cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.24416/uu01-mu2d6u
title: Data Package: Improving the prediction of glassy dynamics by pinpointing the local cage

description: Data package accompanying the publication "Improving the prediction of glassy dynamics by pinpointing the local cage" in the Journal of Chemical Physics. This package provides all the relevant information for the analysis on the cage state associated with three different glass formers  (binary hard spheres, binary harmonic mixture, and binary Kob-Andersen mixture). In the paper we explore whether a simple linear regression algorithm combined with intelligently chosen structural order parameters can reach the accuracy of the current, most advanced machine learning approaches for predicting dynamic propensity. To do this we introduce a method to pinpoint the cage state of the initial configuration – i.e. the configuration consisting of the average particle positions when particle rearrangement is forbidden. We find that, in comparison to both the initial state and the inherent state, the structure of the cage state is highly predictive of the long-time dynamics of the system. Moreover, by combining the cage state information with the initial state, we are able to predict dynamic propensities with unprecedentedly high accuracy over a broad regime of time scales, including the caging regime.
In each directory there are READ_ME files that describe the content. The main directory contains four directories: the directory [FIGURES], which contains the published graphs, the directory [CODES], which contains the codes the obtain the inherent state, the cage state and the structural parameters as described in the paper, the directory [DATA] which contains all the necessary data to do the analysis described in the paper for the three different glassy systems and the directory [OUTPUT], which contains the linear regression files to train the linear regression models, and the associated learned correlations between the measured and predicted propensities for the three different glassy systems.
DOI: 10.24416/uu01-i2tnlh
title: UAV data used for rockfall detection and glacier extent of the Rothorn cirque, Swiss Alps

description: The data set contains point cloud and digital elevation model data derived from UAV flights in 2019 and 2023 in the Rothorn cirque, Turtmann Valley, Swiss Alps. From these data sets rockfall events and glacier extent of the Rothorn glacier was detected.
DOI: 10.24416/uu01-eofr06
title: Molecular simulation data package on the dielectric permittivity of nanoconfined geofluids with various salt concentrations

description: To determine the effect of salinity on the dielectric permittivity of nanoconfined geofluids, we employed molecular dynamics (MD) simulations of saline water confined in calcite slit nanochannels. This data package includes data points, figures, and MD input files to simulate the behaviour of saline water with various NaCl concentrations confined in calcite nanopores at ambient conditions. The dielectric behaviour of nanoconfined saline water deviates significantly compared to the bulk. However, the dielectric properties are weakly dependent on salinity for both the perpendicular and parallel dielectric permittivity components. The data is organized into nine folders referred to as Figure X, where X corresponds to the figure number in the primary publication and a Simulations folder containing the MD input files. All MD simulations were conducted using the LAMMPS package. Detailed information about the files and methods employed can be found in the accompanying readme file.
DOI: 10.24416/uu01-8f4xk2
title: Crystal Nucleation of Highly-Screened Charged Colloids

description: Data package accompanying the publication with the above title in the Journal of Chemical Physics [10.1063/5.0117867]. This package provides all the relevant information for the numerical study of the crystal nucleation of highly-screened charged colloids. We strived to answer the question: when can nearly-hard colloids be seen as hard spheres? To this end, we compared the nucleation barriers and rates of nearly-hard colloids to that of hard spheres by mapping via an effective hard-sphere diameter, which is a common practice in experimental studies. In brief, this package contains the data required to reproduce the graphs, as well as the simulation source code and analysis scripts required to process the raw output. In each directory there are README.txt files that describe the content. The main directory contains three directories: the directory [Figures], which contains the published graphs, and the directories [HS] and [HCYukawa], which contain everything on the systems of, respectively, hard spheres and hard-core Yukawa particles. In these last two directories you will find the directories [Data], [Mathematica], and/or [Code]. The directory [Data] contains all the processed data (.dat format) for that system. Each subdirectory in [Data] contains its own C codes (and bash scripts) used for generating the raw simulation data. The directory [Mathematica] contains all the Mathematica notebooks used for processing the raw data and visualizing the results. Lastly, the directory [Code], when present, contains additional C codes used for analyzing the raw data.
DOI: 10.24416/uu01-3jzdap
title: Data for "DNA fluctuations reveal the size and dynamics of topological domains"

description: These are the data for the manuscript
"DNA fluctuations reveal the size and dynamics of topological domains" 
Willem Vanderlinden, Enrico Skoruppa, Pauline Kolbeck, Enrico Carlon, and Jan Lipfert
PNAS Nexus (2022)

Please cite this reference when using or referring to these data. 

The data sets contain experimental data and data from Monte Carlo simulations 
- The data are organized by which figure in the main text they are presented in.

- The experimental data were generated by single-molecule magnetic tweezers measurements of DNA under defined forces and torques. The consist both of raw extension vs. time traces (both for bare DNA and in the presence of enzymes) and of analyzed data based on these extension time traces.

For Figure 1 and 4 we provide magnetic tweezers traces as text files with 6 columns, in the following format:
Column 1: Time in ms
Column 2: X position in µm
Column 3: Y position in µm
Column 4: Z position in µm
Column 5: Magnet Height (above the flow cell) in mm
Column 6: Magnet Rotation in turns

- The simulation data were generated by Monte Carlo simulations of DNA treated as an elastic rod.
DOI: 10.24416/uu01-prmutt
title: Mechanical and microstructural data used in: “The effect of strain rate on inelastic strain development in porous sandstones deformed under reservoir conditions”

description: Subsurface human activities, such as fluid extraction from oil or gas sandstone reservoirs, frequently leads to surface subsidence and even induced seismicity, as observed in the Groningen Gas Field, the Netherlands. Subsidence is caused by elastic and inelastic reservoir compaction at depth resulting from the increase in effective stress due to pore pressure reduction. The inelastic compaction is partly caused by rate- or time-dependent processes, meaning that compaction may continue even if production is stopped. To reliably evaluate the impact of post-abandonment behavior, mechanism-based rate-/time-dependent compaction laws are needed. 
We performed constant strain rate (rates of 10-3-10-8  s-1) and strain rate stepping (rates varying between 10-4 and 10-9  s-1) experiments under conventional triaxial conditions, on highly porous, clay-bearing Bleurswiller (as an analogue of the Groningen reservoir sandstone) and almost clay-free Bentheimer sandstones. Our results showed a systematic rate effect at differential stresses exceeding 40-50% of the peak differential stress in Bleurswiller sandstone, while this rate effect was only observed at differential stresses exceeding 70% of the peak differential stress in Bentheimer sandstone. Additional experiments investigating the effect of confining pressure, temperature and pore fluid pH, and microstructural analyses on undeformed and deformed materials, suggest that the observed rate effects are likely controlled by rate-dependent intergranular frictional sliding at lower differential stress, with an increased role of stress corrosion cracking at higher differential stress.
The data provided in this dataset include mechanical and microstructural data obtained on our Bleurswiller and Bentheimer sandstone samples. The mechanical data were obtained from 24 conventional triaxial compression experiments at constant strain rate. The microstructural data include backscatter electron (BSE) images obtained for one undeformed sample and two deformed samples, and electron dispersive X-ray spectrometry (EDX) element maps on an undeformed sample.
DOI: 10.24416/uu01-ydnobo
title: Model for topology dependent DNA binding

description: This package contains code that implements a model for topology-dependent binding to DNA.
DOI: 10.5285/472713db-3724-442f-8a24-a1f8834123d9
title: Arrival weights of macaroni penguins at Bird Island, from 1988 to 2025 - VERSION 2.0

description: Macaroni penguins spend the winter at sea and return to colonies on land during the austral spring to reproduce. Arrival weights of male and female Macaroni penguins on Bird Island, South Georgia have been monitored since 1988. The current protocol is that 50 males are weighed on 28th October and 50 females on 8th November.

This dataset is an updated version of Trathan, P., Waluda, C., & Ratcliffe, N. (2021). Arrival weights of Macaroni penguins at Bird Island, from 1988 to 2020 (Version 1.0) [Data set]. NERC EDS UK Polar Data Centre. https://doi.org/10.5285/a5174472-204d-45d4-862c-3befc32b52ca. The update consists of five additional years of data. No changes have been made to the data included in version 1.0 of the dataset.

This work was funded by Natural Environment Research Council (UK) core funding to the British Antarctic Survey.
description: Penguins at the colony at Goldcrest Point (Big Mac) are caught at the main entry point, sexed and weighed. Sex is ascertained by measuring their bill depth at the mandibular symphysis, with males having bill depth &gt; 24mm and females &lt; 24mm. 50 males are weighed on 28th October and 50 females on 8th November. All birds are weighed using a 10kg Pesola and bag. Care is taken to ensure no individual is weighed more than once. All data were collected under permit from the Government of South Georgia and the South Sandwich Islands. All sampling procedures used are regulated by the British Antarctic Survey Ethical Review Committee in collaboration with Cambridge University and the UK Home Office.

This dataset has been updated to add five additional years of counts. The metadata has been updated accordingly.
DOI: 10.24416/uu01-575ewu
title: Contact model and numerical modelling results: “Compaction of the Groningen Gas Reservoir Sandstone: Discrete Element Modelling Using Microphysically Based Grain-Scale Interaction Laws”

description: Reservoir compaction, surface subsidence and induced seismicity are often associated with prolonged hydrocarbon production. Recent experiments conducted on the Groningen gas field’s Slochteren sandstone reservoir rock, at in-situ conditions, have shown that compaction involves both poro-elastic strain and time-independent, permanent strain caused by consolidation and shear of clay films coating the sandstone grains, with grain failure occurring at higher stresses. To model compaction of the reservoir in space and time, numerical approaches, such as the Discrete Element Method (DEM) , populated with realistic grain-scale mechanisms are needed. We developed a new particle-interaction law (contact model) for the classic DEM to explicitly account for the experimentally observed mechanisms of non-linear elasticity, intergranular clay film deformation, and grain breakage. It was calibrated against both hydrostatic and conventional triaxial compression experiments and validated against an independent set of pore pressure depletion experiments conducted under uniaxial strain conditions, using a range of sample porosities, grain size distributions and clay contents. The model obtained was used to predict compaction of the Groningen reservoir. These results were compared with field measurements of in-situ compaction and matched favorably, within field measurement uncertainties. The new model allows systematic investigation of the effects of mineralogy, microstructure, boundary conditions and loading path on compaction behavior of the reservoir. It also offers a means of generating a data bank suitable for developing generalized constitutive models and for predicting reservoir response to different scenarios of gas extraction, or of fluid injection for stabilization or storage purposes.

The data provided in this dataset include the contact model (source codes and the contact model library) developed for the Particle Flow Code (PFC) software, Fish code package for running PFC models, numerical modeling results (tabulated) obtained in the calibration procedure and uniaxial compaction prediction.
DOI: 10.24416/uu01-u63z8w
title: Code for the simulations of rupture steps in  "megaprimer" DNA constructs in magnetic tweezers

description: Code to predict first label positions in DNA constructs obtained by "mega primer" PCR assembly, convert the label positions to step size distributions, and to fit experimental step size data using simulated step size distributions.

The code is first described by 
Yi-Yun Lin, Tine Brouns, Pauline J. Kolbeck, Willem Vanderlinden, and Jan Lipfert
"High-yield, ligation-free assembly of DNA constructs with nucleosome 
positioning sequence repeats for single molecule manipulation assays"
Submitted
Preprint available at 
https://www.biorxiv.org/content/10.1101/2023.01.05.522917v1


There are two Matlab scripts:
- Lin_etal_predict_steps.m is used to generate the step size distribution. It can be run stand alone. Simulation parameters are specified in the script.
It outputs a plot of the simulated step size distribution and also writes the simulated steps to a text file.

- Lin_etal_fit_step_distribution.m reads in simulated steps for different values of the label probability from files in the sub-directory "simulated_distributions".
An example set of simulated step sizes is included in the package. More steps (e.g. for different label probabilities, different sequences, etc.) can readily be computed using the first script Lin_etal_predict_steps.m.
The script Lin_etal_fit_step_distribution.m then reads in experimental data, an example of which is provided as Experimental_Steps_45pN.txt.
The script then compared the simulated distributions to the experimental data using both a chi-squared criterion and the mean step size.
The output are plots that are also exported to png and eps files. Example outputs are included in the package.
DOI: 10.24416/uu01-ckhvkz
title: Determination of Absolute Intramolecular Distances in Proteins by Anomalous X-ray Scattering Interferometry

description: Data set of anomalous small-angle X-ray scattering data to determine intramolecular distances in proteins. Data included are for two variants of the protein MalE, both in the absence and presence of its cognate ligand maltose.
DOI: 10.24416/uu01-elsybj
title: Mechanical and microstructural data used in: “Rate-dependent Inelastic Deformation of Slochteren Sandstone: Implication for Reservoir Compaction in the Groningen Gas Field”

description: Hydrocarbon production from sandstone reservoirs causes elastic and inelastic reservoir compaction, potentially leading to surface subsidence and even seismicity, such as observed in the Groningen Gas Field, Netherlands. Inelastic compaction can partly be instantaneous, though rate-/time-dependent processes may play a role on the longer term. Therefore, compaction may continue even if production is stopped. To reliably evaluate the impact of post-abandonment behaviour, mechanism-based rate-/time-dependent compaction laws are needed. We performed triaxial compression experiments on Slochteren sandstone (reservoir of the Groningen field) samples, with porosity ϕ=14.6-18.9%, to investigate the effect of strain rate (rates of 10-6-10-8  s-1) under conventional triaxial and uniaxial strain (i.e. zero-lateral strain) boundary conditions. Complemented by additional experiments investigating effect of temperature and pore fluid pH, and microstructural analyses on undeformed and deformed materials, suggest that subcritical cracking, coupled with grain rearrangement, was the dominant mechanism causing inelastic deformation under triaxial and uniaxial strain conditions.
The data provided in this dataset include mechanical and microstructural data on our Slochteren sandstone samples. The mechanical data were obtained from 11 conventional triaxial compression experiments at constant strain rate (abbreviated as “triaxial tests”), 9 uniaxial strain triaxial compression experiments at constant strain rate (abbreviated as “uniaxial strain tests”) and a single constant stress (creep) experiment (i.e. a “creep test”). The microstructural data include backscatter electron (BSE) images obtained for one undeformed sample and 6 deformed samples, and electron dispersive X-ray spectrometry (EDX) images on 5 undeformed samples.
DOI: 10.24416/uu01-firi72
title: Unlocking Heterobimetallic Architectures in a Symmetric PNNP ligand Environment

description: The data package consists of NMR data, IR-Spectroscopical data associated with the manuscript "Unlocking Heterobimetallic Architectures in a Symmetric PNNP ligand Environment". NMR files are .mnova files that can be opened using the MestreNova software.
DOI: 10.24416/uu01-a8blmr
title: Data from seismic slip-pulse experiments simulating induced earthquake rupture in the Groningen gas field

description: Rock materials show dramatic dynamic weakening in large-displacement (m), high-velocity (~1 m/s) friction experiments, providing a mechanism for the generation of large, natural earthquakes. However, whether such weakening occurs during induced M3-4 earthquakes (dm displacements) is unknown. We performed rotary-shear experiments on simulated fault gouges prepared from the source-, reservoir- and caprock formations present in the seismogenic Groningen gas field (Netherlands). Water-saturated gouges were subjected to a slip pulse reaching a peak circumferential velocity of 1.2-1.7 m/s and total displacements of 15-20 cm, at 2.5-20 MPa normal stress. The results show 22-81% dynamic weakening within 5-12 cm of slip, depending on normal stress and gouge composition. At 20 MPa normal stress, dynamic weakening from peak friction coefficients of 0.4-0.9 to 0.19-0.27 was observed, probably through thermal pressurization. We infer that similar effects play a key role during induced seismic slip on faults in the Groningen and other reservoir systems.
DOI: 10.24416/uu01-oyke34
title: The Role of Quantum Tunneling in Metal-Ligand Proton Tautomerism 

description: The data package consists of NMR data, IR-Spectroscopical data associated with the manuscript "The Role of Quantum Tunneling in Metal-Ligand Proton Tautomerism". NMR files are .mnova files that can be opened using the MestreNova software.
DOI: 10.15468/dl.r3s6pu
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Moenkhausia aurantia",
 "DecimalLatitude is not null",
 "DecimalLongitude is not null"
 ]
}

 The dataset includes 47 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005445-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.24416/uu01-pb440d
title: µCT data for "A new method for determining fluid flux at high pressures applied to the dehydration of serpentinites"

description: Dehydration of serpentine within a subduction zone setting causes the formation of pore space. The porosity and connectivity of the pores is important for fluid flux through these rocks. The pore space preserved within two recovered high-pressure and high-temperature multi-anvil samples was measured using µCT-scans at the BL20XU experimental hutch 2 of the SPring-8 synchrotron facility. The 3D images were obtained using X-rays with energy of 30 keV and by rotating the sample through 180° in steps of 0.1° (1800 projections) and an exposure time of 60 msec. The voxel size of the 3D images is 0.46 × 0.46 × 0.46 µm. 
This repository contains sliced µCT-scan images (tif-format) for the two experiments (ES367 and V1167). Scans for each experiment are stored in separate folders. Continuous numbers for images are from data acquisition. Scans start and end in the sample, i.e. the subset used for pore space analyses does not include first and last scans because of air above and below the sample. Contact person: Lisa Eberhard - l.eberhard@uu.nl
DOI: 10.24416/uu01-byoftg
title: Hydride as a Leaving Group in Nucleophilic Aromatic Substitution

description: This data set contains the data package belonging to the abovementioned research article.

- NMR data of complexes 1, 1-D, 2, 2-K, 3, 4, 4-D, 5, Int1, Int2 as well as of the mixture of hexadeuterocyclohexadienes.
- IR data of 1, 1-D, 4, 4-D.

#NMR files are .mnova files that can be opened using the MestreNova software.
DOI: 10.24416/uu01-qdqjgx
title: Experimental evidence for deformation-enhanced devolatilization of (carbonated) serpentinite fault gouges

description: We analysed the frictional behaviour of antigorite and carbonated antigorite fault gouges in rotary-shear experiments at Utrecht University. Experiments were conducted at temperatures ranging from 400 - 630 °C, effective normal stresses of 100 - 150 MPa under fluid saturated conditions. This data package includes frictional data from rotary-shear experiments and back-scattered electron (BSE) images of run products. Three samples were analysed by means of micro-computer tomography (µCT). Sliced scans can also be found in this data package.

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 (readME.txt) Contact person is Lisa Eberhard - l.eberhard@uu.nl
DOI: 10.15468/dl.pb5gqq
title: Occurrence Download

description: A dataset containing 2598 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plathymenia reticulata",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 }
 ]
}

 The dataset includes 2598 records from 140 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005446-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18501920
title: Dataset for publication "High-performance thermochromic multilayer coatings with W-doped VO2 nanoparticles dispersed in SiO2 matrix prepared on glass at a low temperature"

description: Dataset for publication "High-performance thermochromic multilayer coatings with W-doped VO2 nanoparticles dispersed in SiO2 matrix prepared on glass at a low temperature"
DOI: 10.5281/zenodo.18501921
title: Dataset for publication "High-performance thermochromic multilayer coatings with W-doped VO2 nanoparticles dispersed in SiO2 matrix prepared on glass at a low temperature"

description: Dataset for publication "High-performance thermochromic multilayer coatings with W-doped VO2 nanoparticles dispersed in SiO2 matrix prepared on glass at a low temperature"
DOI: 10.82209/4066-4z64
title: The legacy effect of Cover Crops on soil structure amelioration: Mean weight diameter (MWD) of soil aggregates has the highest impact on aggregate organic carbon (OC) distribution, followed by soil parameters and cover crop (CC) type.