96| 9.734|MFI 19.278| -31.709| 48| 8.443|MRE 18.035| -31.698| 90| 9.481|MSO 20.417| -31.724| 44| 7.003|MTF 19.227| -31.704| 136| 8.898|MTN 18.542| -31.693| 28| 9.966|MTW 19.137| -31.695| 60| 9.798|PCR 20.037| -31.709| 144| 8.464|PSI 18.843| -31.703| 64| 9.004|SAF 18.371| -31.703| 112| 8.975|STO 19.894| -31.706| 17| 8.671|VET Rows: 20 (showing first 20) Keys: density, energy_per_tsite, iza_code, n_tsites, relative_energy</code></pre> <ul> <li>The quantities shown above are available with the keys (besides standard ASE database keys):</li> </ul> <table> <thead> <tr> <th scope="col">Key</th> <th scope="col">Quantity</th> <th scope="col">Unit</th> </tr> </thead> <tbody> <tr> <td>id</td> <td>Identifier</td> <td> </td> </tr> <tr> <td>formula</td> <td>Chemical formula of the unit cell</td> <td> </td> </tr> <tr> <td>natoms</td> <td>Number of atoms</td> <td> </td> </tr> <tr> <td>volume</td> <td>Unti cell volume</td> <td>Å<sup>3</sup></td> </tr> <tr> <td>mass</td> <td>Atomic mass of the unit cell</td> <td>amu</td> </tr> <tr> <td>density</td> <td>Framework density</td> <td>Si/nm<sup>3</sup></td> </tr> <tr> <td>energy_per_tsite</td> <td>NNPscan energy</td> <td>eV</td> </tr> <tr> <td>n_tsites</td> <td>Number of T-sites</td> <td> </td> </tr> <tr> <td>relative_energy</td> <td>Energy with respect to quartz</td> <td>kJ/(mol Si)</td> </tr> <tr> <td>iza_code</td> <td>only for 'IZA_NNPscan.db'</td> <td> </td> </tr> </tbody> </table> <ul> <li> Comma separated csv files for the quantities listed above: "DEEM_NNPscan.csv" and "IZA_NNPscan.csv"</li> </ul> <p><em>2. Neural network potentials (NNP) for silica</em></p> <ul> <li>SchNet [Schütt18,Schütt19] NNP files trained on DFT data at the PBE+D3 (NNPpbe) and SCAN+D3 level (NNPscan)</li> <li>Simulations can be performed using <a href="https://schnetpack.readthedocs.io/en/stable/getstarted/getstarted.html#references">SchNetPack</a> with its ASE calculator</li> <li>This example shows a simple single-point calculation</li> </ul> <pre><code class="language-python">import ase.io import torch from schnetpack.interfaces import SpkCalculator from schnetpack.environment import AseEnvironmentProvider # check if GPU(s) are available if torch.cuda.is_available(): device = "cuda" else: device = "cpu" # load the NNP model model = torch.load('SiOscan1', map_location=device) # read some structure atoms = ase.io.read( ... ) # define SchNetPack calculator calc = SpkCalculator(model=model, device=device, energy='energy', forces='forces', environment_provider=AseEnvironmentProvider(6.) ) # attach calculator to atoms object atoms.set_calculator(calc) # perform simulations, e.g., single-point calculation energy = atoms.get_potential_energy() print(energy)</code></pre> <p><em>3. Test set used for accuracy evaluation (ASE database: test_set_NNPscan.db)</em></p>
Supplementary data to Dating the timbers from the 'Sparrow-Hawk', a shipwreck from Cape Cod, USA. Journal of Archaeological Science: Reports 103374
<p>This record gives access to all supplementary data that forms the background to the paper: Daly, A., Hocker, F. & Mires, C., 2022. Dating the timbers from the ‘Sparrow-Hawk’, a shipwreck from Cape Cod, USA. Journal of Archaeological Science: Reports https://doi.org/10.1016/j.jasrep.2022.103374</p> <p>In 1626, a vessel making its way to Virginia was forced off course and damaged in a storm, which drove the ship onto the eastern shore of the Cape Cod peninsula, Massachusetts. Onboard were two English merchants and some servants and farmers, many of whom were Irish. In 1863, a storm exposed the weathered remains of a vessel at Old Ship Harbor. At the time, it was hailed as the same ship that had brought the Virginia-bound passengers to Plymouth in 1626. Recent wiggle-match C14 dating and dendrochronology suggests that this is indeed a ship from the early seventeenth century.</p>
Supplementary input data for accounting for component condition and preventive retirement in power system reliability of supply analyses
<div> <div>This data set contains supplementary data used for case studies on accounting for transformer condition in reliability of supply analyses in the following manuscripts: <br>1) H. Toftaker, J. Foros, I. B. Sperstad, "Accounting for component condition and preventive retirement in power system reliability of supply analyses", IET Generation, Transmission & Distribution, vol. 5, no. 1, 2023, DOI: 10.1049/gtd2.12761. <br>2) I. Bjerkebæk, I. B. Sperstad, H. Toftaker, G. Kjølle, "Simulating the Long Term Effect of Asset Management Strategies on Reliability of Supply", pre-print submitted for peer review, 2024. DOI: 10.36227/techrxiv.172107759.95745501/v1.</div> <div> See README.md for details.</div> </div>
Global restoration opportunities in tropical rainforest landscapes - Supplementary Materials - Spatial Data Layers
<p><strong>Global restoration opportunities in tropical rainforest landscapes</strong></p> <p><strong>Sci Adv 5 (7), eaav3223</strong></p> <p><strong>DOI: 10.1126/sciadv.aav3223</strong></p> <p><strong><a href="https://advances.sciencemag.org/content/5/7/eaav3223">https://advances.sciencemag.org/content/5/7/eaav3223</a></strong></p> <p><strong>Supplementary Materials</strong></p> <p><strong><a href="https://advances.sciencemag.org/content/suppl/2019/07/01/5.7.eaav3223.DC1">https://advances.sciencemag.org/content/suppl/2019/07/01/5.7.eaav3223.DC1</a></strong></p> <p><strong>Spatial Data layers:</strong></p> <p><strong><a href="https://doi.org/10.5281/zenodo.3233495">https://doi.org/10.5281/zenodo.3233495</a></strong></p> <p><strong>_OutR10:</strong></p> <p><strong>r_10.img → Global restoration opportunity score (ROS)</strong></p> <p><strong>r_10_sc.img → Global restoration opportunity score (ROS) – rescaled 0-1</strong></p> <p><strong>r_10_nt_sc.img → Neo Tropic restoration opportunity score (ROS) – rescaled 0-1</strong></p> <p><strong>r_10_aa_sc.img → Australiasia restoration opportunity score (ROS) – rescaled 0-1</strong></p> <p><strong>r_10_at_sc.img → Afro Tropic restoration opportunity score (ROS) – rescaled 0-1</strong></p> <p><strong>r_10_im_sc.img → Indo Malay restoration opportunity score (ROS) – rescaled 0-1</strong></p> <p><strong>r_10_nt_sc.img → Neo Tropic restoration opportunity score (ROS) – rescaled 0-1</strong></p> <p> </p> <p><strong>_OutBasics:</strong></p> <p><strong>r_1.img → Study Area</strong></p> <p><strong>r_2.img → Restorable Area</strong></p> <p><strong>r_3.img → Restoration Benefits</strong></p> <p><strong>r_4.img → Restoration feasibility</strong></p> <p><br> <strong>_OutCountry:</strong></p> <p><strong>r_10_XXX_sc.tif → restoration opportunity score (ROS) for country XXX – rescaled 0-1</strong></p> <p><br> <strong>_OutHotspots:</strong></p> <p><strong>r_10_hotspot_XXX_hotspot_area_sc.tif → restoration opportunity score (ROS) for conservation hotspot area XXX – rescaled 0-1</strong></p> <p><strong>r_10_hotspots_upper60.img → Areas with restoration opportunity score (ROS) above 0.6 in conservation hotspots</strong></p> <p><br> <strong>_OutKBA:</strong></p> <p><strong>r_10_XXX_sc.tif → restoration opportunity score (ROS) for Key Biodiversity Area XXX – rescaled 0-1</strong></p> <p><strong>r_10_kba_upper60.img → Areas with restoration opportunity score (ROS) above 0.6 in Key Biodiversity Areas</strong></p> <p><br> <strong>_OutAichi:</strong></p> <p><strong>r_10_aichi_XXX.tif → Top 15% area of with highest restoration opportunity score (ROS) in country XXX</strong></p> <p><strong>r_10_aichi.img → Top 15% area of with highest restoration opportunity score (ROS) global</strong></p> <p><br> <strong>_OutBonn:</strong></p> <p><strong>r_10_XXX_Bonn.img → Area with highest restoration opportunity score (ROS) in country XXX according to their Bonn Challenge commitments</strong></p> <p> </p> <p><strong>_OutParis:</strong></p> <p><strong>r_10_at_paris.img → Area with highest restoration opportunity score (ROS) in Afro Tropic Nationally Determined Contributions to the Paris Climate Agreement</strong></p> <p><strong>r_10_im_paris.img → Area with highest restoration opportunity score (ROS) in Indo Malay Nationally Determined Contributions to the Paris Climate Agreement</strong></p> <p><strong>r_10_nt_paris.img → Area with highest restoration opportunity score (ROS) in Neo Tropic Nationally Determined Contributions to the Paris Climate Agreement</strong></p> <p><br> <strong>_OutTEOW:</strong></p> <p><strong>r_10_ECOREGION_XXX_sc.tif → restoration opportunity score (ROS) for Ecoregion XXX – rescaled 0-1</strong></p> <p><strong>r_10_ECOREGION_upper60.img → Areas with restoration opportunity score (ROS) above 0.6 in Ecoregions</strong></p> <p> </p> <p><strong>_OutAll</strong></p> <p><strong>alltargets.img → Area with highest restoration opportunity score (ROS) according to all targets (excluded from the paper)</strong></p> <p> </p>
Supplementary data: Impact of a global temperature rise of 1.5 degrees Celsius on Asia's glaciers
<p>Supplementary data to <a href="http://doi.org/10.1038/nature23878"><em>Kraaijenbrink, Bierkens, Lutz and Immerzeel, 2017. Impact of a global temperature rise of 1.5 degrees Celsius on Asia’s glaciers, Nature.</em></a> Model code can be found <a href="https://doi.org/10.5281/zenodo.2548689">here</a>.</p> <p>Please note that all data is provided in 7z-archives. To extract the data use the open source software <a href="http://www.7-zip.org/">7zip</a>.</p> <p> </p> <p><strong>Model input: </strong>Raster data</p> <p>The raster data that is required to run the model is available for the entire High Mountain Asia (<em>complete-hma.7z</em>) and for each <a href="https://www.glims.org/RGI/">RGI v5.0</a> sub-region (<<em>region-name>.7z</em>). The 7z-archives hold separate folders for each glacier, which are named by RGI glacier ID. The rasters for each glacier are in GeoTIFF format, have a 30 m resolution, are in local UTM projection (WGS84 datum), and are clipped to the RGI glacier extent.</p> <p>Rasters present for each glacier are:</p> <pre>classification.tif The debris classification made in google earth engine. debris-thickness-50cm.tif Debris thickness estimation based on Landsat 8 surface temperature. ice-thickness.tif Ice thickness determined using the Glabtop2 model ls8-composite-b456.tif Landsat 8 warmest-pixel optical composite (bands RED, NIR, SWIR1) ls8-composite-tsurf.tif Landsat 8 warmest-pixel surface temperature composite srtm-elevation.tif SRTM 1 arc second elevation data srtm-slope.tif Slope of the SRTM 1 arc second data</pre> <p> </p> <p><strong>Model input: </strong>RDS data</p> <p>The general model input data (<em>mbg-model-rds-data.7z)</em> is stored in R’s binary RDS format and <em><a href="https://www.r-project.org/">R</a></em> is required to open and read the data.</p> <p>Files present in the 7z-archive are:</p> <pre>dP_factors_2006-2100.rds Precipitation changes (delta factors) up to 2100 dT_degrees_2006-2100.rds Temperature changes (Kelvin) up to 2100 glacier-data.rds Glacier centroids with current climate and mass balance input ostrem_meancurve.rds The Östrem curve used by the model rgi-subregions.rds RGI sub-region polygons for Asia</pre> <p> </p> <p><strong>Output data</strong></p> <p>Region-aggregated output is available in ESRI Shapefile format for the RGI sub-regions, major river basins, and for a 1×1 degree grid (<em>output-shapefiles.7z</em>). The attribute tables of all shapefiles hold data on the occurrence of debris as well as current glacier area and volume, and volume projections for the end of century.</p> <p>The available shapefile attributes are:</p> <pre>count number of glaciers a_total total glacier area (m2) a_debris glacier area covered by debris (m2) a_ela glacier area below modelled ELA (m2) a_ela_deb glacier area below modelled ELA covered by debris (m2) v_total total glacier volume (m3) v_debris glacier volume covered by debris (m3) v_ela glacier volume below modelled ELA (m3) v_ela_deb glacier volume below modelled ELA covered by debris (m3) m_total_gt total glacier mass (gigaton) volST_EOC volume remaining in end of century under a stable current temperature vol15_EOC volume remaining in end of century under 1.5 degree scenario vol26_EOC volume remaining in end of century for the RCP2.6 model ensemble vol45_EOC volume remaining in end of century for the RCP4.5 model ensemble vol60_EOC volume remaining in end of century for the RCP6.0 model ensemble vol85_EOC volume remaining in end of century for the RCP8.5 model ensemble</pre>
Supplementary Data: Axion global fits with Peccei-Quinn symmetry breaking before inflation using GAMBIT
<p><strong>Description of Supplementary Data</strong></p> <p>This record contains the samples used to create the figures (excluding validation and prior dependence plots) and to derive most of the results in Hoof et al., <em>“Axion global fits with Peccei-Quinn symmetry breaking before inflation using GAMBIT”</em> (available on the <a href="https://arxiv.org/abs/1810.07192">arXiv</a>). Please contact the authors if you are interested in other samples, YAML files or plotting scripts.<br> <br> This record consists of</p> <ul> <li>21 <code>YAML</code> files (6 for <code>T-Walk</code>, 15 for <code>Diver</code>). Running <code>./gambit -f path/to/YAML/file.yaml</code> in the GAMBIT directory will start the scan. However, most users might want to adjust the output file name and directory as well as the settings for the samplers to their systems.</li> <li>21 <code>hdf5</code> files (6 for <code>T-Walk</code>, 15 for <code>Diver</code>). These files contain the actual samples and were compressed using the <code>tar</code> format.</li> <li>Two example <code>pip</code> files (<code>2_QCDAxion_10M1.pip</code> for <code>Diver</code> samples, <code>2_QCDAxion_3041.pip</code> for <code>T-Walk</code> samples) for producing plots from the corresponding <code>hdf5</code> files, using <a href="https://github.com/patscott/pippi"><code>pippi</code></a> and <code>functions.py</code>.</li> </ul> <p>The files follow the naming scheme <code>V_ModelName_[S][C][I][R][E]</code> plus one of the extensions <code>.yaml</code>, <code>.hdf5.tar.gz</code>, or <code>.pip</code>.</p> <ul> <li><code>V</code>: This internal version number can be ignored, but should be quoted when asking for help with the plotting scripts</li> <li><code>ModelName</code>: Corresponds to the axion models in the paper (<em>GeneralALP</em>, <em>QCDAxion</em>, <em>DFSZAxion_I</em>, <em>DFSZAxion_II</em>, <em>KSVZAxion</em>)</li> <li><code>S</code>: Scanner (<code>S=1</code>: <code>Diver</code>, <code>S=3</code>: <code>T-Walk</code>)</li> <li><code>C</code>: Switch to include (<code>C=1</code>) or exclude (<code>C=0</code>) the White Dwarf cooling hints</li> <li><code>I</code>: Setting for the initial misalignment angle <em>θ<sub>i</sub></em> (<code>I=4</code>: flat prior on <em>θ<sub>i</sub></em> with values in [-3.1415, 3.1415]). <code>I=M</code> is used to indicate that the file includes merged samples from other scans in addition to the corresponding <code>I=4</code> scan.</li> <li><code>R</code>: Setting for the DM relic density likelihood (<code>R=1</code>: upper limit, <code>R=2</code>: matching the DM density)</li> <li><code>E</code>: Extra digit for the anomaly ratio <em>E/N</em>; only for <em>KSVZAxion</em> models (<code>E=1</code>: 0, <code>E=2</code>, 2/3, <code>E=3</code>: 5/3, <code>E=4</code>: 8/3), <em>DFSZAxion-I</em> models (<code>E=1</code>: 8/3), <em>DFSZAxion-II</em> models (<code>E=2</code>: 2/3), or some <em>GeneralALP</em> files (<code>E=a</code>: “QCD-like setting” with <em>β</em> = 7.94, <em>T<sub>crit</sub></em> = 147 MeV; <code>E=b</code>: “Simple ALP-like setting” with <em>β</em> = 0, <em>T<sub>crit</sub></em> irrelevant)</li> </ul> <p>For convenience, we provide a mapping between the figures in the paper and the <code>hdf5</code> files:</p> <ul> <li>Fig. 1: none</li> <li>Figs 2 - 11: Validation plots</li> <li>Figs 12 + 13: 2_GeneralALP_10M2</li> <li>Fig. 14: 2_GeneralALP_10M2a, 2_GeneralALP_10M2b</li> <li>Fig. 15: 2_QCDAxion_10M1, 2_QCDAxion_10M2</li> <li>Fig. 16: 2_QCDAxion_3041, 2_QCDAxion_3042</li> <li>Figs 17 + 18: 2_QCDAxion_10M1, 2_QCDAxion_10M2, 2_QCDAxion_30M1, 2_QCDAxion_30M2</li> <li>Fig. 19: 3_KSVZAxion_10M11, 3_KSVZAxion_10M12, 3_KSVZAxion_10M13, 3_KSVZAxion_10M14, 3_DFSZAxion_I_10M11, 3_DFSZAxion_II_10M12</li> <li>Fig. 20: 2_QCDAxion_10M1, 3_KSVZAxion_10M11, 3_KSVZAxion_10M12, 3_KSVZAxion_10M13, 3_KSVZAxion_10M14, 3_DFSZAxion_I_10M11, 3_DFSZAxion_II_10M12</li> <li>Fig. 21: 2_QCDAxion_11M1, 2_QCDAxion_11M2</li> <li>Fig. 22: 2_QCDAxion_3141, 2_QCDAxion_3142</li> <li>Figs 23 + 24: 2_QCDAxion_3041, 2_QCDAxion_3042, 2_QCDAxion_3141, 2_QCDAxion_3142</li> <li>Fig. 25: 2_QCDAxion_3141, 2_QCDAxion_3142</li> <li>Fig. 26: 2_QCDAxion_11M1, 3_DFSZAxion_I_11M11, 3_DFSZAxion_II_11M12</li> <li>Fig. 27: 2_QCDAxion_3141, 3_DFSZAxion_I_31411, 3_DFSZAxion_II_31412</li> <li>Fig. 28: Validation plot</li> <li>Fig. 29: Prior dependence plot</li> </ul> <p>A few caveats to keep in mind:</p> <ul> <li>The YAML files are designed to work with <code>GAMBIT 1.3.1</code>, and the pip files are tested with <code>pippi 2.1</code>, commit 1a08644. They may or may not work with later versions of either software (these working versions/commits can always be obtained via the <code>git</code> history).</li> <li>The <code>pip</code> files will produce an approximately complete, but very basic version of plots in the paper. Re-creating all the plots in the paper requires various manual, undocumented interventions such as additions, deletions and combination of the plotting scripts created by <code>pippi</code>. Users wishing to reproduce the more advanced plots in the paper should contact the authors for tips, scripts, or experiment for themselves.</li> </ul>
Supplementary data for- Heat-evolved microalgae (Symbiodiniaceae) are stable symbionts and influence thermal tolerance of the sea anemone Exaiptasia diaphana
<p>Raw data and R codes for - Heat-evolved microalgae (Symbiodiniaceae) are stable symbionts and influence thermal tolerance of the sea anemone <em>Exaiptasia diaphana</em>. DOI: 10.1111/1462-2920.70011</p>
Supplementary Data: Global rise in forest fire emissions linked to climate change in the extratropics
<p>Supplementary Data for the paper "Global rise in forest fire emissions linked to climate change in the extratropics" by Jones et al. (2024, <em>Science</em>).</p> <p>The records include mapped pyromes and data and code used to delineate the pyromes.</p> <h3><strong>Mapped Pyromes</strong></h3> <p>The data records include mapped pyromes in three forms:</p> <ol> <li><strong>Shapefile</strong> (Jones_etal_2024_Global_Forest_Pyromes.shp.zip). Vector features in shapefile format containing data fields <em>pyrome ID</em> and <em>pyrome name</em>. The zipped file contains .shp, .dbf, .prj, .shx files.</li> <li><strong>Lower-resolution NetCDF </strong>(Jones_etal_2024_Global_Forest_Pyromes_Qdeg.nc). NetCDF version 4 file containing gridded values of <em>pyrome ID</em> at quarter-degree resolution.</li> <li><strong>Higher-resolution NetCDF</strong> (Jones_etal_2024_Global_Forest_Pyromes_005deg.nc). NetCDF version 4 file containing gridded values of <em>pyrome ID</em> at 0.05 degree resolution.</li> </ol> <p>Shapefiles are accessible via GIS programmes such as QGIS or ArcGIS. All files .shp, .dbf, .prj, .shx files must be stored in a single directory</p> <p>NetCDF files can be access by a variety of programming languages such as Python and R. For quick visualisations and access to the data structure, we suggest using the Panoply tool https://www.giss.nasa.gov/tools/panoply/.</p> <h3><strong>Correlation Data</strong></h3> <p>The data records (Correlation_Qdeg.zip) include gridded quarter-degree correlations between forest burned area (BA) and each of the following variables:</p> <ul> <li><em><strong>Fire weather index</strong></em></li> <li><em><strong>Atmospheric instability (continuous Haines index)</strong></em></li> <li><em><strong>Lightning flash density</strong></em></li> <li><em><strong>Soil moisture</strong></em></li> <li><em><strong>Vegetation productivity (Normalised Difference Vegetation Index)</strong></em></li> <li><em><strong>Population density</strong></em></li> <li><em><strong>Cropland cover</strong></em></li> <li><em><strong>Pasture cover</strong></em></li> <li><em><strong>Road density</strong></em></li> <li><em><strong>Potential fuel loads - surface fuels</strong></em></li> <li><em><strong>Potential fuel loads - shrub fuels</strong></em></li> <li><em><strong>Potential fuel loads - canopy and ladder fuels</strong></em></li> <li><em><strong>Terrain ruggedness index</strong></em></li> <li><em><strong>Forest area density</strong></em></li> </ul> <p>The BA data derive from MODIS MCD64A1 collection 6.1 (Giglio et al., 2018). BA data for forests is masked using the MODIS MOD44B product (DiMiceli et al., 2021) with a 30% tree cover threshold. The predictor data derive from multiple sources as desribed by Jones et al. (2024). See Supplementary Methods and Materials.</p> <p>The gridded correlations data are provided in Hierarchical Data Format version 5 (.hdf5) files, zipped to Correlation_Qdeg.zip. File names describe the variables used.<em> Cropland_Pasture_Qdeg.hdf5 </em>contains data for both cropland and pasture. Each file contains layers describing the Spearman's rho (ρ) correlation coefficient and the related p-value.</p> <p>As explained and justified by Jones et al. (2024), the correlation structure used depends on the variable (see Supplementary Methods and Materials) as per the following categories:</p> <ul> <li><strong><em>Fire Weather Index, Atmospheric Instability, and Lightning Flash Density:</em></strong> Monthly correlation between forest BA and each variable across all fire season months in the period 2001-2021 at the quarter-degree resolution.</li> <li><strong><em>Soil Moisture:</em></strong> Inter-annual correlation between (i) mean soil moisture during the fire season and (ii) accumulated forest BA during the fire season at quarter-degree resolution across years 2001-2021. </li> <li><strong><em>Vegetation Productivity (NDVI):</em></strong> Inter-annual correlation between (i) mean NDVI during the prior growing season and (ii) accumulated forest BA during the fire season at quarter-degree resolution across years 2001-2021. </li> <li><strong><em>Population Density, Cropland Cover, Pasture Cover, Road Density, T</em></strong><strong><em>errain Ruggedness Index, Forest Area Density: </em></strong>Spatial correlation between mean annual forest BA and each variable across the 0.05° cells within each quarter-degree cell during 2001-2021.</li> </ul> <p>Note that these grids are provided for insights into spatial variation in the input correlation data. Pyromes are defined based on correlations fitted on the spatial scale of Olson ecoregions, not quarter-degree grid cells (see further details below).</p> <h3><strong>Clustering Code</strong></h3> <p>DEMO_Clustering.zip contains R Statistics code for clustering forest ecoregions into pyromes based on correlations observed between forest BA and 14 predictors at regional level. The <em>Input</em> directory contains a .RData data frame with correlations between forest BA and each predictor for ecoregions. For demonstrative purposes the code is applied to cluster forest ecorgions of North America into pyromes. The <em>Regions</em> directory contains ecoregions of North America in shapefile format. The <em>Output</em> directory contains output generated by M. Jones, which can be used for validation purposes once other users have trialled the code.</p>
East African topography and volcanism explained by a single, migrating plume: supplementary data
<p>These data accompany the following paper:</p> <p>Hassan, R., Williams, S.E., Gurnis, M. and Müller, D., 2020. East African topography and volcanism explained by a single, migrating plume. <em>Geoscience Frontiers</em>, <em>11</em>(5), pp.1669-1680.</p> <p>The data (in simple text form) correspond to the dynamic topography and change in dynamic topography shown in Figure 7.</p>
Supplementary dataset to publication: Oxford nanopore technologies - a valuable tool to generate whole-genome sequencing data for in silico serotyping and the detection of genetic markers in Salmonella, Thomas et al 2023
<p>Bacteria of the genus <em>Salmonella</em> pose a major risk to livestock, the food economy, and public health. <em>Salmonella</em> infections are one of the leading causes of food poisoning. The identification of serovars of <em>Salmonella</em> achieved by their diverse surface antigens is essential to gain information on their epidemiological context. Traditionally, slide agglutination has been used for serotyping. In recent years, whole-genome sequencing (WGS) followed by <em>in silico</em> serotyping has been established as an alternative method for serotyping and the detection of genetic markers for <em>Salmonella</em>. Until now, WGS data generated with Illumina sequencing are used to validate <em>in silico</em> serotyping methods. Oxford Nanopore Technologies (ONT) opens the possibility to sequence ultra-long reads and has frequently been used for bacterial sequencing. In this study, ONT sequencing data of 28 <em>Salmonella</em> strains of different serovars with epidemiological relevance in humans, food, and animals were taken to investigate the performance of the <em>in silico</em> serotyping tools SISTR and SeqSero2 compared to traditional slide agglutination tests. Moreover, the detection of genetic markers for resistance against antimicrobial agents, virulence, and plasmids was studied by comparing WGS data based on ONT with WGS data based on Illumina. Based on the ONT data from flow cell version R9.4.1, <em>in silico</em> serotyping achieved an accuracy of 96.4 and 92% for the tools SISTR and SeqSero2, respectively. Highly similar sets of genetic markers comparing both sequencing technologies were identified. Taking the ongoing improvement of basecalling and flow cells into account, ONT data can be used for <em>Salmonella in silico</em> serotyping and genetic marker detection.</p>
Supplementary data for the article Linguistic system and sociolinguistic environment as competing factors in linguistic variation: A typological approach
<p>This material contains the dataset and the R-scripts from the <a href="https://version.helsinki.fi/gramadapt/linguistic-system-and-sociolinguistic-environment">gitlab repository</a> of the following article. Please cite the article when using the data.</p> <p>Sinnemäki, Kaius 2020. Linguistic system and sociolinguistic environment as competing factors in linguistic variation: A typological approach. <em>Journal of Historical Sociolinguistics</em> 6(2): 20190101. <a href="https://doi.org/10.1515/jhsl-2019-1010">https://doi.org/10.1515/jhsl-2019-1010</a></p>
EXPLO. Ploča Mičov Grad. Supplementary Data for Bolliger et al., 2023, Dendroarchaeology at Lake Ohrid: 5th and 2nd millennia BCE tree-ring chronologies
<p>Supplementary data for the article "Dendroarchaeology at Lake Ohrid: 5th and 2nd millennia BCE tree-ring chronologies from the waterlogged site of Ploča Mičov Grad, North Macedonia" by Bolliger, Maczkowski, Francuz, Reich et al., 2023, published in Dendrochronologia. <a href="https://doi.org/10.1016/j.dendro.2023.126095">https://doi.org/10.1016/j.dendro.2023.126095</a></p> <p> </p> <p>Abstract</p> <p>The prehistoric site of Ploča Mičov Grad (Ohrid, North Macedonia) on the eastern shore of Lake Ohrid yielded a total of 799 wooden samples from a systematically excavated area of nearly 100 square meters. Most of them are pile remains made of round wood with diameters up to almost 40 cm. A comprehensive dendrochronological analysis allows the construction of numerous well-replicated chronologies for different species. High agreements between the chronologies prove that oak, pine, juniper, ash and hop-hornbeam can be crossdated. The chronologies are dated by means of radiocarbon dates and modelling using wiggle matching. An intensive settlement phase is attested for the middle of the 5th millennium BCE. Further phases follow towards the end of the 5th millennium BCE and in the 2nd millennium around 1800, 1400 and 1300 BCE. Furthermore, the exact, relative felling dates allow first insights into the minimum duration of the settlement phases, which lie between 17 and 87 years. The present study lays the foundations for the establishment of a dendrochronological framework for the southwestern Balkans for periods of 6000 years ago. The multi-centennial chronologies presented in this study can be used as a first robust dating basis for future research in the numerous not yet dated prehistoric lake shore settlements of the region with excellently preserved wooden remains.</p>
A2.2a Digital repositories data citation practices. Supplementary material
<p>Data to complement the quantitative analysis of data citation practices in digital repositories based on metadata records from the re3data.org repositories registry.</p> <p>Data was retrieved using re3data.org API on 23-02-2023 and 06-03-2023 and processed using the OpenRefine software.</p> <p>Part of "A FAIR-enabling citation model for Cultural Heritage Objects" project activities.</p>
eSRRF - Supplementary Data
<p><strong>eSRRF supplementary data</strong></p> <p>The eSRRF preprint is available here: https://doi.org/10.1101/2022.04.07.487490</p> <p>Find the code and documentation here: https://github.com/HenriquesLab/NanoJ-eSRRF</p> <p><strong>1a: Set01a_DNA-PAINT_COS7-MT.tif</strong></p> <p>DNA-PAINT of fixed COS-7 cells with indirect immunolabeling against tubulin</p> <ul> <li>Pixelsize: 160 nm</li> <li>Exposure time: 30 ms</li> <li>50 000 frames</li> </ul> <p><strong>1b: Set01b_DNA-PAINT_COS7-MT_bin100.tif</strong></p> <p>Dataset 1a with 100 frames binning to effectivly increase emitter density.</p> <p>eSRRF analysis parameters: </p> <ul> <li>M=5,</li> <li>R=0.5,</li> <li>S=1</li> <li>all frames</li> </ul> <p> </p> <p><strong>2: Set02_HeLa_ffDronpa-MAP4.tif</strong></p> <p>Live-cell TIRF imaging dataset of HeLa cells expressing ffDronpa-MAP4 </p> <ul> <li>Pixelsize: 156 nm</li> <li>Exposure time: 40 ms</li> </ul> <p>eSRRF analysis parameters: </p> <ul> <li>M=4</li> <li>R=2</li> <li>S=4</li> <li>100 frames</li> <li>rolling analysis gap = 50 frames</li> </ul> <p><strong>3: Set03_COS7_PrSS-mEmerald-KDEL.tif</strong></p> <p>Live-cell HiLO-TIRF of COS-7 cells expressing PrSS-mEmerald-KDEL marking the ER lumen.</p> <ul> <li>Pixelsize: 160 nm</li> <li>Exposure time: 5 ms</li> </ul> <p>eSRRF analysis parameters: </p> <ul> <li>M=5</li> <li>R=2</li> <li>S=1</li> <li>100 fr</li> <li>rolling analysis gap = 10 frames</li> </ul> <p><strong>4a: Set4a_MFM_HeLa_TOM20.tif</strong></p> <p>Live-cell MFM of HeLa cells expressing TOM20-HaloTag labeled with JF549 </p> <ul> <li>Pixelsize: 160 nm</li> <li>Exposure time: 20 ms</li> </ul> <p>eSRRF analysis parameters: </p> <ul> <li>M=4</li> <li>R=2</li> <li>S=1</li> <li>100 fr</li> <li>rolling analysis gap = 25 frames</li> <li>3D axial offset = 390 nm</li> </ul> <p><strong>4b: Set4b_MFM_beadcalibration.tif</strong></p> <p>MFM calibration data with TetraSpeck beads immobilized on a coverslip,</p> <ul> <li>Pixelsize: 160 nm</li> <li>z-step 60 nm</li> </ul> <p><strong>5: Set5_LLS_Jurkat_ER.zip</strong></p> <p>Lattice light sheet (LLS) data of the ER in Jurkat cells. The zip-folder contains single image stacks for each z-plane:</p> <p>98 z-planes with 100 fr per plane at 10 ms exposure time 276 nm step size in the z-axis and 104 nm pixelsize. </p> <p>Each z-plane stack was process with eSRRF followed by deskewing with the LLSM plugin (https://monash-merc.github.io/llsm/docs/fiji/index.html) to recover a single 3D volume reconstruction.</p> <p>eSRRF analysis parameters: </p> <ul> <li>M=5 </li> <li>R=3.5 </li> <li>S=2 </li> <li>100 frames</li> </ul> <p><strong>6: Set6_TIRF_NeuronCulture_MT_Skylan-NS.tif</strong></p> <p>TIRF imaging data of cultured neuron expressing Skylan-NS tagged tubulin.</p> <ul> <li>Pixelsize: 64.7 nm</li> <li>Exposure time: 100 ms</li> </ul> <p>eSRRF analysis parameters: </p> <ul> <li>M=4 </li> <li>R=5</li> <li>S=2</li> <li>200 fr</li> </ul> <p><strong>7: Set7_SDC_U2OS_Skylan-S-Actin.tif</strong></p> <p>Live-cell SDC imaging data of U2OS cells transiently expressing SkylanS-ßActin over a time course of 12 hours by acquiring substacks of 50 frames at 10 min intervalls.</p> <ul> <li>Pixelsize: 247.6 nm</li> <li>Exposure time: 500ms</li> </ul> <p>eSRRF analysis parameters: </p> <ul> <li>M=5</li> <li>R=2.5</li> <li>S=1</li> <li>50 frames</li> </ul> <p> </p> <p> </p>
Supplementary data: Agro-morphological and molecular characterization reveal deep insights in promising genetic diversity and marker-trait associations in Fagopyrum esculentum and F. tataricum
<p>Our study focuses on the global/European buckwheat germplasm collected as part of the ECOBREDD project. The potential of this highly diverse collection for organic buckwheat breeding was evaluated at two complementary levels: phenotypic and genetic. Here, we characterized the phenotypic and genetic diversity of a global collection of the two cultivated buckwheat species <em>Fagopyrum esculentum</em> and <em>F. tataricum</em> (190 and 51 accessions, respectively) using 37 agro-morphological traits and 24 SSR markers (Simple Sequence Repeats) (see publication and info sheet of the data).</p>
Supplementary data to: Importance and vulnerability of the world's water towers
<p>This archive contains data produced for a study assessing the importance and vulnerability of the world’s water towers. Code (R-scripts) used to process these files is available on the <a href="https://github.com/mountainhydrology/pub_ngs-watertowers">MountainHydrology Github page</a></p> <p>The archive is organized in directories with specific topics. Each directory contains input files (optional) and output/processed files. The input files can be used in combination with the R-scripts published on <a href="https://github.com/mountainhydrology/pub_ngs-watertowers">Github</a> to generate the processed files included in this archive. In many cases external published data is used as input data for the calculations. In that case the data is not included in this archive but literature references and links to the specific files are provided in the description below. Files which have been preprocessed before use in the R-scripts are included in this archive. For calculation details please see the publication, in particular Extended Data Tables 3 and 4.</p> <p><strong>Archive contents</strong></p> <p>The archives contents are organized in eight separate directories, which are listed here, along with their contents:</p> <ul> <li><strong>ERA5</strong></li> </ul> <p>Precipitation and evaporation data are extracted from ERA5 reanalysis available online in the Copernicus Climate Data Store at https://cds.climate.copernicus.eu</p> <p>This directory includes:</p> <p><em>Input</em></p> <pre><code>ERA5_evaporation_avgannual_2001_2017.nc - Average annual evaporation (mm) for 2001-2017 ERA5_evaporation_ymonmean_2001_2017.nc - Multi-year mean monthly evaporation (mm) for 2001-2017 era5_total-precipitation_ymonmean_2001-2017_global.tif - Multi-year mean monthly precipitation (mm) for 2001-2017 era5_total-precipitation_yearsum_2001-2017.tif - Average annual precipitation (mm) for 2001-2017</code></pre> <p><em>Output</em></p> <pre><code>P_avg_annual_basin_mm.tif - Average annual precipitation 2001-2017 (mm) aggregated to basins P_avg_annual_DS_mm.tif - Average annual precipitation 2001-2017 (mm) aggregated to downstream basins P_avg_annual_mm.tif - Average annual precipitation 2001-2017 (mm) P_avg_annual_WT_mm.tif - Average annual precipitation 2001-2017 (mm) aggregated to Water Tower Units P_var_interannual.tif - Interannual variablity in precipitation 2001-2017 P_var_interannual_basin.tif - Interannual variablity in precipitation 2001-2017 aggregated to basins P_var_interannual_DS.tif - Interannual variablity in precipitation 2001-2017 aggregated to downstream basins P_var_interannual_WT.tif - Interannual variablity in precipitation 2001-2017 aggregated to Water Tower Units P_var_intraannual.tif - Intra-annual variablity in precipitation 2001-2017 P_var_intraannual_basin.tif - Intra-annual variablity in precipitation 2001-2017 aggregated to basins P_var_intraannual_DS.tif - Intra-annual variablity in precipitation 2001-2017 aggregated to downstream basins P_var_intraannual_WT.tif - Intra-annual variablity in precipitation 2001-2017 aggregated to Water Tower Units WTU_P_indicators.csv - Table listing all calculated precipition indicators per Water Tower Unit</code></pre> <ul> <li><strong>Glaciers</strong></li> </ul> <p>Glacier volume and mass balance are derived from published datasets. This directory includes:</p> <p><em>Output</em></p> <pre><code>Glac_area_WT_km2.tif - Glacier area (km2) aggregated for Water Tower Units Glac_volume_WT_km3.tif - Glacier volume (km3) aggregated for Water Tower Units WTU_Glacier_indicators.csv - Table listing all derived glacier indicators per Water Tower Unit WTU_MB.shp - shapefile of Water Tower Units including the glacier mass balance per Water Tower Units as attribute</code></pre> <p><em>External data</em></p> <p>Glacier volume data published in<em> Farinotti et al., 2019, Nature Geoscience</em>, were used.<br> Reference: Farinotti, D. et al. A consensus estimate for the ice thickness distribution of all glaciers on Earth. Nat. Geosci. 12, 168–173 (2019).<br> Glacier volume (km3) and glacier area (km2) at 0.05 degrees spatial resolution were used, which are available <a href="https://www.research-collection.ethz.ch/bitstream/handle/20.500.11850/315707/global_fraction-of-degree_grids.zip?sequence=60&isAllowed=y">here</a>.<br> The used files are <em>p05_degree_glacier_area_km2.tif</em> and <em>p05_degree_glacier_volume_km3.tif</em></p> <p>Glacier mass balance data published by the World Glacier Monitoring Service were used to derive an average glacier mass balance per Water Tower Unit.<br> References:<br> Zemp, M. et al. Global glacier mass changes and their contributions to sea-level rise from 1961 to 2016. Nature 568, 382–386 (2019).<br> World Glacier Monitoring Service. Fluctuations of Glaciers (FoG) Database. (2018). doi:10.5904/wgms-fog-2018-06</p> <ul> <li><strong>HydroLAKES</strong></li> </ul> <p>Surface lake and water storage per Water Tower Unit was calculated. This directory includes:</p> <p><em>Output</em></p> <pre><code>WTU_lake_storage_volume.csv - Table listing lake and reservoir volume (km3) per Water Tower Unit WTU_surface_water_storage_km3.tif - Lake and reservoir storage volume (km3) aggregated to Water Tower Units</code></pre> <p><em>External data</em></p> <p>For surface water lakes and reservoirs the HydroLAKES dataset is used. The shapefile <em>HydroLAKES_polys_v10.shp</em> can be downloaded from <a href="http://https://97dc600d3ccc765f840c-d5a4231de41cd7a15e06ac00b0bcc552.ssl.cf5.rackcdn.com/HydroLAKES_polys_v10_shp.zip">HydroSheds</a></p> <p>Reference: Messager, M. L., Lehner, B., Grill, G., Nedeva, I. & Schmitt, O. Estimating the volume and age of water stored in global lakes using a geo-statistical approach. Nat. Commun. 7, 1–11 (2016).</p> <ul> <li><strong>Indicators</strong></li> </ul> <p>All indicators and subindicators calculated for the Water Tower Index calculation are stored per Water Tower Unit.</p> <p>This directory includes:</p> <pre><code>indicators.csv - Table with all indicators and subindicators per Water Tower Unit</code></pre> <ul> <li><strong>Snow</strong></li> </ul> <p>The MODIS MOD10CM006 snow cover product was used to derive snow persistence.<br> Reference: Hall, D. K. & Riggs, G. A. MODIS/Terra Snow Cover Monthly L3 Global 0.05Deg CMG, Version 6. (2015). doi:10.5067/MODIS/MOD10CM.006</p> <p>This archive includes:<br> <em>Input</em></p> <pre><code>MOD10CM006_yearmean_2001-2017.tif - Annual mean snow cover 2001-2017 MOD10CM006_ymonmean_2001-2017.tif - Multi-year mean monthly snow cover 2001-2017</code></pre> <p><em>Output</em></p> <pre><code>Snow_persistence_avg_annual.tif - Average annual snow persistence 2001-2017 Snow_persistence_avg_annual_WT.tif - Average annual snow persistence 2001-2017 aggregated to Water Tower Units Snow_persistence_var_interannual.tif - Interannaul variability in snow persistence 2001-2017 Snow_persistence_var_interannual_WT.tif - Interannaul variability in snow persistence 2001-2017 aggregated to Water Tower Units Snow_persistence_var_intraannual.tif - Intra-annaul variability in snow persistence 2001-2017 Snow_persistence_var_intraannual_WT.tif - Intra-annaul variability in snow persistence 2001-2017 aggregated to Water Tower Units WTU_Snow_indicators.csv - Table listing all derived snow indicators per Water Tower Unit</code></pre> <ul> <li><strong>Uncertainty</strong></li> </ul> <p>The directory contains the uncertainty ranges used in the uncertainty analysis<br> The directory includes:</p> <pre><code>ET_uncertainty_per_downstream.csv - Table listing SD in evaporation per downstream basin ET_uncertainty_per_WTU.csv - Table listing SD in evaporation per Water Tower Unit P_uncertainty_per_downstream.csv - Table listing SD in precipitation per downstream basin P_uncertainty_per_WTU.csv - Table listing SD in precipitation per Water Tower Unit WTU_IceVol_uncertainty.csv - Table listing uncertainty in ice volume per Water Tower Unit</code></pre> <ul> <li><strong>Water demands</strong></li> </ul> <p>Net water demands for irrigation, industrial and domestic water use, as well as the environmental flow requirement are extracted from PCR-GLOBWB hydrological model output.<br> Reference: Wada, Y., De Graaf, I. E. M. & van Beek, L. P. H. High-resolution modeling of human and climate impacts on global water resources. J. Adv. Model. Earth Syst. 8, 735–763 (2016).</p> <p>The directory includes:<br> <em>Input</em></p> <pre><code>Dom_use_ymonmean_2001_2014_005.tif - Multi-year mean monthly net domestic water demand 2001-2014 at 0.05 degrees resolution (km3) Ind_use_ymonmean_2001_2014_005.tif - Multi-year mean monthly net industrial water demand 2001-2014 at 0.05 degrees resolution (km3) Irr_use_ymonmean_2001_2014_005.tif - Multi-year mean monthly net irrigation water demand 2001-2014 at 0.05 degrees resolution (km3) Tot_use_ymonmean_2001_2014_005.tif - Sum of the three above global_historical_riverdischarge_ymonmean_m3second_5min_2001_2014.nc4 - Multi-year mean monthly natural discharge (m3/s) 2001-2014</code></pre> <p><em>Output</em></p> <pre><code>Domestic_use_avg_annual_basin_km3.tif - Average annual net domestic water demand 2001-2014 aggregated to basins Domestic_use_avg_annual_km3.tif - Average annual net domestic water demand 2001-2014 Industrial_use_avg_annual_basin_km3.tif - Average annual net industrial water demand 2001-2014 aggregated to basins Industrial_use_avg_annual_km3.tif - Average annual net industrial water demand 2001-2014 Irrigation_use_avg_annual_basin_km3.tif - Average annual net irrigation water demand 2001-2014 aggregated to basins Irrigation_use_avg_annual_km3.tif - Average annual net irrigation water demand 2001-2014 Natural_demand_avg_annual_basin_km3.tif - Average annual natural water demand 2001-2014 aggregated to basins Total_human_demand_avg_annual_basin_km3.tif - Average annual net human (sum of domestic, industrial and irrigation) water demand 2001-2014 aggregated to basins Water_gap_average_annual_basin.tif - Average annual water gap 2001-2014 aggregated to basins WTU_Demand_DS_P_available.csv - Table listing dowstream water availability per sector per basin WTU_Demand_indicators.csv - Table listing demand per sector per basin WTU_Domestic_Water_Gap_monthly.csv - Table listing multi-year average monthly domestic water gap per basin WTU_Industrial_Water_Gap_monthly.csv - Table listing multi-year average monthly industrial water gap per basin WTU_Irrigation_Water_Gap_monthly.csv - Table listing multi-year average monthly irrigation water gap per basin WTU_Natural_Water_Gap_monthly.csv - Table listing multi-year average monthly natural water gap per basin WTU_Total_Water_Gap_monthly.csv - Table listing multi-year average monthly water gap per basin</code></pre> <ul> <li><strong>WTU units</strong></li> </ul> <p>The spatial units for all calculations are the Water Tower Units, their downstream basins, and the entire basins (Water Tower Unit + downstream basin). They are extracted using definitions of basins and mountain ranges. This directory includes:</p> <p><em>Output</em></p> <pre><code>basins.tif - Definition of basins with Water Tower Units at 0.05 degrees spatial resolution basins_downstream.tif - Definition of downstream basins at 0.05 degrees spatial resolution basins_vector.shp - Definition of basins with Water Tower Units as vector data downstream_vector.shp - Definition of downstream basins as vector data gmba_all.shp - All GMBA mountain ranges including glacier volume and snow persistence gmba_ss.shp - GMBA mountain ranges included in Water Tower Units WTU.tif - Definition of Water Tower Units as 0.05 degrees spatial resolution WTU_specs.csv - Table with set of specifications of Water Tower Units WTU_vector.shp - Definition of Water Tower Units as vector data</code></pre> <p><em>External data</em></p> <p>FAO's classification of major hydrological basins and FAO's classification of subbasins per continent are used. These are based on HydroSheds and are available as shapefiles at <a href="http://www.fao.org/nr/water/aquamaps/">FAO Aquamaps</a></p> <p>The specific shapefiles used are:</p> <p><a href="http://www.fao.org/geonetwork/srv/en/resources.get?id=38047&fname=Major_hydrological_basins.zip&access=private">major_hydrobasins.shp</a><br> <a href="http://www.fao.org/geonetwork/srv/en/resources.get?id=37039&fname=hydrobasins_asia.zip&access=private">hydrobasins_asia.shp</a><br> <a href="http://www.fao.org/geonetwork/srv/en/resources.get?id=37174&fname=hydrobasins_southam.zip&access=private">hydrobasins_southam.shp</a><br> <a href="http://www.fao.org/geonetwork/srv/en/resources.get?id=38044&fname=hydrobasins_northam.zip&access=private">hydrobasins_northam.shp</a><br> <a href="http://www.fao.org/geonetwork/srv/en/resources.get?id=37299&fname=hydrobasins_neareast.zip&access=private">hydrobasins_neareast.shp</a><br> <a href="http://www.fao.org/geonetwork/srv/en/resources.get?id=37250&fname=hydrobasins_europe.zip&access=private">hydrobasins_europe.shp</a><br> <a href="http://www.fao.org/geonetwork/srv/en/resources.get?id=37173&fname=hydrobasins_centralam.zip&access=private">hydrobasins_centralam.shp</a><br> <a href="http://www.fao.org/geonetwork/srv/en/resources.get?id=37251&fname=hydrobasins_austpacific.zip&access=private">hydrobasins_austpacific.shp</a>:</p>
Supplementary Data to "Disparate regulation of Smad3 phosphorylation and collagen gene transcription by full-length IL-33"
<p>These are Supplementary Figures for the article "Disparate regulation of Smad3 phosphorylation and collagen transcription by full-length IL-33"</p>
Supplementary data for "Machine learning-based prediction of activity and substrate specificity for OleA enzymes in the thiolase superfamily"
<p>Supplementary data for "Machine learning-based prediction of activity and substrate specificity for OleA enzymes in the thiolase superfamily"</p>
Supplementary data: The added value of Bayesian inference for estimating biotransformation rates of organic contaminants in aquatic invertebrates.
<p>Supporting information for the article "<strong>The added value of Bayesian inference for estimating biotransformation rates of organic contaminants in aquatic invertebrates.</strong>"</p> <p>This provides all the R script and .csv files for each dataset. </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.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.