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231 results for “Natural Products”
Dataset for "Formal Single Atom Editing of the Glycosylated Natural Product Fidaxomicin Improves Acid Stability and Retains Antibiotic Activity"
<p>ZIP File:</p> <p>Characterisation data (such as e.g. NMR, IR, MS spectra)</p> <p>NMR raw data, .mnova files</p> <p>DP4+ data (final conformer coordinate files, result tables)</p> <p>DFT simulation data (coordinate files, results table)</p> <p>PDF file:</p> <p>Supporting information for</p> <p>Formal Single Atom Editing of the Glycosylated Natural Product Fidaxomicin Improves Acid Stability and Retains Antibiotic Activity</p>
Identification and Exploration of Immunity-Related Genes and Natural Products for Alzheimer's Disease Based on Bioinformatics, Molecular Docking and Molecular Dynamics
<p>Supplementary material to the article: Identification and Exploration of Immunity-Related Genes and Natural Products for Alzheimer’s Disease Based on Bioinformatics, Molecular Docking and Molecular Dynamics,These data are available to researchers.</p>
Four-Step Access to the Sesquiterpene Natural Product Presilphiperfolan-1β-ol and Unnatural Derivatives via Supramolecular Catalysis
<p>Data underlying the figures in the publication “Four-Step Access to the Sesquiterpene Natural Product Presilphiperfolan-1β-ol and Unnatural Derivatives via Supramolecular Catalysis”, published in <em>ChemCatChem,</em> <strong>2020</strong>, 12, 4512–4516. <a href="https://pubs.acs.org/doi/10.1021/jacs.0c01464">https://pubs.acs.org/doi/10.1021/jacs.0c01464</a></p> <p>Table of contents:</p> <p><strong>1. Crystals</strong>; Word file with the crystallographic data for compounds <strong>4</strong> and <strong>28</strong>.</p> <p><strong>2. Crystal_4</strong>; <em>.cif</em> file for crystal structure of compound <strong>4</strong>.</p> <p><strong>3. Crystal_28</strong>; <em>.cif</em> file for crystal structure of compound <strong>28</strong>.</p> <p><strong>4. Figure_2_NMRs</strong>; MestReNova file containing NMR spectra for compounds in <em>Figure 2.</em></p> <p><strong>5. Figure2_3_GCs</strong>; Zip file containing ASCII text raw data for GC traces relevant to <em>Figures 2</em> and <em>3</em>.</p> <p><strong>6. Figure4</strong>; Word file with the computational data for <em>Figure 4.</em></p> <p><strong>7. Procedures</strong>; Word file with the procedures for <em>Schemes 2 & 3 </em>and<em> Figures 2 & 3.</em></p> <p><strong>8. Scheme_2_NMRs</strong>; MestReNova file containing NMR spectra for compounds in<em> Scheme 2</em>.</p> <p><strong>9. Scheme3_NMRs</strong>; Zip file containing NMR spectra (as .mnova files) for <em>Scheme 3</em>.</p> <p> </p>
Different sources of natural products from the (a) bacterial, (b) archaeal, (c) fungal, (d) protozoan, (e) chromistan, (f) plant and (g) animal kingdoms, the rationale(s) for screening them for antibacterial activity, and associated advantages and disadvantages
<p>This table of information is from the review article 'Bioprospecting for Antibacterial drugs: A Multidisciplinary Perspective on Natural Product Source Material, Bioassay Selection and Avoidable Pitfalls' (<a href="https://doi.org/10.1007/s11095-020-02849-1">https://doi.org/10.1007/s11095-020-02849-1</a>).</p>
IsoAnalyst: A System-Wide Stable Isotopic Labeling Aproach for Connecting Natural Products to Their Cognate Biosynthetic Gene Clusters
<p>Processed mass spectrometry data input used to develop and validate the IsoAnalyst program and the output from these analyses. The S_erythraea folder contains all MS input and output data for <em>Saccharopolyspora erythraea</em>. The Micromonospora_RL09050HVFA folder contains MS input and output data for <em>Micromonopora sp.</em> RL09050HVFA, as well as the full antiSMASH output for the <em>Micromonopora sp.</em> RL09050HVFA genome.</p> <p>Version 2 contains updated IsoAnalyst results for both organisms. </p>
The LOTUS Initiative for Open Natural Products Research: TMAP
<p>TMAP of the compounds present on Wikidata curated in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
Data for: Hedgerows have contrasting effects on pollinators and natural enemies and limited spillover effects on apple production
<p>Agricultural intensification has resulted in a decline in insect biodiversity and threatens the provision of valuable ecosystem services. Agri-environment schemes (AESs) have been implemented in an effort to conserve biodiversity on farmland and increase agricultural sustainability, but their effectiveness can vary widely. To better determine which factors influence AES effectiveness, the relative roles of local habitat features, habitat quality, and landscape context need to be further explored. The aim of this study was to determine the most important factors influencing field margin AES effectiveness in commercial apple orchards, in terms of arthropod biodiversity conservation and ecosystem service provision. We surveyed wild bees and aphid natural enemies in field margins and apple trees in 20 orchards, ten bordered by hedgerow field margins (an AES) and ten with herbaceous field margins (no hedgerows present, not an AES). We considered field margin floral resources and the cover of semi-natural habitat in the surrounding landscape as indicators of local habitat quality and landscape context, respectively. We furthermore quantified pollination and pest control as measures of ecosystem service delivery and the relationship between arthropod communities and apple yield (initial and final fruit set) and quality. We found that hedgerow presence strongly predicted both pollinator and natural enemy communities and that these relationships were more pronounced than those with local habitat quality and landscape context. Hedgerows were negatively related to wild bee richness and abundance within the orchard, and positively related to natural enemy richness and abundance at the field margin but not within the orchard. We found no relationships between local and landscape factors and ecosystem service delivery, and no relationship between wild bee communities and apple yield, suggesting that apple is not pollen limited in our study system. There was, however, a negative relationship between natural enemy richness and initial fruit set. We conclude that annually cut hedgerows can benefit the conservation of natural enemies, but have limited arthropod-mediated private benefits for apple production, and likely need to be supplemented with additional local habitat resources for the conservation of wild bees. Our findings indicate that local habitat factors can strongly influence biodiversity regardless of landscape context, but that AESs likely need to be designed with separate biodiversity and ecosystem service targets, and specific taxonomic groups, in mind.</p>
Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon
<p>Code and data for the article "Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon".</p>
Pushing the boundaries of VCD spectroscopy in natural product chemistry
<p>Database of VCD and IR spectra for a set of monoterpenes, experimental mixtures and essential oils used in the article `Pushing the boundaries of VCD spectroscopy in natural product chemistry'.</p>
Synthetic datasets for end-to-end Relation Extraction of relationships between Organisms and Natural-Products
<p>Synthetic datasets (training/validation) for end-to-end Relation Extraction of relationships between Organisms and Natural-Products. The datasets are provided for reproducibility purposes, but, can also be used to train new models.</p><p>As in the corresponding article, 3 subtypes of synthetic datasets are provided:</p><ul><li><i>Diversity-synt</i>:<strong> </strong>The seed literature references used in the generation process correspond to the top-500 extracted items per biological kingdoms using the <a href="https://github.com/idiap/gme-sampler">GME-sampler</a>.</li><li><i>Random-synt</i>:<strong> </strong>5 datasets of equivalent sizes as <i>Diversity-synt</i>, but using randomly sampled seed literature references.</li><li><i>Extended-synt</i>: A merge of <i>Diversity-synt and the 5 Random-synt datasets.</i><br> </li></ul><p><strong>All </strong>datasets were produced with <a href="https://huggingface.co/lmsys/vicuna-13b-v1.3">Vicuna-13b-v1.3</a>. Like the model, the produced synthetic data are also submitted to the License of the model used for generation, see the original <a href="https://github.com/facebookresearch/llama/blob/llama_v1/MODEL_CARD.md">LLaMA model card</a>.</p><p>LLaMA is licensed under the <a href="https://github.com/facebookresearch/llama/blob/llama_v1/MODEL_CARD.md">LLaMA License</a>, Copyright (c) Meta Platforms, Inc. All Rights Reserved. </p>
Assessing the Pharmacokinetics and Drug Interaction Liability of Kratom, an Opioid-like Natural Product
ClinicalTrials.gov study NCT04392011. IPD Sharing: NO. Countries: 1. Publications: 1.
RCT of Mushroom Based Natural Product to Enhance Immune Response to COVID-19 Vaccination
ClinicalTrials.gov study NCT04951336. IPD Sharing: NO. Countries: 1. Publications: 0.
Autologous DNA mobilization and multiplication expedite natural products discovery from bacteria
Open the record for dataset details and reuse information.
Data from: A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways
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Flower strips and remnant semi-natural vegetation have different impacts on pollination and productivity of sunflower crops
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From weeds to natural enemies: Implications of weed cultivation and bio-pesticides for organic onion production
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Data for: Hedgerows have contrasting effects on pollinators and natural enemies and limited spillover effects on apple production
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Ohio Department of Natural Resources, Division of Wildlife, Reservoir Productivity Assessment Water Chemistry 2006-2007
Limnological data provided represent information collected during 2006–2007 for a total of 153 reservoirs. Some reservoirs were sampled in a single year, others were sampled in both years. Nearly all reservoirs were sampled during July or August near the dam at the deepest part of the reservoir. Additional samples for particular systems were taken in other months and at other sites (i.e., near the inflow). Many samples have complete Secchi transparencies, suspended solids (both total and non-volatile suspended solids), total phosphorus, total nitrogen, and chlorophyll a concentrations. Others are missing various parameters; some samples are represented by only a Secchi transparency measurement. Morphometric data and landuse/land cover data are provided for those systems where it had been previously compiled. All 153 reservoirs are represented in the provided lake shapefile whereas only 117 were included in the watershed shapefile. ' Over a 2-year period (2006 and 2007) we sampled 109 reservoirs (all Ohio reservoiurs > 10 ha), located throughout Ohio, USA, whose watersheds contain a variety of land cover types and a wide range of eutrophication levels. All reservoirs were sampled at least once during July or August in 2006 or 2007. … a subset of 34 of these reservoirs were sampled once in both 2006 and 2007. In addition, 10 reservoirs (“reference reservoirs”) were sampled at least once per month during July and August of both 2006 and 2007. Lakes were sampled by Miami personnel and DOW field crews (Districu3, District 4, and District 5).’
Predicted carbon-13 NMR data of Natural Products (PNMRNP)
<p>PNMRNP is an SDF file that reports the structure, properties and classification of 211,280 natural products.</p> <p>The starting point of this work (January 2019) was <a href="https://github.com/oolonek/ISDB/tree/master/Data/dbs">ISDB</a> which contains csv files of the UNPD data base (Gu J et al., PLOS ONE 2013, 8, e62839, doi:10.1371/journal.pone.0062839) and which are packaged with the ISDB mass spectrometry fragmentation database (Allard PM et al., <em>Anal. Chem.</em> 2016, 88, 6, 3317-3323, doi: 10.1021/acs.analchem.5b04804).</p> <p>Starting from InChI strings of compounds, 2D structures with configuration data were produced mainly from the <a href="http://www.rdkit.org">RDKit cheminformatic toolkit</a>. <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi">Pubchem</a> identifiers were searched for the compounds and used as keys to give names and synonyms to molecules. Carbon atoms in molecular structures were associated to <sup>13</sup>C NMR chemical shift values using <a href="https://nmrshiftdb.nmr.uni-koeln.de">nmrshiftdb2</a>. A three-level classification of compounds according to sub-structure presence is proposed. A compound may be classified as a terpene (level 1) as a sesquiterpene (level 2) and as an eudesmane (level 3).</p> <p>Version 2 of PNMRNP includes the classification of organic compounds according to <a href="http://classyfire.wishartlab.com">ClassyFire</a>.</p> <p>Version 3 of PNMRNP includes <sup>13</sup>C NMR chemical shifts calculated using ACD/Labs C+H NMR Predictors and DB.</p> <p> </p>
Optimising nature conservation outcomes for a given region-wide level of food production
<ol> <li>The land sharing-sparing framework aims to quantify the trade-off between food production and biodiversity conservation, but it has been criticised for offering, for reasons of simplicity, an unrealistically limited set of different land uses.</li> <li>Here, we develop the framework to evaluate a much larger suite of land-use strategies in which the areas and yields of three land-use compartments, natural habitat, high-yield farmland, and lower-yield farmland, are varied simultaneously. For two regions of England, we use functions that relate the local population density of breeding bird species to farm yield to simulate species-specific region-wide population sizes under each strategy.</li> <li>We find that geometric mean population size, averaged across all species, is maximised when farmland yields are higher than the current average yield, and when spared land combines both natural habitat and low-yield farmland. This conclusion is relatively insensitive to the maximum yield considered feasible under extreme land sparing, and holds across a range of region-wide food production targets. </li> <li>To some extent, our conclusion depends on which species groups were included in the assessment. Considered alone, farmland birds preferred a strategy with little or no natural habitat. Nonetheless, the optimal strategy was broadly consistent across all widely-recognised listings of species of conservation concern.</li> <li>Synthesis and applications. Our study looks at landscapes with a long history of agricultural use, and which have little remaining natural habitat, such as those found in lowland England. In these landscapes, conservation outcomes are likely to be maximised by mixed strategies in which high-yield production enables an increase in area of both natural habitat and low-yield farmland elsewhere in the region. </li> </ol>
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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.