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1,582 results for “manuscript”
Dataset for manuscript "Sleep does not influence schema-facilitated motor memory consolidation"
<p>Dataset containing the raw as well as the subject-level data for the two experiments reported in the manuscript "Sleep does not influence schema-facilitated motor memory consolidation".</p>
Supplementary movies for the manuscript "Modelling of Tissue Invasion in Epithelial Monolayers"
<p>Supplementary movies for the manuscript "Modelling of Tissue Invasion in Epithelial Monolayers"</p>
Magnaporthe oryzae transposable elements manuscript additional datasets
<p>Additional datasets for manuscript on transposable elements in <em>Magnaporthe oryzae</em>. </p> <ul> <li>analysis_files.tar.gz - contains selected analysis files generated by scripts in this GitHub repository: <a href="https://github.com/annenakamoto/moryzae_tes">https://github.com/annenakamoto/moryzae_tes</a>. File names correspond to those in the scripts.</li> <li>FungGAP_out.tar.gz - contains gene prediction outputs for all genomes used</li> <li>OrthoFinder_out.tar.gz - contains output from OrthoFinder, run on proteomes of all genomes used</li> <li>tabular_data_for_figures.tar.gz - contains tabular data used to generate figures</li> <li>visualization_files.tar.gz - contains bed and seg files used to visualize all genes, SCOs, effectors, TEs, solo LTRs, and GC content in each representative genome</li> </ul>
Supporting data for the manuscript entitled: Long-term biodegradation of oil under Arctic Conditions: the Baffin Island Oil Spill (BIOS) revisited after almost four decades.
<p>The potential of an unintentional oil spill from ships or upcoming oil development is rising as the Arctic warms up more. It is crucial to understand how oil behaves in this setting and what influences oil biodegradation in the Arctic. On Baffin Island in the Canadian High Arctic, the Baffin Island Oil Spill (BIOS) project staged a number of simulated oil spills on the backshore zone of beaches in the 1980s. Two BIOS sites were revisited in 2019, about 40 years after the first oil pollution, providing a unique chance to research the long-term weathering of crude oil in Arctic conditions. Here, we demonstrate that even after over 40 years, residual oil is still detectable at these locations. Oil at both locations seems to deteriorate relatively slowly, with estimated loss rates ranging from 1.8 to 2.7% annually and appearing to vary across the two locations. We also demonstrate how the locations' sediment microbial communities are still severely impacted by leftover oil, as seen by a decline in diversity, variations in microbial load, and an enrichment of reported oil-degrading bacteria in contaminated sediments. The most enriched putative oil degraders were found in non-oiled control sediments as well, indicating that these degraders are a normal component of the Arctic sediment microbiome even in the absence of oil. Reconstructed genomes of putative oil degraders indicate that only a portion of these degraders have unique adaptations for growth in psychrothermic environments. This study's findings taken together demonstrate that oil spills in the Arctic can linger and have a lasting, major impact on the environment for decades.</p>
Code and data for manuscript: Is phase-dependent stability related to phase-dependent gait robustness?
<p>Code and code data for manuscript: Is phase-dependent stability related to phase-dependent gait robustness?</p>
Data sources for the manuscript on groundwater stress indicators published in Water Resources Research
<p>We computed seven global-scale groundwater stress indicators at the 0.5° grid-cell level and for transboundary aquifers> 20,000 km². All indicators were calculated for current conditions (1981-2010 or 2001-2010) based on a homogenized version of the concatenated WATCH Forcing Data ERA-40 (WFD) and WFD ERA-Interim data sets (WFDEI). In addition, four of the indicators were computed for the 2050s (2041-2070) under the worst-case greenhouse gas emissions scenario RCP8.5 applying ten climate and irrigation scenarios. The scenarios were derived by combining two irrigation scenarios (“AAI constant” and “AAI LandSHIFT”) with model output from the five global climate models GFDL-ESM2M, HadGEM2 -ES, IPSL-CM5A-LR, MIROC-ESM-CHEM, and NorESM1-M.</p> <p>Here, we provide the WaterGAP model output used to compute the groundwater stress indicators. A description of the indicators and the underlying data can be found in the reference below. Moreover, a table with coordinates and grid-cell area [km²] used in WaterGAP is provided for the conversion of units.</p> <p>The model output comprises:</p> <p>1. Monthly groundwater recharge (GWR and GWRswb) 1981-2010 and 2041-2070 [mm/month, km³/month]</p> <p>2. Monthly groundwater withdrawals (WWg) 1981-2010 (constWU, transWU) and 2041-2070 (constWU) [m³/month]</p> <p>3. Monthly net abstractions from groundwater (NAg) 1981-2010 (constWU, transWU) and 2041-2070 (constWU) [m³/month]</p> <p>4. Monthly groundwater discharge (“gwrunoff”) 2001-2010 from a model run with human water use (transWU) [mm/month]</p> <p>5. Monthly groundwater discharge (“gwrunoff”) 2001-2010 from a model run without human water use (NAT) [mm/month]</p> <p>6. Monthly groundwater storage 2001-2010 from a model run with human water use (transWU) [mm]</p> <p>7. Monthly groundwater storage 2001-2010 from a model run without human water use (NAT) [mm]</p>
raw data for a manuscript submitted to Materials and Structures Journal
<p>raw data for a manuscript submitted to Materials and Structures Journal. Includes: coating thickness, jointly with economic and environmental calculations</p>
Dataset for the manuscript "Comparison of Spatiotemporal Distribution and Occurrence Conditions of Large and Small Hail Events in Beijing-Tianjin-Hebei Region"
<p>This data set is a supplement to the journal article " Comparison of Spatiotemporal Distribution and Occurrence Conditions of Large and Small Hail Events in Beijing-Tianjin-Hebei Region".</p> <p>The data set consists of</p> <ul> <li>Hail disaster information included the station NO., hail frequency and the maximum size of hailstone.</li> <li>The atmospheric environment data from ERA-interim data associated with the hail events in this study. </li> <li>VIL and meso-scale rotation parameters correspond to hailstorms. </li> </ul>
Spielbücher, Prognostiken und Textamulette als 'manuscript agents'?
<p>Marco Heiles, Spielbücher, Prognostiken und Textamulette als ‚manuscript agents‘?. Videoaufzeichnung des Vortrags auf der Tagung ‚Was ist historische Wissens- und Gebrauchsliteratur? Theoretische Grundlagen und Parameter der Korpusbildung‘ des Netzwerks Historische Wissens- und Gebrauchsliteratur e.V., Herzog August Bibliothek Wolfenbüttel, 30.08.2022.</p> <p>Schnitt: Melinda Michel (Rheinische Friedrich-Wilhelms-Universität Bonn)</p> <p> </p> <p>Präsentation des Vortrags: </p> <p><a href="https://doi.org/10.5281/zenodo.7515437">https://doi.org/10.5281/zenodo.7515437</a></p> <p> </p> <p>Programm der Tagung: </p> <p>Kathrin Chlench-Priber, Marco Heiles, Sven Limbeck und Simone Schultz-Balluff, Was ist historische Wissens- und Gebrauchsliteratur? Tagungskonzept und Programm, in: Netzwerk Historische Wissensund Gebrauchsliteratur, zuerst Veröffentlicht am 13.06.2022, aktualisierte Version vom 07.11.2022, <a href="https://hwgl.hypotheses.org/1801">https://hwgl.hypotheses.org/1801</a> (PDF: <a href="https://doi.org/10.5281/zenodo.7515385">https://doi.org/10.5281/zenodo.7515385</a>).</p>
Dataset associated with the manuscript: Soil management legacy interacts with wheat genotype to determine access to organic N in a dryland system
<p>Organic nutrient management through the application of compost and/or cover crops provides mineralizable sources of nutrients for plants while often building soil organic matter (SOM) and various aspects of soil health. Variability in nutrient acquisition strategies between crop genotypes may confer advantages under different soil health contexts and could be important for crop selection and breeding, but crop response under field conditions remains unexplored. We investigated the ability of different genotypes of winter wheat (<em>Triticum aestivum</em> L.) to access nitrogen (N) from newly added cover crop residues in two soils with contrasting levels of SOM and biological activity. We planted three previously characterized wheat genotypes in a long-term dryland compost amendment field trial: 1) Byrd (modern, deep roots, low exudation), 2) Cheyenne (historic, drought susceptible, intermediate exudation), and 3) Snowmass (modern, drought-susceptible, high exudation). <sup>15</sup>N-labelled cover crop residue was added to each plot and traced into wheat tissue. In the low SOM soil, the high exudate genotype Snowmass and historic genotype Cheyenne took up the most residue-derived N (6.4-8.1 kg N ha<sup>-1</sup>) compared to the low-exudate genotype Byrd (4.4 kg N ha<sup>-1</sup>), suggesting a strong exudate effect in the more carbon-limited soil. However, the low-exudate, deep rooted genotype, Byrd, took up the most residue N in the high SOM soils (4.6 kg N ha<sup>-1 </sup>vs. 2.8 and 3.3 hg N ha<sup>-1</sup> for Cheyenne and Snowmass, respectively), which indicated higher native N cycling activities and great importance of drought resistance. Enzyme activity, inorganic N, and microbial communities were not influenced by genotype, though did show strong effects of compost application legacy. Our results show that belowground allocation strategies that favor microbial stimulation may be less successful under water limitation, especially when high SOM can support mineralization of residue N without added investment in root inputs. Increased soil health through SOM-building management likely enhances nutrient cycling, and may better support root strategies that invest less in microbial stimulation in favor of other limiting resources.</p>
Dataset for the manuscript: "Three-dimensional species distribution modeling reveals the realized spatial niche for coral recruitment on contemporary Caribbean reefs"
<p>Whether the three-dimensional (3D) structure of habitats influences and partition recruitment niches of corals is unknown. We developed a new method that combined Species Distribution Modeling and Structure from Motion to characterize and map the three-dimensional recruitment niches of two ecosystem engineers on Caribbean coral reefs, scleractinian corals and octocorals. </p> <p>In this repository, we include 48 3D models of small areas of the reef (i.e., within ~ 0.25 m<sup>2</sup> quadrats) reconstructed with Structure-from-Motion, as well as the geospatial data used to characterize and map the realized recruitment niche for scleractinian corals and octocorals on Caribbean coral reefs. We conducted the study at two shallow, fringing reefs off the south shore of St. John, US Virgin Islands, named Grootpan and Europa Bays (18° 18.360’N, 64° 43.140’W, and 18° 19.016’N, 64° 43.798’W, respectively). Within each 0.25 m<sup>2</sup> quadrat, we counted and marked all recruits (octocorals ≤ 5 cm height, and scleractinians ≤ 4 cm wide).</p> <p><em>DATASET DESCRIPTIONS:</em></p> <ul> <li><strong>"Quadname_data.zip":</strong> In each of this folders we included all the data calculated within a quadrat: <ul> <li>ASCII files (.txt).</li> <li>The annotated dense point cloud (.las) for each quadrat.</li> <li>The quadrat 3D model texture (.jpg).</li> <li>The quadrat 3D polygon mesh (.ply).</li> <li>The quadrat 2.5D Digital Elevation Model (i.e., DEM; .tif).</li> <li>Shape files with recruits local coordinates within each quadrat (.dbf, .prj, .shp, .shx).</li> </ul> </li> <li><strong>"datawide.rds": </strong>This is the file needed to run the analyses performed in Martínez-Quintana et al., 2023. This file is obtained after processing all the raw data calculated within each quadrat. All code associated with the workflow used to obtain the datawide.rds file and run the analyses performed in Martínez-Quintana et al., 2023 is available at <a href="https://github.com/AdamWilsonLab/meshSDM">github.com/AdamWilsonLab/meshSDM</a>.</li> </ul> <p><strong>IMPORTANT NOTES: </strong></p> <ul> <li>Quadrat names starting with the letters “eu” indicate the data were collected at Europa Bay, whereas those starting with the letters “ec” indicate that data were collected at Grootpan Bay (commonly named East Cabritte).</li> <li>Each ASCII file (quadname_ASCII_subsampled_X.txt) contains the slope and roughness of the quadrat calculated on the point cloud at 5, 10, 20, and 100 mm scales, and the smooth point cloud used to calculate the topographic exposure index (TEI) described in Martínez-Quintana et al., 2023. Calculations were performed and ASCII files were created with CloudCompare.</li> <li>Each dense point cloud, mesh, texture, and DEM were calculated with Agisoft Metashape.</li> <li>Agisoft Metashape allows the user to classify and annotate groups of points in the dense point cloud. However, the list of classes provided by the software corresponds to the standard list used for terrestrial LiDAR data; these classes cannot be renamed within the software. Thus, for the present study, we coded the automatic semantic classifications available in Metashape as follows: <ul> <li>Ground = Calcareous rock.</li> <li>Building = Igneous rock.</li> <li>High noise = Sand.</li> <li>Low vegetation = Adult Scleractinian corals.</li> <li>Medium vegetation = Adult Octocoral base.</li> <li>High vegetation = Sponge.</li> <li>Water = Octocoral recruit (named also ocr).</li> <li>Road Surface = Scleractinian recruit (named also scr).</li> <li>Unclassified = created points but never classified (excluded from the analyses).</li> <li>Low Point = noise (unreliable points).</li> <li>Transmission tower and Rail = Points outside the quadrat and excluded from the analysis.</li> </ul> </li> </ul>
Raw data files for "A Simple, Transition Metal Catalyst-Free Method for the Design of Complex Organic Building Blocks Used to Construct Porous Metal-Organic Frameworks" manuscript
<p>Raw data files for a manuscript "A Simple, Transition Metal Catalyst-Free Method for the Design of Complex Organic Building Blocks Used to Construct Porous Metal-Organic Frameworks".</p> <p>All files are organized by instrumental methods, except Figure 1 in the manuscript and Figure S1, S52 in the SI, plots for which are reported as separate files. The file headers contain the necessary information such as column designations, units, etc.</p> <p> </p>
Dataset to manuscript "The role of weathering on morphology and rates of escarpment retreat of the rift margin of Madagascar" by Wang et al. (2023) submitted to Journal of Geophysical Research-Earth Surface.
<p>The dataset includes the relevant raw chemical element content data and the chemical weathering condition analysis of river sediment samples of Madagascar. The dataset is a supplement to the manuscript "The role of weathering on morphology and rates of escarpment retreat of the rift margin of Madagascar", by Wang et al. (2023) submitted to the Journal of Geophysical Research-Earth Surface. Commercially sensitive data is hidden but is available by request directly to the corresponding author. The data should <strong>NOT</strong> be used commercially.</p> <p>A MATLAB code for the weathering indices calculation is open-access on GitHub (https://github.com/yanyanwangesd/chemical_weathering). Please contact the corresponding author for more info or technical support on using the code. </p>
Data for the manuscript titled "Solute front shear and coalescence control concentration gradient dynamics in porous micromodel"
<p>Concentration images and data for plots for the manuscript "Solute front shear and coalescence control concentration gradient dynamics in porous micromodel" submitted for publication in Geophysical Research Letters.</p> <p>See the README file for explanations on the data file.</p> <p><strong>Movie captions:</strong></p> <p><strong>Movie S1:</strong> Concentration field for the Péclet Pe = 33 experiment. Solid pillars are represented by the gray discs, and the colormap corresponds to the rescaled concentration <span class="math-tex">\(c/c_\mathrm{max}\)</span>. The black line represents the solute front, which is the boundary of the continuous <span class="math-tex">\(c/c_\mathrm{max} < 0.5\)</span> region within the porous medium. The x- and y-coordinates of the porous medium length and width (respectively) are rescaled by the average pore diameter <span class="math-tex">\(\lambda\)</span>.</p> <p><strong>Movie S2:</strong> Concentration gradient field for the Pe = 33 experiment. Solid pillars are represented by the gray discs, and the colormap corresponds to the rescaled gradient <span class="math-tex">\( a \nabla c / c_\mathrm{max}\)</span>. The x- and y-coordinates of the porous medium length and width (respectively) are rescaled by the average pore diameter <span class="math-tex">\(\lambda\)</span>.</p> <p><strong>Movie S3:</strong> Concentration field for the Pe = 1104 experiment. Solid pillars are represented by the gray discs, and the colormap corresponds to the rescaled concentration <span class="math-tex">\(c/c_\mathrm{max}\)</span>. The black line represents the solute front, which is the boundary of the continuous <span class="math-tex">\(c/c_\mathrm{max} < 0.5\)</span> region within the porous medium. The x- and y-coordinates of the porous medium length and width (respectively) are rescaled by the average pore diameter <span class="math-tex">\(\lambda\)</span>.</p> <p><strong>Movie S4:</strong> Concentration gradients field for the Pe = 1104 experiment. Solid pillars are represented by the gray discs, and the colormap corresponds to the rescaled gradient <span class="math-tex">\( a \nabla c / c_\mathrm{max}\)</span>. The x- and y-coordinates of the porous medium length and width (respectively) are rescaled by the average pore diameter <span class="math-tex">\(\lambda\)</span>.</p>
Raw data for manuscript Semantic context can mask intelligibility declines at above-conversational speech levels in normal-hearing listeners
<p>Raw data for the manuscript in doc file. <br> Copied from the Matlab .m file. used for the analysis.</p> <p>To be updated.</p> <p>For details, contact me at mfer@health.sdu.dk</p>
Data and code for the manuscript:"Female preference for rare males is maintained by indirect selection in Trinidadian guppies"
<p>Data and code for the manuscript "Female preference for rare males is maintained by indirect selection in Trinidadian guppies</p> <p>This project contains three data files and two scripts.</p> <p>Data files:</p> <ul> <li> <p>LL_guppy_data.csv (the mark recapture data from the experimental stream)</p> </li> <li> <p>standardized_locations.csv (the standardized names for pools and riffles each month)</p> </li> <li> <p>pat_data.csv (the classification of male colour patterns by fish id)</p> </li> </ul> <p>Scripts:</p> <ul> <li> <p>data_preparation.R (this script merges the data files, calculates male pattern rarity and novelty, and scores fitness components. RUN THIS FIRST)</p> </li> <li> <p>analysis_and_figures.R (this script builds, runs, and checks the models, summarises the output, and produces the figures. RUN THIS SECOND)</p> </li> </ul>
Supplemental files for manuscript "The circulating phageome reflects bacterial infections"
<p>These are the supplemental files associated with the manuscript "The circulating phageome reflects bacterial infections". These include:</p> <p>1. Supplemental File 1 (Phage Dictionary).csv which is a dictionary connecting bacteriophage accession numbers to their known taxonomic data as well as the taxonomic data of their host if known.</p> <p>2. Supplemental File 2 (Coliphage Characteristics).csv which is a dictionary for phages which infect <em>Escherichia coli</em> including host information to strain if known and characteristics of any known strains.</p> <p>3. Supplemental File 3 (Metadata).xlsx which includes a metadata table for the plasma cfDNA samples sequenced in the associated study, including infection etiology.</p> <p>4. Supplemental File 4 (Negative Controls).xlsx which includes the sequences and identities of short reads from our negative sequencing controls (PBS, Water)</p>
GNSS position time series (.neu files) and seismic velocity strcture (Profil_lat2822_Vp_Vs.dat) used in the manuscript
<p>These are the raw GNSS time series files (in .neu format) and seismic velocity strcture file (Profil_lat2822_Vp_Vs.dat) we used in the manuscript. These data are not allowed to use before the manuscript is accepted.</p>
Saul Flores data for manuscript in ECOLOGY: Extreme drought disrupts plant phenology: insights from 35 years of cloud forest data in Venezuela
<p>Venezuela cloud forest phenology data for tree flowers and fruits.</p>
Python code generating the data of figures 2, 3, 4, 5 and 6 of the manuscript: The evolution of cooperation in the unidirectional linear division of labour of finite roles
<p>The evolution of cooperation is an unsolved mystery, which we see in many social and biological systems. In the study titled "The evolution of cooperation in the unidirectional linear division of labour of finite roles", we investigate under which sanction systems and how the evolution of cooperation happens in the linear division of labour. </p> <p>This python code has been used to produce the results of Figures 2, 3, 4, 5, and 6 of the manuscript. This code shows the evolution of cooperation among the population of various different groups which have different roles to play in the linear division of labour, on the basis of numerical analysis of a partial differential equation system, which originates from the replicator equations used in the evolutionary game theory. We find the locally stable equilibria using this code, which shows the ultimate results of the dynamics in the system under given parameters. Figures 3, 5, and 6 are direct products of the code, showing the dynamics of a system, and figures 2 and 4 are the end results of those dynamics. </p> <p>We found that in a social dilemma situation, cooperation never evolves in the system without punishment. However, with sanction systems by introducing a suitable amount of punishment, while having a suitable findability of the defector, and a suitable initial population structure, cooperation can evolve. These results can be found with this code. We have no legal or ethical concerns regarding this data as this is a numerical analysis based on theoretical equations. </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.