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231 results for “Natural Products”
An assessment of acd_lotus for the structural dereplication of natural products using 13C NMR spectroscopy data.
<p> A method that relies on carbon-13 nuclear magnetic resonance (NMR) spectroscopy, elaborated in earlier works of the author's research group, requires the availability of a dedicated database that establishes relationships between chemical structures, biological and chemical taxonomy, and spectroscopy. The construction of such a database, called <a href="https://doi.org/10.5281/zenodo.6621129">acd_lotus</a>, was reported earlier and its usefulness was only illustrated by <a href="https://doi.org/10.1002/cmtd.202200054">three examples</a>. This dataset provides the results of structure searches carried out starting from 58 carbon-13 NMR data sets recorded on compounds selected in the metabolomics section of BMRB, the biological magnetic resonance bank.</p> <p>Correction in the JSON file of ascochitine.</p> <p>Addition of a CSV file according to <a href="https://doi.org/10.1186/s13321-021-00520-4">Schymanski and Bolton</a> for the description of the selected compounds.</p> <p>Better PNG drawings for compounds 28, 38, 46, and 57.</p> <p>Better PNG drawing for compounds 7 and 26.</p>
Evaluation dataset for Relation Extraction of relationships between Organisms and Natural-Products
<p>A curated evaluation dataset for end-to-end Relation Extraction of relationships between organisms and natural-products.</p> <p>Details about the manual annotation:</p> <ul> <li>For Chemicals: <ul> <li>The chemical labels are annotated as they appear in the abstract.</li> <li>In abstracts, singular chemicals and classes of chemicals produced by a specific organism were distinguished.</li> <li>The "type" attribute {“chemical”, “class”} is used to indicate the nature of the mentioned name.</li> <li>A "class" attribute for chemical entities has also been included if class information is present in the abstract.</li> <li>A Wikidata and PubChem identifiers were assigned to chemicals and classes when available.</li> </ul> </li> <li>For Organisms: <ul> <li>The organism labels are annotated as they appear in the abstract.</li> <li>If in an abstract, the genus name was mention first, e.g. "Plakinastrella sp." and then the specie name e.g "Plakinastrella clathrata" is precise, then only the specie name is used.</li> <li>A Wikidata identifier was assigned to all organisms.</li> <li>In some abstracts, only the genus name is mentioned.</li> </ul> </li> <li>For Relations: <ul> <li>Only the relations explicitly mentioned in the abstract are reported in the output labels.</li> <li>Relations are reported in their order of appearance in the abstract.</li> </ul> </li> </ul>
Integrated experimental and techno-economic modeling of renewable natural gas production from prairie biomass
This study coupled experimental and techno-economic modeling to evaluate the economic prospects of utilizing prairie biomass as a feedstock for anaerobic digestion. Anaerobic digestion experiments were performed using 15 lab-scale bioreactors under semi-continuous operation, designed based off a box-Behnken design with three factors. Response variables included biogas and biomethane yields, in addition to numerous digestate physico-chemical characteristics. Statistical models were developed from the experimental data to predict these responses and were subsequently incorporated into a techno-economic model developed in Python using BioSTEAM. In addition to optimizing key anaerobic digestion parameters, four scenarios were evaluated investigating liquid digestate recirculation, as well as methane recovery from the liquid digestate in a two-stage anaerobic digestion process.
Plant aboveground biomass data: The influence of natural enemies on plant community composition and productivity
The purpose of this experiment is to determine the influences of natural enemies, including plant pathogenic fungi and insect pests, influence plant community composition, productivity, and diversity over time. The experiment is being conducted in an old field that is burned every other year. Within the old field, there are 8 blocks, and within each block there are 6 treatments: foliar fungicide, soil drench fungicide, foliar insecticide, mammal exclosure, the combination of all enemy suppression tactics (pesticides and mammal exclosure), and a nontreated control. The pesticides are applied repeatedly throughout the growing season. Within the plots, community productivity, species composition, percent cover, and pest damage are being quantified over time.
Plant aboveground biomass data: The influence of natural enemies on plant community composition and productivity
The purpose of this experiment is to determine the influences of natural enemies, including plant pathogenic fungi and insect pests, influence plant community composition, productivity, and diversity over time. The experiment is being conducted in an old field that is burned every other year. Within the old field, there are 8 blocks, and within each block there are 6 treatments: foliar fungicide, soil drench fungicide, foliar insecticide, mammal exclosure, the combination of all enemy suppression tactics (pesticides and mammal exclosure), and a nontreated control. The pesticides are applied repeatedly throughout the growing season. Within the plots, community productivity, species composition, percent cover, and pest damage are being quantified over time.
Instantenous rates of ecosystem carbon fluxes: The influence of natural enemies on plant community composition and productivity
The purpose of this experiment is to determine the influences of natural enemies, including plant pathogenic fungi and insect pests, influence plant community composition, productivity, and diversity over time. The experiment is being conducted in an old field that is burned every other year. Within the old field, there are 8 blocks, and within each block there are 6 treatments: foliar fungicide, soil drench fungicide, foliar insecticide, mammal exclosure, the combination of all enemy suppression tactics (pesticides and mammal exclosure), and a nontreated control. The pesticides are applied repeatedly throughout the growing season. Within the plots, community productivity, species composition, percent cover, and pest damage are being quantified over time.
Data set for "Quantitative and Qualitative bibliometric scope toward the Synthesis of Rose Oxide as a Natural Product in perfumery"
<p>This is the bibliometric data for "Quantitative and Qualitative bibliometric scope toward the Synthesis of Rose Oxide as a Natural Product in perfumery" study which were derived from SCOPUS database, on 23<sup>rd</sup> September 2019, based on title search.</p>
In vitro antibacterial activity of microbial natural products against bacterial pathogens of veterinary and zoonotic relevance
<p>Supplemental material to the publication "<i>In vitro</i> antibacterial activity of microbial natural products against bacterial pathogens of veterinary and zoonotic relevance"</p>
Fig. 1 in Natural-Licks Use By Orangutans And Conservation Of Their Habitats In Bornean Tropical Production Forest
Fig. 1. Location maps of Deramakot Forest Reserve in Sabah, Malaysian Borneo (D1 to D4: natural-licks).
Synthetic dataset for end-to-end Relation Extraction of relationships between Organisms and Natural-Products with Vicuna-13b-v1.5
<p>A new synthetic dataset (training/validation) for end-to-end Relation Extraction of relationships between Organisms and Natural-Products.</p><p>The new dataset was generated using <a href="https://huggingface.co/lmsys/vicuna-13b-v1.5">Vicuna-13b-v1.5</a>, derived from LLaMA 2. 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/main/LICENSE">LLaMA 2 license</a>.</p><p>The new dataset was created based on the top-1000 (per biological kingdom) LOTUS literature references extracted with the <a href="https://github.com/idiap/gme-sampler">GME-sampler</a>.</p><p>The dataset contains 10,405 items in the training set and 547 items in the validation set.</p><p>The dataset was generated using the same protocol as described in the <a href="https://github.com/idiap/gme-sampler">article</a>.</p>
ISDB: In Silico Spectral Database (of Natural Products)
<h1><strong>ISDB: In Silico DataBase (of Natural Products)</strong></h1> <h2><strong>Background</strong></h2> <p>The ISDB repository contains in silico fragmented spectra of natural products, generated using <strong>cfm-predict 4</strong> <a href="https://doi.org/10.1021/acs.analchem.1c01465" target="_new" rel="noopener">(DOI: 10.1021/acs.analchem.1c01465)</a>.</p> <p>The initial database preparation and its application for dereplication were first described in:<br><strong>Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication</strong> <a href="https://doi.org/10.1021/acs.analchem.5b04804" target="_new" rel="noopener">(DOI: 10.1021/acs.analchem.5b04804)</a>.</p> <h2><strong>Content</strong></h2> <p>Previous versions of ISDB contained predicted spectra for compounds aggregated within the <strong>LOTUS Initiative</strong> <a href="https://doi.org/10.7554/eLife.70780" target="_new" rel="noopener">(DOI: 10.7554/eLife.70780)</a> and included only "merged" spectra.</p> <p>This version expands beyond taxon-restricted compounds and includes:</p> <ul> <li>Individual in silico spectra predictions (<strong>~1 million</strong>)</li> <li><strong>Substructure annotations</strong></li> <li>Data for compounds from <strong>Wikidata</strong> and <strong>LOTUS</strong></li> </ul> <h2><strong>File Structure</strong></h2> <h3><strong><code>.zip</code> Files</strong></h3> <p>Each <code>.zip</code> file contains:</p> <ul> <li>All original outputs from <strong>cfm-predict 4</strong></li> <li>Substructure annotations</li> </ul> <h3><strong>Wikidata vs LOTUS Files</strong></h3> <ul> <li><strong>Wikidata files</strong>: Contain spectra for nearly all compounds found in Wikidata, obtained using this query: <a href="https://w.wiki/Cvdo" target="_new" rel="noopener">https://w.wiki/Cvdo</a>.</li> <li><strong>LOTUS files</strong>: Contain spectra only for compounds with a "found in taxon" (<code>P703</code>) statement, obtained using this query: <a href="https://w.wiki/D35x" target="_new" rel="noopener">https://w.wiki/D35x</a>.</li> </ul> <h3><strong>Energy Levels: <code>energyAll</code> vs <code>energySum</code></strong></h3> <ul> <li><strong><code>energyAll</code> files</strong>: Include spectra for three individual energy levels plus a summed spectrum (4 spectra per polarity per compound).</li> <li><strong><code>energySum</code> files</strong>: Contain only the summed spectrum (1 spectrum per polarity per compound).</li> </ul> <h2><strong>Related Resources</strong></h2> <ul> <li><strong>Building scripts</strong>: <a href="https://github.com/mandelbrot-project/spectral_lib_builder" target="_new" rel="noopener">https://github.com/mandelbrot-project/spectral_lib_builder</a></li> <li><strong>Matching scripts</strong>: <a href="https://github.com/mandelbrot-project/spectral_lib_matcher" target="_new" rel="noopener">https://github.com/mandelbrot-project/spectral_lib_matcher</a></li> </ul>
NAPRORE-CR (NAtural PROducts REpository - Costa Rica)
<p><strong>Costa Rica</strong> is one of the countries with the greatest biodiversity in the world, thus <strong>NAPRORE-CR</strong> was born as a need to make an inventory of the wealth of isolated and identified natural products in Costa Rica.</p> <p>Within the aims of this repository:</p> <ol> <li> <p>Create an open access repository where natural products isolated and identified in Costa Rica can be found.</p> </li> <li> <p>Characterize the chemical diversity of the compounds in the database using chemoinformatic tools and thus be able to serve as a reference source for the design of new drugs and biomaterials.</p> </li> <li> <p>Be part of and contribute to the <strong>Latin American Natural Product Database (LANaPD)</strong></p> </li> </ol> <p><strong>NAPRORE-CR</strong> was designed and developed in collaboration with the research group of Dr. Jose Medina-Franco from the UNAM. We will shortly release more details about the database in a publication.</p>
Data from: Chrysolaena obovata, A SPECIES NATIVE OF BRAZILIAN CERRADO: GENETIC DIVERSITY AND STRUCTURE OF NATURAL POPULATIONS AND POTENTIAL FOR INULIN PRODUCTION
<p><em>Chrysolaena obovata</em> (Less.) M. Dematteis, an herbaceous Asteraceae species widely distributed across different Brazilian Cerrado physiognomies, has underground organs, named rhizophores, that accumulate high concentrations of inulin-type fructans. These carbohydrates are recognized as beneficial soluble fibers for human health and are currently used in the food and pharmaceutical industries. Considering that fructans, in addition to their economic potential, provide plants with greater tolerance to drought, heat and cold, it is important to understand whether their metabolism is conserved in natural populations. In this work, we aimed to investigate if the levels of genetic diversity in the populations studied allow the selection of localities with a high genetic base and higher fructan content for future programs of <em>in</em> <em>situ</em> conservation and genetic improvement for inulin production. Therefore, we characterized the diversity, structure, and gene flow of seven natural populations from Brazilian Cerrado, using nine microsatellite loci (SSR). In addition, we compared whether the fructan composition varied between populations of different Cerrado phytophysiognomies. Overall, we found that <em>C. obovata</em> populations exhibited moderate levels of genetic diversity, low genetic differentiation, and high gene flow. This study identified two populations with less genetic diversity and therefore, greater attention should be given to conservation programs including these populations. Fructan metabolism is conserved in all populations, indicating that <em>C. obovata</em> is an important genetic resource with high potential for inulin production.</p> <p><strong>File descriptions</strong></p> <p>Population_code.txt - Contains a matrix that indicates the population_code, Population_name, Brazilian-state, Phytophysiognomy, Collection coordinates and Altitudes (m).</p> <p>Date_ Diaz et al.xlsx – Contains Genotypes crude of the individuals analyzed. Primer used for nine microsatellite loci (Camacho <em>et al</em> 2017). </p> <p>Carbohydrates_Diaz et al - Contains data for carbohydrates in <em>C. obovata</em> plant rhizophores in each population (BRA, UB, SD, SP).</p> <p><strong>Location: Brazilian Cerrado</strong></p>
Figure 6: Erythema values before and after 10 minutes from application 57 -STUDIES TOWARDS OBTAINING A PHOTOPROTECTIVE DERMO-COSMETIC COMPLEX PRODUCT WITH NATURAL EXTRACTS OF INORGANIC AND ORGANIC SUBSTANCES
<p>The values of the erythema are relatively low, which indicates that the<br> product is compatible with the skin and has no sensitizing potential (¯gure6).<br> Having a complex composition of ingredients with varying degrees of un-<br> saturation, with the major organic structure, the product is subjected to de-<br> structive processes at the impact of UV radiation and atmospheric oxygen.<br> As a result this organic substances undergo structural changes, embodied in<br> the initial color change, division of chain, forming oxidizing action groups and<br> oxygen free radicals that continue the destructive process. Because of these<br> features, the product was subjected to accelerated tests of thermal and photo<br> destruction. As a result of these tests, the product's characteristics have not<br> changed signi¯cantly.</p>
Figure 2: Variation of the shear stress depending on the speed rate 54-STUDIES TOWARDS OBTAINING A PHOTOPROTECTIVE DERMO-COSMETIC COMPLEX PRODUCT WITH NATURAL EXTRACTS OF INORGANIC AND ORGANIC SUBSTANCES
<p>The evaluation of photodegradation was carried out through the variation<br> of photoprotective factor of the studied product kept 60 minutes under UV<br> radiation at 65±C. The tests revealed the preservation or even a slight increase<br> in the SPF. The use of screen substances in the formulation of photoprotective<br> products results in undesirable sensory characteristics: visible white ¯lm on the<br> skin surface, unpleasant sensation, dry or oily skin after application.</p>
Figure 1: Spreadability (plasticity) Figure-STUDIES TOWARDS OBTAINING A PHOTOPROTECTIVE DERMO-COSMETIC COMPLEX PRODUCT WITH NATURAL EXTRACTS OF INORGANIC AND ORGANIC SUBSTANCES
<p>The physical and chemical methods used to characterize the row<br> materials and the ¯nal products are as following:<br> ² to ¯nd out the amount of inorganic substances (with screening role) the<br> samples were incinerated for two hours at 800±C;<br> ² the quantity of organic substance (with the UV ¯ltering role) was deter-<br> mined by an UV-VIS spectrophotometric method;<br> ² vitamins identi¯cation was done according to the European Pharma-<br> copoeia VI-th edition;<br> ² the photoprotective ability was tested by applying a standard amount of<br> emulsion on a synthetic skin device (0,2g=cm2);<br> ² to test the microbial stability were applied the European Pharmacopoeia<br> VI-th edition stipulations;<br> ² to estimate the compatibility with the human skin a standard quantity<br> of sample (0,2g=cm2) was laid under an occlusive patch.</p>
Figure 4: Determination of hydration of the skin before applying the product-STUDIES TOWARDS OBTAINING A PHOTOPROTECTIVE DERMO-COSMETIC COMPLEX PRODUCT WITH NATURAL EXTRACTS OF INORGANIC AND ORGANIC SUBSTANCES
<p>The volunteers who applied the product on the<br> skin appreciated the sensory characteristics such as: easiness of use, pleasant<br> texture, easy absorption without oily traces, appearance, odor and pleasant<br> color (¯gures 4, 5).</p>
Figure 3: Viscosity variation depending on speed rate Table-STUDIES TOWARDS OBTAINING A PHOTOPROTECTIVE DERMO-COSMETIC COMPLEX PRODUCT WITH NATURAL EXTRACTS OF INORGANIC AND ORGANIC SUBSTANCES-
<p>Microbiological characteristics The total number of aerobic germs and fungi<br> was determined by the decimal dilution method or the multiple tube test. For<br> identifying pathogenic species we have used speci¯c tests (table6).<br> The evaluation of photodegradation was carried out through the variation<br> of photoprotective factor of the studied product kept 60 minutes under UV<br> radiation at 65±C. The tests revealed the preservation or even a slight increase<br> in the SPF. The use of screen substances in the formulation of photoprotective<br> products results in undesirable sensory characteristics: visible white ¯lm on the<br> skin surface, unpleasant sensation, dry or oily skin after application.</p>
Synthetic dataset for end-to-end Relation Extraction of relationships between Organisms and Natural-Products with Mixtral-8x7B-Instruct-v0.1
<p>A new synthetic dataset (training/validation) for end-to-end Relation Extraction of relationships between Organisms and Natural-Products.</p> <p>The new dataset was generated using <a href="https://huggingface.co/mistralai/Mixtral-8x7B-Instruct-v0.1">Mixtral-8x7B-Instruct-v0.1</a>. Like the model, the produced synthetic data are also submitted to the License of the model used for generation (apache-2.0).</p> <p>The new dataset was created based on the top-1000 (per biological kingdom) LOTUS literature references extracted with the <a href="https://github.com/idiap/gme-sampler">GME-sampler</a>.</p> <p>The dataset contains 8,913 items in the training set and 344 items in the validation set.</p> <p>The dataset was generated using the same protocol as described in the article.</p>
Dataset: Nature's Sunshine Products, Inc. (NATR) Stock Performance
This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
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.