Yoda Data Publication Platform of Utrecht University
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From aerial drone to QTL: Leveraging next-generation phenotyping to reveal the genetics of color and height in field-grown Lactuca sativa
No full textThis Dataset contains all the data required to replicate the results presented in the manuscript. A detailed description is available in the readme.txt, the scripts are available at https://github.com/SnoekLab/Dijkhuizen_etal_2025_Drone. The folder R_objects_plots contains the raw data, all the other subfolders contain steps in processing the raw data. All .out objects are R objects that can be loaded into R. The Supplemental_data.xlsx contains the processed data that we use to create all the figures. We also include a weather rapport, this is not used in the manuscript itself but we supply it for if anyone wants to use it. Contact person is Basten Snoek. [email protected]
Paper abstract:
In recent years, the automation of genotyping has significantly enhanced the efficiency of genome-wide association studies. Due to this development, phenotyping is now usually the rate-limiting step, especially in the field. Efforts are now focused on further automating in-field phenotyping. Here we present a GWAS study on 194 field-grown accessions of lettuce (Lactuca sativa). These accessions were non-destructively phenotyped at two time points 15 days apart using an unmanned aerial vehicle. Our high throughput phenotyping approach integrates an RGB camera, a multispectral camera to measure the reflectance at 5 wavelengths (blue, green, red, red edge, near-infrared), and precise height estimation. We used the mean and other descriptives such as median, quantiles, minimum and maximum to quantify different aspects of color and height variation in lettuce from the drone images. Using this approach, we confirm several previously described QTLs, now in populations grown under field conditions and identify several new QTLs for plant-height and color
Synthesis, Characterization and Reactivity of Novel Dipyridine and Pyridinyl Benzoquinoline Complexes of Zinc and Nickel
No full textThis datapackage contains (part of) the spectroscopic (NMR, UV-vis absorption) and electrochemical (CV, CPE) data for this publication
Cerebellar asymmetry of motivational direction: anger‑dependent effects of cerebellar transcranial direct current stimulation on aggression in healthy volunteers
No full textData (individual task, questionnaires and heart rate), preprocessing and analysis scripts, and paper for the study 'Cerebellar asymmetry of motivational direction: anger‑dependent effects of cerebellar transcranial direct current stimulation on aggression in healthy volunteers'
EXCITE_C1_2022_31_SOUP
No full textS.O.U.P. EXCITE Project: Unconventional energy Sources production, storage and release linked to subduction serpentinization: evidence from methane and hydrogen-rich fluid inclusions from the exhumed serpentinized peridotite of Monte Maggiore, Corsic
HYDE data for the Global Carbon Budget (2024)
No full textThis HYDE version 3.4 replaces former HYDE 3.3 version.
This database presents an update and expansion of the History Database of the Global Environment (HYDE, v 3.4).
HYDE is and internally consistent combination of updated historical population estimates and land use. Categories include cropland,
with a new distinction into irrigated and rain fed crops (other than rice) and irrigated and rain fed rice.
Also grazing lands are provided, divided into more intensively used pasture, converted rangeland and non-converted natural (less intensively used) rangeland.
Population is represented by maps of total, urban, rural population and population density as well as built-up area.
The period covered is 10,000 BCE to 2024 CE. Spatial resolution is 5 arc minutes (approx. 85 km2 at the equator), the files are in Arcmap asciigrid format.
Major updates include:
• Radiocarbon data from the IMSET project (Marc Vander Linden, pers.comm.), new estimates for EurAsia of the onset of agriculture (timing and location, gridded maps)
• Implementation of new archaeological expertise from the ArchaeoGlobe Project (Stephens et al, 2019), onset of agriculture (timing and location per region, outside EurAsia)
• Use of most recent and higher resolution satellite information on land cover from the European Space Agency (ESA) consortium for the spatial land use allocation on a yearly basis from 1992 – 2018.
• Use of different remote sensing imagery (MODIS) and statistics (MapBiomas version C8) for Brazil for the 1985-2022 period, and for Indonesia (MB 2.0) for the 2000-2022 period, China for the 1990-2019 period.
• Extension of the database to year 2023
• More input on sub-national level for cropland and grazing land
• netCDF added as output forma
GLOBGM_CMIP6: A Global Hyper-Resolution Groundwater Dataset for Assessing Historical and Future Groundwater Dynamics Under Climate and Socioeconomic Change - [ssp_rcp_average]
No full textThis data package contains outputs from the global groundwater flow model GLOBGM, which was used to estimate global water table depth and groundwater heads at 30 arc-seconds (~1 km) resolution. The model was forced with outputs from the PCR-GLOBWB model, obtained through the HYPFLOWSCI6 project.
We provide long-term average, annual, and monthly estimates of water table depth and groundwater heads at the global scale for a historical reference simulation following the ISIMIP3a protocol, which is designed for model evaluation and impact attribution.
Additionally, we provide outputs following the ISIMIP3b protocol, which focuses on impact attribution and climate change impact assessment. These outputs cover the historical baseline period (1960–2014) and future projections (2015–2100) under three SSP-RCP scenarios (SSP1-2.6, SSP3-7.0, and SSP5-8.5), using five GCM models: GFDL-ESM4, IPSL-CM6A-LR, MPI-ESM1-2-HR, MRI-ESM2-0, and UKESM1-0-LL.
The date here pertains to the long-term average data for the ensemble and GCMSs For a comprehensive overview of the entire dataset and where to access the data please see: https://vanjaarsveldbarry.github.io/globgm_cmip6
PCR-GLOBWB output - 4dHydro working package 5
No full text4dHydro working package 5 is dedicated to provided a set of land-surface and hydrological model community outputs for several calibration/assimilation experiments. These experiments include simulations over different resolutions and calibration/assimilation with earth-observed (EO) satellite products. The aim of these experiments is to investigate the added value of EO products for hydrological simulations. This data package contains the outputs for the PCR-GLOBWB hydrological model (globalhydrology.nl/research/models/pcr-globwb-2-0), which was developed at Utrecht University. See https://opensciencedata.4dhydro.eu/ for links to outputs from other models. Outputs are formatted according to the 4dHydro working package 5 storage protocol. For more information, please contact Bram Droppers ([email protected]) or Niko Wanders ([email protected])
Data supplement to: Allowing natural sedimentation in the Nieuwe Waterweg to reduce salinity intrusion and sea-level rise effects
No full textThree experiments in the Metronome tidal facility were conducted as an idealized representation of the Nieuwe Waterweg (Port of Rotterdam, the Netherlands) without ongoing dredging. The objective was to test the hypotheses that the channel silts up particularly on the landward side, and particularly does so by mud deposition in the harbors and in the upstream reach. Three experiments were conducted: one with sand and a straight channel with fixed banks and without harbors, one with harbors, and one where crushed nutshell was added as mud simulant. The data contains overhead timelapse photography and laser scanning of the dry bed.
Detailed information about the files and information on how the data was processed is given in the explanatory file: Data_description_Nieuwe-Waterweg-experiments_yoda.txt. Contact person is Maarten Kleinhans ([email protected])
Data supplement of Transformative potential of digital systems for promoting human-wildlife coexistence: A systematic literature review
No full textThis is the data set that was produced during the systematic literature review titled "Transformative potential of digital systems for promoting human-wildlife coexistence: A systematic literature review". The data set contains all articles that were included by means of using ASReview during the screening process, and therefore, every article has an ASReview ranking. A group of 11 reviewers then processed those articles and excluded articles based on the exclusion criteria as specified in the paper [EX1, EX2, EX3, EX4]. For the reviewed articles we collected 17 study characteristics (of which 14 were used in the paper), as well as a Digital Maturity score based on 3 digitalization characteristics [Visualizations, Statistical Modelling, Machine Learning] (Raghupathi and Raghupathi, 2021) and [Data Sharing/Storing] (Wilkinson, et al., 2016) and a Systemic Depth score based on 4 system characteristics [Parameters, Feedbacks, Design, Intent] (Abson et al., 2017) and one flag [Explains LP interactions] to mark whether the study explain the interactions between them. Both the Digital Maturity and Systemic Depth scores are then calculated using the equations explained in the paper, and the Transformative Potential is the geometric mean of the two scores.
The data is provided in 1 csv-file. Detailed information about this file is given in the explanatory file README.md. Contact person is Bas Michielsen - [email protected]
Effects of gravity and atmospheric pressure on CO2 sublimation-driven mass flows
No full textThe data presented here originate from CO2-sublimation-driven mass flow experiments, as described in Diamant et al. (2025), and are a supplement. The experiments were conducted in the George -- The Large Dirty Mars Chamber of the Space and Planetary Environments Laboratory at the Open University (Milton Keynes, UK). The data includes (1) raw sensor data from several sensors located in and on top of the flume, (2) digital elevation models of the deposits, and (3) high-speed camera footage of the granular flows (side view). The data is provided in three subfolders. Detailed information about the files in these subfolders, as well as information on how the data is processed, is given in the explanatory file ReadMe_Yoda_Effects_of_gravity_in_sublimationdriven_flows.txt. Contact person is Sharon Diamant - [email protected]