cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25625/kubf1v/9j240a
title: Covariates_Alignment.R

description: :unav
DOI: 10.24416/uu01-nqxn82
title: Data supplement to: Local magnetic anomalies in rugged volcanic terrain explain bias in paleomagnetic data: consequences for sampling

description: The dataset contains measurements made with a fluxgate magnetometer of the ambient geomagnetic field on Mt. Etna, Italy. Measurements were made in April 2018. The purpose of this work was to test how the underlying terrain influences the magnetic field just above the surface of the lava flows.

The FLUX1-5.csv files contains all measurements made with the fluxgate magnetometers at five different sites (FLUX 1-5). Measurements were made at three different paths (Path 1, 2 and 3) at different heights above the surface. For FLUX1-4 this is 100 and 180cm , for FLUX5 it is 25, 75, 125, and 175cm. First columns contains the GPS location of every measurement. The distance between each measurement and the specific height is calculated from the GPS data. Inclination, declination and intensity results are in the last columns.

In this updated version of the dataset an error in FLUX4 has been fixed. Detailed information about the files as well as information on how the data is processed is given in the explanatory file readme.txt. Contact person: Romy Meyer - Researcher - r.meyer@uu.nl
DOI: 10.25625/kubf1v/iieteq
title: SKAT-O_Subtype.R

description: :unav
DOI: 10.25625/kubf1v/4deoj4
title: WGS_descriptiveData.R

description: :unav
DOI: 10.25625/kubf1v/5ovugd
title: input_GLMM.R

description: :unav
DOI: 10.25625/kubf1v/9tyupd
title: family-aware_GLMM.R

description: :unav
DOI: 10.25625/kubf1v/ni9lla
title: SKAT_pheno-preparation_both aims.R

description: :unav
DOI: 10.24416/uu01-aysrsy
title: Raw data for "Anti-cancer compound screening identifies Aurora Kinase A inhibition as a means to favor CRISPR/Cas9 gene correction over knock-out "

description: Raw data used in the analyses presented in the manuscript "Anti-cancer compound screening identifies Aurora Kinase A inhibition as a means to favor CRISPR/Cas9 gene correction over knock-out". Data is structured per figure.
DOI: 10.25625/kubf1v/5vltsu
title: snp_gene_map.txt

description: :unav
DOI: 10.25625/kubf1v/mwcnok
title: preparation_genotype.R

description: :unav
DOI: 10.25625/kubf1v/njhvzk
title: PLINK2_REGENIE_withComments.docx

description: :unav
DOI: 10.24416/uu01-2t4zaa
title: Active wetland restoration kickstarts vegetation establishment, but  natural development promotes greater plant diversity

description: This datafile is part of a study that shows that actively steering wetland restoration by introducing target species and preventing herbivory accelerates vegetation development when compared with natural development. Data was collected on Marker Wadden in the Netherlands from September 2018 to August 2023 (see methods below for more details). 

This file includes (see codebook below for details) data obtained from field measurements on Marker Wadden (Netherlands, datafile ‘Alderson et al. vegetation’ and ‘Alderson et al. organic matter’). The datafiles contain data related to vegetation and soil elevation over time and organic matter. Not all data presented in the data files were used in the manuscript, but are provided as additional information to interested researchers.
DOI: 10.25625/kubf1v/wwogdd
title: SKAT_working.R

description: :unav
DOI: 10.25625/kubf1v/y5r1tn
title: REGENIE.R

description: :unav
DOI: 10.25625/kubf1v/xl3t4l
title: GRAMS Manual.pdf

description: :unav
DOI: 10.25625/kubf1v/knyj6j
title: SKAT-O_Family.R

description: :unav
DOI: 10.25625/kubf1v/ozocjc
title: PRS_AddOns_Plots.R

description: :unav
DOI: 10.25625/kubf1v/1kpfcg
title: gene_pathway_map.txt

description: :unav
DOI: 10.25625/kubf1v/qsajoi
title: Affected vs Unaffected.txt

description: :unav
DOI: 10.25625/kubf1v/urchqb
title: plink preparation.R

description: :unav
DOI: 10.25625/kubf1v/vq7g6v
title: file_processing_postANNOVAR.R

description: :unav
DOI: 10.24416/uu01-i418h9
title: Data supplement to: Burrowing blocks of CO2 ice create sinuous gullies on Martian dunes by explosive sublimation-induced particle transport

description: In this data package, experimental data is stored from experiments in the Mars Chamber at The Open University, Milton Keynes, United Kingdom, and elevation data from Russell crater mega dune on Mars.

The experimental data contains Digital Elevation Models (DEM) of Difference (DoDs) of experiments conducted under Martian atmospheric conditions to simulate the formation of linear dune gullies on Mars by releasing blocks of CO2-ice on a sandy flume slope. Furthermore, the experimental data shows videos of 5 key experiments presented in the manuscript and high speed footage of the two CO2-block transport mechanisms.

The elevation data contains the original HiRISE DEM from the Russell crater mega dune region, and the refined DEM created by Doute, S., & Jiang, C. (2020) - doi:10.1109/TGRS.2019.2937172.

Contact person is Lonneke Roelofs - PhD Candidate - l.roelofs@uu.nl
DOI: 10.25625/kubf1v/dlkpwy
title: preparation.R

description: :unav
DOI: 10.24416/uu01-czdq2m
title: Final report data of the ZonmW project 463002001

description: The dataset refers to research data relative to the ZonMw project 463002001 that is part of the European network EJP-RD "URGENT". The dataset includes: 1) The final scientific report of the URGENT network project 2) The project monitoring of the URGENT network project 3) Hilde Spierenburg final report on the DTDS mutation modeling 4) Hilde Spierenburg final presentation on the DTDS mutation modeling 5) Data report on DTDS mutation modeling with prime editing 6) DTDS mutants (Ala314Val) sequencing data (2024-12-09)
DOI: 10.25625/kubf1v/uxvbha
title: PLINK_RRMS vs Prog.txt

description: :unav
DOI: 10.25625/kubf1v/xcf9sy
title: plots.R

description: :unav
DOI: 10.25625/kubf1v/fwtnjq
title: identify_shared_genes_allControlsAccounted.R

description: :unav
DOI: 10.25625/kubf1v/bdlvei
title: PRS_comparison.R

description: :unav
DOI: 10.25625/kubf1v
title: Dissertation_Supplementary Material

description: This dataset contains the supplementary material for the dissertation "The GRAMS Study: An Approach to Bridging Genomic Data and Deep Phenotyping to Understand Familial Multiple Sclerosis", including the study manual as well as all custom R scripts and PLINK command files used in the analyses.
DOI: 10.24416/uu01-tuwmwb
title: Data package from meandering river experiments with Eurotank facility

description: This datapackage supplements the papers mentioned below on experiments with self-formed braided rivers and meandering rivers, for which vegetation, silica powder or crushed nutshell were used to form floodplains. All experiments were conducted in the Eurotank facility: a flume of 11 by 6 m, so most experiments have river plains of about 10 m long and 3 m wide. This package accommodates files contain gridded digital surface elevation data (DSMs) made by photogrammetry and, for some experiments, overhead images.

The data is provided in 3 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 Data_description_meandering_experiments_yoda.txt. Contact person is Maarten Kleinhans - m.g.kleinhans@uu.nl - https://www.uu.nl/medewerkers/MGKleinhans
DOI: 10.24416/uu01-gjtrtm
title: Understanding Enhanced Rotational Dynamics of Active Probes in Rod Suspensions

description: Data package accompanying the publication with the above title in Soft Matter [10.1039/d2sm00583b]. This package provides all the relevant information for numerically studying Active Brownian particles (APs) exhibiting enhanced rotational diffusion (ERD) in a quasi-two-dimensional suspension of colloidal rods. Activity couples AP-rod contacts to reorientation, with the variance therein leading to ERD. This ERD is captured by a a variant of the coupling used in our previous phenomenological modeling [10.1103/PhysRevLett.125.258002; and associated data package 10.24416/UU01-NXITLI].

In brief, this package contains the data required to reproduce the graphs for the simulations, as well as the simulation source code and analysis scripts required to process the raw simulation output. In each directory there are readme.txt files that describe the content and use of the elements contained therein, e.g., how to run various script to obtain the raw simulation data. The [simulation] directory contains C++ code for the generation of 2D rods-only systems, a passive probe in a rod suspension, and an active probe in a (dense) rod suspension. Using this source code, passive glassy background systems comprising polydisperse 2D spherocylinders can be produced, for which the particles interact via the Weeks-Chandler-Anderson potential. The system containing an AP is modelled similarly; the probe is included as a single disk-shaped particle that, when active, experiences a torque through its interaction with the spherocylinders. This enables the AP to experience ERD, which spikes when the variance of the number of contacts between the probe and the rods in its direct surrounding has a maximum, as described in the associated scientific publication. The directory [analysis] contains C++ codes for the analysis of the data generated using the simulation, such as the self-intermediate scattering functions, mean square displacements, raft and contact analysis, etc., that can be obtained from the raw particle coordinates. Lastly, the directory [data] provides the processed data (.dat files) and scripts (python and bash) to generate the figures in the main text and supplement.
DOI: 10.57903/uj/h4ouev
title: N-Terphenylpicolinamide derivatives designed to target PD-L1 increase activation and proliferation of T cells, and their cytotoxic properties toward cancer cells - research data

description: Raw experimental dataset for the publication "N-Terphenylpicolinamide derivatives designed to target PD-L1 increase activation and proliferation of T cells, and their cytotoxic properties toward cancer cells" (https://doi.org/10.1016/j.ejmech.2026.118652) consist of the inhibitors characerisation (1H,13C NMR, IR, UPLC/MS, HRMS), PD-1/PD-L1 ICB assay, TSA assay, LDPA assay, pharmacocinetics studies and NMR studies, molecular docking and crystallography
DOI: 10.24416/uu01-2xbvkk
title: Data supplement to \"Quantitative water depth determination in large experimental timeseries through combining spectrophotometry and machine learning"

description: This package contains the processed data from specially designed calibration setups in the Metronome (https://www.uu.nl/metronome ) that were used to train and validate the Random Forest models, as well as the Random Forest models themselves and all codes that were developed for calibration, method developing and processing purposes. The provided data contain gridded digital elevation data (DEMs) made by a laser scanner and orthomosaics of overhead camera series. Additionally, the water depth maps of experimental datasets predicted by the Random Forest models are provided (including visualization with timelapse videos of the complete experiments). Detailed information about the files and information on how the data was processed is given in the explanatory file: readme.txt. Contact person is Eise Nota (e.w.nota@uu.nl) or Maarten Kleinhans (m.g.kleinhans@uu.nl).
DOI: 10.24416/uu01-o9k23k
title: Goblet-Cell Interactions Reorient Bundled Mucus Strands for Efficient Airway Clearance

description: Data package accompanying the publication with the above title in PNAS Nexus, which considers the clearance of the respiratory tract of larger animals. This is cleared by sweeping bundled mucus strands along the airway surface. They are produced in submucosal glands and, upon emerging from these glands, the long axis of the bundled strands is oriented along the cilia-mediated flow towards the oral cavity. However, after release, the bundled strands are found to have turned orthogonal to the flow, which maximizes their clearance potential. With a minimal numerical model we showed that adhesive interactions between the bundled mucus strands and mucus threads tethered to goblet cells can reorient the bundled-strand. 

The data package contains the source codes for the numerical study of model bundled mucus strands interacting with model goblet cells (C++), including initialization of the goblet cells. In addition, it contains the data underlying each figure in both the main text and supplemental information, distributed in folders with appropriate labelling. All parts are provided with readme files (.txt) in ASCII format.
DOI: 10.5281/zenodo.18586537
title: Amplified El Niño-Induced Global SST Variability in a Warming World

description: Main results for a paper "Amplified El Niño-Induced Global SST Variability in a Warming World"
DOI: 10.5281/zenodo.14875791
title: Amplified El Niño-Induced Global SST Variability in a Warming World

description: Main results for a paper "Amplified El Niño-Induced Global SST Variability in a Warming World"
DOI: 10.24416/uu01-vyutwt
title: Additional scripts from paper “Realization of a one-dimensional topological insulator in ultrathin germanene nanoribbons”

description: Python code to generate the figures in the Main text and SM of the paper “Realization of a one-dimensional topological insulator in ultrathin germanene nanoribbons”
DOI: 10.24416/uu01-sgm22n
title: Data supplement to "Remote sensing of a gantry-equipped facility: optimizing accuracy by integrating SfM photogrammetry and laserscan computer graphics through fixed base model geometry"

description: This package contains a base model, computed in Agisoft Metashape, raw and processed data from specially designed calibration setups in the Metronome (https://www.uu.nl/metronome ), as well as all codes that were developed for calibration, method developing and processing purposes. 

The provided data contain raw files and produced gridded digital elevation data (DEMs) made by a laser scanner and orthomosaics of fixed overhead camera series and DSLR surveys. Additionally, the orthomosaics of overhead series are provided with timelapse videos of the complete experiments. Because the study compares several methods of DEM construction, the DEMs of each of these methods are presented separately. The resolution of DEMs and orthomosaics are defaulted to 5 mm, but it is possibly to compute them on any grid size between 1 mm and 1000 mm. 

Detailed information about the files and information on how the data was processed is given in the explanatory file: readme.txt. Contact person is Eise Nota (e.w.nota@uu.nl) or Maarten Kleinhans (m.g.kleinhans@uu.nl).
DOI: 10.15468/dl.uadbn8
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is South Africa",
 "TaxonKey is Erythrocebus patas"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005421-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5knds9
title: Occurrence Download

description: A dataset containing 772 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Edrastima uniflora",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 }
 ]
}

 The dataset includes 772 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005424-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vh55jx
title: Occurrence Download

description: A dataset containing 59 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is France",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Quercus faginea"
 ]
}

 The dataset includes 59 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005423-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fjpjs8
title: Occurrence Download

description: A dataset containing 218 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lithophyllum pallescens"
 ]
}

 The dataset includes 218 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005425-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.24416/uu01-ibvnt1
title: The Cellular Potts Model on Disordered Lattices

description: This is the data package for the publication with the above title. The data to reproduce the figures in the manuscript and the Supplementary information is provided in the folder "Data". In the folder "Simulation", we provide all the C++ codes used for the simulation, and the C++ and Python codes used for data analysis and post processing of the raw data generated by the simulation codes. There are readme.txt files in each folder, that describe what the files are, and how to run different codes. Using the simulation codes, the behavior of the cellular Potts model was studied on three different lattices, i.e., square, hexagonal, and disordered lattices. The disordered lattice was itself generated by performing a large-scale simulation on the square lattice with the simulation parameters in fluid-like regime, and applying Voronoi tessellation to the center of mass of the cells. Then the lack of long-range orientational order was assessed by applying fast Fourier transform to these points, using the package ImageJ. On three different lattices, a surface tension induced phase transition was observed based on the behavior of hexatic order of the cells. Also, the shape of the cells was studied across the transition by applying Voronoi tessellation to the center of mass of cells. All the Voronoi tessellations were done using the package Voro++. There is also a folder which specifically contains the overall comparison between the different studied lattices as well as the related data.
DOI: 10.24416/uu01-t9w1m2
title: Data supplement to: Allowing natural sedimentation in the Nieuwe Waterweg to reduce salinity intrusion and sea-level rise effects

description: Three 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 (m.g.kleinhans@uu.nl).
DOI: 10.24416/uu01-czm7sv
title: Data supplement to "Effects of sea-level rise on dredging and dredged estuary morphology"

description: Data was generated for four experimental, sandy estuaries in the 20m long Metronome tidal flume (https://www.uu.nl/metronome). The initial conditions were the same but the second experiment had induced dredging, the third induced sea-level rise and fourth both induced dredging and sea-level rise. The paper contains all information on procedures, settings and data analyses. The data in this supplement is a timeseries of bathymetry and model input and output to calculate the flow fields. The data is provided in 2 subfolders. Detailed information about the files and information on how the data was processed is given in the explanatory file: readme.txt. Contact person is Jana Cox (j.r.cox@uu.nl) or Maarten Kleinhans (m.g.kleinhans@uu.nl).
DOI: 10.24416/uu01-f3slmj
title: Delayed Gravitational Collapse of Attractive Colloidal Gels

description: Data package accompanying the publication with the above title in Journal of Fluid Mechanics. This package provides all the relevant information, scripts, and source codes for numerically studying the gravitational collapse of colloidal gels, using mean field theory. The accompanying publication provides the full details. In brief, this package contains the data required to reproduce the graphs in the paper, as well as the numerical solver source code and analysis scripts required to process the raw simulation output. In the main directory there is a Readme.txt file that describes the content and use of the elements contained therein, e.g., how to run various script to obtain the raw data. These are Python codes, and binary files containing data in a 'numpy array' format.
DOI: 10.24416/uu01-r3zuc9
title: Data supplement to "Estuarine morphodynamics and development modified by floodplain formation"

description: Data was generated for three experimental, sandy estuaries in the 20 m long Metronome tidal flume https://www.uu.nl/metronome. The conditions were the same, except that one experiment had a mud simulant and one had live vegetation. The third experiment was for control with sand only. The paper contains all information on procedures, settings and data analyses. The data in this supplement is a timeseries of bathymetry, an overhead movie of all three experiments for visual inspection of the development, and model input and output to calculate the flow fields.

The data is provided in 4 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 readmeYODA.txt. Contact person is Maarten Kleinhans m.g.kleinhans@uu.nl https://www.uu.nl/medewerkers/MGKleinhans
DOI: 10.24416/uu01-5sdjai
title: Structuring Colloidal Gels via Micro-Bubble Oscillations

description: Data package accompanying the publication with the above title in Soft Matter [10.1039/D3SM00784G]. This package provides all the relevant information, scripts, and source codes for numerically studying the influence of hydrodynamic interactions in the formation and aging of colloidal gels, using Brownian Dynamics, Rotne-Prager-Yamakawa and Stokesian Dynamics. The accompanying publication provides the full details. 

In brief, this package contains the data required to reproduce the graphs for the simulations, as well as the simulation source code and analysis scripts required to process the raw simulation output. In the main directory there is a Readme.txt file that describes the content and use of the elements contained therein, e.g., how to run various script to obtain the raw simulation data. This is a mix of C codes, Python analysis and plotting routines, and text files containing data in a column-wise (ASCII) format.
DOI: 10.24416/uu01-qo36gq
title: Python-JAX-based fast Stokesian dynamics

description: Data package accompanying the publication with the above title in SciPost. This package provides all the relevant information, scripts, and source codes for bench-marking the presented software (jfsd). The accompanying publication provides the full details. In brief, this package contains the data required to reproduce the graphs in the paper, as well as the numerical solver source code and analysis scripts required to process the raw simulation output. In the main directory there is a Readme.txt file that describes the content and use of the elements contained therein, e.g., how to run various script to obtain the raw data. These are Python codes, and binary files containing data in a 'numpy array' format.