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Environmental DNA Marine France Calanques 2022
Description: Fish environmental DNA data set collected in 2022 in the Calanques National Park The eDNA samples were collected in 2022 in two locations (Moyades, M−FPA and “Impérial du large”, I-LPA), during the winter (January- February), the summer (June to August)and fall (mid-September to November) seasons, with the sampling dates depending on the weather conditions. For the M−FPA, samples were collected between Moyades island and Riou island, while for the I-LPA, they were collected on the south side of the “Impérial du large” island. To account for the existing bathymetry, in the M−FPA the samples were taken at two sampling sites with depths of 20 and 40 m, while in the I-LPA they were taken at two sites with depths of 20 and 80 m. At each site, in-situ filtration of seawater was performed using a double-head submersible pump (Subspace, Geneva, Switzerland; nominal flow of ca. 1 L/min) strapped to an underwater scooter with 2 VigiDNA 0.20 µm filtration capsules (SPYGEN, le Bourget du Lac, France), along with disposable sterile tubing. The samples were collected along two horizontal transects (up to 400 m in length) during each closed-circuit rebreather dive, enabling the filtration of a water volume of 15 L/filter per depth, as close as possible to the substrate. Two filter replicates were collected by two divers at each sampling site, except in two cases where bad weather conditions or logistical issues meant that only one replicate was sampled. After the filtration, the remaining seawater was emptied from the capsule back on the boat and replaced by a 80 mL CL1 conservation buffer (SPYGEN, le Bourget du Lac, France). To prevent any contamination, a strict protocol was followed during the entire process, requiring disposable gloves and single-use filtration equipment. Finally, the samples were stored at room temperature. We followed a strict contamination control protocol in both field and laboratory stages. Each water sample processing included the use of disposable gloves and single-use filtration equipment to avoid any risk of contamination. Libraries were prepared with ligation using the MetaFast protocol (Fasteris). Data content: * rawdata/: contains the raw reads for each individual sample. One archive contains the paired-end reads specified by the _R1 or _R2 suffix as well as individually tagged PCR replicates (if available) together with an archive containing all extraction and PCR blank samples of the library. Reads have been demultiplexed using cutadapt but not trimmed, individual demultiplexing tags and primers remain present in the sequences. * taxadata/: contains the table with all detected taxonomy for each sample after bioinformatic processing (see Polanco et al. 2020 for details; https://doi.org/10.1002/edn3.140) and associated field metadata. * metadata/: contains two metadata files, one related to the data collected in the field for each filter, and the second related to the sequencing process in the lab (including the tag sequence, library name, and marker information for each sample)
Alpine3D simulations of future climate scenarios CH2014
Overview The CH2014-Impacts initiative is a concerted national effort to describe impacts of climate change in Switzerland quantitatively, drawing on the scientific resources available in Switzerland today. The initiative links the recently developed Swiss Climate Change Scenarios CH2011 with an evolving base of quantitative impact models. The use of a common climate data set across disciplines and research groups sets a high standard of consistency and comparability of results. Impact studies explore the wide range of climatic changes in temperature and precipitation projected in CH2011 for the 21st century, which vary with the assumed global level of greenhouse gases, the time horizon, the underlying climate model, and the geographical region within Switzerland. The differences among climate projections are considered using three greenhouse gas scenarios, three future time periods in the 21st century, and three climate uncertainty levels (Figure 1). Impacts are shown with respect to the reference period 1980-2009 of CH2011, and add to any impacts that have already emerged as a result of earlier climate change. Experimental Setup Future snow cover changes are simulated with the physics-based model Alpine3D (Lehning et al., 2006). It is applied to two regions: The canton of Graubünden and the Aare catchment. These domains are modeled with a Digital Elevation Model (DEM) with a resolution of 200 m × 200 m. This defines the simulation grid that has to be filled with land cover data and downscaled meteorological input data for each cell for the time period of interest at hourly resolution. The reference data set consists of automatic weather station data. All meteorological input parameters are spatially interpolated to the simulation grid. The reference period comprises only thirteen years (1999–2012), because the number of available high elevation weather stations for earlier times is not sufficient to achieve unbiased distribution of the observations with elevation. The model uses projected temperature and precipitation changes for all greenhouse gas scenarios (A1B, A2, and RCP3PD) and CH2011 time periods (2035, 2060, and 2085). Data Snow cover changes are projected to be relatively small in the near term (2035) (Figure 5.1 top), in particular at higher elevations above 2000 m asl. As shown by Bavay et al. (2013) the spread in projected snow cover for this period is greater between different climate model chains (Chapter 3) than between the reference period and the model chain exhibiting the most moderate change. In the 2085 period much larger changes with the potential to fundamentally transform the snow dominated alpine area become apparent (Figure 5.1 bottom). These changes include a shortening of the snow season by 5–9 weeks for the A1B scenario. This is roughly equivalent to an elevation shift of 400–800 m. The slight increase of winter precipitation and therefore snow fall projected in the CH2011 scenarios (with high associated uncertainty) can no longer compensate for the effect of increasing winter temperatures even at high elevations. In terms of Snow Water Equivalents (SWE), the projected reduction is up to two thirds toward the end of the century (2085). A continuous snow cover will be restricted to a shorter time period and/or to regions at increasingly high elevation. In Bern, for example, the number of days per year with at least 5 cm snow depth will decrease by 90% from now 20 days to only 2 days on average.
Urban bird predation on artificial caterpillars
We established our study sites in the cities of Basel, Lugano and Zurich, and their peri-urban forests. We characterised urban tree cover of each city using a rectangular grid with squares of 100x100 m. Within each square, we measured the area covered by urban trees using the European Union's Copernicus Land Monitoring Service information, Urban Atlas Street Tree Layer 2018 [https://doi.org/10.2909/205691b3-7ae9-41dd-abf1-1fbf60d72c8c](https://doi.org/10.2909/205691b3-7ae9-41dd-abf1-1fbf60d72c8c). Then we assigned each square to four categories of urban tree cover that roughly represented the main types of urban uses: 1) low cover, industrial/commercial areas, 0-20% tree cover; 2) intermediate cover, residential areas, 20-40% tree cover; 3) high cover, urban parks and cemeteries, 40-60% tree cover; 4) peri-urban forests (natural/semi-natural forests), 60-100% tree cover. <br/><br/> Our study sites consisted of eight 1.2 km-long transects in each city, equally distributed across the four tree cover categories. We designed an experimental measurements of bird predation rate on herbivore insect larvae using artificial caterpillars. They mimicked a variety of common, cryptically-coloured herbivorous species, which are usually preyed by birds. We designed caterpillars with green water-resistant modelling clay (Staedtler Noris®), 4-6 cm long and approximately 0.5 cm wide. Caterpillars were threaded to a thin (Ø = 0.6 mm) zinc-plated iron wire and tethered to branches of trees or bushes at a height up to 2 m from the ground. We placed 2-4 caterpillar mimics every 200 m along each transect (five points per transect) or, when not possible due to absence of suitable branches, within 200 m from the point. In total, we placed 270 caterpillar mimics at 115 points during the late breeding season (June-July 2023). Caterpillar mimics were checked after 10-14 days and replaced with new ones at new locations within 10 m from the previous ones. During each of the two visits, we counted the number of bird predation marks.
On the compressive strength of weak snow layers of depth hoar
This repository hosts the experimental data accompanying our publication, “On the compressive strength of weak snow layers of depth hoar,” featured in the Journal of Glaciology. -Compressive Strength Data: Measurements of the compressive strength for 92 artificially grown weak snow samples. -Microstructural CT Data: CT-derived microstructural information for each sample, including: Density Specific surface area Connectivity density Correlation lengths Anisotropy -Additional CT Data: Parent Sample Variability: CT data used to assess the variability of the parent samples. Temporal Evolution: CT data capturing the evolution within the artificial weak layers. Reference Data: Information on the reference CT data sourced from the RHOSSA and MOSAiC campaigns.
The influence of snow microstructure on the compressive mechanical properties of weak snowpack layers
This repository hosts the experimental data accompanying our publication "The influence of snow microstructure on the compressive mechanical properties of weak snowpack layers" feautured in Acta Materialia. - Experimental Data and microstructural descriptors: Full dataset used for the main analysis of the paper. Contains the measured mechanical properties, µCT parameters, further analysis, etc. The column "ID" (e.g. 363) links this data with the 3D µCT dataset (e.g. e0000363). - 3D Data of the segmented µCT scans: Full dataset containing the raw segmented µCT scans in the MetaIO format. They can be opened using the SimpleITK package (`pip install SimpleITK`). Note: the Files can be idenfied by their scan number in the filename, (e.g, e0000363) `import SimpleITK as sitk ` `img = sitk.ReadImage("e0000363_crop_seg.mhd") ` `array = sitk.GetArrayFromImage(img) ` shape: [z, y, x] `array_xyz = np.transpose(array, (2, 1, 0))` (Optional) for array axes in [x, y, z] `spacing = img.GetSpacing() ` voxel size (x,y,z)
CHELSAcerra-daily
CHELSA is a mechanistic downscaling model that links large-scale atmospheric conditions with local topographic factors to produce very high-resolution climate data. It includes commonly used climate variables for impact modeling, such as air temperature, precipitation, humidity, solar radiation, wind speed, and derived variables. CHELSAcerra daily is a high resolution climate dataset for air-temperatures generated with the CHELSA downscaling model using the Copernicus regional reanalysis for Europe (CERRA). Daily summaries are provided for: Daily Mean Near-Surface Air Temperature
Schänis, Switzerland: Long-term forest meteorological data from the Long-term Forest Ecosystem Research Programme (LWF), from 1998 onwards
High quality meteorological data are needed for long-term forest ecosystem research, particularly in the light of global change. The long-term data series published here comprises almost 20 years of measurements for two meteorological stations in Schänis in Switzerland where one station is located within a natural mixed forest stand (SCB) with European beech (_Fagus sylvatica_; 130-150 yrs), European silver fir (_Abies alba_; 130-150 yrs) and European ash (_Fraxinus excelsior_; 130-150 yrs) as dominant tree species. A second station is situated in the very vicinity outside of the forest (field station, SCF). The meteorological time series are presented in hourly time resolution of air temperature, relative humidity, precipitation, photosynthetically active radiation (PAR) and wind speed. Schänis is part of the Long-term Forest Ecosystem Research Programme (LWF) established and maintained by the Swiss Federal Research Institute WSL.
Snow water equivalent for reference date April 1 for Wägital catchment, starting 1943
Total water reserves of the snow cover [mio m3] for Wägital catchment, Switzerland, for reference date April 1. Data is separated in 2 elevation zones 900m-1500m asl and 1500m-2300m asl. Time period 1943-2025, status 2025-04-30. Funded currently or in the past by: - Federal Office of Meteorology and Climatology MeteoSwiss in the context of GCOS Switzerland - Meteodat GmbH - Institute of Geography, University of Zurich - WSL Institute for Snow and Avalanche Research SLF - Institute of Geography, ETH Zurich (IAC ETH Zurich) - AG Kraftwerk Wägital (AXPO and EWZ) See also https://www.meteodat.ch/waegital.html
Soil net nitrogen mineralisation across global grasslands
This dataset contains all data on which the following publication below is based. Paper Citation: Risch, A. C.; Zimmermann, S.; Ochoa-Hueso, R.; Schütz, M.; Frey, B.; Firn, J. L.; Fay, P. A.; Hagedorn, F.; Borer, E. T.; Seabloom, E. W.; et al. Soil net nitrogen mineralisation across global grasslands. Nat. Commun. 2019, 10 (1), 4981 (10 pp.). doi.org/10.1038/s41467-019-12948-2 Please cite this paper together with the citation for the datafile. We conducted coordinated measurements of realised and potential soil net Nmin, and assessed water holding capacity, bulk density, C and N content, texture, pH, pore space, microbial biomass, and archaeal (AOA) and bacterial (AOB) ammonia oxidiser abundance using identical materials and methods across 30 grasslands on six continents. The sites covered a globally relevant range of climatic and edaphic conditions. Climate data was obtained from worldclim - Global climate data https://www.worldclim.org/
Cloud Optimized Raster Encoding (CORE) format
Acknowledgements: The CORE format was proudly inspired by the Cloud Optimized GeoTIFF ([COG](https://www.cogeo.org/)) format, by considering how to leverage the ability of clients issuing HTTP GET range requests for a time-series of remote sensing and aerial imagery (instead of just one image). License: The Cloud Optimized Raster Encoding (CORE) specifications are released to the public domain under a Creative Commons 1.0 CC0 "No Rights Reserved" international license. You can reuse the information contained herein in any way you want, for any purposes and without restrictions. ----------------------- Summary: The Cloud Optimized Raster Encoding (CORE) format is being developed for the efficient storage and management of gridded data by applying video encoding algorithms. It is mainly designed for the exchange and preservation of large time series data in environmental data repositories, while in the same time enabling more efficient workflows on the cloud. It can be applied to any large number of similar (in pixel size and image dimensions) raster data layers. CORE is not designed to replace COG but to work together with COG for a collection of many layers (e.g. by offering a fast preview of layers when switching between layers of a time series). WARNING: Currently only applicable to RGB/Byte imagery. The final CORE specifications may probably be very different from what is written herein or CORE may not ever become productive due to a myriad of reasons (see also 'Major issues to be solved'). With this early public sharing of the format we explicitly support the Open Science agenda, which implies "shifting from the standard practices of publishing research results in scientific publications towards sharing and using all available knowledge at an earlier stage in the research process" (quote from: European Commission, Directorate General for Research and Innovation, 2016. Open innovation, open science, open to the world). CORE Specifications: 1) a MP4 or WebM video digital multimedia container format (or any future video container playable as HTML video in major browsers) 2) a free to use or open video compression codec such as H.264, VP9, or AV1 (or any future video codec that is open sourced or free to use for end users) Note: H.264 is currently recommended because of the wide usage with support in all major browsers, fast encoding due to acceleration in hardware (which is currently not the case for AV1 or VP9) and the fact that MPEG LA has allowed the free use for streaming video that is free to the end users. However, please note that H.264 is restricted by patents and its use in proprietary or commercial software requires the payment of royalties to [MPEG LA](https://www.mpegla.com/programs/avc-h-264/). However, when AV1 matures and accelerated hardware encoding becomes available, AV1 is expected to offer 30% to 50% smaller file size in comparison with H.264, while retaining the [same quality](https://trac.ffmpeg.org/wiki/Encode/AV1). 3) the encoding frame rate should be of one frame per second (fps) with each layer segmented in internal tiles, similar to COG, ordered by the main use case when accessing the data: either layer contiguous or tile contiguous; Note: The internal tile arrangement should support an easy navigation inside the CORE video format, depending on the use case. 4) a CORE file is optimised for streaming with the moov atom at the beginning of the file (e.g. with -movflags faststart) and optional additional optimisations depending on the codec used (e.g. -tune fastdecode -tune zerolatency for H.264) 5) metadata tags inside the moov atom for describing and using geographic image data (that are preferably compatible with the [OGC GeoTIFF standard](https://www.ogc.org/standards/geotiff) or any future standard accepted by the geospatial community) as well as list of original file names corresponding to each CORE layer 6) it needs to encode similar source rasters (such as time series of rasters with the same extent and resolution, or different tiles of the same product; each input raster should be having the same image and pixel size) 7) it provides a mechanism for addressing and requesting overviews (lower resolution data) for a fast display in web browser depending on the map scale (currently external overviews) Major issues to be solved: - Internal overviews (similar to COG), by chaining lower resolution videos in the same MP4 container for fast access to overviews first); Currently, overviews are kept as separate files, as external overviews. - Metadata encoding (how to best encode spatial extent, layer names, and so on, for each of the layer inside the series, which may have a different geographical extent, etc...; Known issues: adding too many tags with FFmpeg which are not part of the standard MP4 moov atom; metadata tags have a limited string length. - Applicability beyond RGB/Byte datasets; defining a standard way of converting cell values from Int16/UInt16/UInt32/Int32/Float32/Float64/ data types into multi-band Byte values (and reconstructing them back to the original data type within acceptable thresholds) Example Notice: The provided CORE (.mp4) examples contain modified Copernicus Sentinel data [2018-2021]. For generating the CORE examples provided, 50 original Sentinel 2 (S-2) TCI data images from an area located inside Switzerland were downloaded from www.copernicus.eu, and then transformed into CORE format using ffmpeg with H.264 encoding using the [x264 library](https://www.videolan.org/developers/x264.html). DISCLAIMER: Basic scripts are provided for the Geomatics peer review (in 2021) and kept as additional information for the dataset. Nevertheless, please note that software dependencies and libraries, as well as cloud storage paths, may quickly become deprecated over time (after 2021). For compatibility, stable dependencies and libraries released around 2020 should be used.