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1,572 results for “Sedimentation”
Supporting data tables and Python scripts for the paper: "Multi Grain-Size Total Sediment Load Model Based on the Disequilibrium Length"
<p>This repository contains all the data tables and Python scripts necessary to generate the results presented in Le Minor et al. (2022): "Multi Grain-Size Total Sediment Load Model Based on the Disequilibrium Length".</p>
Bottom water mediated microplastics distribution in water and sediment in the Yangtze River Estuary and East China Sea
<p>This database included the original data of water parameters, microplastics abundance, microplastics size, shape, color and shape. </p>
Filter and sedimentation place
<p>Filter and sedimentation place.</p> <p>Photo taken on 14.02.2016 in Bulu, Nafra circle, West Kameng, Arunachal Pradesh, India.</p>
Data from: Water level drawdown induces a legacy effect on the seed bank and retains sediment chemistry in a eutrophic clay wetland
<p>The lack of extreme water level fluctuations in managed, non-peat forming wetland ecosystems can result in decreased productivity through the loss of heterogeneity of these ecosystems. Stochastic disruption, such as a water level drawdown, can effectively reverse this effect and return the wetland to a more productive state, associated with higher biodiversity through new vegetation development. Yet, aside from the effect on vegetation dynamics, little is known about longer-term effects (30 years) of a water level drawdown, hereafter referred to as legacy effects, and how this may impact future water level drawdowns.</p> <p>Here, we aim to unravel the legacy effects of a water level drawdown, stand alone and along a water level gradient, on seed bank properties and nutrient availability in a eutrophic clay wetland. To identify these, we studied the hydrologically managed nature reserve Oostvaardersplassen in the Netherlands. Here, one section was subjected to a multi-year water level drawdown and another section was kept inundated. We determined seed bank properties in both areas, spatially and along a soil elevation gradient (20 cm). Nutrient availability was measured by taking sediment samples along the water level gradient and through experimental manipulation of the water level in an indoor mesocosm experiment.</p> <p>Germination was higher in locations with a water level drawdown history, especially at relatively high elevations. Additionally, the proportion of pioneer species in the seed bank was higher in the water level drawdown area. Overall, nutrient concentrations were higher compared to other systems. Nutrient availability was higher in the inundated area and did not respond to the water level gradient. We conclude that 30 years after an induced water level drawdown there is no depletion of nutrients, while we still observe a legacy effect in the number of viable seeds in the seed bank.</p>
Data set for spectral and FT-ICR-MS analysis of dissolved organic matter in sediments of the New Britain Trench axis station
<p> </p> <p>数据集包括原始数据和简单处理所需的数据、图表和文章。</p> <p> </p> <p>表格包含样品数量、收集深度、样品名称以及相应光谱和 FT-ICR-MS 数据的名称。</p> <p> </p> <p>例如,光谱数据包括荧光相对强度、荧光指数,而 FT-ICR-MS 光谱数据包括化合物类型相对强度以及化学式、元素比、等效双键数 (DBE) 和每个样品的芳香指数 (AImod)。</p> <p> </p>
Data from: Burrowing crab effects on the properties and functions of coastal soft sediments
<p>Burrowing ecosystem engineers, such as termites, crabs, marmots, and foxes, can profoundly affect the biological structure and ecosystem functions of their environments. However, the relative importance of burrowing engineers on sediments are challenging to predict and are expected to be influenced by engineer density, engineer functional traits (e.g., burrow morphology), and environmental conditions (e.g., geomorphology, vegetation presence). To develop robust hypotheses predicting the impacts of burrowing ecosystem engineers, we conducted a systematic meta-analysis evaluating the effects of burrowing crabs on sediment properties, nutrient stocks, and ecosystem functions in coastal soft-sediment habitats (e.g., salt marshes, mangrove forests, tidal flats). The data set includes 1422 effect size calculations for the effects of burrowing crabs on sediments collected from 59 total manuscripts. The data suggest that burrowing crabs rework and oxygenate sediments and accelerate rates of nutrient cycling (i.e., nitrification and CO<sub>2</sub> flux). However, the magnitude and direction of burrowing crab effects depend on burrowing crab superfamily, the presence of vegetation, and their interaction. Crab burrow density does not consistently predict burrowing engineer effects on sediments. </p>
SedDNA results along the sediment core of the Dzoumogné reservoir, Mayotte Island, Comoros Archipelago, France
<p>This repository is made up of two main folders containing information about the metadata and the database variables:</p> <ul> <li><em>Metadata_SedDNA_dzoumogne_reservoir_afoucher.xlsx</em> (description of the metadata associated with the sediment samples)</li> <li><em>Variable_description_dzoumogne_reservoir_afoucher.xlsx</em> (description of the database variables)</li> </ul> <p>as well as 6 folders containing the data sets for each genetic marker:</p> <ul> <li><em>Balitzki_12S-afoucher.xlsx</em></li> <li><em>Hardy_18S-afoucher.xlsx</em></li> <li><em>Kelly_16S-afoucher.xlsx</em></li> <li><em>Pornon_ITS-afoucher.xlsx</em></li> <li><em>Prosser_rtbl-afoucher.xlsx</em></li> <li><em>White_ITS-afoucher.xlsx</em></li> </ul> <p>Related publication: Foucher et al. submitted</p> <p>---------------------------------------------------------</p> <p><strong>Context:</strong> Sediment DNA was extracted from 12 layers along a sediment core (<strong>IGSN number: 10.58052/IEFOU0003</strong>) collected in 2021 in the Dzoumogné reservoir (Mayotte Island, Comoros Archipelago, France), covering the 2012-2021 period. The aim of these analyses was to evaluate the consequences of landscape defragmentation, induced by deforestation and intensification of agricultural practices, on changes in biological communities.</p> <p><strong>Sample collection, storage and subsampling:</strong> Sediment core was collected using an Uwitec gravity corer equipped with a 63mm PVC liner. The core was stored at 4°C in a cold and dark room for 3 weeks prior to subsampling. The sediment core was opened and subsampled in a previously sterilized hoot (DNA cleaner and UV) in a dedicated biological room at the University of Paris-Saclay. Each sample was extracted from the sediment core using sterilized metal plates inserted on either side of the layer to be sampled (the central part of this sample was then sub-sampled to remove the part of the sediment in contact with the PVC tube of the core and the cutting tools). During this process the operators were equipped with gloves, masks and headgear to avoid any risk of contamination. A blank was placed in the fume cupboard to control contamination during core opening and sampling.</p> <p><strong>Extraction and assignation:</strong><em> Sed</em>DNA was retrieved using a standardized protocol that combines the use of commercial kits (Nucleospin soil – Macherey-Nagel) and the extracellular DNA pre-treatment described in Taberlet et al. (1). In order to limit amplification biases and to improve the metabarcoding sensitivity, a combination of 7 genetic markers was used to PCR-amplify each targeted taxonomic group (plants - 50-70 bp – trnL (2), plants - 150 bp – rbcL (3), plants/fungi – 320 bp –ITS (4), plants – 380 bp – ITS , metazoa – 200 bp – 16S (5), Eukaryotes – 200 bp – 18S (6), vertebrates – 200 bp – 12S (7)). PCRs were realized in octuplicates with positive and negative controls. Extraction controls were also amplified with the dedicated primers. PCR products were cleaned using the MinElute purification kit (QIAGEN) and all purified amplicons were pooled in equimolar concentrations at the exception of the extraction and the PCR negative controls as they were not concentrated enough. Then, each sample pool was run on an Agilent Bioanalyzer using the DNA High Sensitivity LabChip kit (Agilent Technologies, Santa Clara, CA, USA) to verify amplicon length and each sample was finally quantified with a Qubit fluorometer (Invitrogen, Carlsbad, CA, USA). <br>Libraries were generated with a PCR-free protocol in order to tremendously reduce the number of chimeras induced by the metabarcoding approach. One microgram of each purified PCR products pool was submitted to molecular end-repair and then ligated to Illumina adapters prior to sequencing on Illumina platforms (Next-Generation Sequencing; Fasteris, Switzerland) using a NovaSeq instrument (Illumina, San Diego, CA, USA) with a paired-end read mode covering the amplicon lengths. The objective was to obtain approximately 1 million reads per marker and per sample. <br>Bioinformatics analyses were performed using the OBITools (8) and QIIME2 (9) pipelines. Reads were first demultiplexed using OBITOOLS. Then erroneous sequences were removed, and singletons were filtered out. Sequences were then clustered at 97% identity using VSEARCH (10). Sequences that were found in the extraction blanks were removed from the downstream analysis. Taxonomic assignment was realized in two steps. First, sequences were assigned by blasting them against a custom database generated from the GenBank latest release curated and restricted to all the documented taxa. Sequences with over 95% identity match were kept and their last common ancestor was computed using MEGAN (11). A second assignment pass was made using a Naïve Bayesian Classifier using QIIME’s rescript plugin (12).<em><br><br></em></p> <p><strong>Data validation:</strong> Discuss in the related paper.</p> <p> ----------------------------------------------------------</p> <p>References:</p> <p><br>1. P. Taberlet, S. M. Prud’Homme, E. Campione, J. Roy, C. Miquel, W. Shehzad, L. Gielly, D. Rioux, P. Choler, J. C. Clément, C. Melodelima, F. Pompanon, E. Coissac, Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies. Mol. Ecol., doi: 10.1111/j.1365-294X.2011.05317.x (2012).<br>2. P. Taberlet, E. Coissac, M. Hajibabaei, L. H. Rieseberg, Environmental DNA. Mol. Ecol. 21, 1789–1793 (2012).<br>3. S. W. J. Prosser, P. D. N. Hebert, Rapid identification of the botanical and entomological sources of honey using DNA metabarcoding. Food Chem. 214, 183–191 (2017).<br>4. T. J. White, T. J. White, T. Bruns, S. Lee, J. Taylor, Amplification and Direct Sequencing of Fungal Ribosomal RNA Genes for Phylogenetics (Academic press, New York, USA, 1990).<br>5. R. P. Kelly, Making environmental DNA count. Mol. Ecol. Resour. 16, 10–12 (2016).<br>6. C. M. HARDY, E. S. KRULL, D. M. HARTLEY, R. L. OLIVER, Carbon source accounting for fish using combined DNA and stable isotope analyses in a regulated lowland river weir pool. Mol. Ecol. 19, 197–212 (2010).<br>7. B. Balitzki-Korte, K. Anslinger, C. Bartsch, B. Rolf, Species identification by means of pyrosequencing the mitochondrial 12S rRNA gene. Int. J. Legal Med. 119, 291–294 (2005).<br>8. F. Boyer, C. Mercier, A. Bonin, Y. Le Bras, P. Taberlet, E. Coissac, obitools : a unixinspired software package for DNA metabarcoding. Mol. Ecol. Resour. 16, 176–182 (2016).<br>9. E. Bolyen, J. R. Rideout, M. R. Dillon, N. A. Bokulich, C. C. Abnet, G. A. Al-Ghalith, H. Alexander, E. J. Alm, M. Arumugam, F. Asnicar, Y. Bai, J. E. Bisanz, K. Bittinger, A. Brejnrod, C. J. Brislawn, C. T. Brown, B. J. Callahan, A. M. Caraballo-Rodríguez, J. Chase, E. K. Cope, R. Da Silva, C. Diener, P. C. Dorrestein, G. M. Douglas, D. M. Durall, C. Duvallet, C. F. Edwardson, M. Ernst, M. Estaki, J. Fouquier, J. M. Gauglitz, S. M. Gibbons, D. L. Gibson, A. Gonzalez, K. Gorlick, J. Guo, B. Hillmann, S. Holmes, H. Holste, C. Huttenhower, G. A. Huttley, S. Janssen, A. K. Jarmusch, L. Jiang, B. D. Kaehler, K. Bin Kang, C. R. Keefe, P. Keim, S. T. Kelley, D. Knights, I. Koester, T. Kosciolek, J. Kreps, M. G. I. Langille, J. Lee, R. Ley, Y.-X. Liu, E. Loftfield, C. Lozupone, M. Maher, C. Marotz, B. D. Martin, D. McDonald, L. J. McIver, A. V. Melnik, J. L. Metcalf, S. C. Morgan, J. T. Morton, A. T. Naimey, J. A. Navas-Molina, L. F. Nothias, S. B. Orchanian, T. Pearson, S. L. Peoples, D. Petras, M. L. Preuss, E. Pruesse, L. B. Rasmussen, A. Rivers, M. S. Robeson, P. Rosenthal, N. Segata, M. Shaffer, A. Shiffer, R. Sinha, S. J. Song, J. R. Spear, A. D. Swafford, L. R. Thompson, P. J. Torres, P. Trinh, A. Tripathi, P. J. Turnbaugh, S. Ul-Hasan, J. J. J. van der Hooft, F. Vargas, Y. Vázquez-Baeza, E. Vogtmann, M. von Hippel, W. Walters, Y. Wan, M. Wang, J. Warren, K. C. Weber, C. H. D. Williamson, A. D. Willis, Z. Z. Xu, J. R. Zaneveld, Y. Zhang, Q. Zhu, R. Knight, J. G. Caporaso, Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).<br>10. T. Rognes, T. Flouri, B. Nichols, C. Quince, F. Mahé, VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).<br>11. D. H. Huson, A. F. Auch, J. Qi, S. C. Schuster, MEGAN analysis of metagenomic data. Genome Res. 17, 377–386 (2007).<br>12. M. S. Robeson, D. R. O’Rourke, B. D. Kaehler, M. Ziemski, M. R. Dillon, J. T. Foster, N. A. Bokulich, RESCRIPt: Reproducible sequence taxonomy reference database management. PLOS Comput. Biol. 17, e1009581 (2021).</p>
Sediment core dataset for "Shift away from Nile incision at Luxor ~4,000 years ago impacted ancient Egyptian landscapes"
<p>This dataset contains all sedimentary core information used for reconstructing the Holocene evolution of the Nile Valley landscape near Luxor in Egypt.</p> <p>Sedimentary information from 81 sediment cores retrieved by a combination of hand-operated Eijkelkamp augers and a gasoline-powered Cobra TT percussion corer was used to investigate the Nile’s Holocene fluvial deposits in its valley near Luxor, Egypt. Sediment samples were studied in ~10 cm intervals and had their characteristics such as sedimentary texture (conforming to USDA standards), grain size, Munsell colour, degree of sorting, mica occurrence and rhizolith percentages logged on-site. Boreholes reached to an average depth of ~8 m — with many penetrating >10 m. Their spacing varied from ~20 to 200 m, depending on the heterogeneity of the subsurface. The cross-section was strategically placed to span the entire valley, perpendicular to the main axis of the Nile Valley and the current river, while following governmental policies and regulatory procedures working in and around Egyptian Antiquities areas. Coring locations were recorded in UTM36N and the Survey of Egypt vertical datum using a Leica RTK-GNSS positioning system, and subsequently stored together with the sedimentary logs for future reference. Subsequently, UTM36N coordinates were converted to degrees, minutes, seconds for publication purposes. </p> <p>This dataset consists of one Microsoft Excel workbook:</p> <p>1_sedimentary_core_dataset.xlxs</p> <p>Further details can be found in Peeters et al. "Shift away from Nile incision at Luxor ~4000 years ago impacted ancient Egyptian landscapes" (Nature Geoscience, 17, July 2024, p. 645–653, <a href="https://www.nature.com/articles/s41561-024-01451-z" target="_blank" rel="noopener">https://www.nature.com/articles/s41561-024-01451-z</a>). </p> <p>Contact information:</p> <p>Dr Angus Graham (angus.graham@arkeologi.uu.se)</p> <p>Dr Jan Peeters (j.peeters1.uu@gmail.com)</p>
Dataset of sediment cores and box cores collected in Central Basin, Ross Sea (Antarctica)
<p>dataset of sediment cores and box cores collected in Central Basin, Ross Sea (Antarctica)</p>
Dataset for the Global Prediction Of Total Organic Carbon In Marine Sediments Using Deep Neural Networks (nn-toc)
<p>The data folder contains the raw features and labels used for training machine learning models to predict total organic carbon in marine sediments. </p> <p>The data folder has three subfolders:</p> <ol> <li>raw : contains the labels, features and other data used to train the machine learnign models</li> <li>interim : transformed data, which has to be reproduced</li> <li>output : output from the models, used for analysis and visualisation</li> </ol> <p>The data folder has to be integrated in the Git repository nn-toc, to execute the code.</p> <p> </p> <p> </p>
General video about the PROMISCES project - Preventing Recalcitrant Organic Mobile Industrial chemicalS for Circular Economy in the Soil sediment water system
<p>General video presentation about the PROMISCES project.</p>
Data: Characterizing the sediment dynamics through in-situ measurements in the abyssal Manila Trench, northeast South China Sea
<p>Along the Manila Trench, a total of four moorings were deployed in <a name="OLE_LINK5"></a>September 2019 and recovered in August 2020. The field measurements in velocity and turbidity were resampled to create hourly dataset.</p>
Beryllium Isotopes in Maar Lake Sediments Response to Rapid Climate Change Since the Last Deglaciation
<p>Data for "<span>Beryllium Isotopes in Maar Lake Sediments Response to Rapid Climate Change Since the Last Deglaciation</span>"</p>
Balancing the oceanic Zn isotope budget: the key role of deep-sea pelagic sediments
<p><span>Supplementary</span><span> i</span><span>nformation</span><span> present analytical methods, figures, and tables.</span></p> <p><span><span>Supplementary Table present geochmical data of deep-sea sediments from the Indian and Pacific.</span></span></p>
Holocene and glacial individual foraminiferal analyses (IFA) of stable isotopes in Globigerinoides ruber tests from Line Islands sediment cores (central equatorial Pacific)
<p>This dataset contains individual foraminiferal analyses (IFA) stable isotopic (δ¹⁸O and δ¹³C) measurements of planktic foraminifera <em>Globigerinoides ruber</em> tests from modern and Last Glacial Maximum (LGM; ~20 ka) sediments from offshore the Line Islands, located in the central equatorial Pacific Ocean.</p>
Dataset for Paul et al., "Trace metals in coastal marine sediments: Natural and anthropogenic sources, correlation matrices, and proxy potentials", Science of The Total Environment (STOTEN-175789, 2024)
<p>The datafile (.xlsx format) contains the solid phase data for all study sites presented in the associated STOTEN publication <a href="https://doi.org/10.1016/j.scitotenv.2024.175789" target="_blank" rel="noopener">(10.1016/j.scitotenv.2024.175789)</a></p> <ol> <li>specifics on the ICP-MS and ICP-OES analysis</li> <li>solid-phase data (Pb, Cd, Cu, Zn, Sb, Sn, Ni, As, Tl, V, Mo, U, Re, TOC, S, Fe, Mn, and Al)</li> <li>coefficient of variation test results (as a basis for evaluating the applicability of data normalizations to the data; i.e. calculation of Enrichment Factors, cf. method section of the original publication)</li> </ol> <p>Please note that the title of the paper and the publication number has changed upon final publication. The Excel file description still refers to the original manuscript number and title "Trace metals in coastal marine sediments: anthropogenic sources, correlation patterns, and proxy potentials".</p>
Quantifying vertical fluxes near the sediment water interface
<p>Field and laboratory observations used in GRL article "<a href="http://onlinelibrary.wiley.com/doi/10.1002/2017GL076789/abstract?campaign=wolacceptedarticle">Determining near-bottom fluxes of passive tracers in aquatic environments</a>" DOI: 10.1002/2017GL076789.</p>
Data for "The impacts of bioturbation by common marsh crabs on sediment erodibility: a laboratory flume investigation"
<p>This repository contains supporting data for the paper, "The impacts of bioturbation by common marsh crabs on sediment erodibility: a laboratory flume investigation." This includes data collected during the flume experiment described within the paper, and flow velocity data collected during field validation.</p>
Effects of the Invasive Freshwater Mussel Limnoperna fortunei on Sediment Properties and Accumulation Rates
<p>Environmental data and results of an experiment conducted in the vicinity of the Río de la Plata Estuary (Argentina), aimed at assessing the influence of the invasive mussel <em>Limnoperna fortunei</em> on sediment properties and accumulation rates. In the experiment, eighteen 20 L flow-through experimental units with and without mussels were used monitoring where changes in the mass and characteristics of the sediments accumulated throughout a yearly cycle in monthly, biannual and annual intervals.</p>
Shapefiles and data associated with the study of "Subsurface Sediment Mobilization in the Southern Chryse Planitia on Mars"
<p>This zip file contains the shapefiles for ArcGIS project with the positions of the five types of edifices within the southern part of the Chryse Planitia on Mars which were subject of the study "Subsurface Sediment Mobilization in the Southern Chryse Planitia on Mars" by Brož et al. (2019, JGR-Planets).</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.