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Air/Snow temperature vertical profiles at different nodes of the 'Limnopolar Lake' CALM site, in Byers Península Livingston Island, Antarctica (2013-2022)
<div> <div> </div> </div> <div> <p>Air or seasonal snow temperature data were collected at different heights above the ground between 2013 and 2022 using an array of temperature micro-loggers (iButton models by Maxim) mounted on vertical wooden masts. These measurements were conducted at various nodes within the 100x100 m 'Limnopolar Lake' CALM site (A25) grid of the PERMATHERMAL network, managed by the University of Alcalá, Madrid, Spain, to monitor active layer thickness on Byers Peninsula, Livingston Island, South Shetland Islands, Antarctica.</p> <p>In 2013, nine arrays were installed at nodes with relative coordinates (00,00), (00,05), (00,10), (05,00), (05,05), (05,10), (10,00), (10,05), and (10,10). Measurements were taken at heights of 2.5, 5, 10, 15, 20, 25, 30, and 40 cm above the ground surface using DS1921G iButton loggers, which recorded air/snow temperatures every 4 hours. This experiment, referred to as 'Mini', was active for only one year and is now discontinued.</p> <p>Between 2017 and 2022, three arrays were installed at nodes (00,00), (05,05), and (10,10). These arrays measured air/snow temperatures at heights of 2.5, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 120, 140, and 160 cm above the ground surface using DS1922L iButton loggers, which recorded temperatures every 3 hours. This experiment, referred to as 'HR', has also been discontinued.</p> </div>
Air/Snow temperature vertical profiles at different sites in Livingston Island, Antarctica (2006-2023)
<p>Air or seasonal snow temperature data collected at different heights above the ground (2.5, 5, 10, 20, 40, 80, and 160 cm), generally recorded every 3 hours between 2006 and 2023, using an array of temperature micro-loggers (iButton models by Maxim) mounted along a vertical wooden mast. These measurements were taken at various stations of the PERMATHERMAL network, managed by the University of Alcalá, Madrid, Spain, to monitor the thermal dynamics of frozen soils on Livingston Island, South Shetland Islands, Antarctica.</p>
Air/Snow temperature vertical profiles at different sites in Deception Island, Antarctica (2008-2023)
<p>Air or seasonal snow temperature data collected at different heights above the ground (2.5, 5, 10, 20, 40, 80, and 160 cm), generally recorded every 3 hours between 2006 and 2023, using an array of temperature micro-loggers (iButton models by Maxim) mounted along a vertical wooden mast. These measurements were taken at various stations of the PERMATHERMAL network, managed by the University of Alcalá, Madrid, Spain, to monitor the thermal dynamics of frozen soils on Deception Island, South Shetland Islands, Antarctica.</p>
Air/Snow temperature vertical profiles at different nodes of the 'Crater Lake' CALM site in Deception Island, Antarctica (2012-2023)
<p>Air or seasonal snow temperature data were collected at different heights above the ground between 2012 and 2023 using an array of temperature micro-loggers (iButton models by Maxim) mounted on vertical wooden masts. These measurements were conducted at various nodes within the 100x100 m 'Crater Lake' CALM site (A16) grid of the PERMATHERMAL network, managed by the University of Alcalá, Madrid, Spain, to monitor active layer thickness in Deception Island, South Shetland Islands, Antarctica.</p> <p>In 2012, nine arrays were installed at nodes with relative coordinates (00,00), (00,05), (00,10), (05,00), (05,05), (05,10), (10,00), (10,05), and (10,10). Measurements were taken at heights of 2.5, 5, 10, 15, 20, 25, 30, and 40 cm above the ground surface using DS1921G iButton loggers, which recorded air/snow temperatures every 4 hours. This experiment, referred to as 'Mini', was active until early 2021.</p> <p>Between 2017 and 2023, four arrays were installed at nodes (00,010), (05,05), (06,00), and (10,00). These arrays measured air/snow temperatures at heights of 2.5, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 120, 140, and 160 cm above the ground surface using DS1922L iButton loggers, which recorded temperatures every 3 hours. Three of the arrays of this experiment, referred to as 'HR', has also been discontinued in early 2021, althought one of them was active until early 2024.</p>
Dataset for: Pre-pandemic artificial MERS analog of polyfunctional SARS-CoV-2 S1/S2 furin cleavage site domain is unique among spike proteins of genus Betacoronavirus
<table> <tbody> <tr> <th> </th> <td> <div> <h3><strong>Data File Descriptions and Methods</strong></h3> <ol> <li><strong>Data file 1 [betacov_matching_IPR042578.fasta]</strong>: Representative set of 2,465 betacoronavirus S protein overlapping homologous superfamily sequences retrieved in fasta format on 4 December 2022 from the InterPro repository at https://www.ebi.ac.uk/interpro/entry/InterPro/IPR042578/.<br><br></li> <li><strong>Data File 2 [betacov_matching_IPR042578_motif.fasta]</strong>: With Data File 1 as input, extracted 98,122 furin cleavage site (FCS) output motifs of 20 amino acids length, including overlapping and redundant sequences, produced with the FindFur algorithm with preset parameters as described by (Gu, 2020). FindFur as used was deposited on 15 December 2020 at the GitHub software repository at https://github.com/chwisteeng/FindFur.<br><br></li> <li><strong>Data File 3 [table_s1s2_hits_betacov_polyf.pdf]</strong>: Compiled summary table of sequence hits (PDF) of spike S1/S2 domains across genus <em>Betacoronavirus. </em>The compiled table of hits removed from Data File 2 sequences corresponding to spike protein fragments (incomplete length spike proteins as deposited at GenBank) and duplicates (redundant parts identically overlapping within the 20 amino acids motif windows), and then selected one sequence representative for multiple but identical sequences.<em> </em>Collection dates and geographical locations were retrieved from the NCBI Genbank protein database at https://www.ncbi.nlm.nih.gov/protein/. For SARS-CoV-2 spike variants, these data were also cross-validated with the SARS-CoV-2 lineage mutation tracker (Gangavarapu, 2023) available at https://outbreak.info which was based on extensive sequencing data from the global GISAID initiative (https://gisaid.org/). Solid lines (-) depict pat7 NLS, asterisks (*) O-glycosites, and circumflex (^) symbols FCS.<br><br></li> <li> <p><strong>Data File 4 [table_s1s2_hits_betacov_polyf.xlsx]</strong>: Compiled summary table of sequence hits (MS Excel) of spike S1/S2 domains across genus <em>Betacoronavirus. </em>The compiled table of hits removed from Data File 2 sequences corresponding to spike protein fragments (incomplete length spike proteins as deposited at GenBank) and duplicates (redundant parts identically overlapping within the 20 amino acids motif windows), and then selected one sequence representative for multiple but identical sequences.<em> </em>Collection dates and geographical locations were retrieved from the NCBI Genbank protein database at https://www.ncbi.nlm.nih.gov/protein/. For SARS-CoV-2 spike variants, these data were also cross-validated with the SARS-CoV-2 lineage mutation tracker (Gangavarapu, 2023) available at https://outbreak.info which was based on extensive sequencing data from the global GISAID initiative (https://gisaid.org/). Solid lines (-) depict pat7 NLS, asterisks (*) O-glycosites, and circumflex (^) symbols FCS.<br><br></p> </li> <li> <p><strong>Data File 5 [betacov_s1s2_nls_pat7_furin_psort.txt]: </strong>Nuclear localization signal (NLS) detection output for 5 representative betacoronavirus spike sequence domains, including the positive hits for pat7 in SARS-CoV-2 and for MERS-MA30 CoV. NLS predictions used the PSORT algorithm available as a webservice at https://wolfpsort.hgc.jp/ which is based on the work of Nakai and Horton (Nakai and Horton, 1999). Numbering refers to Data File 3 and Data File 4.<br><br></p> </li> <li> <p><strong>Data File 6 [betacov_s1s2_oglyc_netogly.txt]: </strong>Detection output for 5 representative betacoronavirus spike sequence domains tested for Thr/Ser O-glycosite residue pairs with the standard prediction software NetOGlyc4.0 (Steentoft et al., 2013) as available at https://services.healthtech.dtu.dk/services/NetOGlyc-4.0/. Positive hits have scores above 0.5. Numbering refers to Data File 3 and Data File 4.<br><br></p> </li> <li> <p><strong>Data File 7 [betacov_s1s2_nls_pat7_furin_blastp.txt]</strong>: Comprehensive sequence database searches using were performed using the NCBI protein BLAST (blastp) algorithm with webservice available at https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins. The following blastp search parameters and settings were used: Word size=2; Expect value=200000; Hitlist size=500; Gapcosts=9,1; Matrix=PAM30; Filter string=F; Genetic Code=1;Window Size=40; Threshold=11; Composition-based stats=0; Database Posted date=Jan 19, 2023 2:59 AM; Number of letters=17,117,563; Number of sequences=10,766; Entrez query: Includes: Betacoronavirus (taxid:694002); Excludes: SARS-CoV-2 (taxid:2697049). The six polyfunctional input query consensus motif sequences were TXXPR(K/H/R)XRSX and TXXPRX(K/H/R)RSX.</p> </li> </ol> <h3><strong>References</strong></h3> <p>Gu, C., 2020. FindFur: A Tool for Predicting Furin Cleavage Sites of Viral Envelope Substrates. Master’s Thesis, San Jose State University, CA, USA. doi: <a href="https://doi.org/10.31979/etd.4ahv-9jya">10.31979/etd.4ahv-9jya</a> </p> <p>Gangavarapu K, Latif AA, Mullen JL, Alkuzweny M, Hufbauer E, Tsueng G, Haag E, Zeller M, Aceves CM, Zaiets K, Cano M, Zhou X, Qian Z, Sattler R, Matteson NL, Levy JI, Lee RTC, Freitas L, Maurer-Stroh S; GISAID Core and Curation Team; Suchard MA, Wu C, Su AI, Andersen KG, Hughes LD. Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations. Nat Methods. 2023. 20(4):512-522. doi: <a href="https://doi.org/10.1038/s41592-023-01769-3">10.1038/s41592-023-01769-3</a>.</p> <p>Nakai, K., Horton, P., 1999. PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem Sci 24, 34–36. doi: <a href="https://doi.org/10.1016/s0968-0004(98)01336-x">10.1016/s0968-0004(98)01336-x</a></p> <p>Steentoft, C., Vakhrushev, S.Y., Joshi, H.J., Kong, Y., Vester-Christensen, M.B., Schjoldager, K.T.-B.G., Lavrsen, K., Dabelsteen, S., Pedersen, N.B., Marcos-Silva, L., Gupta, R., Bennett, E.P., Mandel, U., Brunak, S., Wandall, H.H., Levery, S.B., Clausen, H., 2013. Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology. EMBO J 32, 1478–1488. doi: <a href="https://doi.org/10.1038/emboj.2013.79">10.1038/emboj.2013.79</a></p> </div> </td> </tr> </tbody> </table>
Online Resources for Strullu-Derrien et al - The 330–320 Million-Year-Old Tranchée des Malécots (Chaudefonds-sur-Layon, South of the Armorican Massif, France): a Rare Geoheritage Site Containing In Situ Palaeobotanical Remains
<p>This repository contains the following files associate with "The 330–320 Million-Year-Old Tranchée des Malécots (Chaudefonds-sur-Layon, South of the Armorican Massif, France): a Rare Geoheritage Site Containing In Situ Palaeobotanical Remains" by Christine Strullu-Derrien, Alan RT Spencer, Christopher J Cleal and Victor O. Leshyk.</p> <p><strong>Online Resource 1</strong> Model data as a .zip archive (301.5MB) containing .obj/.mtl and texture files for each 3D reconstruction (Models #1-4, whole site reconstruction, detailed reconstruction of the trench, and model of the mine site).</p> <p><strong>Online Resource 2</strong> Video animation showing whole site 3D model (.mp4 | 37.7MB), with quick fly-through of the Tranchée des Malécots showing exposed rock and bedding of the SW wall.</p> <p><strong>Online Resource 3</strong> Video animation showing 3D Model #1 (.mp4 | 35.1MB).</p> <p><strong>Online Resource 4</strong> Video animation showing 3D Model #2 (.mp4 | 83.5MB).</p> <p><strong>Online Resource 5</strong> Video animation showing 3D Model #3 (.mp4 | 45.3MB).</p> <p><strong>Online Resource 6</strong> Video animation showing 3D Model #4 (.mp4 | 65.8MB).</p> <p><strong>Online Resource 7</strong> Video animation showing 3D model of the Malécots mine headframe (.mp4 | 14.9.0MB).</p>
Temple sites and earthquake zones in central India
<p>Temple sites and earthquakes zones in central India, showing distribution of damaged and undamaged buildings based on a partial survey undertaken in March 2020 (red=damaged; green = undamaged).</p><ul><li><a href="https://www.wikidata.org/wiki/Q116762395">Sihoniya सिहोनिया </a>(District Morena, Madhya Pradesh). <a href="https://doi.org/10.5281/zenodo.6576874">Kakanmath</a>.</li><li><a href="https://www.wikidata.org/wiki/Q2487545">Gwalior Fort ग्वालियर का क़िला</a> (District Gwalior, Madhya Pradesh). <a href="https://www.wikidata.org/wiki/Q7424948">Sās Bahu</a>.</li><li><a href="http://wikimapia.org/#lang=en&lat=25.952179&lon=78.177338&z=12&m=w&show=/17811820/Amrol">Amrol अमरोल</a> (District Gwalior, Madhya Pradesh). <a href="https://www.wikidata.org/wiki/Q97946694">Śiva temple</a>.</li><li><a href="https://www.wikidata.org/wiki/Q178948">Khajuraho खजुराहो</a> (District Chhatarpur, Madhya Pradesh). <a href="https://www.wikidata.org/wiki/Q26258435">Temple group</a>.</li><li><a href="http://wikimapia.org/#lang=en&lat=24.503199&lon=78.961573&z=15&m=bs&show=/42266012/Sun-temple-Umri">Umri उमरी</a> (District Tikamgarh, Madhya Pradesh). <a href="https://www.wikidata.org/wiki/Q97101444">Sun temple</a>.</li><li><a href="https://www.wikidata.org/wiki/Q6991044">Nemawar नेमावर</a> (District Dewas, Madhya Pradesh). <a href="https://www.wikidata.org/wiki/Q116182801">Siddhanāth</a>.</li><li><a href="https://www.wikidata.org/wiki/Q12416611">Un उन</a> (खरगोन ज़िला, Madhya Pradesh). <a href="https://doi.org/10.5281/zenodo.3733042">Śiva temple</a>.</li><li><a href="http://wikimapia.org/#lang=en&lat=21.986667&lon=76.021807&z=16&m=bs&show=/40057101/Temple&search=Boruth">Boruth बोरुथ</a> (खरगोन ज़िला, Madhya Pradesh). <a href="https://doi.org/10.5281/zenodo.3732976">Ruined temple</a>.</li><li><a href="https://www.wikidata.org/wiki/Q12446456">Māndhātā ओंकारेश्वर मांधाता</a> (District Khandwa, Madhya Pradesh). <a href="https://doi.org/10.5281/zenodo.5773997">Ruins of a temple destroyed by earthquake.</a></li><li><a href="https://www.wikidata.org/wiki/Q25247863">Udaypur उदयपुर</a> (District Vidisha, Madhya Pradesh). <a href="https://commons.wikimedia.org/wiki/File:Udaipur_Temple,_west_side.jpg">Śiva temple</a>.</li><li><a href="https://www.wikidata.org/wiki/Q28173479">Kadwaya कदवाया</a> (District Ashoknagar, Madhya Pradesh). <a href="https://commons.wikimedia.org/wiki/File:Matha_or_Monastery_at_Kadwaha.tif">Maṭha</a> and <a href="https://doi.org/10.5281/zenodo.8359697">Bhūteśvar temple</a>, and <a href="https://doi.org/10.5281/zenodo.8359659">adjacent mosque</a>.</li><li><a href="https://www.wikidata.org/wiki/Q115858066">Terahī तेरही</a> (District Shivpuri, Madhya Pradesh). <a href="https://www.wikidata.org/wiki/Q115859520">Temples and maṭha</a>.</li><li><a href="https://www.wikidata.org/wiki/Q56293237">Jagat जगत</a> (District Udaipur, Rajastan). <a href="https://www.wikidata.org/wiki/Q4741465">Ambikā Mātā temple</a>.</li><li><a href="https://www.wikidata.org/wiki/Q1425430">Ranakpur रणकपुर</a> (Rajasthan). <a href="https://upload.wikimedia.org/wikipedia/commons/8/86/Chaumukha_Jain_temple_at_Ranakpur_in_Aravalli_range_near_Udaipur_Rajasthan_India.jpg">Chaumukha Jain temple</a>.</li><li><a href="http://wikimapia.org/#lang=en&lat=23.142047&lon=78.711483&z=17&m=bs&show=/42165691/Ruined-temple">Gorakhpur गोरखपुर</a> (District Raisen रायसेन, Madhya Pradesh). <a href="https://doi.org/10.5281/zenodo.10028195">Temple destroyed by earthquake</a>.</li></ul>
Tree diameter growth and increment core δ13C data from a recently thinned forestry-drained site (Lettosuo) in southern Finland.
<p>Dataset includes increment core data from Lettosuo drained peatland forest site. The study site locates in the Tammela municipality in southern Finland (60° 38’ 31’’ N, 23° 57’ 35’’ E). Increment cores were analysed for the ring widths for dominant and suppressed Norway spruce trees, and for the ring δ<sup>13</sup>C values from suppressed Norway spruce trees. Data was collected as a part of BiBiFe (”Biogeochemical and biophysical feedbacks from forest harvesting to climate change”) consortium that is funded by the Academy of Finland. </p> <p> </p> <p>Sampling for increment cores was done during October 2020 for sample trees (10 in total, of which 5 were suppressed trees from thinned area and 5 suppressed trees from control area) and additional sampling was conducted for annual diameter increment for 3 tree groups to increase sample size for diameter growth (suppressed trees in thinned area [n=20], dominant trees in thinned area [n=22] and suppressed trees in control area[n=20]) during March 2021. </p> <p> </p> <p><strong>Tree </strong><strong>ring carbon isotope data</strong></p> <p> </p> <p>Laser ablation IRMS method was applied in the Stable Isotope Laboratory of Luke (SILL) to quantify δ<sup>13</sup>C values in 10 increment cores for the time period 2010–2020, following principles of Schulze et al. (2004) and described in Lehtonen et al (manuscript). Up to 11 evenly spaced “spots” for each annual tree ring were measured to obtain information on the intra-annual variation of δ<sup>13</sup>C of the samples. </p> <p> </p> <p>(1) File: Lettosuo_d13C.xls</p> <p>File includes d13C measurements</p> <p> </p> <p><strong>Data column description below for isotope data: </strong></p> <p> </p> <p><strong>id</strong> stands for tree id [id includes tree identity, year and also spot number]</p> <p><strong>year</strong> is the year of the tree ring</p> <p><strong>nr</strong> is an index for data </p> <p><strong>tree</strong> indicates tree identity "C" for control and "H" for harvest</p> <p><strong>treatment</strong> indicates the treatment of the sampling area (control / harvest)</p> <p><strong>d13C</strong> gives the measured d13C value based on the LA-IRMS measurements</p> <p><strong>season </strong>indicates whether observation originated from the earlywood (EW) or latewood (LW) period, where 1 is EW and 2 is LW</p> <p> </p> <p><strong>Tree ring width measurements</strong></p> <p> </p> <p>In addition to the δ<sup>13</sup>C values, also the ring widths were measured. Here, also additional dominant trees were measured. </p> <p> </p> <p>(3) Files:</p> <p>controlRW.csv</p> <p>dominantRW.csv</p> <p>thinningRW.csv</p> <p> </p> <p>Files include increment core data (in micrometers) from isotope sample trees and additional increment core trees from the control area and harvested area of the site. Dominant trees were measured only from the thinned area. </p> <p> </p> <p>In the .csv files individual columns are for ring widths for individual trees. In the controlRW.csv and thinningRW.csv files first 5 columns include diameter increments from sample trees (those that have also d13C measurements).</p> <p> </p> <p><strong>References:</strong></p> <p> </p> <p>Lehtonen A, Leppä K, Sahlstedt E, Schiestl-Aalto P, Heikkinen J, Young G, Korkiakoski M, Peltoniemi M, Rinne-Garmston K, Sarkkola S, Lohila A, Mäkipää R (manuscript). Fast recovery of Norway spruce trees after thinning from above on a drained peatland forest site.</p> <p> </p> <p>Korkiakoski M, Ojanen P, Penttilä T, Minkkinen K, Sarkkola S, Rainne J, Laurila T, Lohila A (2020) Impact of partial harvest on CH<sub>4</sub> and N<sub>2</sub>O balances of a drained boreal peatland forest. Agric For Meteorol 295:108168.</p> <p> </p> <p>Schulze B, Wirth C, Linke P, Brand WA, Kuhlmann I, Horna V, Schulze E-D (2004) Laser ablation-combustion-GC-IRMS--a new method for online analysis of intra-annual variation of 13C in tree rings. Tree Physiol 24:1193–1201.</p>
Environmental context observed during the Tara Pacific Expedition 2016-2018, simplified version at site level
<p>This dataset provide a site level-compilation of previous datasets provided at the event level (see https://zenodo.org/record/6445609#.YlP8B5NByEA). In some cases, certain parameters were not available at specific sampling sites due to technical issues or sensor availability, however, various basin scale studies and statistical tests require a complete dataset for all sampled sites. During the Tara Pacific expedition, many parameters were concurrently measured in-situ, estimated from remote sensing and/or modeled. For instance, sea surface temperature was measured on the boat using the thermosalinograph included in the underway system, but also with satellite and estimated from a model. Each of these three modes of acquisition have their caveat and accuracy, however, within a certain confidence interval, missing in-situ data can be replaced by its remotely sensed or modeled equivalent. We provide here a simplified version at the sampling site level by replacing missing in-situ data by their closest and most accurate satellite or modeled equivalent. In each case, in-situ data was considered as the most accurate source of data, with a preference to HPLC pigments analysis followed by measurements done by the ACS, while satellite and modeled data were used only if in-situ data was not available. We evaluated the accuracy of ACS and of each satellite and modeled datasets by linear regressions with their in-situ counterparts. A bias of the modeled or satellite data was identified when the slope of the regression was different to 1 and/or an intercept was different to 0. The satellite and modeled data were forced to match the in-situ data by dividing by the slope and subtracting the intercept. This is the case for SST. When large bias persisted between matchups with observations, the corrected data was not used to replace missing in-situ data. This is the case for chl. The same approach was then applied to fill missing data with modeled values (MERCATOR-Copernicus).</p> <p>A correction for the bias in the following variable was applied for SST, SSS, PO4, and SiOH. As previously done, if large bias persisted between observations and corrected data, they were not used to replace missing in-situ data. This is the case for chl, NO3, and Fe.</p> <p>The [MTE] samples were sometimes sampled in the afternoon instead of the morning alongside all the other water samples, thus were located in between two sampling stations. These [MTE] samples could not be assigned to a sampling station following the criterion presented in the section 3, therefore, the missing values of the corresponding morning stations were interpolated linearly.</p> <p>The same approach was used for pH measurements, with a preference from measurements provided by total carbonate system quantifications, followed by direct pH measurements and then modeled values (MERCATOR-Copernicus).</p>
Rosalia: An experimental research site to study hydrological processes in a forest catchment - data repository
<p>This repository is a supplement to the paper <strong>Fürst, J., et al. (2021). “Rosalia: an experimental research site to study hydrological processes in a forest catchment.” Earth Syst. Sci. Data 13(8): 4019-4034.</strong></p> <p>Experimental watersheds have a long tradition as research sites in hydrology and have been used as far back as the late 19<sup>th</sup> and early 20<sup>th</sup> century. The University of Natural Resources and Life Sciences Vienna (BOKU) has been operating the experimental research forest site called “Rosalia” with an area of 950 ha since 1875 to support and facilitate research and education. Recently, BOKU researchers from various disciplines extended the “Rosalia” instrumentation towards a full ecological-hydrological experimental watershed. The overall objective is to implement a multi-scale, multi-disciplinary observation system that facilitates the study of water, energy and solute transport processes in the soil-plant-atmosphere continuum.</p> <p>This repository contains the datasets collected by a monitoring network of 4 discharge gauging stations, 7 rain-gauges, together with observations of air and water temperature, relative humidity and conductivity. In four profiles, soil water content and temperature are recorded in different depths. In 2019, additionally a program to collect isotopic data in precipitation and discharge was started. On one site, also Nitrate, TOC and turbidity are monitored. All data collected since 2015, including in total 56 high resolution time series data (10 min sampling interval), are provided to the scientific community.</p>
Mapping the Atlantic Ocean i.e. the Gulf of Maine to identify suitable cultivation sites for kelp species
<p>Input source:</p> <ul> <li>Temperature data</li> <li>Depth data</li> <li>Wave data</li> <li>Nutrients data</li> <li>Current data</li> <li>Marine use data</li> </ul> <p><strong>All from other available sources outside the project</strong></p> <p> </p> <p>DATA SET GENERATED:</p> <ul> <li>Environmental data</li> <li>Training/validation data</li> <li>The socioeconomic datasets</li> </ul> <ul> <li>Map of suitable sites</li> <li>Model using GIS</li> </ul>
Stack Exchange Open Source site questions categorization
<p>This dataset contains the posts of Open Source Stack Exchange site, collected at the end of 2020, along with the categorization of the posts. For each post a category, and potentially a second one is indicated, along with the cluster (generic group) each category belongs to. The coding task of assigning each question to a category was performed by two independent coders for each question (the categorization of each coder is also provided in the dataset). The dataset contains also (in a separate file) a dictionary of the most correlated unigrams and bigrams per category.</p>
Simulation Parameters for Two Cooperative Binding Sites Sensitize PI(4,5)P2 Recognition by the Tubby Domain
<p>Dataset to perform the coarse-grained MD simulations presented in "Two cooperative binding sites sensitize PI(4,5)P2 recognition by the tubby domain". The dataset includes protein structures and GROMACS simulation files such as mdp, itp, gro, and index files for the tubby domain as well as PLC-delta1 PH domain.</p>
JavaScript Libraries From Top 1 Million Sites
<p>Scraped data from top 1 million domains as reported by Majestic 1 Million on June 5th, 2022. The homepage of each domain is scraped and all encountered javascript script source URLs are extracted.</p> <p>You can find the source code at <a href="https://github.com/get-set-fetch/scraper/tree/main/datasets">github.com/get-set-fetch/scraper</a> and detailed documentation at <a href="https://getsetfetch.org">getsetfetch.org</a>.</p>
A meteorology and snow dataset from adjacent forested and meadow sites at Crested Butte, CO, USA
<p>This dataset contains meteorology and snow observation data collected at sites in the southwestern Colorado Rocky Mountains during water years 2019-2021. Data collection had an emphasis on paired open-forest sites and included three forested elevations. In total, we present 270 snow pit observations, 4,019 snow depth measurements, and three years of meteorological forcing from two weather stations (one in a meadow, the other in an adjacent forest). The dataset is described in a forthcoming publication of the same name: <em>A meteorology and snow dataset from adjacent forested and meadow sites at Crested Butte, CO, USA</em> (Bonner et al., 2022).</p> <p>All snow observation and meteorological forcing data are available as both .nc and .mat files.<br> Additionally, original digitized copies of snow pit observations are provided as .gsheet/.xlxs files.</p> <p>This dataset will continue to be updated, via this repository, as additional years of data are collected.</p>
Datasets and Supporting Materials for the IPIN 2021 Competition Track 3 (Smartphone-based, off-site)
<p>This package contains the datasets and supplementary materials used in the IPIN 2021 Competition.</p> <p><strong>Contents:</strong></p> <ul> <li>IPIN2021_Track03_TechnicalAnnex_V1-02.pdf: Technical annex describing the competition</li> <li>01-Logfiles: This folder contains a subfolder with the 105 training logfiles, 80 of them single floor indoors, 10 in outdoor areas, 10 of them in the indoor auditorium with floor-trasitio and 5 of them in floor-transition zones, a subfolder with the 20 validation logfiles, and a subfolder with the 3 blind evaluation logfile as provided to competitors.</li> <li>02-Supplementary_Materials: This folder contains the matlab/octave parser, the raster maps, the files for the matlab tools and the trajectory visualization.</li> <li>03-Evaluation: This folder contains the scripts used to calculate the competition metric, the 75th percentile on the 82 evaluation points. It requires the Matlab Mapping Toolbox. The ground truth is also provided as 3 csv files. Since the results must be provided with a 2Hz freq. starting from apptimestamp 0, the GT files include the closest timestamp matching the timing provided by competitors for the 3 evaluation logfiles. It contains samples of reported estimations and the corresponding results.</li> </ul> <p><strong>Please, cite the following works when using the datasets included in this package:</strong></p> <ul> <li>Torres-Sospedra, J.; et al. Datasets and Supporting Materials for the IPIN 2021 Competition Track 3 (Smartphone-based, off-site). http://dx.doi.org/10.5281/zenodo.5948678</li> </ul>
PALEODEM/ Supplementary materials of the manuscript "Unraveling Early Holocene occupation patterns at El Arenal de la Virgen (Alicante, Spain) open-air site: an integrated palimpsest analysis"
<p>This repository hosts the R code scripts and datasets that allow reproducibility and replicability of the intra-site spatial analyses implemented in the paper:</p> <p>Rabuñal, J.R., Gómez-Puche, M., Polo-Díaz, A., Fernández-López de Pablo, J., 2022. Unraveling Early Holocene occupation histories at open-air sites through integrated chronological, archaeostratigraphical, lithic refitting and spatial analyses: the Arenal de la Virgen (Villena, Alicante) study case. SocArXiv.</p> <p>Contents:</p> <p>AV_Spatial_database.xlsx: main dataset for the intra-site spatial analysis.</p> <p>AV_Lcross_database.xlsx: dataset for the implementation of the cross-type L function.</p> <p>AV_2clusters.rds: dataset for the calculation of the artifact metrics.</p> <p>AV_MovingWindow_Results.csv: dataset with the results of the calculation of the Burnt Microdebris Index and its spatial autocorrelation analysis.</p> <p>AV_DBSCAN_Separation.R: R file containing the code used for the separation of the lithic spatial distribution using the DBSCAN automated density-based clustering algorithm.</p> <p>AV_Spatial_analysis.R: R file containing the code used for the intra-site spatial analysis.</p> <p>AV_MWA_Moran.R: R file containing the code for implementing the calculation and spatial autocorrelation analysis of the Burnt Microdebris Index.</p>
Intermolecular interactions in G protein-coupled receptor allosteric sites at the membrane interface from molecular dynamics simulations and quantum chemical calculations
<p>Allosteric modulators are called to be promising candidates in G protein-coupled receptor (GPCR) drug development by displaying target selectivity and fewer side effects. Among the allosteric sites known to date, extrahelical cavities represent an uncharacteristic binding location that raises many questions about the ligand interactions and stability; the binding site structure, and how all of these are affected by lipid molecules. In this work, we analyze the dynamics and interactions in the PAR2, C5aR1, and GCGR receptors unbound and bound to allosteric modulators at the receptor-lipid interface using molecular dynamics simulations in three lipid compositions. In addition, we performed quantum chemical calculations to further explore electrostatic interactions and the strength of atom pairwise contacts in the stabilization of the ligand-receptor complexes. We show that besides classical hydrogen bonds weak polar interactions such as O-HC, O-Br, and S-HC contacts and aromatic interactions contribute to the binding of allosteric modulators at the extrahelical sites in the middle of the membrane. The allosteric cavities are open and detectable in various membrane compositions but not always predicted as druggable. The availability of polar atoms for interactions in such cavities can be assessed by water molecules from the simulations. Although ligand-lipid interactions are weak, the lipid tails play a role in sizing and shaping the large part of the allosteric cavity. </p> <p>You will find the following files:</p> <ul> <li>Input files of the equilibration and production protocols of MD simulations (MD_simulations_inputs.zip)</li> <li>Input files and coordinate files of F-SAPT and NCIPLOT calculations (quantum_chemical_coordiates_inputs.zip)</li> </ul>
"Chronomodel" Bayesian chronological models for East Borneo, based on data from the Liang Abu and Kimanis sites
<p>Bayesian chronological models generated using the <a href="https://chronomodel.com"><em>ChronoModel</em></a> software East Borneo (Indonesia), based on data from the Liang Abu and Kimanis (Arifin, 2017) archaeological sites.</p> <p>Two models were generated:</p> <ul> <li> a “<strong>conservative</strong>” model, observing the Bayesian approach and the distinction between<br> prior and posterior information;</li> <li>a “<strong>restricted</strong>” model: excluding possible outliers and without application of a “Fresh-<br> water reservoir effect” correction.</li> </ul> <p>Four files are provided:</p> <ul> <li>abu-kimanis-conservative-model.chr: model specification for the “conservative” model</li> <li>abu-kimanis-conservative-model_synthetic-stats-table.csv: results for the “conservative” model</li> <li>abu-kimanis-restricted-model.chr: model specification for the “restricted” model</li> <li>abu-kimanis_restricted-model_synthetic-stats-table.csv: results for the “restricted” model</li> </ul> <p>The .chr files can be open and edited using the <em>ChronoModel</em> software.</p>
ODP Site 807 benthic foraminiferal carbon and oxygen isotopes during the early Pleistocene
<p>The early Pleistocene benthic isotopic data of ODP 807 generated by this study are available.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.