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108 results for “environmental monitoring”
Supplementary material 6 from: Ushio M, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics 2: e23297. https://doi.org/10.3897/mbmg.2.23297
The numbers of eDNA copies of marine fish species quantified by metabarcoding with the internal standard DNA
Supplementary material 8 from: Ushio M, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics 2: e23297. https://doi.org/10.3897/mbmg.2.23297
The relationship between MiSeq sequence reads and DNA copy numbers quantified by qPCR. Correlations for the total fish eDNA (all data, a; enlarged figure, b), Japanese anchovy (Engraulis japonicus; all data, c; enlarged figure, d) and Japanese jack mackerel (Trachurus japonicus; all data, e; enlarged figure, f). Dashed and soild lines indicate 1:1 line and linear regression line, respectively. Regression lines in the enlarged figures were drawn by excluding outliers. All regression lines, except for the lines for total fish eDNA, were significant (P < 0.05). Dotted boxed regions in a, c and e correspond to the range of the graphs in b, d and f, respectively. The intensity of red colour indicates the slope of the regression line used to convert sequence reads to the copy numbers.
Supplementary material 4 from: Ushio M, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics 2: e23297. https://doi.org/10.3897/mbmg.2.23297
The relationship between MiSeq sequence reads and copy numbers of standard DNAs for 52 samples. Blue line indicates the linear regression between sequence reads and copy numbers. The regression lines are used to convert the MiSeq reads into the calculated copy numbers. Numbers in a grey region indicate sampling date. Note that regression slopes are different amongst samples, i.e. the number of sequence reads generated per eDNA copy is different amongst samples.
Supplementary material 5 from: Ushio M, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics 2: e23297. https://doi.org/10.3897/mbmg.2.23297
The relationship between regression residuals and copy numbers of standard DNAs for 52 samples. Dashed line indicates zero residuals.
Monitoring of the UHPFRC strengthened Chillon viaduct under environmental and operational variability
<p>Datasets corresponding to 3 months of data of the monitoring of Chillon viaduct.</p> <p>Each file contains: </p> <ul> <li>the vibration data from 11 acelerometers, in vertical direction</li> <li>the sampling ratio</li> <li>Temperature </li> <li>Humidity</li> </ul> <p>The accelerometer positions are illustarted in the pdf "accelerometres Position.pdf". </p> <p>When employing this dataset, please cite:"Martín-Sanz, Henar, Konstantinos Tatsis, Vasilis K. Dertimanis, Luis David Avendaño-Valencia, Eugen Brühwiler, and Eleni Chatzi. "Monitoring of the UHPFRC strengthened Chillon viaduct under environmental and operational variability." <em>Structure and Infrastructure Engineering</em> (2019): 1-31."</p>
Data from: Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding
Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present into the environment. In this study, we tested if an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, in vitro, and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI = 0.90-0.99) versus 0.58 (CI = 0.50-0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA-based approach has the potential to become the next-generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.
Data from: A general-purpose spatial survey design for collaborative science and monitoring of global environmental change: the global grid
Recent guidance on environmental modeling and global land-cover validation stresses the need for a probability-based design. Additionally, spatial balance has also been recommended as it ensures more efficient sampling, which is particularly relevant for understanding land use change. In this paper I describe a global sample design and database called the Global Grid (GG) that has both of these statistical characteristics, as well as being flexible, multi-scale, and globally comprehensive. The GG is intended to facilitate collaborative science and monitoring of land changes among local, regional, and national groups of scientists and citizens, and it is provided in a variety of open source formats to promote collaborative and citizen science. Since the GG sample grid is provided at multiple scales and is globally comprehensive, it provides a universal, readily-available sample. It also supports uneven probability sample designs through filtering sample locations by user-defined strata. The GG is not appropriate for use at locations above ±85° because the shape and topological distortion of quadrants becomes extreme near the poles. Additionally, the file sizes of the GG datasets are very large at fine scale (resolution ~600 m × 600 m) and require a 64-bit integer representation.
Monitoring the birds and the bees: Environmental DNA metabarcoding of flowers detects plant–animal interactions
<p>Animal pollinators are vital for the reproduction of ~90% of flowering plants. However, many of these pollinating species are experiencing declines globally, making effective pollinator monitoring methods more important than ever before. Pollinators can leave DNA on the flowers they visit, and metabarcoding of these environmental DNA (eDNA) traces provides an opportunity to detect the presence of flower visitors. Our study, collecting flowers from seven plant species with diverse floral morphologies, for eDNA metabarcoding analysis, illustrated the value of this novel survey tool. eDNA metabarcoding using three assays, including one developed in this study to target common bush birds, recorded more animal species visiting flowers than visual surveys conducted concurrently, including birds, bees, and other species. We also recorded the presence of a flower visit from a western pygmy possum; to our knowledge, this is the first eDNA metabarcoding study to simultaneously identify the interaction of insect, mammal, and bird species with flowers. The highest diversity of taxa was detected on large inflorescence flower types found on <em>Banksia arborea </em>and <em>Grevillea georgeana</em>. The study demonstrates that the ease of sample collection and the robustness of the metabarcoding methodology have profound implications for future management of biodiversity, allowing us to monitor both plants and their attendant cohort of potential pollinators. This opens avenues for rapid and efficient comparison of biodiversity and ecosystem health between different sites and may provide insights into surrogate pollinators in the event of pollinator declines.</p>
Continuous air pollution monitoring data for the Kanto region (Japan) derived from original observations by the National Institute for Environmental Studies Environmental Observatory (https://tenbou.nies.go.jp/download/).
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Environmental and Biological Monitoring Pilot Study for Polycyclic Aromatic Hydrocarbons in Linxian, China
ClinicalTrials.gov study NCT00342472. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Data from: Long-term environmental monitoring for assessment of change: measurement inconsistencies over time and potential solutions
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Data from: Environmental monitoring through protist NGS metabarcoding: assessing the impact of fish farming on benthic foraminifera communities
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In situ monitoring reveals cellular environmental instabilities in human pluripotent stem cell culture
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Data from: An environmental DNA-based method for monitoring spawning activity: a case study, using the endangered Macquarie perch (Macquaria australasica)
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Data from: Using occupancy modeling to compare environmental DNA to traditional field methods for regional-scale monitoring of an endangered aquatic species
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The Bug in a teacup – Monitoring arthropod-plant associations with environmental DNA from dried plant material
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Occupancy in dynamic systems: accounting for multiple scales and false positives using environmental DNA to inform monitoring
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Spatiotemporal monitoring of the rare Northern dragonhead, Dracocephalum ruyschiana (Lamiaceae): SNP genotyping and environmental niche modelling herbarium specimens
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Data from: A general-purpose spatial survey design for collaborative science and monitoring of global environmental change: the global grid
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Data from: Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding
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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.