Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
7,370
datasets available to search
ShareScore release 0.9.0
Dataset results
7,370 results for “supplementation”
Table S2 supplemental material to COMMSENV-22-1356B manuscript
<p>Table S2 supplemental material to COMMSENV-22-1356B manuscript</p>
Supplement: Functional strain redundancy and persistent phage infection in a Swiss hard cheese starter culture
<p>Undefined starter cultures are bacterial communities used in cheese making. They are phenotypically stable and propagated under constant conditions in milk. This makes them interesting to understand the eco-evolutionary dynamics of microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to analyze historical samples spanning 22 years and continuous propagation for 123 generations of an important Swiss cheese starter culture. We found that the bacterial community is highly stable and dominated by two species, Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Each species is represented by a few coexisting strains. Genome sequencing, metabolomics analysis, and co-culturing experiments show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large diversity of matching CRISPR spacers. Our findings provide novel insights into strain-level diversity in domesticated microbial communities and highlight an important role of bacteria-phage interactions in cheese starter cultures. </p>
Supplements: Comparison of different validation methods for single-step genomic evaluations based on a simulated cattle population
<p><strong>Supplementary Figures</strong></p> <p>Supplemental Figures to show true and estimated dispersion for the different scenarios</p>
Supplemental Data Set for "Constraining Changes in Surface Dust Thickness on Mars Using Diurnal Surface Temperature Observations from EMIRS"
<p>Supporting data set for manuscript "Constraining Changes in Surface Dust Thickness on Mars Using Diurnal Surface Temperature Observations from EMIRS". Provides the binned and averaged EMIRS surface temperatures acquired before and after the January 2022 dust storm for each region of interest to derive changes in surface dust thickness.</p>
Garaffa_et_al_OE_2023_Supplemental_Information
<p>Supplemental Information. Garaffa et al., Stocktake of G20 countries' climate pledges reveals limited macroeconomic costs and employment shifts, One Earth (2023), https://doi.org/10.1016/j.oneear.2023.10.012 </p><p>List of policies included in the scenarios (CurPol, NDC-LTS and 1.5C)</p>
nielsjdewinter/TE_circadian: Revised supplement
<p>Updated code for producing figure S13 (small change to linetypes and colors)</p>
FIGURE 3 in A supplement of the genus Phlugiolopsis Zeuner, 1940 (Tettigoniidae: Meconematinae) from Yunnan, China
FIGURE 3. Phlugiolopsis curvis sp. nov., male: A–B. head and pronotum: A. dorsal view; B. lateral view; C–F. apex of abdomen: C. dorso-lateral view; D. dorsal view; E. dorso-apical view; F. ventral view; female: G. subgenital plate in ventral view; H. ovipositor in lateral view; I. apex of ovipositor in lateral view. Abbreviation: a. anterior margin of triangular process.
FIGURE 1 in A supplement of the genus Phlugiolopsis Zeuner, 1940 (Tettigoniidae: Meconematinae) from Yunnan, China
FIGURE 1. Phlugiolopsis expansis sp. nov., male: A–B. head and pronotum: A. dorsal view; B. lateral view; C–F. apex of abdomen: C. dorsal view; D. right cercus in dorsal view; E. dorso-apical view; F. ventral view; female: G. subgenital plate in ventral view; H. ovipositor in lateral view; I. apex of ovipositor in lateral view. Abbreviation: p. process of lamellar expansion of cercus.
Supplemental Data for Blood Pressure Heritability Study by Lee et al.
<ul> <li> <p><strong>Data S1</strong>: Lists of top 5,000, 6,000, 7,000, 8,000, 9,000, and 10,000 expressed genes for the four BP relevant tissues and their coordinates (hg19).</p> </li> <li> <p><strong>Data S2</strong>: MACS2 peak files in the narrowPeak format for all tissues. The coordinates are in GRCh38.</p> </li> <li> <p><strong>Data S3</strong>: S-LDSC result files for analyses.</p> </li> <li> <p><strong>Data S4</strong>: gkmQC results for all chromatin accessibility peak sets, including both BP relevant and BP irrelevant tissues.</p> </li> <li> <p><strong>Data S5</strong>: Training regions (positive and negative sets) of gkm-SVM, final trained models, deltaSVM positive variants, and motif enrichment analysis results for the BP relevant tissues.</p> </li> <li> <p><strong>Data S6:</strong> The list of genes predicted to exert BP relevant function in a specific tissue.</p> </li> </ul>
Effects of maternal calcium propionate supplementation on offspring productivity and meat metabolomic profile in sheep
<p>data set from meat metabolome from lambs</p>
Supplemental material and data for Phys. Rev. Lett. 128, 066801 2022
<p>Supplemental material and data for Phys. Rev. Lett. 128, 066801 (2022)</p>
Supplement to zenodo doi 10.5281/zenodo.8122347 Data Archive for the NASA DAILI CubeSatMission:NASA Award Number: 80NSSC18K0973
<p>In the zenodo archive 10.5281/zenodo.8122347 the idl save sets include an array, raw_image, that had no actual data. The save-sets here fill that array with the actual data. These images are the actual images obtained with each DAILI exposure. In the original DAILI archive the portions of each exposure needed for retrieval of the science parameters were correctly included. Hence, the arrays here are just for completeness although they do document the dark counts between the regions where light is admitted.</p>
Data Supplement: Dataset with Tweets containing the terms "digital" and "peacebuilding", 03/2006-12/2021
<p>This dataset was developed for the empirical analysis of public social media discourse on the topic of digital peacebuilding. It contains tweets with the terms “digital” and “peacebuilding” posted in the period March 2006 - December 2021. The tweets were collected via the Academic Research API, using the academictwitteR R package. Retweets were excluded from the data collection. Furthermore, Twitter IDs, duplicates and emojis were removed from the data. The data was subsequently coded with the Qualitative Data Analysis (QDA) software 'Atlas.ti'. The coding was carried out in-vivo, using text and GREP search auto-coding. All codes were manually reviewed and then clustered into seven code groups, to which each of the intellectual maneuvers in the article speaks. Given this approach, no code book was necessary. The second sheet (“Code Groups”) contains the codes associated with each code group. The third sheet („Tweets“) contains all tweets and indicates how they have been coded, i.e., 0 means they code has not been assigned, 1 means the code has been assigned. </p>
Electronic Supplement to "Bedload transport's scaling behavior: what if Bagnold was right?"
<p>Here we provide all the data used for our paper entitled "Bedload transport's scaling behavior: what if Bagnold was right?". The deposit contains:</p> <ol> <li>All the Mathematica notebooks used for plotting the figures in the article and its supplement.</li> <li>Five spreadsheets with all the data: pipe-data (bedload data from pipe flows), flume-data (bedload data from laboratory flumes), Data_Bunte (bedload in the Rockies), Data_USFD (bedload in Idaho and Nevada), and Data_other_sites (bedload in other sites)</li> <li>An electronic supplement providing further information.</li> </ol>
Supplemental 3D Model Data - Hapalosiphonacean cyanobacteria (Nostocales) thrived amid emerging embryophytes in a 407-million-year-old landscape
<p>Three-dimensional reconstruction models of cyanobacteria from a 407 million year old fossil from the Lower Devonian Rhynie chert, UK. Thin sections SU.PB. 2023.0.1.2.8 from the Palaeobotany Collection in the Pôle Collections scientifiques et patrimoniales. Bibliothèque de Sorbonne Université, Paris (France).</p> <p>Imaris files (.IMS) can be viewed using the Imaris Viewer software, freely available in both Windows and Mac versions from https://imaris.oxinst.com/imaris-viewer. </p>
Natural products structure database LOTUS supplemented with predicted 13C NMR chemical shifts.
<p>A structure database of natural products in SDF format was created from <a href="https://zenodo.org/record/6582124">the LOTUS database version 9</a> .</p> <p>This database is intended to facilitate the <a href="https://www.mdpi.com/1420-3049/26/3/637">dereplication of natural products</a>.</p> <p>The LOTUS database was described in <a href="https://elifesciences.org/articles/70780">this publication</a> (free download).</p> <p>File 220916_frozen_metadata.csv was downloaded from <a href="https://zenodo.org/record/7085063">the LOTUS database version 9</a> and the SMILES chains of the compounds were collected.</p> <p>The SMILES chains were translated to 2D chemical structures using python scripts relying on the <a href="https://github.com/rdkit/rdkit">RDKit</a> library.</p> <p>Each compound was associated to predicted <sup>13</sup>C NMR chemical shifts by means of an already reported <a href="https://www.mdpi.com/2673-4532/2/3/6">procedure</a> (free download).</p> <p>Each compound was also supplemented with metadata from file 220916_frozen_metadata.csv .</p> <p>Archive file acd_lotusv9.sdf.zip contains acd_lotusv9.sdf with 218,478 compound descriptions inside.</p> <p>Archive file acd_lotusv9.NMRUDB.zip is a compressed version of acd_lotusv9.NMRUDB, itself created by importation of file acd_lotusv9.sdf in an ACD/Labs database file (new with version 0.0.4).</p> <p>The description of the first compound was copied in file firstmolv9.sdf and is provided for a quick inspection of the database content.</p> <p>The title line in firstmolv9.sdf is Q43656_2, meaning that more data about this compound may be found by searching in <a href="https://www.wikidata.org/">Wikidata</a> for Q43656 and that the initial data was given by line 2 in file 220916_frozen_metadata.csv .</p> <p>Files acd_lotusv9.sdf acd_lotusv9.NMRUDB contain biological taxonomy data from file 220916_frozen_metadata.csv that were not exploited in acd_lotusv7. Sub-files dealing with a particular taxon can be easily produced now.</p> <p>Chemical shift calculations for <sup>13</sup>C nuclei using the HOSE code approach are available <a href="https://zenodo.org/record/7047760">here</a> for the compounds in acd_lotusv7.</p> <p> </p>
Stressed economies respond more strongly to climate extremes - Data and Code Supplement
<p>This repository provides data and code to reproduce the results of the publication "R. Middelanis, S. N. Willner, K. Kuhla, L. Quante, C. Otto, and A. Levermann (2023). Stressed economies respond more strongly to climate extremes. Environmental Research Letters."</p> <p> </p> <p><strong>dependencies:</strong></p> <ul> <li>a working environment is provided in environment.yml</li> <li>the Acclimate post-processing package can be downloaded from the respective GitHub repostory with <code>git@github.com:acclimate/post-processing.git</code>. Switch to the develop branch with <code>git checkout develop</code> and install the package with <code>conda develop .</code> from within the repository</li> </ul> <p> </p> <p><strong>data:</strong></p> <ul> <li>See <code>./data/README.md</code> for the required data and sources for those data that are not included in this repository.</li> </ul> <p> </p> <p><strong>Steps to reproduce the results:</strong></p> <p>1. Generate Acclimate input data</p> <ul> <li>Direct loss time series are obtained from "Kuhla et al. (2021). Ripple resonance amplifies economic welfare loss from weather extremes. <em>Environmental Reserach Letters</em>".</li> <li>Acclimate input data (cf. <code>./data/README.md</code>) are generated with <code>./code/forcing.py</code></li> <li>The input data used in the pubilcation are available at <code>./data/acclimate_input</code></li> </ul> <p>2. Run Acclimate</p> <ul> <li>the Acclimate model can be downloaded from the respective GitHub repository at <a href="https://github.com/acclimate/acclimate">https://github.com/acclimate/acclimate</a></li> </ul> <p>3. Run the analyses</p> <ul> <li>Acclimate output files of the calibration runs and the scenario runs are aggregated with functions <code>aggregate_calibration_ensemble </code>and <code>aggregate_ensembles</code> in <code>./code/utils.py</code>, respectively.</li> <li>Aggregated ready-to-use output data is located in <code>./data/acclimate_output</code></li> <li>All figures can be reproduced with <code>./code/plotting.py</code></li> </ul>
test upload for anonymous review supplemental material
<p>test upload for anonymous review</p>
Molecular portraits of morphotypes - large supplemental tables
<p>This is a collection of large tables accompanying the article https://doi.org/10.1101/2023.01.24.525310</p>
Supplemental Fig. S1–2
<p>Supplemental Figures in Journal of Physiological Genomics on the Short Report titled "Changes in Fecal Gut Microbiome of Home Healthcare Patients with Disabilities through Consumption of Malted Rice Amazake"</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.