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253 results for “data publishing”
otoole et al (2023) apobec3 published data
<p>Contents</p> <p>Data<br> - 3 XML files (epoch model, exponential model and skygrid model with 2 APOBEC3 partitions defined).<br> - 4 phylogenies (B.1 and Clade IIb, Clade I and Clade IIa, outgroup pruned)<br> - 4 state reconstruction files (B.1 and Clade IIb, Clade I and Clade IIa)<br> - 4 branch SNP reconstruction files (B.1 and Clade IIb, Clade I and Clade IIa)<br> - 4 amino acid reconstruction files (B.1 and Clade IIb, Clade I and Clade IIa)<br> - 4 snp count files (B.1 and Clade IIb, Clade I and Clade IIa) <br> - 2 heptamer count files for Clade IIb (internal and all branches)<br> - 4 root-to-tip data files (B.1 and Clade IIb, Clade I and Clade IIa)<br> - 1 mutation count file including data from Clade IIb and B.1<br> <br> Scripts<br> - all_in_one notebook (notebook of most work from the paper- reconstructs the branch snps from the state files, generates tree figures, calculates amino acid information, calculates root-to-tip data for regression, code for generating figures present in the manuscript, sliding window calculations)<br> - analysis_until_roottotip (stand alone notebook to get root-to-tip data)<br> - cleaner_apobec_work (earlier version of analysis, including sankey diagram code)<br> - get_ml_tree_with_reconstruction (shell commands for aligning, generating ml tree, reconstructing states and pruning off outgroup)<br> - make_partitions (extraction of code for generating the two partitions of the alignment, apobec3 and non-apobec3)<br> - roottotip.R (regression analysis using roottotip data)<br> - synonprob.R (probability of getting x synonymous mutations given the data)</p>
Knowledge Exchange - Data from the survey on Alternative Publishing Platforms
<p>The survey data are available in two formats (.csv and .xlsx). They each contain the answers of 45 respondents to the survey conducted at the start of 2023.</p> <p>The <a href="https://docs.google.com/forms/d/e/1FAIpQLScXVQ_4UqZzPh6tj4lGna_SLA4iD0DF5DGjkYKu4HlVJ9AitA/viewform">survey form is still open</a>.</p>
Data pertaining to the published article "Quantitative T1 mapping detects blood-brain barrier breakdown in apparently non-enhancing multiple sclerosis lesions" by Donatelli et al., 2023.
<p>Data pertaining to the published article "Quantitative T1 mapping detects blood-brain barrier breakdown in apparently non-enhancing multiple sclerosis lesions" by Donatelli et al., NeuroImage: Clinical (2023). </p><p>PMID: <strong>37717382; </strong>PMCID: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/pmc10514220/">PMC10514220</a>; DOI: <a href="https://doi.org/10.1016/j.nicl.2023.103509">10.1016/j.nicl.2023.103509</a></p>
Landscape composition and life‐history traits influence bat movement and space use: Analysis of 30 years of published telemetry data
Open the record for dataset details and reuse information.
Lab Standards for Benthic Macroinvertebrate Sequencing (repackaging of occurrences published by the NEON Biorepository Data Portal)
These DNA extracts are community standard or mock standard of macroinvertebrate DNA created at NEON headquarters, and used as a positive control for macroinvertebrate and zooplankton metabarcoding data.
Source code for models of floral initiation in pea and gene expression data extracted from published sources
<p>The dataset contains the source code for computational models of a gene network controlling transition to flowering in pea (<em>Pisum sativum</em>). The models were based on ordinary differential equations (ODE) or neural networks. It also includes data on the expression dynamics of genes involved in the network, which was used for model fitting. The expression data was extracted from the following papers: </p> <p>Hecht, V., Laurie, R. E., Schoor, K. Vander, Ridge, S., Knowles, C. L., Liew, L. C., Sussmilch, F. C., et al. (2011). The Pea GIGAS Gene Is a FLOWERING LOCUS T Homolog Necessary for Graft-Transmissible Specification of Flowering but Not for Responsiveness to Photoperiod. 23, 147–161. doi:10.1105/tpc.110.081042</p> <p>Sussmilch, F. C., Berbel, A., Hecht, V., Schoor, K. Vander, Ferrándiz, C., Madueño, F., et al. (2015). Pea VEGETATIVE2 Is an FD Homolog That Is Essential for Flowering and Compound In fl orescence Development. 27, 1046–1060. doi:10.1105/tpc.115.136150</p> <p>The source code of the DEEP software used for parameter optimization in the model fitting can be found in the Gitlab repository (https://gitlab.com/mackoel/deepmethod/-/tree/master).</p> <p>The files are the supplement to the following manuscript, submitted to Frontiers in Genetics:</p> <p>"Dynamical Modeling of the Core Gene Network Controlling Transition to Flowering in <em>Pisum sativum</em>" by Polina Pavlinova, Maria G. Samsonova, and Vitaly V. Gursky.</p> <p>All possible questions can be sent to: Polina Pavlinova (polina.pavlina1004@gmail.com), Vitaly Gursky (gursky@math.ioffe.ru).</p>
Data Tables from contribution titled "Joint geophysical-petrological modeling on the Ivrea geophysical body beneath Valsesia, Italy: Constraints on the continental lower crust" published in Geochemistry, Geophysics, Geosystems
<p><strong>TABLE CAPTIONS</strong></p> <p><strong>Table 1: </strong>Average and specific bulk compositions of the representative exposed primitive rocks of the deep lower crust and upper mantle of the IVZ (Balmuccia and Lower Mafic Complex in Valsesia, Finero in Val Cannobina, and Sessera river in Val Sessera) used for the Perple_X calculations using the two thermodynamic models STX11 and HP02. Mn, Ni, P, and Cr were not used for the Perple_X calculations. Mg# is calculated as Mg / (Mg + Fe) (mole fractions). Symbols in the last row indicate the rock compositions that are reported (✓) and not reported (✗) in Figure 5. Average compositions are normalized to 100 wt.% on a volatile-free basis; specific compositions report original totals and H<sub>2</sub>O contents estimated based on the volumetric proportions hydrous minerals (amphibole and phlogopite) at the scale of the bulk rock. References: 1) Voshage et al. (1990); 2) Voshage et al. (1990), Shervais and Mukasa (1991), Hartmann and Wedepohl (1993), Rivalenti et al. (1995), and Mukasa and Shervais (1999); 3) Pin and Sills (1986); 4) Pin and Sills (1986), Shervais and Mukasa (1991), Hartmann and Wedepohl (1993), Rivalenti et al. (1995), and Mukasa and Shervais (1999); 5) Shervais and Mukasa (1991) and Mazzucchelli et al. (2009); 6) Sinigoi et al. (1991; 2011); 7) Hartmann and Wedepohl (1993); 8) Coltorti and Siena (1984); 9) Siena and Coltorti (1989), Lu et al. (1997a; b), and Stähle et al. (2001).</p> <p> </p> <p><strong>Table 2: </strong>Summary of <em>V<sub>P</sub></em> and <em>r</em> from the thermodynamic calculations based on representative rock compositions listed in Table 1. Mineral abbreviations: Pl = plagioclase, Spl = spinel, Grt = garnet, Ky = kyanite, Px = pyroxene, Cr-Di = Cr-diopisde, Am = amphibole, Phl = phlogopite.</p>
Raw data and analysis results in paper by Cho and Iwata published in JGR
<p>Thirty-two microtremor arrays were analyzed in Cho and Iwata (2021) (Cho, I., & Iwata, T., 2021, Limits and benefits of the spatial autocorrelation microtremor array method due to the incoherent noise, with special reference to the analysis of long wavelength ranges. Journal of Geophysical Research: Solid Earth, 126, e2020JB019850. https://doi.org/10.1029/2020JB019850). This archive includes the raw digital data of microtremors and analysis results, plots of the processing results of individual arrays, and script files to plot some graphs.</p> <p> </p>
Data used in the paper entitled: Damaged Speleothems and Collapsed Karst Chambers Indicate Paleoseismicity of the NE Bohemian Massif (Niedźwiedzia Cave, Poland), published in TECTONICS
<p>Multiphase speleothem damage and passage collapse in Niedźwiedzia Cave (E: 16°50′36,65″, N: 50°14′04,26″) NE Bohemian Massif, Poland, were studied with an integrative approach to decipher the cause of damage during the last 320 ka. Since the most likely trigger of damage in the cave was an earthquake, we support our interpretation with a probable seismic intensity prediction to define a seismogenic source and to calculate the expected macroseismic intensity and peak ground acceleration (PGA) at the research site. Finally, we evaluate probable seismic effects in the cave with the elastic properties of speleothems to ascertain a threshold value of failure.<br> The relative range of earthquake hazards for a particular site depends significantly on the decrease in the ground motion amplitude (or intensity) with distance from all surrounding potential seismic sources, event size, and type of acting mechanism. The ground motion relation generally depends on the depth of focus, earthquake mechanism, and geological conditions along the path (Schenková et al., 1981). Therefore, to discuss probable seismic effects in Niedźwiedzia caves and their vicinities, we used the attenuation curves presented previously for the research area (Schenková et al., 1981; <a href="https://doi.org/10.1007/BF00878971;">https://doi.org/10.1007/BF00878971;</a> see the coefficient for the 13th zone). Dataset 2020TC006459_ds_to fig.5 contains a calculation of the attenuation curves, i.e., decrees of the intensity (on the MSK scale) and PGA (m/s2) with distance from the epicenter. We used these data to estimate (or to predict) the expected values of intensities ranging with distance from the seismogenic source region. This approach is a steady-state approximation because we assumed that isoseismal spread is regularly distributed around the epicenter and that the local influence of discontinuities is omitted.<br> The failure criteria resulting in speleothem damage were evaluated on a prismatic cantilever beam supported at one end. The parameters describing these criteria are the speleothem natural frequency and the corresponding critical horizontal ground acceleration (m/s2), which depend on elastic properties of the speleothem and the following geometric dimensions: height, H, and diameter, D, measured in situ (we acquired geometric measurements for 50 broken speleothems in Niedźwiedzia Cave). The horizontal ground acceleration is the limit value when at which speleothems breaks. The natural frequency (Hz) indicates that the failure process is more likely to occur if the natural frequency (or resonance frequency) is in accordance with the seismic wave frequency affecting the speleothem. If both frequencies match, the speleothem resonates, enhancing the oscillation effect, which may lead to damage. Dataset 2020TC006459_ds_to fig.6 contains H and D measurements of 50 broke speleothems and calculated natural frequency and critical horizontal ground acceleration for each measured speleothem. The values of both failure parameters depend on elastic properties that can be assessed in laboratory tests in which the following parameters are estimated: P- and S-wave velocities, Vp and Vs, respectively, using an acoustic measurement system, density, ρ, (from the measured mass and volume), Young’s modulus, E, and tensile stress, σt. The AMS tests were carried out at the Institute of Earth Sciences, University of Silesia, Sosnowiec, Poland. The failure stress was estimated based on the uniaxial compressive stress test carried out in the external laboratory of AP GEOTECHNIKA, Katowice, Poland, using a universal testing machine. The strength tests were conducted for two 0.05x0.05 m (height/dimension, h/d = 1) speleothems samples.</p>
WDS-RDA Publishing Data Workflows Working Group Analysis sheet
<p>The information was further refined by adding color: pink indicates “project” (4 entries), blue shows “repository” (14 entries), yellow is “journal” (7 entries) and green for “hybrid” (1 entry). Future versions of the spreadsheet are planned, which can be filtered via other categories, for example: discipline-specific vs discipline-agnostic, funding model, level of editing/intervention, etc.</p> <p>The collection and analysis of data took place between 1 February and 30 June 2015</p>
WDS-RDA-F11 Publishing Data Workflows WG Synthesis FINAL CORRECTED
<p>Final, revised version of http://dx.doi.org/10.5281/zenodo.33413 (published 6 November 2015)</p>
WDS-RDA Publishing Data Workflows Working Group Analysis sheet FINAL
<p><strong>NB: This dataset is superseded by:</strong></p> <p>Murphy, Fiona et al.. (2015). WDS-RDA-F11 Publishing Data Workflows WG Synthesis FINAL CORRECTED. Zenodo. 10.5281/zenodo.33899</p> <p>Data Publishing Workflows collected and analysed between 1 February - 30 June 2015. Fields were populated using a combination of consultation and desk research. This is a refined version of the previous spreadsheet also lodged in Zenodo: </p> <p>Murphy, Fiona et al.. (2015). WDS-RDA Publishing Data Workflows Working Group Analysis sheet. Zenodo. 10.5281/zenodo.19107</p> <p>Publication date: 29 June 2015</p> <p>Keyword(s): <strong>data publishing, workflows, journals, repositories, research data</strong></p>
Ionosphere-Thermosphere Data Published in "Responses of the Thermosphere and Ionosphere System to Concurrent Solar Flares and Geomagnetic Storms"
<p>This dataset supports the Journal of Geophysical Research publication "Responses of the Thermosphere and Ionosphere System to Concurrent Solar Flares and Geomagnetic Storms" by Qian et al., 2019. The data files are selected output and related analyses from the thermosphere-ionosphere-electrodynamics general circulation model (TIEGCM). The format of the data files are either IDL save files or NetCDF files or ASCII.</p>
Supplementary data for "Increasing risks of extreme salt intrusion events across European estuaries in a warming climate", published in Communications Earth & Environment
<p>This data repository contains python scripts and post-processed climate model and salt intrusion length data to reproduce figures in the paper below.</p> <p>====================</p> <p>Title: Increasing risks of extreme salt intrusion events across European estuaries in a warming climate (<a href="https://www.nature.com/articles/s43247-024-01225-w">Link to the full paper</a>)</p> <p>Author: Jiyong Lee, Bouke Biemond, Huib de Swart, and Henk A. Dijkstra</p> <p>Journal: Communications Earth & Environment</p> <p>Year: 2024</p> <p>Publisher: Nature</p> <p>====================</p>
Data for the research article "High-Temperature Deformation of Enstatite-Olivine Aggregates" published in JGR Solid Earth
<p>The data available in this repository is the original data presented in the research article: Bystricky, M., Lawlis, J., Mackwell, S., & Heidelbach, F. (2024). High-temperature deformation of enstatite-olivine aggregates, Journal of Geophysical Research: Solid Earth, 129, e2023JB027699. https://doi.org/10.1029/2023JB027699.</p> <p>Version v1: data at time of original submission (2023)</p> <p>Version v2: data at time of publication (2024)</p>
Data referring to the Article "Harmonized Skies: A Survey on Drone Acceptance across Europe" published in Drones Journal
<p><span>The material provided is part of the article "Harmonized Skies: A Survey on Drone Acceptance across Europe," published in the Drones Journal (https://doi.org/10.3390/drones8030107). This article describes a study investigating civil drone acceptance in six different EU countries. This study was part of the USpace4UAM project (Grant Agreement No 101017643). The material includes the data set for the study described and the Python codes for the random forest analysis carried out to investigate the influence of demographic and personnel factors on drone acceptance.</span></p>
Data and scripts for the article on 'Affectedness and Differential Object Marking in Turkish and Uzbek', published in Linguistics
<p>Data and scripts for the article on 'Affectedness and Differential Object Marking in Turkish and Uzbek', published in Linguistics; see the publication for details</p>
Data from: Landscape composition and life-history traits influence bat movement and space use: analysis of 30 years of published telemetry data
<p><span><b>Aim: </b>Animal movement determines home range patterns, which in turn affect individual fitness, population dynamics and ecosystem functioning. Using temperate bats, a group of particular conservation concern, we investigated how morphological traits, habitat specialization and environmental variables affect home range sizes and daily foraging movements, using a compilation of 30 years of published bat telemetry data.</span></p> <p><span><b>Location</b>: Northern America and Europe.</span></p> <p><span><b>Time period</b>: 1988 – 2016.</span></p> <p><span><b>Major taxa studied</b>: Bats.</span></p> <p><span><b>Methods</b>: We compiled data on home range size and mean daily distance between roosts and foraging areas at both colony and individual levels from 166 studies of 3,129 radiotracked individuals of 49 bat species. We calculated multi-scale habitat composition and configuration in the surrounding landscapes of the 165 studied roosts. Using mixed models, we examined the effects of habitat availability and spatial arrangement on bat movements, while accounting for body mass, aspect ratio, wing loading and habitat specialization.</span></p> <p><span><b>Results:</b><i> </i>We found a significant effect of landscape composition on home range size and mean daily distance at both colony and individual levels. On average, home ranges were up to 42% smaller in the most habitat-diversified landscapes while mean daily distances were up to 30% shorter in the most forested landscapes. Bat home range size significantly increased with body mass, wing aspect ratio and wing loading, and decreased with habitat specialization.</span></p> <p><span><b>Main conclusions: </b>Promoting bat movements through the landscape surrounding roosts at large spatial scales is crucial for bat conservation. Forest loss and overall landscape homogenization lead temperate bats to fly farther to meet their ecological requirements, by increasing home range sizes and daily foraging distances. Both processes might be more detrimental for smaller, habitat-specialized bats, less able to travel increasingly longer distances to meet their diverse needs.</span></p>
Data for article on "Selectives ("topic markers") on subordinate clauses", published in Linguistics
<p>Dataset for study on "Selectives (“topic markers”) on subordinate clauses" (Appendix F)</p>
Conceptualizing relationships among hyporheic exchange, storage, and water age: data represented in published figures
<p>Hyporheic exchange is a key driver of ecosystem processes in streams, yet stream ecologists often fail to leverage detailed conceptual models developed by engineers and hydrologists describing the relationship between water storage, water balance, and water age (time elapsed since a conceptual parcel of water entered the hyporheic zone) in hyporheic zones. In a companion paper (G.C. Poole et al. <em>Hyporheic Hydr</em><em>au</em><em>lic Geometry: Conceptualizing relationships among hyporheic exchange, storage, and water age</em>, published in PLoS ONE; doi:<a href="https://doi.org/10.1371/journal.pone.0262080">10.1371/journal.pone.0262080</a>), we provide visualizations of these relationships in an effort to allow non-hydrologists to grasp four primary concepts along with associated research and management implications: 1) the rate of hyporheic exchange, size of the hyporheic zone, and hyporheic water age are inexorably linked; 2) such linkages can be leveraged to build understanding of hyporheic processes; 3) the age distribution of hyporheic water and hyporheic discharge is heavily skewed toward young water ages -- at any temporal scale of observation (minutes, hours, days, or months) older hyporheic water is rare relative to younger water; 4) the age distribution of water discharged from any hyporheic zone is not the same as the age distribution of water stored within that hyporheic zone. The data set presented here represents the numerical values represented by the figures published in the companion paper.</p>
ScienceDex guides
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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.