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4,276 results for “Estimation”
High-resolution spatialization for estimation of precipitation in the Cordillera Blanca, Peru
<p>Supplementary materials for the article "High-resolution spatialization for estimation of precipitation in the Cordillera Blanca, Peru"</p>
Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision and Reproducibility - Dataset
<p>This zip contains all input structures for paper the: Alchemical Free<br> Energy Estimators and Molecular Dynamics<br> Engines: Accuracy, Precision and Reproducibility</p> <p>Authors: Alexander D. Wade, Agastya P. Bhati, Shunzhou Wan, Peter V.Coveney</p> <p>The structures of the folders are protein/ligand_transformation/alchemical_leg/input/files</p> <p>The ligand transformation are derived from previous work by wang et al. (https://pubs.acs.org/doi/10.1021/ja512751q)</p> <p>There are two files for the solvent alchemical leg: complex.pdb and complex.prmtop</p> <p>complex.pdb is structure file that also denotes the alchemical atoms in the pdb beta column. complex.prmtop is an AMBER parameter/topology file</p> <p>For the complex alchemical leg there is an additional file constraints.pdb that contains the constraint information in the pdb beta column.</p> <p>These files can be used with TIES_MD (https://ucl-ccs.github.io/TIES_MD/) or other molecular dynamics engiens that take AMBER input.</p>
Global estimates of marine gross primary production based on machine‐learning upscaling of field observations
<p>4 variables (excluding dimension variables):</p> <p>double GPP_LD_MLD_RF[Lon,Lat,Month] <br> units: mmol O2 m-2 d-1<br> fill value: NaN<br> long_name: Monthly mixed-layer integration of gross primary production trained from the<br> dataset determined by the light-dark bottle incubation using Random Forest<br> algorithm<br> coordinates: [Longitude, Latitude Month]</p> <p>double GPP_LD_ZEU_RF[Lon,Lat,Month] </p> <p> units: mmol O2 m-2 d-1<br> fill value: NaN<br> long_name: Monthly euphotic-zone integration of gross primary production trained from<br> the dataset determined by the light-dark bottle incubation using Random<br> Forest algorithm<br> coordinates: [Longitude, Latitude Month]</p> <p>double GPP_Triple_MLD_RF[Lon,Lat,Month] <br> units: mmol mmol O2 m-2 d-1<br> fillvalue: NaN<br> long_name: Monthly mixed-layer integration of gross primary production trained from<br> the dataset determined by the triple isotopes of dissolved oxygen using<br> Random Forest algorithm<br> coordinates: [Longitude, Latitude Month]<br> <br> double GPP_Triple_ZEU_RF[Lon,Lat,Month] <br> units: mmol O2 m-2 d-1<br> fill value: NaN<br> long_name: Monthly euphotic-zone integration of gross primary production trained from<br> the dataset determined by the triple isotopes of dissolved oxygen using<br> Random Forest algorithm</p> <p>3 dimensions:</p> <p> Lon Size:181<br> units: degree_north<br> long_name: Longitude</p> <p> Lat Size:91<br> units: degree_east<br> long_name: Latitude</p> <p> Month Size:13<br> units: Jan, Feb, Mar, Apr, May, Jun, Jul, Aug, Sep, Oct, Nov, Dec, Annuual_mean<br> long_name: Month</p> <p><br> Author: Yibin Huang & Nicolas Cassar<br> Correspond: nicolas.cassar@duke.edu<br> <br> Request_for_citation: If you use these data in publications or presentations, please cite: Huang,<br> Y., Nicholson, D., Huang, B., & Cassar, N. (2021). Global estimates of<br> marine gross primary production based on machine‐learning upscaling of<br> field observations. Global Biogeochemical Cycles, 35, e2020GB006718.<br> https://doi.org/10.1029/2020GB006718<br> <br> Creation date: Dec/6th/2021</p>
FIG. 8. Estimated phylogenetic relationships from a in Fourteen New, Endemic Species Of Shrew (Genus Crocidura) From Sulawesi Reveal A Spectacular Island Radiation
FIG. 8. Estimated phylogenetic relationships from a maximum likelihood analysis of 983 concatenated ultraconserved elements. Samples from Sulawesi are labeled with the species name, locality, and catalog number. Asterisks indicate type specimens from Miller and Hollister (1921). Ultrafast bootstrap values <95 are shown.
Dataset of the study "Thirty seconds sit-to-stand test as an alternative for estimating peak oxygen uptake and six-minutes walking distance in women with breast cancer: a cross-sectional study"
<p>Data was collected to study the usefulness of the thirty seconds sit-to-stand test as an alternative for estimating peak oxygen uptake and six-minutes walking distance in women with breast cancer, which is a cross-sectional study derived from the ONCORE project (Randomized controlled trial on comprehensive exercise-based cardiac rehabilitation program for the prevention of anthracyclines and/or anti-HER2 antibodies-induced cardiotoxicity in breast cancer), ClinicalTrials.gov Identifier: NCT03964142</p> <p> </p> <p>DATASET FILE (xlsx) includes 4 sheets:<br> - Dataset_variables: all variables collected pre-post intervention<br> - Descriptive data (baseline): variables used for the descriptive analysis before the intervention (baseline)<br> - Data_CPET-30STS(pre-post): pooled data from CPET-30STS pre-post intervention<br> - Data_6MWD-30STS(pre-post): pooled data from 6MWD-30STS pre-post intervention</p>
Estimation of Air Pollution with Remote Sensing Data: Revealing Greenhouse Gas Emissions from Space
<p><strong>Description</strong></p> <p>This dataset contains remote sensing data from the ESA Copernicus missions Sentinel-2 and Sentinel-5P (tropsopheric NO2 column density) in the 2018-2020 timespan. The satellite measurements each cover ~3100 locations in Europe and ~100 on the US Westcoast, each with a size of 1.2x1.2km. The locations are selected such that each measurement is centered at the location of an air quality measurement station on the ground (from the European Environment Agency or the US Environmental Protection Agency, measuring NO2). This makes it possible to analyze spatiotemporally aligned remote sensing and ground-based measurements.</p> <p> The 13 Sentinel-2 bands are upsampled (bilinear) to 10m resolution and cropped to 120x120 pixel. For some locations multiple Sentinel-2 images are available. The images are stored as binary numpy `.npy` files organized into directories based on their locations. </p> <p>The Sentinel-5P data was pre-processed by mapping the measurements from consecutive satellite overpasses onto a common rectangular grid of 0.05×0.05◦(∼5×5km) across Europe. To harmonize the Sentinel-2 (10m to 60m, upscaled to 10m) and Sentinel-5P (5×3.5km, rescaled to 5×5km) imaging resolutions, the Sentinel-5P data is linearly interpolated to 10m resolution and cropped to 120×120 pixel around the locations of interest. Additionally, all measurements with a QA flag (qa_value) below 75 were discarded, following ESA recommendations. The Sentinel-5P data are stored as `.netcdf` file, organized by location. For each location, three such files are available, containing averaged Sentinel-5P measurements at different temporal frequencies (2018-2020, quarterly, monthly).</p> <p>The <p>samples_{frequency}_{area}.csv</p> files provide a list of observations with the corresponding file paths to a (cloud-free) Sentinel-2 image, the Sentinel-5P measurement, and the average NO2 concentration measurement by the EEA or EPA ground station. These files can be used for easy data-loading.</p> <p><strong>Content</strong></p> <p>The data is organized into the following files:</p> <ul> <li>README.md - this file</li> <li>sentinel-2-eea.tar.gz [33.1GB]</li> <li>sentinel-5p-eea.tar.gz [80.1GB]</li> <li>samples_2018_2020_eea.csv </li> <li>samples_quarterly_eea.csv</li> <li>samples_monthly_eea.csv</li> <li>sentinel-2-epa.tar.gz [0.15GB]</li> <li>sentinel-5p-epa.tar.gz [1.8GB]</li> <li>samples_2018_2020_epa.csv</li> <li>samples_quarterly_epa.csv</li> <li>samples_monthly_epa.csv</li> </ul> <p><strong>Acknowledgement</strong></p> <p>If you use this data set, please cite our publication:</p> <p><em>Scheibenreif, L., Mommert, M., Borth, D., "</em>Estimation of Air Pollution with Remote Sensing Data: Revealing Greenhouse Gas Emissions from Space<em>", Tackling Climate Change with Machine Learning workshop at ICML 2021.</em></p> <p>Please refer to this publication for additional information on the data set.</p> <p>This data set contains modified Copernicus Sentinel data acquired in 2018-2020, processed by ESA.</p> <p> </p> <p><strong>Responsible Author</strong></p> <p>Linus Scheibenreif<br> University of St. Gallen, Institute of Computer Science<br> Chair Artificial Intelligence and Machine Learning<br> linus.scheibenreif ( at ) unisg.ch</p>
A hierarchical dependent double-observer method for estimating waterfowl breeding pairs abundance from helicopters
<p>We applied a dependent double-observer method for helicopter surveys and developed a hierarchical Bayesian model as a means to adjust counts of waterfowl for incomplete detection. We conducted our study using 52 plots in Labrador, Canada. A designated pair of primary observers reported counts and location of all waterfowl flocks that they detected to a pair of secondary observers, including details regarding the species, age and sex of observed birds. Secondary observers then reported any additional flocks observed by them but missed by the primary observers. The pairs of observers alternated between primary and secondary roles during the course of the survey, as well as position (front or back) within the helicopter. We used hierarchical Bayesian models to estimate detection probabilities of waterfowl flocks, as well as derive species-specific detection-corrected abundance and sex composition estimates of flocks. The hierarchical model output allowed us to derive estimates of indicated breeding pairs for each species in the survey area corrected for incomplete detection. Observers seated in the back of the helicopter had higher detection probabilities (0.89; 90% Bayesian Credible Intervals [BCI] = 0.82 – 0.95) than those in the front (0.74; 90% BCI = 0.66 – 0.83), and observer experience had a limited effect on detection. Total crew detection probabilities ranged between 0.99 (90% BCI = 0.97 – 1.00) and 0.97(90% BCI = 0.94 – 0.99), depending on the individual observers' position and role in the helicopter. Detection probabilities were higher for sea ducks and diving ducks and lower for dabbling ducks. Observers generally missed less than 5% of the total indicated pairs for all species. We recommend that detection in helicopter surveys be measured to control for observer turnover, observer experience, and aircraft-related differences in visibility.</p>
Improving estimates of the ionosphere during geomagnetic storm conditions through assimilation of thermospheric mass density
<p>Swarm A/B/C neutral mass density normalized to 400 km to be assimilated by the CTIPe physics based model coupled with the thermosphere ionosphere data assimilation scheme (TIDA). Swarm-A is assimilated and B/C are used for validation purposes. The selected period is March 2015 that contains the St. Patrick's Day storm 2015 between 16-18 of that month.</p>
An estimation of the absolute number of axons indicates that human cortical areas are sparsely connected
<p>This is a collection of preprocessed data and standalone Matlab analysis code for the PLoS: Biology article of the same name, <a href="https://doi.org/10.1371/journal.pbio.3001575">https://doi.org/10.1371/journal.pbio.3001575</a>. The primary processed diffusion MRI connectivity data was reported and previous distributed in our eNeuro article <a href="http://doi.org/10.1523/ENEURO.0416-20.2020">https://doi.org/10.1523/ENEURO.0416-20.2020</a>. The replication dataset was reported and previous distributed by Arnatkeviciute et al. 2021, Nature Communications (<a href="http://doi.org/10.1038/s41467-021-24306-2">https://doi.org/10.1038/s41467-021-24306-2</a>). Please cite these publications when using relevant code or data. Files with the .mat extension are Matlab v7.3 data files. The raw imaging data from which these files were derived are available from <a href="https://db.humanconnectome.org/">https://db.humanconnectome.org</a>.</p>
DoPose: dataset for object segmentation and 6D pose estimation
<p>DoPose (Dortmund Pose)is a dataset of highly cluttered and closely stacked objects. The dataset is saved in the <a href="https://github.com/thodan/bop_toolkit/blob/master/docs/bop_datasets_format.md">BOP format</a>. The dataset includes RGB images, Depth images, 6D Pose of objects, segmentation mask (all and visible), COCO Json annotation, camera transformations, and 3D model of all objects. The dataset contains 2 different types of scenes (table and bin). Each scene contains different view angles. For the bin scenes, the data contains 183 scenes with 2150 image views. In those 183 scenes 35 scenes contain 2 views, 20 contains 3 views and 128 contains 16 views. And for table scenes, the data contains 118 scenes with 1175 image views. in Those 118 scenes, 20 scenes contain 3 views, 50 scenes with 6 images, and 48 scenes with 17 images. So in total, our data contains 301 scenes and 3325 view images. Most of the scenes contain mixed objects. The dataset contains 19 objects in total.</p> <p>For more info about the dataset content and collection process please refer to our <a href="https://arxiv.org/abs/2204.13613">Arxiv preprint</a></p> <p>If you have any questions about the dataset, please contact <strong>anas.gouda@tu-dortmund.de</strong></p>
Nimble Output for MCMC Estimation of Source Apportionment; Accompaniment for Journal Article
<p>Paper <em>A dependent Bayesian Dirichlet Process model for source apportionment of particle number size distribution</em> contributed to the <em>Environmetrics</em> Special Issue on <em>Environmental Data Science</em>. In this paper, a fairly extensive Bayesian model is run using the <em>Nimble</em> probabilistic programming language. To allow for user reproducibility, the output of this model (full, not summary), is provided here.</p>
Small mammal ARTS: Orion receiver data for site radiomapping and vole tracking, and scripts and results for localization and activity estimates
<p class="FirstParagraph">This data set accompanies "An Automated Radio-Telemetry System (ARTS) for Monitoring Small Mammals". </p> <p class="FirstParagraph">The behavior of small fossorial mammals, such as voles, is extremely difficult to observe in natural environments. Small mammals were traditionally studied with labor intensive methods such as trapping and recapture or radio telemetry via homing, which require week/months of work and produce static home range estimates.</p> <p class="FirstParagraph">In pursuit of better understanding natural history and behavioral ecology we implemented an automated radio telemetry system (ARTS) to continuously monitor small mammals. We used an isotropic antenna array coupled with broadband receivers to estimate animal positions with nonlinear least squares, nonparameteric, and Bayesian trilateration methods. We then used Lomb-Scargle periodograms to estimate activity patterns of freely-behaving Prairie voles.</p>
SSP: An R package to estimate sampling effort in studies of ecological communities
<p>SSP (simulation-based sampling protocol) is an R package that uses simulations of ecological data and dissimilarity-based multivariate standard error (MultSE) as an estimator of precision to evaluate the adequacy of different sampling efforts for studies that will test hypothesis using permutational multivariate analysis of variance. The procedure consists in simulating several extensive data matrixes that mimic some of the relevant ecological features of the community of interest using a pilot data set. For each simulated data, several sampling efforts are repeatedly executed and MultSE calculated. The mean value, 0.025 and 0.975 quantiles of MultSE for each sampling effort across all simulated data are then estimated and standardized regarding the lowest sampling effort. The optimal sampling effort is identified as that in which the increase in sampling effort does not improve the highest MultSE beyond a threshold value (e.g. 2.5 %). The performance of SSP was validated using real data. In all three cases, the simulated data mimicked the real data and allowed to evaluate the relationship MultSE – n beyond the sampling size of the pilot studies. SSP can be used to estimate sample size in a wide variety of situations, ranging from simple (e.g. single site) to more complex (e.g. several sites for different habitats) experimental designs. The latter constitutes an important advantage in the context of multi-scale studies in ecology. An online version of SSP is available for users without an R background.</p>
Correlation spectroscopy with multi-qubit-enhanced phase estimation: data
<p>This directory contains the data shown in Figures 2-8 of the paper "Correlation spectroscopy with multi-qubit-enhanced phase estimation" (https://doi.org/10.48550/arXiv.2203.12656). Each data set is stored as matlab .mat file containing variables described in the accompagnying .text document</p>
On the estimation of landslide intensity, hazard and density via data-driven models.
<p>The geographic prediction of landslide occurrence is undertaken by assessing whether a slope may be stable or unstable. In other words, current practices treat slopes where a single landslide occurred in the same way as slopes where many landslides occurred. At the slope scale, this procedure inevitably underestimates the effect of multiple landslides.<br> Here we model the number of landslides per slope instead. Then, thanks to the close relation that the number of failures shows with respect to landslide size, we convert the estimated number of landslides into estimated landslide areas. Ultimately, we also estimate the expected proportion of a slope affected by landslides. This framework is more informative than the stable/unstable paradigm and may help landslide risk mitigation strategies.</p>
The implications of incongruence between gene tree and species tree topologies for divergence time estimation
<p>Phylogenetic analyses are increasingly being performed with datasets that incorporate hundreds of loci. Due to incomplete lineage sorting, hybridization, and horizontal gene transfer, the gene trees for these loci may often have topologies that differ from each other and from the species tree. The effect of these topological incongruences on divergence time estimation has not been fully investigated. Using a series of simulation experiments and empirical analyses, we demonstrate that when topological incongruence between gene trees and the species tree is not accounted for, the temporal duration of branches in regions of the species tree that are affected by incongruence is underestimated, whilst the duration of other branches is considerably overestimated. This effect becomes more pronounced with higher levels of topological incongruence. We show that this pattern results from erroneous estimation of the number of substitutions along branches in the species tree, although the effect is modulated by the assumptions inherent to divergence time estimation, such as those relating to the fossil record or among-branch-substitution-rate variation. By only analysing loci with gene trees that are topologically congruent with the species tree, or only taking into account the branches from each gene tree that are topologically congruent with species tree, we demonstrate that the effects of topological incongruence can be ameliorated. Nonetheless, even when topologically congruent gene trees or topologically congruent branches are selected, error in divergence time estimates remains. This stems from temporal incongruences between divergence times in species trees and divergence times in gene trees, and more importantly, the difficulty of incorporating necessary assumptions for divergence time estimation.</p>
An ensemble of 48 perturbed-physics model (Noah-MP) estimates of the 1/8° runoff over the conterminous United States, 1980–2015
<p>This dataset contains the 1980–2015 monthly evapotranspiration simulated by a 48-member perturbed-physics ensemble configured from the Noah LSM with multi-physics options (Noah‑MP v3.6). Simulation outputs include the surface and subsurface runoff. The file name has four parts: the variable collection, the used parameterization, the time scale, and the suffix.</p> <p>The 48 physics configurations are generated by combining four runoff parameterizations (run1: SIMGM, run2: SIMTOP, run3: NOAHR, run4: BATS), two parameterizations of stomatal conductance (can1: Ball–Berry, can2: Jarvis), three parameterizations of soil moisture stress factor (btr1:NOAHB, btr2: CLM, btr3: SSiB), and two parameterizations of near-surface atmospheric turbulence (tub1: M-O, tub2: Chen97).</p> <p>The simulation domain covers the all of conterminous United States (25°–53°N, 125°–67°W), which is also called the NLDAS-2 testbed (Xia et al., 2012a, b). The simulations were performed at a spatial resolution of 0.125°, which is the same as for NLDAS-2 models. Details of the simulation settings and spin-up run can be found in Section 2.3 of Zheng et al. (2019) and Section 2.2 of Fei et al. (2021).</p>
An ensemble of 48 perturbed-physics model (Noah-MP) estimates of the 1/8° ET over the conterminous United States, 1980–2015
<p>This dataset contains the 1980–2015 monthly evapotranspiration simulated by a 48-member perturbed-physics ensemble configured from the Noah LSM with multi-physics options (Noah‑MP v3.6). Simulation outputs include total evapotranspiration and its constituents (canopy evaporation, soil evaporation, and transpiration). The file name has four parts: the variable collection, the used parameterization, the time scale, and the suffix.</p> <p>The 48 physics configurations are generated by combining four runoff parameterizations (run1: SIMGM, run2: SIMTOP, run3: NOAHR, run4: BATS), two parameterizations of stomatal conductance (can1: Ball–Berry, can2: Jarvis), three parameterizations of soil moisture stress factor (btr1:NOAHB, btr2: CLM, btr3: SSiB), and two parameterizations of near-surface atmospheric turbulence (tub1: M-O, tub2: Chen97).</p> <p>The simulation domain covers the all of conterminous United States (25°–53°N, 125°–67°W), which is also called the NLDAS-2 testbed (Xia et al., 2012a, b). The simulations were performed at a spatial resolution of 0.125°, which is the same as for NLDAS-2 models. Details of the simulation settings and spin-up run can be found in Section 2.3 of Zheng et al. (2019) and Section 2.2 of Fei et al. (2021).</p>
An ensemble of 48 perturbed-physics model (Noah-MP) estimates of the 1/8° terrestrial water storage over the conterminous United States, 1980–2015
<p>This dataset contains the 1980–2015 monthly terrestrial water storage simulated by a 48-member perturbed-physics ensemble configured from the Noah LSM with multi-physics options (Noah‑MP v3.6). Simulation outputs include the total terrestrial water storage and its constituents (snow water equivalent, four-layer soil water content from the surface down to 2 m, and the groundwater storage anomaly). The file name has four parts: the variable collection, the used parameterization, the time scale, and the suffix.</p> <p>The 48 physics configurations are generated by combining four runoff parameterizations (run1: SIMGM, run2: SIMTOP, run3: NOAHR, run4: BATS), two parameterizations of stomatal conductance (can1: Ball–Berry, can2: Jarvis), three parameterizations of soil moisture stress factor (btr1:NOAHB, btr2: CLM, btr3: SSiB), and two parameterizations of near-surface atmospheric turbulence (tub1: M-O, tub2: Chen97).</p> <p>The simulation domain covers the all of conterminous United States (25°–53°N, 125°–67°W), which is also called the NLDAS-2 testbed (Xia et al., 2012a, b). The simulations were performed at a spatial resolution of 0.125°, which is the same as for NLDAS-2 models. Details of the simulation settings and spin-up run can be found in Section 2.3 of Zheng et al. (2019) and Section 2.2 of Fei et al. (2021).</p>
Supplementary Materials for 'Mobile device-based Bluetooth Low Energy Database for range estimation in collaborative positioning'
<p>Supplementary Materials for 'Mobile device-based Bluetooth Low Energy Database for range estimation in collaborative positioning'</p> <p>This package contains a collaborative BLE-RSS database, which considers different collaborative set-ups involving five mobile devices. The database is composed of three main subdirectories (Raw-Data, Processed-Data, and Code). The Code directory contains the Matlab script files used to process the raw data, visualize the processed data, and usage examples of the data provided. Further information is provided in the Readme file.</p>
ScienceDex guides
Understand access before you commit
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.