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3,206 results for “property (T)”
QM7-X: A comprehensive dataset of quantum-mechanical properties spanning the chemical space of small organic molecules
<p>Here, we introduce QM7-X, a comprehensive dataset of > 40 physicochemical properties for ~4.2 M equilibrium and non-equilibrium structures of small organic molecules with up to seven non-hydrogen (C, N, O, S, Cl) atoms. To span this fundamentally important region of chemical compound space (CCS), QM7-X includes an exhaustive sampling of (meta-)stable equilibrium structures---comprised of constitutional/structural isomers and stereoisomers, e.g., enantiomers and diastereomers (including cis-trans-and conformational isomers)---as well as 100 non-equilibrium structural variations thereof to reach a total of ~4.2 M molecular structures. Computed at the tightly converged quantum-mechanical PBE0+MBD level of theory, QM7-X contains global (molecular) and local (atom-in-a-molecule) properties ranging from ground state quantities (such as atomization energies and dipole moments) to response quantities (such as polarizability tensors and dispersion coefficients). By providing a systematic, extensive, and tightly converged dataset of quantum-mechanically computed physical and chemical properties, we expect that QM7-X will play a critical role in the development of next-generation machine-learning based models for exploring greater swaths of CCS and performing <em>in silico</em> design of molecules with targeted properties.</p> <p>The dataset is provided in eight HDF5 based files (compressed in .XZ files). One can also find here a README file with technical usage details and examples of how to access the information stored in the dataset (see createDB.py). </p> <p>*The paper explaining the generation of data stored in QM7-X can be found in <em>Sci Data</em> 8, 43 (2021). DOI: 10.1038/s41597-021-00812-2 . arXiv: https://arxiv.org/abs/2006.15139 .</p>
Data from: Properties of Markov chain Monte Carlo performance across many empirical alignments -- part I
<p>Nearly all current Bayesian phylogenetic applications rely on Markov chain Monte Carlo (MCMC) methods to approximate the posterior distribution for trees and other parameters of the model. These approximations are only reliable if Markov chains adequately converge and sample from the joint posterior distribution. While several studies of phylogenetic MCMC convergence exist, these have focused on simulated datasets or select empirical examples. Therefore, much that is considered common knowledge about MCMC in empirical systems derives from a relatively small family of analyses under ideal conditions. To address this, we present an overview of commonly applied phylogenetic MCMC diagnostics and an assessment of patterns of these diagnostics across more than 18,000 empirical analyses. Many analyses appeared to perform well and failures in convergence were most likely to be detected using the average standard deviation of split frequencies, a diagnostic that compares topologies among independent chains. Different diagnostics yielded different information about failed convergence, demonstrating that multiple diagnostics must be employed to reliably detect problems. The number of taxa and average branch lengths in analyses have clear impacts on MCMC performance, with more taxa and shorter branches leading to more difficult convergence. We show that the usage of models that include both Γ-distributed among-site rate variation and a proportion of invariable sites are not broadly problematic for MCMC convergence but are also unnecessary. Changes to heating and the usage of model-averaged substitution models can both offer improved convergence in some cases, but neither are a panacea.</p>
Data from: Properties of Markov chain Monte Carlo performance across many empirical alignments --part II
<p>Nearly all current Bayesian phylogenetic applications rely on Markov chain Monte Carlo (MCMC) methods to approximate the posterior distribution for trees and other parameters of the model. These approximations are only reliable if Markov chains adequately converge and sample from the joint posterior distribution. While several studies of phylogenetic MCMC convergence exist, these have focused on simulated datasets or select empirical examples. Therefore, much that is considered common knowledge about MCMC in empirical systems derives from a relatively small family of analyses under ideal conditions. To address this, we present an overview of commonly applied phylogenetic MCMC diagnostics and an assessment of patterns of these diagnostics across more than 18,000 empirical analyses. Many analyses appeared to perform well and failures in convergence were most likely to be detected using the average standard deviation of split frequencies, a diagnostic that compares topologies among independent chains. Different diagnostics yielded different information about failed convergence, demonstrating that multiple diagnostics must be employed to reliably detect problems. The number of taxa and average branch lengths in analyses have clear impacts on MCMC performance, with more taxa and shorter branches leading to more difficult convergence. We show that the usage of models that include both Γ-distributed among-site rate variation and a proportion of invariable sites are not broadly problematic for MCMC convergence but are also unnecessary. Changes to heating and the usage of model-averaged substitution models can both offer improved convergence in some cases, but neither are a panacea.</p>
Reproduction package for the paper "Correlating spectral and timing properties in the evolving jet of themicro blazar MAXI J1836-194"
<p>Basic reproduction package for the paper in the title; it contains all the necessary information and scripts required to replicate the results and plots, minus the proprietary code used (which can be found on github on request).</p>
Unique dynamics and exocytosis properties of GABAergic synaptic vesicles revealed by three-dimensional single vesicle tracking
<p>This data set includes x, y, and z trajectories of all GABAergic synaptic vesicles that we used for the study. These GABAergic synaptic vesicles in inhibitory presynaptic terminals of living primary hippocampal neurons were labeled by single quantum dots (QDs) conjugated with anti-VGAT antibody under electrical stimulation, and were tracked three-dimensionally by using a dual-focus imaging in real-time. Each trajectory data indicates x, y, and z positions (nanometer-scale) over time from the start of imaging to the moment of vesicle fusion. The electrical stimulation to the neurons was applied for 120 s, starting from 20 s.</p>
Gene Regulatory Network inference in long lived C.elegans reveals modular properties that are predictive of novel ageing genes - Database of Physical gene-gene Interactions in young adult C.elegans.
<p>This repository contains Supplementary Information for manuscript Suriyalaksh et al Gene Regulatory Network inference in long lived C.elegans reveals modular properties that are predictive of novel ageing genes corresponding to the curation of physical gene-gene interactions for young adult C elegans worms </p> <p>We manually curated 239,001 regulatory interactions from 289 young adult wild-type (WT) C.elegans datasets, consisting of 126 genes and 495 unique transcription factors (see TableS1_datasets_for_prior.csv for references). </p> <p>This repository contains 3 different files:</p> <p>TableS1_datasets_for_prior.csv - contains datasets used as sources for physical gene-gene or TF-gene interactions</p> <p>TableS2_physical_priors.xlsx - contains three tabs:<br> ChIPATAC - contains physical TF-gene interactions from 115 L4 or young-adult ChIP-seq datasets from modERN (Kudron et al., 2018) + ChIP-seq datasets (GSE28350, GSE81521) from (Hochbaum et. al, 2011, Li et. al, 2016).</p> <p>eY1HATAC- contains 3,501 TF-gene interactions from eY1H assay by Fuxman Bass et al. (2016).</p> <p>motifATAC - contains 202 unique TF DNA recognition motifs using “direct evidence” option from CiS-BP motif database (Weirauch et al., 2014), obtained through RTFBSDB R package (Wang et al., 2016) - see TableS1</p> <p>TableS3_WT_functional_priors.csv - contains functional knockdown data that we use as gold standard to validate inferred networks in Suriyalaksh et al. (see TableS1_datasets_for_prior.csv for sources)</p> <p>---</p> <p>Description of methodology to obtain regulatory interactions in TableS2:</p> <p>Regulatory sequences for each gene were acquired from ENSEMBL (Aken et al., 2017), obtained using biomaRt R package (accessed on 31st Oct 2017). This study used WBcel235/ce11 version of the C. elegans genome, and WormBase WS260 genome annotations.</p> <p>For motifs, TFs whose motifs overlapped with an open ATAC-seq region by at least one base pair were kept. For ChIP-seq, TF binding sites that overlapped with an open ATAC-seq region by at least one base pair were kept using bedtools intersect and bedtools merge commands.</p> <p>An interaction from a TF to a gene was inferred by aligning transcription start sites (TSS) using bedtools window commands with 1000 bp window size to the TF-binding locations from ChIP-seq and motifs.</p> <p>For eY1H data, an interaction is included if the TSS site of the target gene overlaps with an open ATAC-seq region by at least one base pair.</p> <p>For gene-gene interactions, of the 298 studies compiled in WormExp v1.0 database (Yang et al, 2016, updated 27/07/16), 98 studies were included in the database spanning 126 different genes (see Table S1 in this repository).</p>
Dataset for publication Cuevas K., Chougan M., Martin F., Ghaffar SH, Stephan D., Sikora P. 3D printable lightweight cementitious composites with incorporated waste glass aggregates and expanded microspheres – Rheological, thermal and mechanical properties. Journal of Building Engineering (2021) 44, 102718
<p>Dataset consisting of G-code for 3D mortar specimen's printing path and particle size distribution (Origin file) of materials used in the study Cuevas K., Chougan M., Martin F., Ghaffar SH, Stephan D., Sikora P. 3D printable lightweight cementitious composites with incorporated waste glass aggregates and expanded microspheres – Rheological, thermal and mechanical properties. Journal of Building Engineering (2021) 44, 102718. <a href="https://doi.org/10.1016/j.jobe.2021.102718">https://doi.org/10.1016/j.jobe.2021.102718</a></p>
Structural and luminescent properties of Y2Mo4O15: Eu3+ red phosphor calcined at different temperatures
<p>Data from the preprint of the manuscript published in the Physica status solidi (b) journal</p> <p> Jelena Papan, Zoran Ristić, Aleksandar Ćirić, Sanja Kuzman, Miroslav D. Dramićanin, <strong>Structural and luminescent properties of Y<sub>2</sub>Mo<sub>4</sub>O<sub>15</sub>: Eu<sup>3+</sup> red phosphor calcined at different temperatures, </strong>Physica status solidi (b), Vol. 257, Iss. 8, 1900454.</p> <p><a href="https://doi.org/10.1002/pssb.201900454">https://doi.org/10.1002/pssb.201900454</a></p>
Dataset: On the Properties of Next Generation Wireless Backhaul
<p>This dataset contains all the data used in the Paper: "On the Properties of Next Generation Wireless Backhaul" sent to Transaction of Network Science and Engineering.</p> <p>It is divided into three main archives:</p> <ul> <li>The first archive, called <strong>geodata.zip</strong>, contains the Data Surface Model (DSM) and the topographical maps used to generate the intervisibility graphs. These maps have been aggregated from different sources and they are all released under a CC-BY-SA 4.0 license. It is divided into two folders: 'dsm' and 'topo_maps': <ul> <li> 'dsm' contains the Data Surface Model (DSM) of the nine areas used in our research. Each area is saved in a separate .tif file and can be used directly from the tool. The projection system is EPSG:3003.</li> <li>'topo_mapsì contains the PostGIS dump of the tables containing the topographical maps of the cities. In order to use them, you have to import those in PostGIS and connect our tool to the PostGIS DB.<br> The CTR files (technical region maps) are divided by region, while the openstreetmap file (osm.tar) contains the whole Italian peninsula. All the geographical data are projected in the reference system EPSG:3003. The CTR of Campania is unavailable due to licensing incompatibilities.</li> </ul> </li> <li>The second archive, called <strong>visibility_graphs.zip</strong>, contains the visibility graph we have generated using our tool. It is released as a CC-BY-SA 4.0 license. It is divided into folders, one for each area of the analysis. Each folder contains two files: <ul> <li>best_p.csv : contains the ids of the nodes associated with their coordinates on a cartesian projection. The projection is EPSG:3003</li> <li>intervisibility.adj : contains the intervisibility graph represented as an adjacency matrix. It can be read by common libraries such as networkx or igraph. The intervisibility has been calculated 2m above the building.</li> </ul> </li> <li>The third folder, called <strong>network_topologies.zip</strong>, contains the network topologies we have computed using a State-of-the-Art algorithm from Polese et Al. The folder is divided into two folders: '30gNB' and '60gNB', corresponding to the density of base stations for square km. It s further divided in 9 folders (one for each area), then divided on the basis of the model we use for the visibility graph. You can find more information about these models in section V of the paper. In this last folder we have two sets of 50 files, which are the intervisibility graph of that set of Base Stations and the topology produced. This dataset has been released under a CC-BY-SA 4.0 license.</li> </ul> <p>All the results can be replicated using our code which will be released with an open-source license as soon as the article is published.</p>
Dataset on soil hydraulic properties under contrasted plant covers and agricultural practices
<p>Complete dataset on the temporal variation of soil infiltrability along a homogeneous fluvisol, on bare soil or soil planted with two plant species with contrasted root systems (a Malvaceae with a tap-root system and a Poaceae with a fibrous root system), and impacted by three different management practices (burning, mowing, and chemical weeding). An original protocol, based on specific ring infiltrometers, able to measure the temporal dynamics of soil infiltrability was used. This dispositive takes into account the variability of the measurement across space.</p> <p> </p>
Properties of flat-spectrum radio-loud Narrow-Line Seyfert 1 Galaxies
<p>Numerical tables of the Spectral Energy Distributions (SEDs) of Figs. 8-13 of the paper http://arxiv.org/abs/1409.3716v2</p>
Material properties of bovine intervertebral discs across strain rates - dataset
<p>Raw experimental data from axial compression tests of each of the bovine intervertebral disc specimens and the .dat files from each of the subject specific FE models at each strain rate.</p>
Data of the publication: Nuclear spin coherence properties of 151Eu3+ and 153Eu3+ in a Y2O3 transparent ceramic by J. Karlsson et al.
<p>Data corresponding to the figures of the publication "Nuclear spin coherence properties of 151Eu3+ and 153Eu3+ in a Y2O3 transparent ceramic" by J. Karlsson et al., (https://doi.org/10.1088/1361-648X/aa529a). A text file describes data in each compressed folder, please refer to the caption in the publication for more details. </p>
Black Sea thermohaline properties: Long-term trends and variations
<p>3D velocity (m/s), temperature (°C) and salinity fields for the Black Sea are simulated by the use of the General Estuarine Ocean Model (GETM) and General Ocean Turbulence Model (GOTM). Data sets consists of monthly mean value on a horizontal grid of 423x172 data points (2 longitude minutes x 2 latitude minutes) and 70 vertical levels. Simulations are performed for the period from 1960 to 2015 (56 years). The 3D monthly mean vertical coordinate, temperature and salinity are stored in monthly NetCDF data files available for download.</p> <p>Detailed description: The 3D hydrodynamic model comprises of 3D GETM and 1D GOTM initialized on high resolution 2 x 2 min latitude–longitude horizontal grid. The model bathymetry grid is produced from ETOPO1 global bathymetric grid with horizontal resolution of 1 min. Linear programming procedure was applied to smooth slightly the bathymetry. The maximum depth of the model domain is 2200 m with a 70 levels general vertical grid which is compressed towards the surface. A detailed description of the GETM equations can be found in Stips et al. [2004].One way to minimize dissipation and dispersion is to use a numerical method which satisfies the Total Variation Diminishing (TVD) property. Flux-limiter methods satisfy the TVD property and switch between a second-order approximation when the field is smooth and a first-order approximation when it is near a discontinuity. Flux-limiter methods have been applied to the different numerical approaches so that oscillations present in the numerical solution can be minimized. The second-order monotone scheme with the Superbee limiter is used herein [Burchard and Bolding 2002]. The meteorological forcing from the European Centre for Medium Range Weather Forecast (ECMWF) available from http://www.ecmwf.int, has been applied, namely, ERA-40 project (1958-2001) and ERA-Interim project (1979-2015). Two model runs have been chosen: Run1 with ERA-40 (1958-1979) followed by forcing with ERA-Interim (1980-2015) and Run2 forced with ERA-Interim (1979-2015), in order to study the effect of the starting year and forcing data and to identify possible artificial trends due to computational and forcing uncertainties. Freshwater input has been evaluated using the values from the Global Runoff Data Centre (GRDC, http://www.bafg.de/GRDC) runoff. Being an estuarine basin, the Black sea is very sensitive to variations in the fresh water input. The resulting buoyancy flow induced by the river runoff is essential for establishing the basin circulation. Comparison between runoff data sets from different data centres has revealed similar climatological mean annual cycles for all rivers considered herein [Miladinova-Marinova et al., 2016]. The mode has been forced the GRDC data because it contains long term daily records of the Danube River. Water exchange in the Bosphorus and Kerch Straits is simulated as a river flow that contains surface outflow/inflow and bottom inflow/outflow. Assuming the long term steady state water and salt budgets in the Black Sea, the monthly averaged volume fluxes have been estimated [Miladinova-Marinova et al., 2016] and used further as a forcing condition. The model is initialized by means of temperature and salinity 3D fields coming from the project MEDAR/MEDATLAS II (http://www.ifremer.fr/medar). The MEDAR data set for the Black Sea reflects the main features known from observations – the strong halocline at 70-150 m, the CIL at approximately 25-70 m and the doming of the isohalines due to the cyclonic Rim current. The detailed model setup and an extended validation is presented in Miladinova-Marinova et al. [2016]. Burchard, H., and K. Bolding (2002), Getm: A general estuarine transport model. Scientific documentation, Joint Research Centre Ispra Tech. Rep. EUR 20253 EN, Eur. Comm; Stips, A., K. Bolding, T. Pohlmann, and H. Burchard (2004), Simulating the temporal and spatial dynamics of the North Sea using the new model GETM (General Estuarine Transport Model), Ocean Dynam., 54, 266-283; Miladinova-Marinova S., A. Stips, E. Garcia-Gorriz, D. Macias Moy (2016), Black Sea ecosystem model: setup and validation, EUR 27786, doi: 10.2788/601495</p> <p>Simulation zip files from Run1, BLACK_SEA_HYDRO1_YEAR_MONTH.zip, and simulation zip files from Run2, BLACK_SEA_HYDRO2_YEAR_MONTH.zip, are stored herein.</p>
Probabilistic state-level estimates of US coastal storm property damages from climate change
<p>Probabilistic estimates of property damage (2010 USD) by damage mechanism, sea level measure, region, and time period. Values are derived from <em>Estimates of US coastal damages by local sea level </em>(doi: https://doi.org/10.5281/zenodo.820149) using the code at https://github.com/ClimateImpactLab/acp-impacts</p> <p>Direct (surge + wind) and business-interruption storm damage estimates as well as estimated property below sea level are projected by estimating damages as a function of local sea level (LSL). These damage functions are then applied to probabilistic estimates of local sea level from Kopp et al (2014) using a Monte Carlo simulation. Percentiles of the resulting distributions are presented in the included files. Estimates of property below sea level are calculated for both mean sea level (MSL) as well as mean higher high water (MHHW).</p> <p>In each period, estimates of the cumulative value of inundated property, or property below sea level, are removed from the exposure data set when computing future storm damages; therefore, projections of future storm damages differ between the two measures of sea level.</p>
Global scale leaf broadband optical properties derived from CliMA Land and associated CESM simulations
<p>Leaf level broadband reflectance and transmittance computed from leaf traits.</p> <ul> <li>clm_refl_tran_1m_weighted.nc: monthly data (144*96 pixels)</li> <li>surfdata_CMIP6_fluspect_v3.nc: surface data to run CESM (144*96 pixels)</li> </ul> <p>Global scale simulation results</p> <ul> <li>research_data_coupled_future_v2.nc: CESM coupled future simulations</li> <li>research_data_coupled_history_v2.nc: CESM coupled historical simulations</li> <li>research_data_uncoupled_history_v2.nc: CESM uncoupled future simulations</li> <li>research_data_uncoupled_ssp_v2.nc: CESM uncoupled SSP245 and SSP585 simulations</li> </ul> <p>Code changes</p> <ul> <li>SurfaceAlbedoMod.F90: modified CLM module</li> <li>Julia-and-Python-Code.tar.gz: code used for processing the data and plot the figures</li> </ul>
Supplementary material for the publication: "Efficient Surrogate Models for Materials Science Simulations: Machine Learning-based Prediction of Microstructure Properties"
<p><span><span><span>This dataset contains supplementary code, images and models for the publication „Efficient Surrogate Models for Materials Science Simulations: Machine Learning-based Prediction of Microstructure Properties“.</span></span></span></p> <p> </p> <p><span><span><span>The content will be updated and additionally linked to the corresponding git repositories.</span></span></span></p>
Raw data for the submitted manuscript: Effects of microplastics on enchytraeid multigeneration reproduction and soil physicochemical properties
<p>Survival and reproduction data from multigenerational single species tests involving four types of plastic materials.</p> <p> </p>
Dataset of physical, biological and chemical soil properties from 10 European long-term experiments
<p>This dataset contains all measurements that were conducted within the Workpackage #2 of the SoilX Project (2022-2024). The data contains physical, chemical and biological soil parameters that were measured in ten European long-term field experiments, as well as soil management indicators calculated with the SoilManageR packager for R. Each data table contains different parameters, and they can be linked by the identifying columns (LTE, treatment, depth, block, replicate). Further information can be found in the ReadMe.txt.</p> <pre> </pre>
Vertical profiles of stable water isotopes and thermodynamic properties from research flights during the L-WAIVE field campaign in June 2019
<p>This datasets contains the measurements of stable water isotopes conducted during the Lacustrine-Water vApor Isotope inVentory Experiment (L-WAIVE) field campaign taking place in June 2019 in the Annecy valley in the French Alps (Chazette et al. 2021). The measurements were conducted using a Picarro laser spectrometer L2130-i that was installed on an ultralight aircraft. The Picarro measurements of atmospheric humidity are merged measurements of thermodynamic properties by a fast-response temperature and humidity probe (iMet XQ-2; see also Chazette et al. 2021) interpolated on 10s temporal resolution.</p> <p>The data is provided on a one file per flight. All variables are described in README.</p> <p>This dataset has been used in Thurnherr et al. (submitted) for a comparison study of stable water isotopes measurements from various platforms and COSMOiso model simulations.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.