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106 results for “Chemical structure”
Dataset for "Structural and molecular indices in common carp (Cyprinus carpio L.) fed n-3 PUFA enriched diet. Food and Chemical Toxicology, 151, 112146."
<p>Dataset for "<strong><em>Eljasik P, Panicz R, Sobczak M, Sadowski J, Tórz A, Barbosa V, Marques A, Dias J. (2021). </em></strong><em>Structural and molecular indices in common carp (Cyprinus carpio L.) fed n-3 PUFA enriched diet. </em><strong><em>Food and Chemical Toxicology, 151, 112146. </em></strong><em>DOI: <a href="https://www.sciencedirect.com/science/article/abs/pii/S0278691521001794?via%3Dihub">doi.org/10.1016/j.fct.2021.112146</a>"</em></p>
Nanoscale chemical characterization of secondary protein structure of F-Actin using mid-infrared photoinduced force microscopy (PiF-IR)
<p>Raw data for manuscript for special issue in Spectrochimica Acta related to ECSBM 2022</p> <p> </p>
Data from: Chemical structure predicts the effect of plant-derived low-molecular weight compounds on soil microbiome structure and pathogen suppression
Open the record for dataset details and reuse information.
Data from: Insights into chemical and structural order at planar defects in Pb2(MgW)O6 using multislice electron ptychography
Open the record for dataset details and reuse information.
Supplementary information for 'Structural and chemical properties of superconducting Co-doped BaFe2As2 thin films grown on CaF2'
<p>This repository contains supplementary information for the journal article '<a href="https://iopscience.iop.org/article/10.1088/1361-6668/abcecf">Structural and chemical properties of superconducting Co‑doped BaFe<sub>2</sub>As<sub>2</sub> thin films grown on CaF<sub>2</sub></a>'.</p> <p>The Jupyter notebooks (.ipynb) demonstrate data treatment for Fig. 4b (folder "HyperSpy EDXS Analysis") and Fig. 10a (folder "Atomap"). The notebooks can be run with the provided datasets. HTML files are also provided for quick inspection of the used procedures in a web browser. Supplementary video files (.mp4) show electron-beam-induced radiation damage at the BaFe<sub>2</sub>As<sub>2</sub>-CaF<sub>2</sub> interface.</p> <p>Please visit the websites of the <a href="https://hyperspy.org/">HyperSpy</a> and <a href="https://atomap.org/">Atomap</a> projects for more information.</p> <p>If there are any questions or bugs, please contact me under lukas.gruenewald_at_kit.edu.</p> <p> </p> <p> </p>
Data from: Effect of plant chemical variation and mutualistic ants on the local population genetic structure of an aphid herbivore
1.Plants exhibit impressive genetic and chemical diversity, not just between species but also within species, and the importance of plant intraspecific variation for structuring ecological communities is well known. When there is variation at the local population level, this can create a spatially‐heterogeneous habitat for specialized herbivores potentially leading to non‐random distribution of individuals across host‐plants. 2.Plant variation can affect herbivores directly and indirectly via a third species, resulting in variable herbivore growth rates across different host plants. Herbivores also exhibit within‐species variation, with some genotypes better adapted to some plant variants than others. 3.We genotyped aphids collected across two years from a field site containing ~200 patchily‐distributed host plants that exhibit high chemical diversity. The distribution of aphid genotypes, their ant mutualists, and other predators was assessed across the plants. 4.We present evidence that the local distribution of aphid (Metopeurum fuscoviride) genotypes across host‐plant individuals is associated with variation in the plant volatiles (chemotypes) and non‐volatile metabolites (metabotypes) of their host plant tansy (Tanacetum vulgare). Furthermore, these interactions in the field were influenced by plant‐host preferences of aphid‐mutualist ants. 5.Our results emphasize that plant intraspecific variation can structure ecological communities not only at the species level but also at the genetic level within species, and that this effect can be enhanced through indirect interactions with a third species.
Structural and chemical changes in He+ bombarded polymers and related performance properties
<p><span>Folder zawiera pliki excel, każdy z nich odpowiada jednemu wykresowi z publikacji i zawiera dane pozwalające na wykonanie wykresu.</span></p>
Figure S1 Chemical structures of the phospholipids used in the present study.
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Dataset for "Broad chemical transferability in structure-based coarse-graining"
<p>Dataset for "Broad chemical transferability in structure-based coarse-graining"</p>
Highly Selective Oxidative Dehydrogenation of Ethane to Ethylene via Chemical Looping with Oxygen Uncoupling through Structural Engineering of the Oxygen Carrier
<p>Raw data for the article "Highly Selective Oxidative Dehydrogenation of Ethane to Ethylene via Chemical Looping with Oxygen Uncoupling through Structural Engineering of the Oxygen Carrier", already published in Advanced Energy Materials. <a href="https://doi.org/10.1002/aenm.202200405">https://doi.org/10.1002/aenm.202200405</a></p> <p>All details concerning conditions and equipment for measurements can be found in the main text, supporting information of the article, and in text files contained in the folder.</p>
Interrelated chemical-microstructural-nanomechanical variations in the structural units of the cuttlebone of Sepia officinalis
<p>Raw data for our paper: "Interrelated chemical-microstructural-nanomechanical variations in the structural units of the cuttlebone of <em>Sepia officinalis</em>" <strong>DOI: </strong>10.1063/1.4993202</p>
Chemical and Structural In-Situ Characterization of Model Electrocatalysts by Combined Infrared Spectroscopy and Surface X-Ray Diffraction
<p>Raw and treated data</p>
Data for PhD Thesis: "Chemical and electronic structure of Cu$_2$O, NiO, and Cu$_2$O-NiO combinatorial material libraries as hole-transport material for halide perovskite solar cells"
<p>Here, the whole data measured during the PhD time of L. CW. Bodenstein-Dresler + Labbook is uploaded. T data in the "data"-folder was measured at HZB with XPS, UPS and IPES. </p> <p> </p> <p>The PEYS and CPD and XRD data was measured by A. Kama at BIU. </p> <p> </p>
Exploring the chemical and structural change of copper porphyrins upon charging by means of synchrotron X-ray absorption spectroscopy
<h2><span>Abstract</span></h2> <p><span>In response to the growing demand for battery materials, researchers explore alternative resources with a focus on sustainability. Among these, organic electrode materials—including porphyrins—have emerged as promising candidates due to their advantageous properties, such as rapid charging capabilities and high energy densities. However, despite their potential, the precise charging mechanism of these alternatives remains elusive. To address this gap, our study delved into copper porphyrins, with a primary focus on [5,15-bis(ethynyl)-10,20-diphenylporphinato] copper(II) (CuDEPP). Employing synchrotron X-ray absorption spectroscopy in <em>operando</em> mode, we probed the evolution in chemical and electronic structure of Cu in CuDEPP. Our findings unequivocally demonstrate the participation of copper as a redox center during reversible charge storage, shedding light on its superior electrochemical performance. Furthermore, a combined approach involving extended X-ray absorption fine structure (EXAFS) studies and theoretical calculations provided deeper insights into the observed structural distortion during the charge storage process. Notably, our results support the hypothesis that redox processes, specifically those involving the aromatic porphyrin ring, drive the electrochemical activity of CuDEPP. In summary, our investigation offers important insights into the charging mechanism of copper porphyrins—an essential step toward advancing sustainable organic materials for batteries. </span></p>
Investigating the interplay between RNA structural dynamics and RNA chemical probing experiments
<p>Normalized SHAPE reactivity for pre-miR20b and CDE2GG as reported in 'Investigating the interplay between RNA structural dynamics and RNA chemical probing experiments'.</p>
Exploring the Chemical Space of Glycosylation in Noncovalent Protein Complexes: an Expedition along Different Structural Levels of Human Chorionic Gonadotropin Employing Mass Spectrometry
<p><strong>Supplementary files for "Exploring the Chemical Space of Glycosylation in Noncovalent Protein Complexes: an Expedition along Different Structural Levels of Human Chorionic Gonadotropin Employing Mass Spectrometry"</strong></p> <p><strong>Introduction</strong></p> <p>This data repository contains all previously unpublished raw data files for the manuscript “Exploring the Chemical Space of Glycosylation in Noncovalent Protein Complexes: an Expedition along Different Structural Levels of Human Chorionic Gonadotropin Employing Mass Spectrometry” by Maximilian Lebede<sup>||</sup>, Fiammetta Di Marco<sup>||</sup>, Wolfgang Esser-Skala, René Hennig, Therese Wohlschlager, Christian G. Huber.</p> <p><strong>Files</strong></p> <p>This repository contains 9 files:</p> <ul> <li><strong>Dimer Raw Files.zip</strong> folder containing 4 files of native-MS data (*.raw, Thermo RAW file format) of two batches of the drug product Ovitrelle® at native dimer level. </li> <li><strong>H11M9 Ovitrelle BA056714 Glycopeptide R1 230920_07.zip</strong> folder containing 1 file of HPLC-MS/MS glycopeptide data (*.raw, Thermo RAW file format) of one batch of the drug product Ovitrelle®.</li> <li><strong>H11M9 Ovitrelle BA056714 Glycopeptide R2 230920_08.zip</strong> folder containing 1 file of HPLC-MS/MS glycopeptide data (*.raw, Thermo RAW file format) of one batch of the drug product Ovitrelle®.</li> <li><strong>H11M9 Ovitrelle BA056714 Glycopeptide R3 230920_09.zip</strong> folder containing 1 file of HPLC-MS/MS glycopeptide data (*.raw, Thermo RAW file format) of one batch of the drug product Ovitrelle®.</li> <li><strong>H11M9 Ovitrelle BA059433 Glycopeptide R1 240920_15.zip</strong> folder containing 1 file of HPLC-MS/MS glycopeptide data (*.raw, Thermo RAW file format) of one batch of the drug product Ovitrelle®.</li> <li><strong>H11M9 Ovitrelle BA059433 Glycopeptide R2 240920_16.zip</strong> folder containing 1 file of HPLC-MS/MS glycopeptide data (*.raw, Thermo RAW file format) of one batch of the drug product Ovitrelle®.</li> <li><strong>H11M9 Ovitrelle BA059433 Glycopeptide R3 240920_17.zip</strong> folder containing 1 file of HPLC-MS/MS glycopeptide data (*.raw, Thermo RAW file format) of one batch of the drug product Ovitrelle®.</li> <li><strong>MoFi Settings.zip</strong> folder containing 12 files of MoFi settings (*.xml) to annotate deconvoluted spectra of hCG subunits and dimer of two Ovitrelle® batches, untreated and after desialylation. A typical MoFi setting file is build from protein sequence (*.FASTA), monosaccharide and frequent modification atomic composition (*.csv), glycan or glycoform library (*.csv) and deconvoluted spectrum in centroid (*.csv). Files are named as following: Settings_Ovitrelle_Batch number (BA056714 or BA059433)_Structural level (Alpha, Beta or Dimer)_Enzymatic treatement (Untreated or Sialidase).</li> <li><strong>Subunit Raw Files.zip</strong> folder containing 8 files of HPLC-MS data (*.raw, Thermo RAW file format) of two batches of the drug product Ovitrelle® at intact subunit level. </li> </ul> <p>Raw files are named as following: Instrument, Drug product (Ovitrelle), Batch number (BA056714 or BA059433), Structural level (Dimer, Subunits or Glycopeptides), Enzymatic treatment (untreated, Sialidase, PNGase F or PNGase F + Sialidase) and date. Glycopeptide data includes 3 replicates (R1-3).</p> <p><strong>License</strong></p> <p>This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit <a href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</a> .</p> <p> </p>
Performance of chemical structure string representations for chemical image recognition using transformers dataset
<p>The datasets contain string representations used for DECIMER short communication paper.</p> <p><strong>ChEMBL dataset:</strong></p> <p>Train and test datasets downloaded from ChEMBL and curated. Contains data with and without stereochemistry. Separated as Canonical and Isomeric.</p> <p>String representations contain SMILES, DeepSMILES, SELFIES and InChIs.</p> <ul> <li>Train dataset: 1.5 Mio molecules</li> <li>Test dataset: ~100K molecules</li> </ul> <p><strong>Pubchem dataset:</strong></p> <p>Train and test datasets downloaded from PubChem and curated. Contains data with and without stereochemistry. Separated as Canonical and Isomeric.</p> <p>String representations contain SMILES, DeepSMILES and SELFIES.</p> <ul> <li>Train dataset: 3 Mio molecules</li> <li>Test dataset: 250K molecules</li> </ul>
Data for Structural Features of Interfacial Water Predict the Hydrophobicity of Chemically Heterogeneous Surfaces
<p>Scripts, raw and processed data, Jupyter notebooks, and force field files for the simulations performed in:</p> <p>B. C. Dallin, A. S. Kelkar, and R. C. Van Lehn. “Structural Features of Interfacial Water Predict the Hydrophobicity of Chemically Heterogeneous Surfaces.” <em>Chemical Science </em><strong>2023</strong>.</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>
Nine years of warming and nitrogen addition in the Tibetan grassland promoted loss of soil organic carbon but did not alter the bulk change of chemical structure
<p>Understanding the changes in soil organic carbon (SOC) storage and chemical stabilization dynamics is important for accurately predicting ecosystem C sequestration and/or potential C loss, but the relevant information, especially for the intervention of environmental controls on grassland soil is limited in Tibetan plateau regions. Here we used a 9-year two-way factorial experiment involving warming with open top chambers (+1.80 °C in the daytime and +0.77 °C in the nighttime at the soil surface) and multilevel nitrogen (N) enrichment treatments (0, 5, 10, and 15 g m<sup>-2</sup> year<sup>-1</sup>) in the Tibetan plateau to investigate the changes in SOC pool size and chemical structure. 9-year warming treatment significantly decreased SOC stock in the Tibetan grassland. We observed decreasing SOC concentrations which may be related to changes in the C degrading enzymes. Surprisingly, the SOC molecular structure remained unchanged in all N enrichment and warmed plots, suggesting that both treatments had affected all forms of SOC, from simple and complex polymeric in a similar way. Our results suggest that long-term warming stimulates soil C loss but no preference in SOC loss with different chemical structure.</p>
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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.