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1,773 results for “Supplementary data,”
Supplementary data for analysis of TEs in Atlantic salmon genome
<p>This dataset contains the data used to generate the figures in the manuscript "The role of transposon activity in shaping cis-regulatory element evolution after whole genome duplication".</p> <p>The scripts for the figures can be found at https://gitlab.com/sandve-lab/TE-CRE</p>
Supplementary data for the article Fichtner et al., 2024, A&A, 690, A72
<p>Supplementary data for the paper:<br>Fichtner Y. A., Mackey J., Grassitelli L., Romano-Díaz E., Porciani C., 2024, A&A, 690, A72, Connecting stellar and galactic scales: Energetic feedback from stellar wind bubbles to supernova remnants, DOI: https://doi.org/10.1051/0004-6361/202449638 </p> <p>Paper abstract:<br>Context. Energy and momentum feedback from stars is a key element of models for galaxy formation and interstellar medium dynamics, but resolving the relevant length scales to directly include this feedback remain out of reach of current-generation simulations.<br>Aims. We aim to constrain the energy feedback by winds, photoionisation and supernovae (SNe) from massive stars.<br>Methods. We measure the thermal and kinetic energy imparted to the interstellar medium on various length scales, calculated from high-resolution 1D radiation-hydrodynamics simulations. Our grid of simulations covers a broad range of densities, metallicities, and state-of-the-art evolutionary models of single and binary stars.<br>Results. A single star or binary system can carve a cavity of tens-of-pc size into the surrounding medium. During the pre-SN phase, post-main-sequence stellar winds and photoionisation dominate. While SN explosions dominate the total energy budget, the pre-SN feedback is of great importance by reducing the circumstellar gas density and delaying the onset of radiative losses in the SN remnant. Contrary to expectations, the metallicity dependence of the stellar wind has little effect on the cumulative energy imparted by feedback to the ISM; the only requirement is the existence of a sufficient level of pre-SN radiative and mechanical feedback. The ambient medium density determines how much and when feedback energy reaches to distance >= 10 − 20 pc and affects the division between kinetic and thermal feedback.<br>Conclusions. Our results can be used as a sub-grid model for feedback in large-scale simulations of galaxies. The results reinforce that the uncertain mapping of stellar evolution sequences to SN explosion energy is very important to determining the overall feedback energy from a stellar population.</p> <p>General description of the data release:<br>The data release contains tables with the cumulative flows of kinetic energy, thermal energy, mass and metal mass as a function of time for every simulation presented in the corresponding paper. The cumulative flows are calculated at three different distances from the stellar source (5, 10 and 20 pc). Exemplary parameter files of the simulations and readme files are also included.<br>The tables could be used in a sub-grid model of stellar feedback to determine the amount of feedback ejecta (mass, metals, thermal and kinetic energy) that can be injected, taking into account the circumstellar medium. It is possible to do so as a function of time, ambient metallicity and ambient density. The data release includes simulations of different stellar models of single and binary stars, making it possible to choose between different stellar populations.<br>It is also possible to use the data for a comparison to other work.</p>
Supplementary Data for: Benchmark of density functional theory in the prediction of chemical shielding anisotropies for anisotropic NMR based structural elucidation
<p>Additional Data for the research paper titled: Benchmark of density functional theory in the prediction of chemical shielding anisotropies for anisotropic NMR based structural elucidation.</p> <p>Anisotropy Benchmark for Carbon NS372:</p> <ul> <li>Chemical Shielding Tensor for the molecules in the NS372 test set for carbon (XLSX)</li> <li>Coordinate files for the molcules of the NS372 test set that contained carbon (in NS372-Carbon-COORD-Files.zip)</li> </ul> <p>DFT Benchmark for RCSA for Natural Products:</p> <ul> <li>Chemical Shielding Tensor used for the RCSA analysis of 6 Natural Products (CSV)</li> <li>Turbomole Input and Ouput files for the DFT calculation of the natural products (in RAW_DATA_for_RCSA_Analysis.zip)</li> <li>ConArch+ Input and Ouput files for the RCSA analysis using (in RAW_DATA_for_RCSA_Analysis.zip)</li> <li>Coordinate files used for the RCSA analysis (in RAW_DATA_for_RCSA_Analysis.zip)</li> </ul> <p> </p>
Supplementary data to: Characterizing regional oceanography and bottom environmental conditions at two contrasting sponge grounds on the northern Labrador Shelf.
<p>Supplementary data to the article: </p> <p><strong>Characterizing regional oceanography and bottom environmental conditions at two contrasting sponge grounds on the northern Labrador Shelf.</strong></p> <p> </p> <p> </p> <p>Published in Biogeosciences in 2024: https://bg.copernicus.org/articles/21/5407/2024/</p> <p><a href="https://bg.copernicus.org/articles/21/5407/2024/">BG - Characterizing regional oceanography and bottom environmental conditions at two contrasting sponge grounds on the northern Labrador Shelf</a></p> <p>DOI : https://doi.org/10.5194/bg-21-5407-2024</p> <p>Abstract: </p> <p>Deep-sea sponge grounds are distributed globally and are considered hotspots of biological diversity and biogeochemical cycling. To date, little is known about the environmental conditions that allow high sponge biomass to develop in the deep sea. Here, we characterize oceanographic conditions at two contrasting sites off the northern Labrador Shelf with high- and low-sponge-biomass. Data were collected by year-long benthic lander deployments equipped with current meters, a turbidity and chlorophyll-<em>a</em> measuring device, and a sediment trap. Additionally, regional oceanography was described by analyzing vertical conductivity-temperature-depth (CTD) casts, Argo float profiles, and surface buoy drifter data for the northern Labrador Shelf from 2005 to 2022. Stable isotopic composition of benthic fauna was determined to investigate food web structure at the sponge grounds. Our results revealed strong (0.26 ± 0.14 m s<sup>-1</sup>; mean ± SD) semidiurnal tidal currents at the high-sponge-biomass site, but twofold weaker currents (0.14 ± 0.08 m s<sup>-1</sup>; mean ± SD) at the low-sponge-biomass site. Tidal analysis suggests that, at the high-sponge-biomass site, kinetic energy is dissipated from barotropic tide to baroclinic tide/turbulence, which could enhance food availability for benthic organisms. Bottom nutrient concentrations were elevated at the high-sponge-biomass site which would benefits growth in deep-sea sponges. Organic matter flux to the seafloor was increased at the high-sponge-biomass site and consisted of fresher material. Finally, both sponge grounds demonstrated tight benthic-pelagic coupling prior to the onset of stratification. Stable isotope signatures indicated that soft corals (<em>Primnoa resedaeformis</em>) fed on suspended particulate organic matter, while massive sponges (<em>Geodia</em> spp.) likely utilized additional food sources. Our results imply that benthic fauna at the high-sponge-biomass site benefit from strong tidal currents, which increases food supply, and favourable regional ocean currents that increase nutrient concentration in bottom waters.</p>
Supplementary data for the discussion of the PhD thesis entitled Engineering Oleaginous Yeast for Bio-Based Future.
<p>Supplementary data corresponding to the discussion of PhD thesis named Engineering Oleaginous Yeast for Bio-Based Future.</p> <p>Authors:</p> <p>Zeynep Efsun Duman-Özdamar<sup>a,b,c</sup>, Maria Suarez-Diez<sup>b</sup></p> <p><sup>a</sup>Bioprocess Engineering, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands</p> <p><sup>b</sup>Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE, Wageningen, the Netherlands</p> <p><sup>c</sup>Wageningen Food & Biobased Research, Wageningen University & Research, 6708 WE, Wageningen, The Netherlands</p> <p> </p> <p> </p>
Supplementary material for the paper "Data-Limited Continuous Experimentation (dlCE): A Literature Review"
<p>This is supplementary material for a paper, "Data-Limited Continuous Experimentation (DLC): A Literature Review", published at the 15th International Conference on Software Business (ICSOB 2024). It contains a list of included papers from a literature review, their experimentation cases and extracted data related to contextual and experimentation factors, as well as their relevance to dlCE scenarios.</p>
Supplementary data for: "Emergence of Potential Anadromous Arctic Charr (Salvelinus alpinus) Habitats in the Svalbard Archipelago after the End of the Little Ice Age"
<p><strong>Supplementary data for: “Emergence of Potential Anadromous Arctic Charr (<em>Salvelinus alpinus</em>) Habitats in the Svalbard Archipelago after the End of the Little Ice Age” </strong></p> <p><a href="https://doi.org/10.1029/2024JG008367">https://doi.org/10.1029/2024JG008367</a></p> <p> </p> <p>Abstract: Glaciers in the Svalbard Archipelago are retreating rapidly in response to climate change. The retreat of glaciers leads to alteration of the hydrological and thermal regimes of the freshwater ecosystems. In this delicate context, existing anadromous Arctic charr (<em>Salvelinus alpinus</em>) populations are at severe risk and might disappear from the archipelago. However, the retreat of glaciers also promotes the formation of new lake systems that might be suitable for colonization by anadromous Arctic charr. These systems may provide a substantial opportunity for the establishment of new populations of anadromous charr, potentially buffering the decline in existing systems. To date, there is a lack of information on the number of recently deglaciated lake systems that have emerged since the end of the Little Ice Age (ca. 1920) that might be suitable for charr colonization. Therefore, the goal of this paper is to provide an initial assessment of the number of these lakes. To this end, and in accordance with previously published research, this study assesses whether a recently deglaciated lake system is potentially open to colonization based on gradient, river length, and lake surface area. Depending on the applied threshold (four in total), up to 24 lake systems are classified as potentially open to colonization by anadromous Arctic charr, with Spitsbergen emerging as a colonization hotspot. The findings of this paper might serve as basis for new studies and for implementing proactive management and conservation strategies to protect anadromous charr populations.</p> <p> </p> <p><strong>Data description:</strong></p> <p> </p> <p><em>Recently_Deglaciated_Systems</em> [EPGS: 25833] - Shapefile containing the information of 168 lake systems that emerged between 1936/1938 and 2020 in the Svalbard Archipelago</p> <p>ID: Identification number</p> <p>X: Easting</p> <p>Y: Northing</p> <p>Fall?: Presence of the lake system in fall (with dates when the lake was visible in satellite images)</p> <p>Spring?: Presence of the lake system in spring (with dates when the lake was visible in satellite images)</p> <p>Info: information regarding the type of system (i.e., larger lake surrounded by lakes and ponds or system of multiple lakes and ponds). If blank, lake is considered single.</p> <p> </p> <p><em>Analysis</em> [EPGS: 25833] - Shapefile containing the analysis of 125 lake systems with connection to the ocean.</p> <p>ID: Identification number</p> <p>X: Easting</p> <p>Y: Northing</p> <p>Surface (km<sup>2</sup>): Surface of the connected recently deglaciated lake system (km<sup>2</sup>)</p> <p>Elevation (m): Elevation of the outlet (m)</p> <p>Length (m): River length (m)</p> <p>Slope (%): Slope of the river (%)</p> <p>SV1: Result of the classification with SV1</p> <p>SV2: Result of the classification with SV2</p> <p>HY: Result of the classification with HY</p> <p>NO: Result of the classification with NO</p>
Supplementary data to "Protocol to image, segment and quantify cortical contractions in maturing mouse oocytes"
<p>This dataset contains supplementary materials for the "Protocol to image, segment and quantify cortical contractions in maturing mouse oocytes" manuscript.</p> <p>This dataset contains two timelapse images of maturing oocytes (control_oocyte.tif and ArpC4_KO_oocyte.tif) with the corresponding Region of Interest files for FIJI (control_oocyte_UnetCortex.zip and ArpC4_KO_oocyte_UnetCortex.zip). The .csv files contain raw measurements produced by Radioak plugin for FIJI, and the .xlsx files contain the quantifications based on the raw data. The units in .csv and .xlsx files are microns.</p> <p> In the timelapse images the time resolution is 1 min, each pixel is 0.1135 micrometers.</p>
Supplementary Data for Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2
<p>This repository includes:<br> The global tree in Newick format: global_2_13_21.main.tre<br> The global, ultrametric tree in Newick format: global_2_13_21.ultra.tre<br> All metadata used in this study including the GISAID acknowledgements: metadata.tgz<br> Tables S1-S4 in plain text format.</p>
Supplementary data for "Enhancing Resource-based Test Case Generation For RESTful APIs with SQL Handling"
<p>Supplement to: <em>Enhancing Resource-based Test Case Generation For RESTful APIs with SQL Handling</em></p> <p>In this repository, we provide <em>tests</em> and their <em>coverage reports</em> (conducted by Intellij coverage reports) that are used in the Discussion section of the paper.</p>
Supplementary data for the manuscript: Image2SMILES: Transformer-based Molecular Optical Recognition Engine
<p>This is the supplementary data for the manuscript: <a href="https://chemrxiv.org/engage/chemrxiv/article-details/60c758c6469df4169bf45744">Image2SMILES: Transformer-based Molecular Optical Recognition Engine</a></p> <p>It contains pairs of image-string, generated from 1M SMILES strings. These strings were randomly chosen from PubChem database.<br> It was prepared using the code, published at <a href="https://github.com/syntelly/img2smiles_generator/">https://github.com/syntelly/img2smiles_generator/</a></p> <p>To unpack do:<br> <em>tar xvf subset_1M.tar.xz && tar xvf subset_1M_dump.tar.gz && rm subset_1M_dump.tar.gz</em></p> <p>You'll get the following data:</p> <ul> <li>subset_1M.smi - list of 1M source SMILES</li> <li>subset_1M_dump - directory with images </li> <li>subset_1M_result.csv - list of pairs FGSMILES - pathcode, first 3 chars of pathcode are corresponding subdirs in subset_1M_dump</li> <li>subset_1M_fails.csv - list of failed molecules from subset_1M.smi</li> <li>subset_1M_grpcounter.lst - list of counted groups, used in this generation</li> </ul> <p>You can generate your own data using <a href="https://github.com/syntelly/img2smiles_generator/">https://github.com/syntelly/img2smiles_generator/</a> </p>
Supplementary Data for "Molecular dynamics simulations provide structural insight into binding of cyclic dinucleotides to human STING protein"
<p>Supplementary Data for "Molecular dynamics simulations provide structural insight into binding of cyclic dinucleotides to human STING protein", Journal of Biomolecular Structure and Dynamics, 2021, 10.1080/07391102.2021.1942213</p> <p>A random selection of 10 representative structures from each MSM state of STING/CDN complexes is provided in .pdb file format. The selected MSM representatives are aligned and available as PyMOL session files.</p>
Supplementary Data for: Whole genome sequencing elucidates the species-wide diversity and evolution of fungicide resistance in the early blight pathogen Alternaria solani
<p>Supplementary Data for: Whole genome sequencing elucidates the species-wide diversity and evolution of fungicide resistance in the early blight pathogen Alternaria solani</p> <p>This repository contains:</p> <p>SNP call data / VCF file</p> <p>Scripts for all processing steps from mapping up to PCA and phylogenetic analyses (script.ts)<br> Scripts for population genomic analyses with LEA and PopGenome (scripts.SE)<br> All script names are self explanatory.</p>
Supplementary Data to: "A single nucleotide mutation in DUOX2 gene causes some of the panda's unique metabolic phenotypes"
<p>This file contains the data set associated with the manuscript entitled: "A single nucleotide mutation in the dual-oxidase 2 (<em>DUOX2</em>) gene causes some of the panda’s unique metabolic phenotypes", National Science Review, DOI: <a href="http://dx.doi.org/10.1093/nsr/nwab125">10.1093/nsr/nwab125</a></p>
Supplementary tables and figures - Excluding loci with substitution saturation improves inferences from phylogenomic data
<p>Supplementary tables and figures - Excluding loci with substitution saturation improves inferences from phylogenomic data</p>
Fast measurement of angular velocity in air-driven flat rotors with periodical features - Supplementary Data
<p>Supplementary Movie and data files used for generating Figure 4 in the main text. The files are compressed pickled pandas Dataframes and can be read with:</p> <pre><code class="language-python">import pandas as pd df = pd.read_pickle('/folder/file.xz', compression='xz')</code></pre> <p>Along with those files there are .txt files containing the physical information of each experiment.</p>
GENES supplementary data
<p>The origin of plasma-derived bacterial extracellular vesicles in healthy individuals and patients with inflammatory bowel disease: A pilot study</p> <p> </p> <p>Supplementary Data:</p> <p> </p> <p>Table S1: Taxa (ASV level) abundance in protocol control and plasma samples.</p> <p>Table S2: Differential genera in protocol control and plasma samples identified by classical univariate analysis (CUA).</p> <p>Table S3: Taxa (ASV level) abundance in healthy control (HC), Crohn’s disease (CD) and ulcerative colitis (UC) plasma samples.</p> <p>Table S4: Differential genera in healthy control (HC), Crohn’s disease (CD) and ulcerative colitis (UC) plasma samples identified by classical univariate analysis (CUA).</p> <p> </p>
Fault trace data and supplementary table and figures of "Fault trace corrugation and segmentation as a measure of fault structural maturity"
<p>Fault trace data and supplementary information to the paper "Fault trace corrugation and segmentation as a measure of fault structural maturity" by Manighetti I., Mercier A., and de Barros L., Sept. 2021</p>
Cleaned data from Supplementary Table S1 from "Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method"
<p>This data is derived from <a href="https://doi.org/10.5281/zenodo.5277805">https://doi.org/10.5281/zenodo.5277805</a>. As of 2021-09-08, <a href="https://doi.org/10.5281/zenodo.5277805">https://doi.org/10.5281/zenodo.5277805</a> contained an Excel file with md5:8907e7444f49d02d58fdef9fb2a1089a and filename "TableS1.xlsx"; the file was licensed under <a href="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</a>.</p> <p>In "TableS1.xlsx" there were, among others, worksheets with the names "Table S1. TECRDB Keqs" and "Table S2. TECRDB ΔrH data".</p> <p>Worksheet "Table S1. TECRDB Keqs" was exported as a csv with filename "TableS1_Keq.csv". A column "id" was added with a persistent identifier created in w3id.org.</p> <p>Worksheet "Table S2. TECRDB ΔrH data"" was exported as a csv with filename "TableS1_deltaH.csv". A column "id" was added with a persistent identifier created in w3id.org.</p> <p>No other corrections were made.</p>
Supplementary data for: Does Phobos reflect solar wind protons? Mars Express special flyby operations with and without the presence of Phobos
<p>Supplementary data to reproduce figures for "Does Phobos reflect solar wind protons? Mars Express special flyby operations with and without the presence of Phobos".</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.