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1,923 results for “compounds”
Data for evaluation of modelled versus observed NMVOC compounds at EMEP sites in Europe
<p>Data (model outputs, emission files, python scripts) for the publication of "<span>Evaluation of modelled versus observed NMVOC compounds at </span><span>EMEP sites in Europe".</span></p>
COMPOUND CAPITAL
Low resolution 3d model of corinthian capital in a roman ville of Fuente Alamo, (Cordoba, Spain). Source: Objaverse 1.0 / Sketchfab
Organic compounds drive growth in phytoplankton taxa from different functional groups
<p>Phytoplankton are usually considered autotrophs, but an increasing number of studies shows that many taxa are able to also utilise organic carbon. Acquiring nutrients and energy from different sources might enable an efficient uptake of required substances and provide a strategy to deal with a varying resource availability, especially in highly dynamic ecosystems such as estuaries. In our study we investigated the effects of 31 organic carbon sources on the growth (proxied by differences in cell counts after 24 h exposure) of 17 phytoplankton strains from the Elbe estuary spanning four functional groups. All of our strains were able to make use of at least 1 and up to 26 organic compounds for growth. Pico-sized green algae such as <em>Mychonastes</em>, as well as the nano-sized green alga <em>Monoraphidium </em>in particular were positively affected by a high variety of substances. Reduced light availability, typically appearing in turbid estuaries and similar habitats, resulted in an overall poorer ability to utilise organic substances for growth, indicating that organic carbon acquisition was not primarily a strategy to deal with darkness. Our results give further evidence for mixotrophy being an ubiquitous ability of phytoplankton and highlight the importance to consider this trophic strategy in research.</p>
More to legs than meets the eye: Presence and function of pheromone compounds on heliothine moth legs
<p><span>Chemical communication is ubiquitous in nature and chemical signals convey species-specific messages. Despite their specificity, chemical signals may not be limited to only one function. Identifying alternative functions of chemical signals is key to understanding how chemical communication systems evolve. Here, we explored alternative functions of moth sex pheromone compounds. These chemicals are generally produced in, and emitted from, dedicated sex pheromone glands, but some have recently also been found on the insects' legs. We identified and quantified the chemicals in leg extracts of the three heliothine moth species </span><em><span>Chloridea </span><span>(</span><span>Heliothis</span><span>)</span></em><span><em> virescens</em>, <em>Chloridea </em></span><em><span>(</span><span>Heliothis</span><span>)</span><span>subflexa</span></em><span>, and <em>Helicoverpa armigera</em>, compared their chemical profiles and explored the </span><span>biological function of pheromone compounds on moth legs. </span><span>Identical pheromone compounds were present on the legs in both sexes of all three species, with no striking interspecies or intersex differences. Surprisingly, we also found pheromone-related acetate esters in leg extracts of species that lack acetate esters in their female sex pheromone. When we assessed gene expression levels in the leg tissue, we found </span><span>known and putative pheromone biosynthesis genes expressed, which </span><span>suggests that moth legs may be additional sites of pheromone production</span><span>. To determine possible additional roles of the pheromone compounds on legs, we explored whether these may act as oviposition-deterring signals, which does not seem to be the case. However, when we tested whether these chemicals have antimicrobial properties, we found that two pheromone compounds (16:Ald and 16:OH) reduce bacterial growth. Such an additional function of previously identified pheromone compounds likely coincides with additional selection pressures and, thus, should be considered in scenarios on the evolution of these signals.</span></p>
Pseudomonas aeruginosa secretes compounds that kill Acanthamoeba castellanii trophozoites
<p>Microscopy of A. castellanii trophozoites incubated with cell-free supernatant from P. aeruginosa strain PA14 overnight cultures in LB. Time elapsed 2 hours. Video acquired using a Canon Vixia HFS200 camera and Nikon Eclipse TS100 microscope (20x objective).</p>
Mangroves as nature-based mitigation for ENSO-driven compound flood risks in a large river delta: supporting data - high water levels
<p>This dataset contains modelled high water levels in the Guayas delta supporting the paper 'Mangroves as nature-based mitigation for ENSO-driven compound flood risks in a large river delta' published in HESS 2024.</p> <p>The dataset is organised through two folders:</p> <ul> <li>mangroves: all data from the scenarios with mangroves included in the domain</li> <li>no_mangroves: all data from the scenarios without mangroves included in the domain</li> </ul> <p>Each folder is further divided along 6 subfolders:</p> <ul> <li>I: El Niño Ocean & river</li> <li>II: El Niño Ocean</li> <li>III: El Niño river</li> <li>IV: Neutral</li> <li>I_50per: 50 % increase in seaward El Niño anomalies</li> <li>I_150per: 150 % increase in seaward El Niño anomalies</li> </ul> <p>Each folder contains two files:</p> <ul> <li>vars.csv - each row represents a mesh node and there are three columns: <ul> <li>X: x value of the model mesh node [m]</li> <li>Y: y value of the model mesh node [m]</li> <li>HIGH_WATER: high water level [m]</li> </ul> </li> </ul>
List of charge transport low molecular weight compound geometry files
<p>The dataset comprises geometry files for low molecular weight compounds related to electron transport and hole transport. These files store information about atoms and bonds. The optimization of molecular geometry is performed using Avogadro software. These molecular structural files can subsequently be utilized to calculate energy levels for molecules, for instance, using Gaussian software.</p>
Bioactive compounds from Crataegus Oxycantha Protects myocardium against important proteins of atherosclerosis. An in-depth analysis using molecular simulation studies
<p>We are submitting this data as a raw file for the submission of our manuscript to the peer reviwed journals. </p>
Exploring Beneficial Properties of Haskap Berry Leaf Compounds for Gut Health Enhancement
<p>Data and the publication to which they are related</p>
Supplemental data for the publication: "Algal methylated compounds shorten the lag phase of Phaeobacter inhibens bacteria"
<p><strong>Data S1: </strong><em>P. inhibens </em>feature table (genes) with results from co-cultivation RNA-sequencing run. The dataset includes bacterial gene accession numbers, functional annotations, transcript abundances (TPM normalized read counts) and results of DESeq2 differential gene expression analysis. (Fig. 1, figs. S1A, S3-S4, tables S1-S2). </p> <p><strong>Data S2: </strong><em>P. inhibens </em>feature table (genes) with results from lag phase RNA-sequencing run. The dataset includes bacterial gene accession numbers, functional annotations, transcript abundances (TPM normalized read counts) and results of DESeq2 differential gene expression analysis. (Fig. 4A, figs. S10-S13, tables S6-S7). </p> <p><strong>Data S3: </strong><em>Emiliania huxleyi </em>CCMP3266 sGenome gene annotation file version 2 (GFF3 format).</p> <p><strong>Data S4: </strong>Feature quantification obtained using Compound Discoverer. The table presents the output analysis using Compound Discoverer (v3.3) with a putative identification of metabolites. Each identified metabolite (each row) contains a sub-table under the + tab (on the left side) that specifies the feature quantification in each analyzed sample. Sample ID appears in the “Study File ID” column in each sub-table. Values in the columns “Exchange Rate [%]: 0” and “Exchange Rate [%]: 1” represent relative abundances of the molecules in their unlabeled form and with single <sup>13</sup>C-label (M+1 isotopologue), respectively. Compounds marked with “1” in the “Tags” column were further validated using standards. The average M+1 isotope abundance [%] for <em>S</em>-Adenosylmethionine (SAM) and 5'-<em>S</em>-Methyl-5'-thioadenosine (MTA)—as reported in Fig. 4D—were calculated by averaging the values in the “Exchange Rate [%]: 1” column from samples supplemented with <sup>13</sup>C-labeled and unlabeled DMSP, respectively. Detailed information regarding the isotope abundances of SAM and MTA can be found in the tab “SAM and MTA isotope abundance” in the table. In the tab “Features Positive Mode” samples F10, F12, F14, and F16 were supplemented with <sup>13</sup>C-labeled DMSP and samples F2, F4, F6, F8 were supplemented with unlabeled DMSP. In the tab “Features Negative Mode” samples F2, F3, F4, and F5 were supplemented with <sup>13</sup>C-labeled DMSP and samples F10, F11, F12, F13 were supplemented with unlabeled DMSP.</p>
Data for "Association of western US compound hydrometeorological extremes with Madden-Julian oscillation and ENSO interaction"
<p>The files in this dataset are used to reproduce the figures in a paper entitled "Association of western US compound hydrometeorological extremes with Madden-Julian oscillation and ENSO interaction", submitted to <em>Communications Earth & Environment</em>.</p> <p>The data are in the NetCDF format including the climatological frequency of compound precipitation and temperature extremes over the western US and their changes associated with Madden-Julian oscillation and ENSO. Reanalysis ERA5 data contain the geopotential height, integrated vapor transport, and temperature advections. </p>
NMR data for "Application of a Hydrophobic Polyglutamate Bearing a Triphenylphosphine Group for the Orientation of Pharmaceutically Active Compounds and the Measurement of Residual Dipolar Couplings"
<p>NMR raw data for the work titled:</p> <p>"Application of a Hydrophobic Polyglutamate Bearing a Triphenylphosphine Group for the Orientation of Pharmaceutically Active Compounds and the Measurement of Residual Dipolar Couplings"</p> <p>The archive consists of NMR spectra of all compounds synthesized and the NMR spectra used for the determination of RDCs (isotropic and anisotropic).</p>
Tailored topotactic chemistry unlocks heterostructures of magnetic intercalation compounds
<p>The uploaded files include the raw datasets used to generate the figures presented in the main text and supplementary information of the paper titled 'Tailored Topotactic Chemistry Unlocks Heterostructures of Magnetic Intercalation Compounds'.</p>
Supplement for "Mesoscopic hydrodynamic model for spreading, sliding and coarsening compound drops"
<p>This repository contains the<strong> data sets</strong> and <strong>source code</strong> corresponding to the following publication</p> <p> </p> <p>Diekmann, J. and Thiele, U.<br>“Mesoscopic hydrodynamic model for spreading, sliding and coarsening compound drops”<br>Phys. Rev. Fluids <strong>10</strong>, 024002, 2025<br>DOI: <a href="https://doi.org/10.1103/PhysRevFluids.10.024002">https://doi.org/10.1103/PhysRevFluids.10.024002</a></p> <p> </p> <p>Please consider the README for more details.</p>
CARA: Benchmarking Compound Activity Prediction for Real-World Drug Discovery Applications
<p>Identifying active compounds for target proteins is fundamental in early drug discovery. Recently, data-driven computational methods have demonstrated promising potential in predicting compound activities. However, there lacks a well-designed benchmark to comprehensively evaluate these methods from a practical perspective. To fill this gap, we propose a benchmark, named CARA.Through carefully distinguishing assay types, designing train-test splitting schemes and selecting evaluation metrics, CARA can consider the biased distribution of current real-world compound activity data and avoid overestimation of model performances. We observed that current models can make successful predictions for certain proportions of assays, while the performances varied across different assays. In addition, evaluation of several few-shot training strategies demonstrated different performances related to task types. Overall, we provide a high-quality dataset for developing and evaluating compound activity prediction models, and the analyses in this work may inspire better applications of data-driven models in drug discovery.</p>
A new, fluorescence-based method for visualizing the pseudopupil and assessing optical acuity in the dark compound eyes of honeybees and other insects
<p>Images reported here are the raw Data set acquired to obtain Figure 6 in the manuscript Rigosi et al, “A new, fluorescence-based method for visualizing the pseudopupil and assessing optical acuity in the dark compound eyes of honeybees and other insects” accepted in Scientific Reports (DOI: 10.1038/s41598-021-00407-2).</p> <p>Please check the Methods section for a description of the analysis of the eye map obtained with these images.<br> Note that all the images are 16-bit.</p>
Supplementary Material for "Model-Free Analysis of Experimental Residual Diploar Couplings in Small Organic Compounds"
<p>NMR Spectra (CLIP-HSQC, perfectCLIP-HSQC, TSE-PSYCHEDELIC) of isopinocampheol in six alignment conditions.</p> <p>Simulation input (experimental RDC data in six alignment media, input geometries, keywords) and output files (simulation / geometry trajectories, alignment data, SECONDA analysis) for isopinocampheol runs with the TITANIA software.</p>
Table of SwissADME Analysis of Flavonoid Compounds
<p>Tabulation of SwissADME Analysis for Journal Article: <em>In Silico Study</em> of Flavonoid Compound: Utilization of Molecular Simulation to Discover Drug Candidate for COVID-19</p>
Simulation Input Data for "Molecular simulation of lignin-related aromatic compound permeation through Gram-negative bacterial outer membranes"
<p>This is the reduced data behind an upcoming manuscript investigating permeability across the outer membranes of Gram-negative bacteria. The data is taken directly from the directory structure that contains both the simulation and analysis, with excluded trajectory files and intermediate products to fit within the zenodo upload limit. The tar command used to generate this tarball was:</p> <pre><code class="language-bash">tar --exclude="*BAK" --exclude="*dcd" --exclude="*xsc" --exclude="*vel" --exclude="*coor" --exclude="*csv" --exclude="*old" --exclude="*log" --exclude="*state" --exclude="*watpos/*npz" --exclude="*new*png" --exclude="*frame*png" --exclude="*ppm" --exclude="*mp4" --exclude="*bayesdata*npy" --exclude="*run.npy" -zcvf OM.tgz OuterMembrane</code></pre> <p>Within the OuterMembrane directory, there are 3 primary subdirectories.</p> <ul> <li><strong>Build </strong>contains the scripts and files to build the simulation systems, including the CHARMM-GUI output</li> <li><strong>Equilibrium</strong> contains the equilibrium simulation inputs and the analysis scripts (subdirectory <strong>Analysis</strong>)</li> <li><strong>REUS2</strong>, which has the replica exchange inputs and essential output. It also contains an <strong>Analysis</strong> subdirectory that carries out the analysis within the text.</li> </ul>
Raw data for "A-Proof-of -Concept: In vivo Volatile Organic Compounds Secretion Monitoring as a Tool for Prediction of Natural Pest Control Ability"
<p>This upload refers to work entitled "A-Proof-of -Concept: In vivo Volatile Organic Compounds Secretion Monitoring as a Tool for Prediction of Natural Pest Control Ability" and contains the unprocessed data obtained during experiments perform. </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.