Find research datasets worth reusing

Stochastic Occupancy Grid Map Prediction in Dynamic Scenes: Dataset

Three occupancy grid map (OGM) datasets for the paper titled "Stochastic Occupancy Grid Map Prediction in Dynamic Scenes" by Zhanteng Xie and Philip Dames 1. OGM-Turtlebot2: collected by a simulated Turtlebot2 with a maximum speed of 0.8 m/s navigates around a lobby Gazebo environment with 34 moving pedestrians using random start points and goal points 2. OGM-Jackal: extracted from two sub-datasets of the socially compliant navigation dataset (SCAND), which was collected by the Jackal robot with a maximum speed of 2.0 m/s at the outdoor environment of the UT Austin 3. OGM-Spot: extracted from two sub-datasets of the socially compliant navigation dataset (SCAND), which was collected by the Spot robot with a maximum speed of 1.6 m/s at the Union Building of the UT Austin The relevant code is available at:  OGM prediction: https://github.com/TempleRAIL/SOGMP OGM mapping with GPU: https://github.com/TempleRAIL/occupancy_grid_mapping_torch

Data set for the publication entitled "Azithromycin alters spatial and temporal dynamics of airway microbiota in idiopathic pulmonary fibrosis"

Set of files containing data used for microbiota analysis by 16S rRNA amplicon sequencing. The study cohort included patients with idiopathic pulmonary fibrosis from four centres in Switzerland, treated with azithromycin or placebo, sampled sequentially by oropharyngeal swab. This work is available in medRxiv and has been submitted

ALS-based DEMs (100 cm): the dynamics of the prehistoric communities located in the Mostiștea Valley and Danube Plain (between Oltenița and Călărași)

This dataset is part of a larger project on the dynamics of the prehistoric communities located in the Mostiștea Valley and Danube Plain (between Oltenița and Călărași), supervised by the ArchaeoSciences Division of the Research Institute of the University of Bucharest (ICUB)  and Kiel University (Germany), in partnership with HOGENT, University of Applied Sciences and Arts (Belgium), Museum of Bucharest, Museum of the Lower Danube Călărași, Museum of Gumelnița Civilization Oltenița, and "Vasile Pârvan" Institute of Archaeology (Romania), under the "Sultana School of Archaeology" initiative. Spatial data play a crucial role in archaeological research, and orthophotos, digital elevation models, and 3D models are frequently used for the mapping, documentation, and monitoring of archaeological sites. Thanks to the availability of compact and low-cost uncrewed airborne vehicles, the use of UAV-based photogrammetry is well matured in this field over the last two decades. More recently, compact airborne systems are also available that allow the recording of thermal data, multispectral data, and airborne laser scanning. For this project, various platforms and sensors are applied at the Chalcolithic archaeological sites in the Mostiștea Basin and Danube Valley (Southern Romania). By analyzing the performance of the systems and the resulting data, insight is given into the selection of the appropriate system for the right application. This analysis requires thorough knowledge of data acquisition and data processing as well. As both laser scanning and photogrammetry typically result in very large amounts of data, a special focus is also required on the storage and publication of the data. Hence, the objective of this project is to provide a full overview of various aspects of 3D data acquisition for UAV-based mapping. Based on the conclusions drawn in our related publications, it is stated that photogrammetry and laser scanning can result in data with similar geometrical properties when acquisition parameters are appropriately set. On the one hand, however, the used ALS-based system outperforms the photogrammetric platforms in terms of operational time and the area covered. On the other hand, conventional photogrammetry provides flexibility that might be required for very low-altitude flights, or emergency mapping. Furthermore, as the used ALS sensor only provides a geometrical representation of the topography, photogrammetric sensors are still required to obtain true color- or false color composites of the surface. Lastly, the variety of data, like pre- and post-rendered raster data, 3D models, and point clouds, requires the implementation of multiple methods for the online publication of data. Various client-side and server-side solutions are presented to make the data available for other researchers.

opencc-by-4.0Jul 2022View details →

Dynamic full-field imaging of rupture radiation: Material contrast governs source mechanism

Datasets related to the research article 'Dynamic full-field imaging of rupture radiation: Material contrast governs source mechanism'.  A readme with the necessary Matlab code to load the data is included. Tested on Matlab2020b For the analytic rupture radiation simulation code please check the linked github repository.

MS-based orthophotos (50 cm): the dynamics of the prehistoric communities located in the Mostiștea Valley and Danube Plain (between Oltenița and Călărași)

Model codes and simulation data for "Modeling demographic-driven vegetation dynamics and ecosystem biogeochemical cycling in NASA GISS's Earth system model (ModelE-BiomeE v.1.0)"

ModelE-BiomeE v1.0 model codes and data This folder contains the simulation data and model codes that were used in the paper ‘Modeling demographic-driven vegetation dynamics and ecosystem biogeochemical cycling in NASA GISS’s Earth system model (ModelE-BiomeE v.1.0)’ (https://doi.org/10.5194/gmd-2022-72). We included the data simulated by ModelE-BiomeE v.1.0 with settings of full demography (folder FullDemography) and single cohort (folder SingleCohort), and initial settings of land grids and vegetation data (folder GlobalVegetation). The codes include the full ModelE 2.1, module BiomeE files in ModelE, and the standalone BiomeE. In the folder FullDemography, we have 4 netcdf files for global output and 25 files for single grids output. The files ‘FullDM_2588_JAN.nc’ and ‘FullDM_2588_JUL.nc’ are the original model output of January and July in the year 2588. The file ‘FullDM_2588_Annual.nc’ is the yearly summary of model simulations. The file ‘FullDM_Selected.nc’ is an annual summary of 588 years of model simulation only with selected variables. The csv files are for single grids output at the time steps of daily and yearly. The last digit 1~8 represents the sites of 'BNC','MNT','HF','OKR','KZ','SV','WGK','TPJ', respectively (Table 1). Table 1 Site ID and file number ['BNC',  'MNT',   'HF',  'OKR',  'KZ',   'SV',   'WGK',  'TPJ'] ['8991', '8992', '8993', '8994', '8995', '8996', '8997', '8998'] ['8971', '8972', '8973', '8974', '8975', '8976', '8977', '8978'] ['8961', '8962', '8963', '8974', '8965', '8966', '8977', '8968'] Please refer to Table 2 in the paper for the detail of these 8 sites. ‘DailyLAIGPP.csv’ is a summary of all ‘DailyEcosystem’ files with LAI and GPP data. We included the Python scripts that can be used to generate the figures in out paper (Plotting-BiomeE-MsTMIP.py, Plotting-Scatter-Comparison.py, PlottingBiomeEMaps.py, and PlottingGridOutput.py). For the convenience of readers (in reproducing our figures), we included the summary of reanalysis of the data from observations and MsTMIP in folder ‘Sum-Obs-Simu’. Please refer to the original sources listed in our paper for the detail of these data.

opencc-by-4.0May 2022View details →

Developmental timing of programmed DNA elimination in Paramecium tetraurelia recapitulates germline transposon evolutionary dynamics

With its nuclear dualism, the ciliate Paramecium constitutes an original model to study how host genomes cope with transposable elements (TEs). P. tetraurelia harbors two germline micronuclei (MIC) and a polyploid somatic macronucleus (MAC) that develops from the MIC at each sexual cycle. Throughout evolution, the MIC genome has been continuously colonized by TEs and related sequences that are removed from the somatic genome during MAC development. Whereas TE elimination is generally imprecise, excision of ~45000 TE-derived Internal Eliminated Sequences (IESs) is precise, allowing for functional gene assembly. Programmed DNA elimination is concomitant with genome amplification. It is guided by non-coding RNAs and repressive chromatin marks. A subset of IESs are excised independently of this epigenetic control, raising the question of how they are targeted for elimination. To gain insight into the determinants of IES excision, we determined the developmental timing of DNA elimination genome-wide by combining fluorescence-assisted nuclear sorting with next-generation sequencing. Essentially all IESs are excised within one endoduplication round only (32C to 64C), while TEs are eliminated at a later stage. We show that time, rather than replication, controls the progression of DNA elimination. Further analyses defined four IES classes according to excision timing and revealed that the earliest excised IESs tend to be independent of epigenetic factors, display strong sequence signals at their ends and originate from the most ancient integration events. We conclude that old IESs have been optimized during evolution for early and accurate excision, by acquiring stronger sequence determinants and escaping epigenetic control.

opencc-by-4.0Jun 2022View details →

Cohesin and CTCF control the dynamics of chromosome folding

The dataset contains all the tracking data from Mach et al 2022 paper. Each file has the following header: x,y,z: spot coordinate. For dual color imaging, the distance along x,y and z across channels track: track id frame: time frame cell: cell id

opencc-by-4.0Oct 2022View details →

Low Frequency Ambient Noise Dynamics and Trends: Cape Leeuwin, Australia

Data files and code for : Low Frequency Ambient Noise Dynamics and Trends: Cape Leeuwin, Australia R version 4.X used for plots and analysis. Packages: entropy, foreach, rEDM <ol> <li>Plots.R : Create plots for manuscript. </li> <li>MI.R : Evaluate lagged Mutual Information of random data segments</li> <li>CCM.R : Convergent cross mapping of Ambient Noise with teleconnections</li> <li>EMM_Surrogate.R : Evaluate CCM significance with randomized surrogates</li> </ol> Python 3.X used for plots and analysis. Packages: pandas, matplotlib, emd, pyEDM <ol> <li>Figure5,py  Figure14.py : Create plots for manuscript</li> <li>EMD.py : Compute empirical mode decompositions</li> </ol>

opencc-by-4.0Sep 2017View details →

Bottom water acidification and warming on the western Eurasian Arctic shelves: Dynamical downscaling projections. Data archive.

This archive includes one .mat file (MATLAB format) containing all the data and interpolated SINMOD model used for skill assessment and bias correction, and several NetCDF files containing the SINMOD SRES A1B projections (bias corrected where possible) for the bottom water in the pan-Arctic model domain for years 2001-2099 inclusive. Temporal resolution is biweekly and spatial resolution is 20km (see grid info in NetCDF files).

opencc-by-4.0Sep 2017View details →

Ab-initio molecular dynamics trajectories of fully hydrated TiO2 surfaces

This data set contains trajectories of ab-initio molecular dynamics simulations of TiO2 surfaces in water described in the paper: L.Agosta, E.G.Brandt and A.P.Lyubartsev "Diffusion and reaction pathways of water near fully hydrated TiO2 surfaces from ab initio molecular dynamics", J.Chem.Phys., 147, 024704 (2107) doi: http://dx.doi.org/10.1063/1.4991381 Trajectories of 6 fully hydrated TiO2 surfaces are stored under respective names. Each trajectory file contains 50 ps of simulation with frames saved every 0.0005 ps. Format: PDB, gzipped.

opencc-by-4.0Oct 2017View details →

Evolutionary dynamics of mycorrhizal symbiosis in land plant diversification - phylogenetic data

This submission supplements the manuscript entitled Evolutionary dynamics of mycorrhizal symbiosis in land plant diversification by Frida A.A. Feijen, Rutger A. Vos, Jorinde Nuytinck & Vincent S.F.T. Merckx. The contents of this submission are dating analysis results for rootings of the land plant topology. Contains the following files: <ul> <li>*.log.gz BEAST logs</li> <li>*.trees.gz BEAST trees</li> <li>*.tiff screen dumps of tracer, showing the burn-in</li> <li>*.consensus.trees produced with treeannotator</li> </ul> For more information: https://github.com/naturalis/mycorrhiza/tree/v1.0.0

Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α-Fig. 2def

smTIRF-FRET Data for Fig 2, for "Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α"

Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α-Fig. 7cde

smTIRF-FRET Data for Fig 7, for "Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α"

Dynamical mean field theory data for single band Hubbard model

Dynamical mean field theory (DMFT) data for the half filled repulsive single band Hubbard model on four lattices: cubic, diamond, hypercubic in \(d=\infty\), and hyperdiamond in \(d=\infty\). It is allowed for long range antiferromagnetic ordering, i.e., the self-consistency condition as seen in Eq. 97 of Georges et al., Rev. Mod. Phys. 68, 13 is used. The simulations are done for different temperatures between \(\beta t = 3\) and \(\beta t = 40\). The interaction \(U\) is chosen in steps of 0.1 centered around the respective Mott transitions. Available data are <ul> <li>interacting Greens function on Matsubara frequencies</li> <li>self energy on Matsubara frequencies</li> <li>double occupation</li> <li>spin up and spin down occupation</li> </ul> Data is generated using triqs 1.4 and the continous time quantum Monte Carlo application 1.4, compare homepage at https://triqs.ipht.cnrs.fr The data are used in the publication "First-order metal-insulator transitions in the extended Hubbard model due to self-consistent screening of the effective interaction" available on the arXiv (arXiv:1706.09644). There it is used to calculate derivatives of the double occupancy w.r.t. the interaction U. The data are available in hdf5 archives and can easily be accessed, e.g., with python and h5py. An example python script is included. Relevant input parameters are included in the h5 files.

Soil Carbon Dynamics in Soybean Cropland and Forests in Mato Grosso, Brazil

These files contain the carbon content, radiocarbon, and stable isotope data for soils collected to 2 m deep in forest and soybean cropland in Mato Grosso, Brazil.

opencc-by-4.0Jan 2018View details →

Molecular dynamics simulation trajectory of an anionic lipid bilayer: 100 mol% DOPS with Na+ counterions using ff99 Ions

System: Symmetric bilayer of anionic DOPS (1,2-Dioleoyl-sn-glycero-3-phosphoserine 100 mol-%) lipids with sodium (Na+) counter ions. Number of DOPS: 128. Number of Na+-ions: 128. Number of waters: 4480. Lipid model: Amber Lipid 17 [IR Gould, AA Skjevik, CJ Dickson, BD Madej, RC Walker: "Lipid17: A Comprehensive AMBER Force Field for the Simulation of Zwitterionic and Anionic Lipids" in prep. (2018)]. Ion models:  Amber ff99 [J Åqvist J. Phys. Chem. 94 8021 (1990)]. Water model: TIP3P [WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein J. Chem. Phys. 79 926 (1983)]. Simulation engine: Amber16 [DA Case et al. AMBER 2017 UCSF (2017)]. Number of independent repeats per setup: 2. Trajectory lengths per repeat: 400 ns + 100 ns. Previously equilibrated for: 100 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Langevin' at T = 303 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984); J. Chem. Phys. 103 10252 (1995)] with xy and z coupled separately at p = 1.0 bar with no surface tension. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Theory Comput. 9 3878 (2013)]. Van der Waals: Turned off between 1.0 nm and 1.5 nm. Constraints: Lengths of covalent bonds involving Hydrogens in lipids using SHAKE [J. Comput. Phys. 23 327 (1977)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: OHS Ollila et al. "NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PS lipids" in prep (2018).

opencc-by-4.0Jan 2018View details →

Molecular dynamics simulation trajectory of an anionic lipid bilayer: 100 mol% POPS with Na+ counterions using Joung-Cheatham Ions

System: Symmetric bilayer of anionic POPS (palmitoyl-oleoyl-phosphatidylserine 100 mol-%) lipids with sodium (Na+) counter ions. Number of POPS: 128. Number of Na+-ions: 128. Number of waters: 4480. Lipid model: Amber Lipid 17 [IR Gould, AA Skjevik, CJ Dickson, BD Madej, RC Walker: "Lipid17: A Comprehensive AMBER Force Field for the Simulation of Zwitterionic and Anionic Lipids" in prep. (2018)]. Ion model: Joung–Cheatham [IS Joung, TE Cheatham III J. Phys. Chem. B 112 9020 (2008)]. Water model: TIP3P [WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein J. Chem. Phys. 79 926 (1983)]. Simulation engine: Amber16 [DA Case et al. AMBER 2017 UCSF (2017)]. Number of independent repeats per setup: 2. Trajectory lengths per repeat: 400 ns + 100 ns. Previously equilibrated for: 100 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Langevin' at T = 298 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984); J. Chem. Phys. 103 10252 (1995)] with xy and z coupled separately at p = 1.0 bar with no surface tension. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Theory Comput. 9 3878 (2013)]. Van der Waals: Turned off between 1.0 nm and 1.5 nm. Constraints: Lengths of covalent bonds involving Hydrogens in lipids using SHAKE [J. Comput. Phys. 23 327 (1977)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: OHS Ollila et al. "NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PS lipids" in prep (2018).

opencc-by-4.0Apr 2024View details →

Quantifying Dissolution Dynamics in Porous Media Using a Spatial Flow Focusing Profile

The diverse range of patterns in porous media formed by dissolution processes depends on the relative magnitude of flow, transport, and chemical reactions at pore surfaces. However, distinguishing between regimes often relies solely on qualitative, visual comparisons of emergent structures. Here, we propose a quantitative measure capable of identifying different regimes using the concept of the spatial flow focusing profile, which segments the medium into cross sections along the flow direction to calculate the flow focusing index for each section. We employ this measure in numerical simulations of a dissolving porous medium using a pore-network model. We obtain a morphological phase diagram of dissolution patterns, which we characterize using the flow focusing profile. In particular, we demonstrate that analyzing the temporal changes in the profile allows one to quantitatively distinguish between wormholing and channeling. The transition between them is shown to be affected by the heterogeneity of the system.