Find research datasets worth reusing

opencc-by-4.0Mar 2022View details →

Amyloid-beta 16-22 peptide dimer simulation (without salt) with the CHARMM-Drude force field and OpenMM (Run 3)

MD simulations of the Amyloid-beta 16-22 dimer at 0 mM NaCl concentration with CHARMM-Drude force field and OpenMM. Initial structure is obtained from CHARMM-GUI. In the initial configuration, two amyloid-beta 16-22 monomers are not interacting. This repository contains the third out of three independent runs. All the simulation parameters and force field files are uploaded into this repository. Simulations are done with OpenMM v. 7.5.1.

opencc-by-4.0Mar 2022View details →

Amyloid-beta 16-22 peptide dimer simulation (without salt) with the CHARMM-Drude force field and OpenMM (Run 1)

MD simulations of the Amyloid-beta 16-22 dimer at 0 mM NaCl concentration with CHARMM-Drude force field and OpenMM. Initial structure is obtained from CHARMM-GUI. In the initial configuration, two amyloid-beta 16-22 monomers are not interacting. This repository contains the first out of three independent runs. All the simulation parameters and force field files are uploaded into this repository. Simulations are done with OpenMM v. 7.5.1.

Muonic Force Carriers

The datasets contain Muonic Force Carriers (MFC) events generated with Monte Carlo simulations. They describe the scattering of an incoming muon and a target nucleus of the detector material of the ATLAS detector, which produces an outgoing muon, the outgoing target and a MFC. The datasets are given in function of the energy of the incoming muon, ranging from 50 to 200 GeV, in step of 25 GeV. The shape of each dataset is of (100'000,5,3), where 100'000 is the number of events, 5 corresponds to the different particle (incoming muon, target at rest, outgoing muon, outgoing target, MFC), and 3 to the different features (energy, transversal momentum, pseudorapidity).

Ocean-forced instability of the West Antarctic Ice Sheet since the mid-Pleistocene

This data file contains the IRD abundance, clay mineralogy, water content in Excel file 'Wang et al.xlsx (sheet: sedimentology)', and Sr-Nd isotopes in Excel file 'Wang et al.xlsx (sheet: Sr-Nd isotope)' in gravity core ANT34/A2-10 (LATITUDE: -67.036111 and LONGITUDE: -125.591944) from the Amundsen abyssal plain since 770 ka. Supplement to Jiakai Wang et al., Ocean-forced instability of the West Antarctic Ice Sheet since the mid-Pleistocene. Geochemistry Geophysics Geosystems (in review).

2D honeycomb transformation into dodecagonal quasicrystals driven by electrostatic forces

This repository contains the SXRD data measured for the 48-18-6 approximant in Sr-Ti-O on Pt(111). The data has been acquired at the SixS beamline of the Synchrotron SOLEIL in France on 19.09.2019. Monochromatic x-rays with photon energy of 11 keV were used to avoid Pt fluorescence (at 11.1 and 13 keV) and consequently reduced the background signal. The diffraction experiment was performed under grazing incidence at an angle of 0.2 °. The orientation matrix was defined relative to the Pt substrate lattice with its lattice constants of a = 392 pm. Additionally, the 3D voxel map generated from the raw data for further use in the binoculars software is provided as well as the input and output of SHELXL, which has been used for structure relaxation.

opencc-by-4.0Jul 2022View details →

THREE-DIMENSIONAL VOLUMETRIC EVALUATION OF ROOT RESORPTION IN MAXILLARY ANTERIORS FOLLOWING EN-MASSE RETRACTION WITH VARYING FORCE VECTORS - A RANDOMIZED CONTROL TRIAL

To assess the severity of root resorption (RR) during retraction of maxillary anteriors with and without skeletal anchorage (three different force systems); and analyze it comprehensively using cone-beam computed tomography (CBCT) superimpositions.

opencc-by-4.0Feb 2023View details →

Terminus Traces for publication 'Ocean-forcing and glacier-specific factors drive differing glacier response across the 69 oN boundary, east Greenland' (Version 1)

Dataset supporting publication 'Brough, S., Carr, J.R., Ross, N., Lea, J.M. (2023) Ocean-forcing and glacier-specific factors drive differing glacier response across the 69 oN boundary, east Greenland. J. Geophys. Res. Earth Surf. <a href="https://doi.org/10.1029/2022JF006857">https://doi.org/10.1029/2022JF006857</a>.' This dataset provides GIS ready shapefiles of mapped terminus traces for 24 east Greenland glaciers between 2013 and 2020 for the aforementioned publication. Data are provided in both geographic (EPSG: 4326; WGS84) and projected (EPSG:3413; NSIDC Sea Ice Polar Stereographic North) coordinate systems. As each terminus trace has metadata appended, including the unique path identifier, it is possible to directly and easily identify the original image used in the mapping process. Both shapefiles are compatible for ingestion into the Google Earth Digitisation Tool (GEEDiT) Reviewer (<a href="https://liverpoolgee.wordpress.com/">https://liverpoolgee.wordpress.com/</a>) for reviewing and sub-setting the dataset (see Lea, J.M. [2018] Earth Surf. Dynam. 6, 551–561. <a href="https://doi.org/10.5194/esurf-6-551-2018">https://doi.org/10.5194/esurf-6-551-2018</a>).   When using this data product in a publication, please include the following citations: Brough, S., Carr, J.R., Ross, N., Lea, J.M. (2023). Terminus Traces for publication 'Ocean-forcing and glacier-specific factors drive differing glacier response across the 69 oN boundary, east Greenland' (Version 1) [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.6904219">https://doi.org/10.5281/zenodo.6904219</a>. Brough, S., Carr, J.R., Ross, N., Lea, J.M. (2023) Ocean-forcing and glacier-specific factors drive differing glacier response across the 69 oN boundary, east Greenland.  J. Geophys. Res. Earth Surf. <a href="https://doi.org/10.1029/2022JF006857">https://doi.org/10.1029/2022JF006857</a>.

opencc-by-4.0Jul 2022View details →

Additional movies for a manuscript titled 'Leaf epidermal cells respond to application and removal of mechanical force by distinct cytosolic calcium waves'

This repository provides 21 additional videos that highlight the spectrum of mechanically stimulated calcium responses observed in the leaf epidermis of Arabidopsis t. expressing the genetically encoded calcium indicator R-GECO1. These movies correspond to figures in a manuscript entitled 'Leaf epidermal cells respond to application and removal of mechanical force by distinct cytosolic calcium waves'. In each movie, a cantilever exerts approximately 5 mN force to the epidermis (where the cantilever looks like a shadow in the movies). Each movie contains a scale bar and the relative time (hr:min:sec). Placement of the cantilever generally occurs after approximately 1 minute.

GNSS and Digisonde sporadic-E maps produced by Air Force Institute of Technology

Spatial maps of sporadic-E are produced by combining COSMIC-2 RO data with Digisonde measurements, using the S4-based approach described by Carmona et al. (2022). Images from the TEC-based approach used in other studies are also included for reference.    Carmona, R. A., Nava, O. A., Dao, E. V., & Emmons, D. J. (2022). A Comparison of Sporadic-E Occurrence Rates Using GPS Radio Occultation and Ionosonde Measurements. Remote Sensing, 14(3), 581.

Calibrated Western USA Noah-MP Parameter Set Forced by ERA5-WRF

These three files include the default (original) Noah-MP parameter set for the Western USA, and parameter sets based on calibration to daily streamflow data and monthly streamflow data.

Effects of Reanalysis Forcing Fields on Ozone Trends and Age of Air from a Chemical Transport Model

This dataset is based on the global off-line 3-D chenmical transport model (TOMCAT/SLIMCAT) forced with ECMWF reanalyses (ERA-Interim and ERA5) to compare the performance of the stratospheric ozone simulations. Each field is separately saved as NETCDF file. Each field is show on geographic coordinates, which can be longitude, latitude, vertical hybrid-pressure level (for zonal mean fields, such as ozone, temperature and age-of-air). The dimensions in each field are: lat --> latitude lon --> longitude lev --> hydrid pressure level time --> months of the simulation The output of the total column ozone from the TOMCAT/SLIMCAT simulations forced with ERA-Interim and ERA5 for Figures 1-4 and  Figure S2 in the supplement are in files: toz_A_ERAI.nc toz_B_ERA5.nc The output of the stratospheric column ozone (SCO) in Figure S1 in the supplement are in the file (levels1-3 are SWOOSH, B_ERA5 and A_ERAI SCO data, respectively): sco_SWOOSH_A_ERAI_B_ERA5.nc The output of zonal mean ozone profiles from the TOMCAT/SLIMCAT simulations forced with ERA-Interim and ERA5 for Figures 5-7, 9 and Figures S3-4 are in files: O3_mm_A_ERAI.nc O3_mm_B_ERA5.nc The output of zonal mean temperature from the TOMCAT/SLIMCAT simulations forced with ERA-Interim and ERA5 for Figure 8 are in files: te_mm_A_ERAI.nc te_mm_B_ERA5.nc The output of zonal mean age-of-air from the TOMCAT/SLIMCAT simulations forced with ERA-Interim and ERA5 for Figures 10-12 are in files: Age_mm_A_ERAI.nc Age_mm_B_ERA5.nc The output of the zonal mean ozone, temperature and age-of-air from the ERA5.1 reanalysis corrected simulations during the period from 2000 to 2006 in all Figures above using ERA5 are in files: ERA5_1_O3_2000_18.nc ERA5_1_te_2000_18.nc ERA5_1_Age_2000_18.nc

2D honeycomb transformation into dodecagonal quasicrystals driven by electrostatic forces

This repository contains the key input and output files used for the density fucntional theory calculations of the paper "Mechanism of 2D Oxide Quasicrystal formation from honeycomb structures" by Sebastian Schenk, Oliver Krahn, Eric Cockayne, Holger L. Meyerheim, Marc deBoissieu, Stefan F"orster, and Wolf Widdra (2022). The calculations were performed using the DFT code VASP, version 5.4.4 [Commercial software is mentioned in this README file to adquately described the procedure. This does not imply an endorsement or recommendation by the National Institute of Standards and Technology, nor that the software used is necessarily the best for the given purpose.] The subfolder large_approximant contains the files for the large Sr48Ti132O204 approximant on a Pt monolayer.  Subfolders honeycomb/PtN and sigma/PtN contain the files for honeycomb and sigma Ba8Ti24O36 structures on Pt trilayers with N Pt per layer per periodic cell. Subfolders honeycomb/PtN/substrate contain the corresponding files for the Pt substrate alone.  The honeycomb and sigma structures are at the equilibrium strain as determined by matching interpolated stress results, as described in the Supplementary Information associated with the main Article. The input files are the standard VASP input files: POSCAR (structure information), POTCAR_TITEL (pseudopotential information. Because the VASP pseudopotential files are proprietary, only the titles of the pseudopotentials used are given), KPOINTS (k-point generation) and INCAR (most calculation details). To accelerate the DFT van der Waals calculation, the file vdw_kernel.bindat from the VASP package (not included here) should also be used.  The output files are OSZICAR (summarizes energy at each iteration) and OUTCAR (full ouput).

Increasing the thermodynamic driving force of the phosphofructokinase reaction in Clostridium thermocellum

Glycolysis is an ancient, widespread, and highly conserved metabolic pathway that converts glucose into pyruvate. In the canonical pathway, the phosphofructokinase (PFK) reaction plays an important role in controlling flux through the pathway. Clostridium thermocellum has an atypical glycolysis and uses pyrophosphate (PPi) instead of ATP as the phosphate donor for the PFK reaction. The reduced thermodynamic driving force of the PPi-PFK reaction shifts the entire pathway closer to thermodynamic equilibrium, which has been predicted to limit product titers. In this work, we replace the PPi-PFK reaction with an ATP-PFK reaction. We demonstrate that the local changes are consistent with thermodynamic predictions: the ratio of fructose 1,6-bisphosphate to fructose-6-phosphate increases, and the reverse flux through the reaction (determined by 13C labeling) decreases. The final titer and distribution of fermentation products, however, do not change, demonstrating that the thermodynamic constraints of the PPi-PFK reaction are not the sole factor limiting product titer.

opencc-zeroSep 2022View details →

dryad36/100

Reduced isometric knee extensor force following anodal transcranial direct current stimulation of the ipsilateral motor cortex

Background: The goal of this study was to determine if 10-min of anodal transcranial direct current stimulation (a-tDCS) to the motor cortex (M1) is capable of modulating quadriceps isometric maximal voluntary contraction (MVC) force or fatigue endurance contralateral or ipsilateral to the stimulation site. Results: The main finding of this study was a significant interaction effect for stimulation condition x leg tested x time [F(1,60) =7.156, p = 0.010, ηp2 = 0.11] which revealed significant absolute KE MVC force impairments in the contralateral leg following s-tDCS (p < 0.001, d =1.2) and in the ipsilateral leg following a-tDCS (p < 0.001, d = 1.09). A significant interaction effect for condition x leg tested [F(1,56) = 8.12, p = 0.006, ηp2 = 0.13], showed a significantly lower left quadriceps (ipsilateral to tDCS) relative MVC force with a-tDCS, versus s-tDCS [t(15) = -3.07, p = 0.016, d = -0.77]. There was no significant difference between the relative right quadriceps (contralateral to tDCS) MVC force for a-tDCS and s-tDCS. Although, there was an overall significant [F(1,56) = 8.36, p < 0.001] 12.1% force decrease between the first and twelfth MVC repetitions, there were no significant main or interaction effects for fatigue index force. Conclusion: Hence, a-tDCS may be ineffective at increasing maximal force or endurance and instead may be detrimental to quadriceps force production.

opencc-by-4.0Sep 2022View details →

Scaling protein-water interactions in the Martini 3 coarse-grained force field to simulate transmembrane helix dimers in different lipid environments

This dataset contains molecular dynamics (MD) trajectories used for preparation of the following manuscript:  "Scaling protein-water interactions in the Martini 3 coarse-grained force field to simulate transmembrane helix dimers in different lipid environments".

opencc-by-4.0Sep 2022View details →

Data samples for Flow-matching -- efficient coarse-graining molecular dynamics without forces

CG samples generated during the training and validation processes in the flow-matching project. Accompanying the preprint "Flow-matching -- efficient coarse-graining molecular dynamics without forces": https://arxiv.org/abs/2203.11167. Detailed descriptions can be found in the preprint as well as the included README.

opencc-by-4.0Oct 2022View details →

Data that are used to Explain the Forcing Efficacy with Pattern Effect and Feedback Nonlinearity"

This dataset is for the draft "Explaining the Forcing Efficacy with Pattern Effect and Feedback Nonlinearity".     The netcdf file "last150yravg_picontrol.nc" represents the time-average fields for the last 150 years of PI-control experiment. Netcdf files beginning with "last20yravg" represent the time-average fields for the last 20 years (Year131-150) of abrupt forcing experiments.  Note that "0p5co2" in the file name denotes 0.5xCO2, "4psolar" denotes +4% solar radiation, and "m2psolar" denotes -2% solar radiation.     The netcdf files beginning with "fixedsst" represent the time-average fields for fixed-SST experiments, where the file "fixedsst_control.nc" denotes the fixed SST control experiment.     The netcdf files beginning with "uni" represent the time-average fields for uniform warming/cooling experiments, where the magnitude of SST change is indicated by the file names (m2K denotes -2K).     The text file "GFA_partialR_over_partial_SST" denote the value of partial_R over partial_SST for each grid, and its grid (96x144) is same as other netcdf files in this datasets .

dryad36/100

Separability of human motor memories during reaching adaptation with force cues

Judging by the breadth of our motor repertoire during daily activities, it is clear that learning different tasks is a hallmark of the human motor system. However, for reaching adaptation to different force fields, the conditions under which this is possible in laboratory settings have remained a challenging question. Previous work has shown that independent movement representations or goals enabled dual adaptation. Considering the importance of force feedback during limb control, here we hypothesised that independent cues delivered by means of background loads could support simultaneous adaptation to various velocity-dependent force fields, for identical kinematic plan and movement goal. We demonstrate in a series of experiments that indeed healthy adults can adapt to opposite force fields, independently of the direction of the background force cue. However, when the cue and force field were in the same direction but differed by their magnitude, the formation of different motor representations was still observed but the associated mechanism was subject to increased interference. Finally, we highlight that this paradigm allows dissociating trial-by-trial adaptation from online feedback adaptation, as these two mechanisms are associated with different time scales that can be identified reliably and reproduced in a computational model.

opencc-zeroOct 2022View details →

opencc-by-4.0Oct 2022View details →

Dataset for High-resolution mantle flow models reveal importance of plate boundary geometry and slab pull forces on generating tectonic plate motions

This repository contains the plugin and dataset used to setup models in the manuscript: "High-resolution mantle flow models reveal importance of plate boundary geometry and slab pull forces on generating tectonic plate motions". The material model plugin used in our models is in the "plugins" folder. The "models" folder contains the reference input parameter file described in the paper. All other model configurations shown in the paper can be obtained by modifying this parameter file.  The input files used to set up the models are in the respective folder. Additionally, the Jupyter notebook used to compute residuals of our models is provided in the "scripts" folder.