AndreaBozzo/ceres-open-data-index huggingface dataset:
Three-dimensional debris flow simulation tool debrisInterMixing

Here debrisInterMixing until version 7 is provided for download. Further versions as well as installation instructions and tutorials and discussion forums (mostly in german) can be acessed at murgang.org (choose "als Gast anmelden" and then scroll to the bottom). The first OpenFoam-compatible Version 2.3.x are available as supplement to v. Boetticher, A., Turowski, J. M., McArdell,W. B., Rickenmann, D., Hürlimann, M., Scheidl, C., and Kirchner, J. W.: DebrisInterMixing-2.3: A Finite Volume solver for three dimensional debris flow simulations based on two calibration parameters. Part two: model validation with experiments. Geoscientific Model Development, 10, 11: 3963-3978. doi: 10.5194/gmd-10-3963-2017.
DebrisInterMixing is a Volume-of-Fluid based Finite Volume code that accounts for shear-thinning sensitive shares of fine sediment suspension together with pressure-sensitive components of the gravel grains within debris flow mixtures. All model properties can be derived from a material sample except for a grid-sensitive calibration parameter.
For more information, please contact albrecht.vonboetticher@wasserbau.ch. 
For a recent summary on applications see the DFHM8 contribution at https://www.e3s-conferences.org/articles/e3sconf/abs/2023/52/e3sconf_dfhm82023_02024/e3sconf_dfhm82023_02024.html - DOI: https://doi.org/10.1051/e3sconf/202341502024
UPDATE: DebrisInterMixing for OpenFOAM-7 is available, please contact albrecht.vonboetticher@wasserbau.ch. DebrisInterMixing with OpenFOAM-10 is ready but not yet validated.

Tags: barrier-impact-simulation, dberisintermixing, debris-flow, finite-volumes, hangmuren, interfoam, murgang, natural-hazard, shallow-landslide
Urban birds point counts data

The study area included the cities of Basel, Lugano and Zurich. The sampling design reflected four main city districts related to four categories of tree cover (Figure 1): 1) industrial/commercial areas, 0-20% tree cover; 2) residential areas, 20-40% tree cover; 3) urban parks and cemeteries, 40-60% tree cover; 4) peri-urban forests (natural/semi-natural forests), 60-100% tree cover. The tree cover gradient was evaluated across a square grid with a square side length of 100 m. For each square, we evaluated the area covered by urban trees using the Urban Atlas Street Tree Layer 2018 (European Union’s Copernicus Land Monitoring Service information, 2021). 
In each city, we established eight transects of 1.2 km, two for each tree cover category. Transects crossed contiguous grid squares belonging to the same tree cover categories as much as possible. We performed aural-visual point counts of birds every 200 m along each transect (six points per transect) during the breeding season (April-June 2024) (Bibby et al., 2000). The transects were walked at the time of highest activity of birds, which is from thirty minutes after sunrise until 4 hours later. Each transect was walked twice, 20-60 days apart, to account for imperfect detection of birds and sample completeness (Balestrieri et al., 2017; Kéry et al., 2005).

Tags: biodiversity, birds, environmental-gradients, periurban, spatially-distributed-sampling, urban
Steigerwald_Artificial_Dendrotelms

This dataset comprises environmental and insect larval data from 24 artificial dendrotelms (water-filled tree holes) created in beech trees (Fagus sylvatica) in six old-growth forest patches connecting two forest nature reserves in the Steigerwald in Germany.

Tags: body-size, dendrotelms, diversity, european-beech, fagus-sylvatica, forest, germany, insects, invertebrates, metacommunity, old-growth-islands, steigerwald, stepping-stones, trems, water-filled-tree-holes
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.

Tags: biodiversity, biodiversity-experiment, birds, insect-herbivores, periurban, pest-invasion, urban, urban-biodiversity, urban-ecology
Urban bird capture data with prey species and fungal community

We captured birds in urban parks and peri-urban forests in the cities of Lugano and Zurich. The urban sites were located in an urban forest (Lugano) and in a cemetery (Zurich), and the bird assemblages were comparable with those of the surrounding forests.
We captured individual birds during sessions lasting multiple days using mist-nets, concentrating the activities within 3-4 hours after sunrise and before sunset. We extracted birds from nets using single-use nitrile gloves and gently wiped their body parts with a dry foam swab MW940 (Medical Wire & Equipment), which was then placed in a screw-capped tube (2 ml), which was previously filled with 1 ml ethanol puriss. (Sigma-Aldrich) under sterile conditions.Then, we marked each bird with an alphanumeric leg band, identified the species, determined the sex and age whenever possible, measured for relevant biometrics (e.g. wing chord), the amount of body fat and pectoral muscle (i.e. body condition), and weighed.
Afterwards, we placed each bird in a disposable paper bag within a cotton bag that ensured respiration and left it for few minutes in a safe and calm place to allow for defecation and the collection of faecal samples. The faecal sample was collected from insectivorous and omnivorous birds, and few granivorous birds that are known to occasionally eat invertebrates, such as the house sparrow Passer domesticus.
After releasing the bird, we stored the faecal sample in a screw-capped tube (2 ml), which was previously filled with 1 ml ethanol puriss. (Sigma-Aldrich) under sterile conditions. We wore single-use nitrile gloves and used sterile toothpicks to collect solid samples. The tubes were initially stored in the refrigerator during the field campaign and no later than seven days after collection at -20°C until prepared for DNA extraction.
DNA extraction and library preparation was performed at WSL Phytopathology facilites, Sequencing was performed at Lausanne Genomic Technologies Facility (University of Lausanne; [https://wp.unil.ch/gtf/](https://wp.unil.ch/gtf/)) on an AVITI benchtop sequencing system (Element Biosciences). Bioinformatics was performed at the Genetic Diversity Center (ETH Zurich) using a custom pipeline.

Tags: biodiversity, birds, fungal-pathogen, fungi, insects, urban, urban-biodiversity, urban-ecology
Stable isotope data from 73 tree and shrub species in a common garden in Basel Switzerland

This dataset contains hydrogen and carbon isotope data from 73 tree and shrub species grown in a common garden (Kannenfeldpark) in Basel, Switzerland. Leaf and twig samples were collected in August 2019. The isotope measurements cover various organic compounds, including sugars, cellulose, and (lignin) methoxy groups, as well as leaf and twig xylem water. Details on sample preparation and isotope analysis are provided in Schuler et al. (2023) for carbohydrates and water, and in Wieland et al. (in review) for methoxy groups.

Tags: carbohydrates, common-garden, isotopes, methoxy-groups, tree-species
Soil microbial diversity and multifunctionality across European biomes

The diversity and network complexity of prokaryotic and fungal communities and their relationships with soil multifunctionality (SMF) – an integrative index for C-, N- and P-cycling functions – was investigated along a 3,000-km latitudinal transect across Europe (37° to 62°N), spanning biomes from Mediterranean drylands, temperate to boreal forests.

Tags: fungi, latitudinal-gradient, microbial-biodiversity, prokaryotes, soil-microbiome, soil-mulitfunctionality
Modeled and measured fluxes of latent and sensible heat and snow transport at S17 near Syowa in Antarctica

This dataset supports a related publication (Sigmund et al., 2025) and contains
- results of four **large-eddy simulations** (LES) coupled to a Lagrangian model (LM) for snow transport, aiming to reproduce field measurements, especially latent heat fluxes, at the S17 site near Syowa Station, East Antarctica, in conditions of drifting and blowing snow,
- references to the **source code** of the LES-LM model,
- the source code and results of a simple **one-dimensional (1D) model** inspired by the large-scale model CRYOWRF (Sharma et al., 2023), aiming to reproduce the LES-LM results,
- post-processed **measurements** shown in the figures of the related publication,
- **programming code** for post-processing and plotting the results.
The LES-LM simulations solve the Navier-Stokes equations for incompressible flows and advection-diffusion equations for air temperature and specific humidity in a domain of 19.2 x 18.32 x 18.32 m³. In these simulations, the airflow is driven by a prescribed large-scale pressure gradient. We assume that the air density is constant (1.18 kg/m³) and the snow particles have a spherical shape and a density of 918.4 kg/m³. Further methodological details are described in the related publication. The 1D model and post-processing code was created using the R software version 4.3.2 (R Core Team, 2024).
References
- Sharma, V., Gerber, F., & Lehning, M. (2023): Introducing CRYOWRF v1.0: multiscale atmospheric flow simulations with advanced snow cover modelling. Geosci. Model Dev. 16, 719–749. [https://doi.org/10.5194/gmd-16-719-2023](https://doi.org/10.5194/gmd-16-719-2023)
- Sigmund, A., Melo, D. B., Dujardin, J., Nishimura, K., & Lehning, M. (2025). Parameterizing snow sublimation in conditions of drifting and blowing snow. Journal of Advances in Modeling Earth Systems, 17, e2024MS004332. [https://doi.org/10.1029/2024MS004332](https://doi.org/10.1029/2024MS004332)

Tags: antarctica, blowing-snow, drifting-snow, large-eddy-simulation, parameterization, snow-sublimation, turbulence
Overland and topsoil interflow time series from the Studibach - summer 2022

The dataset comprises the time series of overland flow (OF) and topsoil interflow (TIF) discharges from 14 small runoff plots (1 x 3 m) over 27 rainfall events in 2022 across the Studibach in the Alptal, a typical pre-Alpine catchment in Switzerland. 
The runoff plots were installed on different topographic indices and vegetation covers in order to study the spatio-temporal variability of OF and TIF. 
The runoff was collected into self-made "Upwelling Bernoulli Tubes" and the water level inside these tubes was measured by pressure sensors (DCX-22-CTD, Keller Druck, Switzerland) at a 5-min resolution. The discharge was derived from the water level. 
The precipitation was measured with a tipping bucket at the Erlenhöhe meteorological station and has a 10-min resolution.

Tags: alptal, land, overland-flow, plot, rainfall, runoff, studibach, time-series, topsoil-interflow
Metabarcoding of urban and forest bird faecal samples

We captured birds in urban parks and peri-urban forests in the cities of Lugano, Zurich (Switzerland) and Napoli (Italy). The urban sites were located in urban forests (Lugano, Napoli) and in a cemetery (Zurich). Bird faecal samples were stored in a screw-capped tube (2 ml), which was previously filled with 1 ml ethanol puriss. (Sigma-Aldrich) under sterile conditions. We wore single-use nitrile gloves and used sterile toothpicks to collect solid samples. The tubes were initially stored in the refrigerator during the field campaign and no later than seven days after collection at -20°C until prepared for DNA extraction.
DNA extraction and library preparation was performed at WSL Phytopathology facilites, Sequencing was performed at Lausanne Genomic Technologies Facility (University of Lausanne; https://wp.unil.ch/gtf/) on an AVITI benchtop sequencing system (Element Biosciences). Bioinformatics was performed at the Genetic Diversity Center (ETH Zurich) using a custom pipeline.

Tags: arthropoda, birds, dna-metabarcoding, trophic-networks, urban-biodiversity
Urban bird predation on horse chestnut leaf miner Cameraria ohridella in three Swiss cities

We established our study sites in the cities of Basel, Lugano and Zurich. 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 three 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.
-br/--br/-
We measured bird predation rate on the non-native insect larvae of the horse chestnut leaf miner (HCLM) Cameraria ohridella, an invasive moth that lays eggs and completes its larval and pupal development stages within the leaves of the horse chestnut Aesculus hippocastanus. The larvae feed on leaf fluids and tissue while creating mines within the leaf, which ultimately results in early leaf browning and loss of photosynthetic activity. We collected roughly ten twigs from each tree, including five twigs from the inner and five from the outer crown. Each twig carried 2-4 leaves, for a total of 3408 leaflets. Leaves were stored for ~10 weeks in a refrigerated room at 4 degrees C. We checked all HCLM mines using a stereo microscope and distinguished among open and close mines.
Open mines were further divided based on the opening hole, whether it was a small round exit hole of the larva or the parasitoid, or an irregularly shaped, large bird predation hole.

Tags: biodiversity, birds, insect-herbivores, insects, larvae, plant-insect-interaction, urban-biodiversity, urban-ecology
Application of CRISPR-Dx and metabarcoding to catchment-level eDNA for terrestrial mammal detection

General description
Data associated with the publication "CRISPR-Dx and metabarcoding perform similarly for monitoring mammals with eDNA on the catchment level in high-alpine ecosystems".  The data set contains the cleaned metabarcoding reads per site/catchment, the CRISPR-Dx detection per species and site, the site coordinates and a species checklist obtained from the Swiss National Park with the species known to occur at the sampling time point in the respective catchments.
 Authors
Flurin Leugger, Martina Lüthi, Michel Schmidlin, Sarah Marie-Antoine Turnheer, Zacharias Kontarakis and Loïc Pellissier
 Contact
flurinleugger@gmail.com
loic.pellissier@usys.ethz.ch
 Project description 
We collected eDNA samples in the Swiss National Park in September 2022 using VigiDNA filters. We extracted the samples in the clean lab at ETH using a modified extraction protocol of Pont et al. (2018). We used the Mamm01 primer (Tabarlet et al. 2018) for metabarcoding and for CRISPR analysis. We applied CRISPR-Dx for eight species occurring in the Swiss National Park. Additionally, we compared the eDNA detections to species inventories per catchment obtained from the Swiss National Park. See publication for more details.
 Folders
 catchments
Shape file containing the catchments sampled in the Swiss National Park.
 metadata
Folder containing files with overview of site names and extract number. Second file with metadata per site (e..g., sampling date). Column called "EVS" (Environmental sample) is the key between the two files.
 data
Folder containing a folder for eDNA and species_inventory (traditional monitoring), respectively.
 eDNA folder
CRISPR_classifications.csv: CRISPR-Dx classifications per extract (and PCR pool).
metabarcoding_seqs_all_cleaned.csv: all DNA sequences from metabarcoding after removing all sequences found in the negative controls.
 species_inventory
Species per catchment reported by the Swiss National Park, based on traditional monitoring including. visual surveys and other opportunistic records. 2: known presence in 2022, 1: maybe present in 2022, 0: not recorded in 2022

Tags: catchment, crispr-dx, dna-metabarcoding, edna, mammals, metabarcoding, national-park
Robot-aided measurement of insect diversity on vegetation using environmental DNA

Traditional methods of biodiversity monitoring are often logistically challenging, time-consuming, require experienced experts on species identification and sometimes include destruction of the targeted specimens. Here, we investigated a non-invasive approach of combining the use of drones and environmental DNA (eDNA) to monitor insect biodiversity on vegetation.
We aimed to assess the efficiency of this novel method in capturing insect diversity and comparing insect composition across different vegetation types (grassland, shrub, and forest) in Switzerland. A commercial, off-the-shelf drone was equipped with a specialised probe that autonomously swabbed vegetation and collected eDNA. Then, samples were processed using rapid third-generation Oxford Nanopore sequencing. The obtained data were analysed for insect diversity, comparing taxonomic richness, evenness and community composition across the three habitat types using statistical techniques. Sequencing of the samples yielded 76 hexapods taxa, revealing an insect community with notable differences in taxonomic richness but not in evenness across grassland, shrub, and forest habitats.
Our study demonstrates the potential of drone-based sampling integrated with eDNA and nanopore sequencing for biodiversity monitoring, offering a non-destructive method for detecting insect occurrence on plant surfaces. Integrating robotics and eDNA technology provides a promising solution for fast, large-scale, non-invasive biodiversity monitoring, potentially improving conservation efforts and ecosystem management.

Tags: drone, edna, ins16s, insect, minion, switzerland
Psychophysiological effects of walking in forests and urban built environments with disparate road traffic noise exposure

This repository contains data related to the field experiments of the RESTORE project. This project is a collaboration between the Swiss Federal Institute for Forest, Snow and Landscape Research (WSL) and the Swiss Federal Laboratories for Materials Science & Technology (EMPA). It has received funding from the Swiss National Science Foundation. The overall objective of the RESTORE project was to assess the effects of green spaces as facilitators and noise as impediment to recover from stress in people's daily environments across Switzerland.
We conducted a randomized, controlled field study to compare the psychophysiological benefits of exposure to forests and urban built environments with different levels of road traffic noise in healthy adults during 30-minute walks in Zürich, Switzerland to explore:
1) The psychophysiological effects of walking in forests and urban built environments with disparate road traffic noise exposure 
2) The effects of walking in urban forests and urban built environments with disparate road traffic noise exposure on repetitive negative thinking and connectedness with the non-human world  
3) The effects of a mindful walking intervention in urban forests for healthy adults
Accordingly, this repository includes data and documentation for the 3 scientific articles:
Scientific article 1. “Psychophysiological effects of walking in forests and urban built environments with disparate road traffic noise exposure: study protocol of a randomized controlled trial", BMC Psychology, 2024. https://doi.org/10.1186/s40359-024-01720-x
Scientific article 2. "Psychophysiological effects of walking in forests and urban built environments with disparate road traffic noise exposure: A randomized controlled trial“. Journal of Environmental Psychology, 2025. 
Scientific article 3. “The effects of walking in urban forests and urban built environments with disparate road traffic noise exposure on repetitive negative thinking and connectedness with the non-human world: A randomized controlled trial". To be submitted to PLOS One, 2025.
Scientific article 4: "Effects of a mindful walking intervention in urban forests for healthy adults". To be submitted to Current Psychology, 2025.

Tags: field-data, forest, restoration, traffic-noise, urban-landscape
Compilation of normalized  crack propagation speeds

Compilation of normalized crack-propagation speeds (expressed as a fraction of the slab shear-wave speed).
The dataset contains crack-propagation speeds from DEM simulations (79 flat and 6 tilted; Bobillier et al., 2024), MPM simulations (48 flat and 191 tilted; Trottet et al., 2022), and field measurements: PSTs (222 data points, including 192 from low-angle terrain - 30°; van Herwijnen et al., 2016) and avalanche-video analyses (6 cross-slope and 5 down-slope speeds; Trottet et al., 2022).
The dataset also includes Python scripts that generate the relative-frequency distribution of the compiled, normalized crack-propagation speeds.
Bobillier, G., Bergfeld, B., Dual, J., Gaume, J., van Herwijnen, A., 55 and Schweizer, J.: Numerical investigation of crack propagation regimes in snow fracture experiments, https://doi.org/10.1007/s10035-024-01423-5 2024
Trottet, B., Simenhois, R., Bobillier, G., Bergfeld, B., van Herwijnen, A., Jiang, C. F. F., and Gaume, J.: Transi- 55 tion from sub-Rayleigh anticrack to supershear crack propagation in snow avalanches, Nat. Phys., 18, 1094–1098, https://doi.org/10.1038/s41567-022-01662-4, 2022.
van Herwijnen, A., Gaume, J., Bair, E. H., Reuter, B., Birkeland, K. W., and Schweizer, J.: Estimating the effective elastic modulus and specific fracture energy of snowpack layers from field experiments, J. Glaciol., 62, 997–1007, https://doi.org/10.1017/jog.2016.90, 2016a.

Tags: crack-propagation, crack-speed, dry-snow-avalanche, field-data, numerical-simulations, weak-layer