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9,113 results for “Sampling”
Labeled sampling of related discussion posts
<p>This is a labeled sampling of (uN)related discussion posts. Each file contains master_discussion_id;target_discussion_id;R or N</p> <p>The label R means that the master_discussion and target_discussion are related.</p> <p>The label N means that the master_discussion and target_discussion are unrelated.</p> <p>Projects: Gatsby, Homebrew, and Next.js </p> <p>https://github.com/gatsbyjs/gatsby/discussions/</p> <p>https://github.com/orgs/Homebrew/discussions/</p> <p>https://github.com/vercel/next.js/discussions/</p> <p> </p>
Unraveling the secrets of plant roots: Simplified method for large scale root exudate sampling and analysis in Arabidopsis thaliana
<p>Plants exude a plethora of compounds, both above- and below ground, to communicate with their environment. Although much is known about this communication above ground, we are only beginning to fathom the identity, level of variation, and role of below-ground chemical signals in a plant’s life. There have been many challenges associated with establishing a standardized methodology for studying root-exuded compounds, thus their role in plant-environment communication is still not well described.</p> <p>Here, we develop an interdisciplinary workflow to explore the natural variation in root exudate chemical composition of the model plant <em>Arabidopsis thaliana</em>. We highlight key challenges associated with sampling strategies and develop a framework for analyzing narrow and broad-scale patterns in root exudate composition of a large sample set of natural <em>A. thaliana</em> accessions.</p> <p>Our method consists of <em>in vitro</em> cultivation of individual seedlings inside a plastic mesh followed by a short hydroponic sampling period in micro quantities of ultrapure water. The mesh eases handling individual plants of varying sizes, thus making this setup advantageous for large-scale characterization of root exudates of individual plants in axenic conditions, and can be easily extended for prolonged temporal exudate collection experiments. Furthermore, a short sampling duration minimizes the experiment duration from days to mere hours, and is validated by yielding sufficient signal even with the small volume of sampling solution. An untargeted metabolic profiling analytical approach using ultra-high performance liquid chromatography coupled with mass spectrometry (UHPLC-QTOF-MS), followed by compound identification using open access software MZMine3 and SIRIUS 5, was used to capture a broad picture of the root exudate composition of <em>A. thaliana</em> accessions. This methodology can be broadly applied for investigating the role of root exudates as signals involved in plant belowground interactions. We report the first findings from the analysis here with results from Columbia genotype.</p> <p>We include here</p> <p> </p> <p>In <strong>Raw datafiles</strong>: The raw datasets obtained from MZmine 3 analysis, which contains aligned features of Columbia genotypes (Sheet1) as well as control samples (Sheet2). The dataset consists of <em>feature (row)ID, average (mass-to-charge ratios) m/z</em> and <em>retention times (RT)</em> across samples for individual features. It also includes sample-specific information including <em>feature status, name, m/z, RT, feature peak height,</em> and <em>area</em>. We also include a filtered datasheet excluding the features obtained in control as well as samples (Sheet3). Sheet 4 contains the phenotypic data on the number of leaves and rosette size of the 28 replicates at the time of sampling, along with the total peak area for each sample from MZmine data.</p> <p>In <strong>Supplementary tables</strong>: The 354 metabolites obtained after filtering out control features are listed with their <em>mass-to-charge ratios</em>, <em>retention times, and the mean, variance and coefficient of variation of the peak areas </em>(Supplementary Table 1). Supplementary Table 2 details the features identified by SIRIUS 5 with their <em>mass-to-charge ratios, retention times, chemical formula, chemical annotations,</em> and corresponding <em>probabilities scored by SIRIUS</em></p> <p>In <strong>Extended data analysis:</strong> Contains supporting data analysis for reproducibility and validity of our method for root exudate collection and analysis in <em>Arabidopsis thaliana.</em> These extended data analyses enhance the understanding of the relationship between plant phenotypic traits, peak area, and variation in compound abundance</p>
Raw data for the Article "Cyclopentadienone Iron Complex-Catalyzed Hydrogenation of Ketones: An Operando Spectrometric Study Using Pressurized Sample Infusion-Electrospray Ionization-Mass Spectrometry"
<p>This data set contains the raw data (NMR, LC-MS, ESI-MS, HRMS, Elemental Analysis) for the article "Cyclopentadienone Iron Complex-Catalyzed Hydrogenation of Ketones: An <em>Operando</em> Spectrometric Study Using Pressurized Sample Infusion-Electrospray Ionization-Mass Spectrometry" published in <em>Organometallics</em>, DOI:</p> <p><a href="https://doi.org/10.1021/acs.organomet.2c00341">https://doi.org/10.1021/acs.organomet.2c00341</a></p> <p>The compound names correspond to the ones used in the article and its supporting information.</p>
Size, age, telomere and ecophysiology data of Gallotia galloti lizard species sampled in Tenerife
<p>The dataset is used in the manuscript "Nina Serén, Rodrigo Megía-Palma, Tatjana Simčič, Miha Krofel, Fabio Maria Guarino, Catarina Pinho, Anamarija Žagar, Miguel A. Carretero. Functional responses in a lizard along a 3.5 km altitudinal gradient. Journal of Biogeography (under review)."</p> <p>The dataset consists of measurements of individual lizards of the species Gallotia galloti, each tagged with a unique CODE. Data include year of sampling, population name, exact elevation (in meters above sea level) and approximate elevation (rounded to the nearest hundred, in meters), and sex. Measurements were as follows: Snout Vent Length (in millimeters), Mass (in grams), AGE_Consensus (in years), Relative Telomere Length, PMA(29ºC, 33 ºC and 37ºC) (Potential metabolic activity measured at experimental conditions of 29˚C, 33ºC and 37ºC, respectively,in µLO2/mg prot/h), Catalase (in relative units U/mg protein), EWLa (accumulated evaporative water loss (in grams) and Temperature_8AM-5PM (measurements of cloacal temperature at hourly intervals starting at 8AM and ending at 5PM).</p>
Bayesian Analysis for Remote Biosignature Identification on exoEarths (BARBIE) I: Using Grid-Based Nested Sampling in Coronagraphy Observation Simulations for H2O
<p>We present all of the data across our SNR and abundance study for the molecule H2O for an exoEarth twin. The wavelength range is from 0.515-1 micron, with 25 evenly spaced 20% bandpasses in this range. The SNR ranges from 3-16, and the abundance values range from log10(VMR) = -3.5 to -1.5 in steps of 0.5 and 0.25 (all presented in VMR in the associated table). We present the lower and upper wavelength per bandpass, the input H2O value (abundance case), the retrieved H2O value (presented as the log10(VMR)), the lower and upper limits of the 68% credible region (presented as the log10(VMR)), and the log-Bayes factor for H2O. For more information about how these were calculated, please see Bayesian Analysis for Remote Biosignature Identification on exoEarths (BARBIE) I: Using Grid-Based Nested Sampling in Coronagraphy Observation Simulations for H2O, accepted and currently available on arXiv. </p> <p>To open this csv as a Pandas dataframe, use the following command:</p> <p>your_dataframe_name = pd.read_csv(f'zenodo_table.csv', dtype={'Input H2O': str})</p>
Fusarium associated with Banana - DArT-seq Cuban and Latin-American samples
<p>Using genotyping-by-sequencing and whole genome comparisons, we investigated the genetic diversity across this suite of isolates and compared it with the genetic diversity in a global <em>Fusarium</em> panel.</p>
THz TDS results of PPFe and PPFu samples
<p>Transmission spectra of the wafer covered with pre-exposed and post exposed PPF. The results are almost identical but of attenuated magnitude in comparison to transmission values obtained for a bare Si substrate.</p>
MURI Metabarcoding Sample Dataset
<p>This is a test dataset for the metabarcoding_QAQC_pipeline repo: <a href="https://github.com/MMARINeDNA/metabarcoding_QAQC_pipeline">https://github.com/MMARINeDNA/metabarcoding_QAQC_pipeline</a> . These are fastq files of eDNA metabarcoding sequences that were sequenced on the Illumina Miseq platform, as well as the Miseq sample sheet.</p>
Zambia land use and land cover field samples
<p><strong>General Description</strong></p> <p>This data set consists of 697 land use and land cover (LULC) sample locations and reference labelling collected over Muchinga and Copperbelt provinces, Zambia. The data available in ESRI shapefile format (spatial reference system: WGS 84, EPSG: 4326) was collected in a field campaign realized between May and June 2023. The dataset can be used for training and to evaluate the performance of the classification models.</p> <p><strong>Land Use and Land Cover Classes</strong></p> <p>The five LULC classes collected are:</p> <table> <tbody> <tr> <td>Label</td> <td>Code</td> </tr> <tr> <td>Forest land</td> <td>1</td> </tr> <tr> <td>Cropland</td> <td>2</td> </tr> <tr> <td>Grassland</td> <td>3</td> </tr> <tr> <td>Wetland</td> <td>4</td> </tr> <tr> <td>Other land</td> <td>5</td> </tr> </tbody> </table> <p><strong>Data set Details</strong></p> <ul> <li><strong>Time period:</strong> May / June 2023</li> <li><strong>Type of data:</strong> land use and land cover samples</li> <li><strong>How the data was collected:</strong> KoboCollect app</li> <li><strong>Coordinate reference system:</strong> EPSG:4326</li> <li><strong>Bounding box (Xmin, Ymin, Xmax, Ymax):</strong> (27.5472562965098682,-13.8722138995139996 : 32.0291093994995890,-11.2161515458659427)</li> <li><strong>File format:</strong> shapefile</li> </ul> <p> </p> <p> </p>
MicroBooNE BNB Inclusive Overlay Sample (No Wire Info)
<p>MicroBooNE samples are provided for collaborative development in two different formats: HDF5, targeting the broadest audience, and artroot, targeting users that are familiar with the software infrastructure of Fermilab neutrino experiments and more in general of HEP experiments. The HDF5 files are stored on Zenodo, together with a list of artroot files accessible with xrootd.</p> <p>This sample includes simulated interactions of neutrinos from the Booster Neutrino Beam (BNB), overlaid on top of cosmic ray data. The sample is inclusive, i.e. it includes all types of neutrinos and interactions, with relative abundance matching our nominal flux and cross section models. Interactions are simulated in in the whole cryostat volume.</p> <p>The HDF5 files in this sample do not include the information at the wire waveform level ("NoWire" label), allowing for larger number of events to be included in the data set.</p> <p>More documentation, including detailed description of content, recipes, and example usage, at <a href="https://github.com/uboone/OpenSamples/tree/v02">https://github.com/uboone/OpenSamples</a>.</p> <p>Suggested text for acknowledgment is the following:<br> <em>We acknowledge the MicroBooNE Collaboration for making publicly available the data sets [data set DOIs] employed in this work. These data sets consist of simulated neutrino interactions from the Booster Neutrino Beamline overlaid on top of cosmic data collected with the MicroBooNE detector [2017 JINST 12 P02017].</em></p> <p>In addition, we request that software products resulting from the usage of the datasets are also made publicly available.</p>
Results of the test for the sampling period described in D7.3: Madrid pilot report
<p>This datasets provides further information about section 9.4 Monitorisation and results of D7.3. This public deliverable describes Madrid pilot project report. CARTIF share this dataset with the results of the test carried out during the sampling period regarding particulate matter and nitrogen oxides.</p>
Database 2 - Second-year samplings in the CodeRe-farm pilot sites in Greece
<p>This database contains the results of the second year of AWIN assessments and general data recordings in the Greek goat pilots participating in the Code: Re-farm research project.</p>
Synthetic data set "Synth1" for the paper "Adaptive Sampling of 3D Spatial Correlations for Focus+Context Visualization"
<p>Synthetic data set "Synth1" for the paper "Adaptive Sampling of 3D Spatial Correlations for Focus+Context Visualization".<br>Preprint of the paper available at: <a href="https://arxiv.org/abs/2309.03308">https://arxiv.org/abs/2309.03308</a></p>
Variation of and associations with the depth and evenness of sequencing coverage in a sample of archived plastid genomes
<p>Depth and evenness of sequencing coverage are considered potential indicators of genome assembly quality. In plastid genomics, where new data generation has outpaced the development of suitable assembly quality indicators, these coverage metrics could offer insights into the quality of plastomes of different sizes, structures, or taxonomic origins. However, the typical variation of sequencing depth and evenness among archived plastid genomes, their variability between plastome partitions, and any association with methodological factors have yet to be evaluated. This study explores the variation of sequencing depth and evenness across a sample of publicly accessible plastid genomes and their potential associations with plastome structure, assembly accuracy, and the methodological provenance of the genome data using statistical tests. Our results indicate significant differences in sequencing depth across the four structural partitions as well as between the coding and non-coding sections of the genomes, a significant correlation between sequencing evenness and the number of ambiguous nucleotides, and a significant difference in sequencing evenness between several DNA sequencing platforms. These findings highlight that many publicly accessible plastid genomes are based on sequence data with highly variable sequencing depth and evenness and that this variation is influenced, at least partially, by genome structure and methodological factors.</p>
Quantity and composition of POM and MAOM in 156 soil samples collected from 20 National Ecological Observatory Network (NEON) sites in 2019
While it is generally assumed that particulate organic matter (POM) and mineral associated organic matter (MAOM) have distinct biogeochemical characteristics, it remains unresolved where and why POM and MAOM differ in their composition and relationships to total SOM decomposition among heterogenous soils. To address these questions, we analyzed elemental, isotopic, and chemical composition, including diffuse reflectance infrared Fourier transform (DRIFT) spectra, of POM and MAOM in 156 soil samples collected from 20 National Ecological Observatory Network (NEON) sites spanning diverse ecosystems (tundra to tropics) across North America in 2019. We used a classic size separation method for POM (53–2000 µm) and MAOM (< 53 µm) following chemical dispersion.
Kelp forest fish communities environmental DNA samples from Santa Barbara Channel
The dataset in this package is the processed fish community structure inferred from 12S eDNA metabarcoding in the Santa Barbara Channel. 49 water samples were collected across 11 sites in 2017 and the taxa were identified to the highest resolution possible. The raw DNA sequence has been archived in the Sequence Read Archive (SRA) database (https://www.ncbi.nlm.nih.gov/sra) under the accession number PRJNA667508. This dataset is used to support manuscript: Lamy, T., Pitz, K.J., Chavez, F.P. et al. Environmental DNA reveals the fine-grained and hierarchical spatial structure of kelp forest fish communities. Sci Rep 11, 14439 (2021). https://doi.org/10.1038/s41598-021-93859-5
Winter sampling microclimatic data using handheld devices at a shrub gradient across Californian drylands.
During a two-week sampling period in February 2023, we collected microclimatic data, including temperature and relative humidity, at shrubs and in the open across 9 sites in California. We collected ambient and ground temperatures.
Small reservoir grab sample data, Parker, Ipswich, Lamprey, and Oyster River Watersheds, 2015 - 2020
This dataset contains water quality data from the inputs and outputs of eight reservoirs located in southeastern New Hampshire and northeastern Massachusetts. Samples were filtered in the field using Whatman GF/F filters with a nominal pore size of 0.7 µm and stored on ice until returned to the lab where they were frozen until analysis. Samples were analyzed for anions (NO3-, Cl-, SO4-, Br-) via ion chromatography on a Dionex Ion Chromatograph; NH4+ using a colorimetric method on a SmartChem Chemistry Analyzer; and total dissolved nitrogen (TDN) and dissolved organic carbon (DOC) via high-temperature oxidation on a Shimadzu TOC-V. DON was calculated as the difference between TDN and DIN (NO3- + NH4+). Samples correspond with individual sample names. Site (n = 8) indicate which reservoir each sample belongs to. Location indicates whether a sample was collected at the outflow or inflow ("UP", for reservoirs with one inflow) or "UP_1", "UP_2", or "UP_3" for sites with up to three inflows. CArea.km2 is the upstream drainage area estimated from the reservoir outflow while SArea.km2 is the surface area of each reservoir calculated via NHD+ polygons in GIS software. Temp.C is water temperature at the reservoir outflow on the day of sample collection while Discharge.m3s is the daily discharge scaled to the reservoir outflow from the nearest USGS gaging station. DIN.mgL, DON.mgL, and TDN.mgL are concentrations of dissolved inorganic nitrogen, dissolved organic nitrogen, and total dissolved nitrogen, respectively, in mg/L.
Xylem water oxygen and hydrogen isotopes of Ponderosa Pine trees and soil samples in the southwestern U.S. 2018 and 2021
Across seven sites in southern Utah and northern Arizona, we collected precipitation, xylem water, and soil water isotope samples during two years: 2018 and 2021. All xylem water samples were collected from mature Ponderosa pine forests. At each site, xylem water samples were collected from the same 15 trees during two periods during 2018, and three periods during 2021. Soil pits were dug close to the trees and soil samples were collected at 5, 25, and 45cm depth close to the tree xylem samples. In 2021, we also collected precipitation isotopes using a rain gauge that was topped with mineral oil to prevent evaporation.
South Bay Salt Pond Restoration Project – Phase-1 (2014-2017) Fish Sampling for Mercury Studies.
The South Bay Salt Pond Restoration Project, the largest wetland restoration project in the western United States, is conducting an adaptive management experiment to restore tidal flows to the tidally muted pond A8 complex. The A8 pond complex is a series of interconnected ponds (A8, A7, and A5) located at the interface of the Guadalupe River with Alviso Marsh in Lower South San Francisco Bay that has had a legacy of mercury contamination from cinnabar open-pit mining in the Guadalupe River watershed. As a result, restoration of salt pond habitats in the Alviso Marsh has taken an adaptive management approach whereby fish populations, water and sediment were monitored for mercury contamination before and after restoration actions and data was used to inform further restoration actions in the A8 complex. In this study, UC Davis conducted fish sampling to collect 2-sentinel species, the Three-spine Stickleback and Mississippi Silverside to assess whole-body mercury concentrations. Fish were collected seasonally (4-5 surveys-year) from spring 2014 through winter 2017 at two slough locations exchanging water with the A8 complex, one in upper Alviso Slough (ALSL-2) at the Alviso Municipal Marina boat launch and on in lower Alviso Slough (ALSL-3) near the pond A7 water control structure, and in two reference sloughs, Artesian/Mallard Slough just downstream from the San Jose-Santa Clara Regional Wastewater Facility outfall and Guadalupe Slough at the confluence with the Sunnyvale Wastewater Treatment Plant. Fish sampling consisted of beach seine, minnow trap and fyke netting with various levels of effort to capture the requisite number and size of sentinel fishes. Therefore, much of the sampling efforts were not conducted in a manor conducive of making fish abundance or species assemblage comparisons amongst the sampling locations. In addition to the slough sampling, we sampled for fish in tidal muted ponds A8, A7, A5, A3N, A3W and A16 from spring 2014 through winter of 201
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.