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1,600 results for “input”
Road salt inputs alter biogeochemistry but not plant community composition in exurban forested wetlands
<p class="MsoNoSpacing">Forested wetlands of the temperate north are increasingly exposed to deicing salts, but it is unclear how this may alter wetland biogeochemistry and plant community composition. To investigate potential effects of deicing salts on exurban forested wetlands in southern New England, we employed a multi-site field study to describe spatiotemporal patterns of soil physiochemical, water quality, and vegetation characteristics with distance from road deicing salt source. We surveyed nine road-adjacent, red maple-dominated wetlands to quantify a suite of soil parameters (Na<sup>+</sup>, K<sup>+</sup>, Mg<sup>2+</sup>, Ca<sup>2+</sup>, pH, electrical conductivity (EC), heavy metals, N, P, soil moisture), as well as surface and groundwater salinity, and vegetation communities. With increasing distance from roads along 165-m transects penetrating into each wetland, soil salinity (EC, Na<sup>+</sup>) decreased, while soil base cation<sup> </sup>concentrations (Mg<sup>2+</sup>, Ca<sup>2+</sup>) increased, likely due to cation exchange (Na<sup>+</sup> displacing other base cations). <a name="_Hlk73441264">We also measured foliar chemistry and observed elevated Na<sup>+</sup> and reduced Mg<sup>2+ </sup>of<sup> </sup>dominant species leaf tissue near roads, suggesting plant nutrient uptake responds to road-salt related changes in soil physicochemical variables. </a>Despite this, we did not detect differences in plant community composition (ground, shrub layers) along road-salt induced soil chemistry gradients in the field, likely because surface and ground water salinities were relatively low (maximum: 0.64 ppt). To determine at which field salinities we could potentially expect changes in wetland plant communities, we conducted a full-factorial, manipulative seed bank experiment to examine how NaCl concentration (0, 0.5, 1, 2, 4, 8 parts per thousand (ppt)), frequency of salt exposure (pulse, constant) and water level (surface, 2-cm below surface) affected soil seed bank responses. Seedling richness was reduced at salinities exceeding 1 ppt, and seedling density was reduced above 2 ppt, but pulsing tended to alleviate salt-induced reductions in seed bank responses. As salinization of freshwater ecosystems continues to increase, our results suggest that field salinity levels of exurban New England forested wetlands are nearing yet still typically below the threshold for which we expect to see strong plant community responses. </p>
mosartwmpy sample input data; 1980 - 1985
<p>Sample input data spanning the years 1980-1985 for running the mosartwmpy water routing and management model: https://github.com/IMMM-SFA/mosartwmpy</p>
Underestimated input of terrestrial dissolved organic carbon to the ocean
Open the record for dataset details and reuse information.
Input data for RemoTeC synthetic measurements and retrieval
<p>RemoTeC is a retrieval algorithm developed for the retrieval of trace gas column-averaged dry air mole fractions from measured level 1b radiance spectra in the near-infrared (NIR) and shortwave-infrared (SWIR) bands. It is open access software developed by The Netherlands Institute for Space Research (SRON) and Karlsruhe Institute for Technology (KIT). </p> <p>The dataset available here is the input data for the RemoTeC synthetic measurement and retrieval code. The source code for these algorithms can be found at:</p> <p><a href="https://bitbucket.org/sron_earth/remotec_synthetic_measurements/src/master/">https://bitbucket.org/sron_earth/remotec_multi_purpose/src/main/</a></p> <p>Here we provide the data for both of these algorithms. The retrieval code should be used in conjunction with the synthetic measurement generator, but the synthetic measurement generator can be used as stand alone code. Any publications from using either of these codes should reference DOI for this dataset.</p>
Implementing Riverine Biogeochemical Inputs in ECCO-Darwin: A Sensitivity Analysis of Terrestrial Fluxes in a Data-Assimilative Global Ocean Biogeochemistry Model
<p>Resolving riverine biogeochemical inputs in ocean biogeochemistry models is pivotal for capturing the spatiotemporal variability of nutrients and carbon in coastal regions and in the global ocean. ECCO-Darwin is a pioneering data-assimilative global-ocean biogeochemistry model, which, to date, has focused on the pelagic zone. In this work, we use an optimized version of ECCO-Darwin to perform a sensitivity analysis to quantify the response of the open ocean and coastal margins to lateral inputs of carbon and nutrients. We generate riverine inputs by combining point-source freshwater discharge from JRA55-do with the Global NEWS 2 watershed model, accounting for lateral inputs from 5171 watersheds worldwide. While adding carbon and nutrients along with freshwater improves biogeochemical skill in river plume regions and coastal waters, the open-ocean response may be overestimated due to an excess of carbon and nutrients advected offshore. This highlights the need for a more nuanced representation of land-to-ocean and nearshore processes for quantifying how global ocean primary production and carbon cycling respond to land-to-ocean inputs.</p>
Input files and dataset for CD3CN+F Reaction sampling in CHARMM
<p>The input files and resulting trajectory data for the CD3CN application described in:</p> <p><a href="https://pubs.rsc.org/en/content/articlelanding/2016/fd/c6fd00138f#!divAbstract">Adaptive free energy sampling in multidimensional collective variable space using boxed molecular dynamics</a>, by O'Connor et al.</p>
More Flexible Number Formats for High-Accuracy Simulations - Randomized Inputs
<p>The random input matrices and vectors used in the thesis "More Flexible Number Formats for High-Accuracy Simulations".</p>
Inputs (forcing and observations) ready for use by 'MuSA: The Multiscale Snow Data Assimilation System (v1.0)'
<p>MuSA is a snow data assimilation system that can fuse observations with snowpack simulations generated by the Flexible Snow Model (FSM2). This repository contains meteorological forcing developed with the Micromet model and 5 m resolution snow depth observations in the Izas basin (central Spanish Pyrenees) generated with drones, ready to be used in MuSA.</p>
LHM fresh-salt 4.1 input data
<p>This dataset includes the necessary input file to run the LHM fresh-salt workflow, version 4.1. After checkout of the git-repository at https://gitlab.com/deltares/imod/nhi-fresh-salt/-/tags/LHM_fresh-salt_4.1_final, extract the zipfile to the location ./data/1-external.</p> <p>The data can be viewed and downloaded separately at the NHI dataportal: https://data.nhi.nu</p>
Results and assumptions for: Modeling the Circular Economy in Environmentally Extended Input-Output Tables: methods, software and case study
<p>This dataset presents supplementary information for <em>"Modeling the Circular Economy in Environmentally Extended Input-Output Tables: methods, software and case study" </em><a href="https://doi.org/10.1016/j.resconrec.2019.104508">https://doi.org/10.1016/j.resconrec.2019.104508</a></p> <p>The data was processed and results were obtained through https://cmlplatform.github.io/pycirk/</p> <p> </p> <p><br> Annex I: Scenario assumptions and modeling choices and complete results (file Annex_I.xlsx) <br> Annex II: Contains analysis of other software, database modifications, and list of affected categories (file Annex_II.docx) <br> Results: settings, assumptions, results and their analysis from the case study presented in the paper (file Donati_CE_EEIO_Mo_SI.tar.gz)</p>
JMLKelinci+: Detecting Semantic Bugs and Covering Branches with Valid Inputs using Coverage-Guided Fuzzing and Runtime Assertion Checking
<p>Testing to detect semantic bugs is essential, especially for critical systems. Coverage-guided fuzzing and runtime assertion checking (RAC) are two well-known approaches for detecting semantic bugs. Coverage-guided fuzzing aims to generate inputs tests with high code coverage. However, while coverage-guided fuzzers are equipped with sanitizers that can detect a fixed set of semantic bugs, they can otherwise only detect bugs that lead to a crash. Thus, the first problem we address is how to help fuzzers detect previously unknown semantic bugs that do not lead to a crash. Moreover, a coverage-guided fuzzer may not necessarily cover all branches with valid inputs, although invalid inputs are useless for detecting semantic bugs. So, the second problem is how to guide a fuzzer to cover all branches in a program using only valid inputs. On the other hand, RAC monitors the expected behavior of a program dynamically and can only detect a semantic bug when a valid input test shows that the program does not satisfy its specification. <br> Thus, the third problem is how to provide high-quality input tests for a RAC that can trigger potential bugs.<br> The combination of a coverage-guided fuzzer and RAC solves these problems and can cover branches with valid inputs and detect semantic bugs effectively. Our study uses RAC to guarantee that only valid inputs reach the program under test using the program's specified preconditions and it also uses RAC to detect semantic bugs using specified postconditions. A prototype tool was developed for this study, named JMLKelinci+. Our results show that combining a coverage-guided fuzzer with RAC will lead to executing the program under test only with valid inputs and that this technique can effectively detect semantic bugs. <br> Also, this idea improves the feedback given to a coverage-guided fuzzer, enabling it to cover all branches faster in programs with non-trivial preconditions.</p>
Abeshu-etal_2023_GMD: Model Input and Output data
<p>1. Input data required to conduct the experiment</p> <p>2. Model output data for reproducing the manuscript figures</p>
MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"
<p>Input files and trajectories of n-alkane/lipid systems used in the article: ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids".</p> <p>Equilibrated starting configurations were created using CHARMM36. Otherwise, filenames specifiy the force field used (C36 or SL), Temperature and system composition.</p> <p>.xtc trajectories were created using gmx trjconv with options -pbc nojump -dt 10. run2 equals simulations from 100-200ns, run3 equals 200-300ns. The first 100ns were excluded from the analysis and are not included in this dataset.</p> <p>Exemplary .mdp files have been included for both force-fields. Please refer to the manuscript for the force field sources and additional information.</p>
SimBEV input data (probabilities)
<p>This dataset includes aggregated probabilities for the creation of vehicle driving profiles used in the simulation tool <a href="https://github.com/rl-institut/simbev">SimBEV</a>. The probabilies are based on the survey <a href="https://www.mobilitaet-in-deutschland.de/publikationen2017.html">Mobilitaet in Deutschland 2017</a>.</p>
Input parameters for manuscript "Understanding drug skin permeation enhancers using Molecular Dynamics Simulation"
<p>Input parameters used for Gromacs simulations in publication with title: "Understanding drug skin permeation enhancers using Molecular Dynamics Simulation"</p>
Input data for "Characterisation of the mechanism of Bile Salt Hydrolase substrate specificity by experimental and computational analyses"
<p>Topologies, coordinates, input and analysis scripts for Amber20 simulations performed in "Characterisation of the mechanism of Bile Salt Hydrolase substrate specificity by experimental and computational analyses", Structure, 2023</p>
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations: Simulations Topology, Coordinate, Parameters, Input and Output files
<p>The simulation data for the article: Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations.</p> <p>ck_metad.tar.gz: Includes the topology files, coordinates files and gromacs parameter input file (.mdp) used for WT-MetaD-HREX simulations with different c(K+), which are newly added runs for resubmission. The corresponding script files and Plumed files are in GitHub.</p> <p>eq_mini.tar.gz: Includes the parameter files required for the equilibration and minimization protocol.</p> <p>standard_md.tar.gz: Includes the topology files and coordinate files for all systems built in the article. Also include the hbfix parameters file required on the MD run, and the MD script file.</p> <p>metad.tar.gz: Includes the topology files, coordinates files and gromacs parameter input file (.mdp) used for WT-MetaD-HREX simulations. The corresponding script files and Plumed files are in GitHub.</p> <p>metad*fe*.tar.gz: Plumed HILLS files and metad.bias data used for drawing the free energy landscapes.</p> <p>ions.tar.gz: Data used for Figure.3 in the manuscript</p> <p>si_data.tar.gz: All data used for SI figures.</p>
EFECT Modelling Mission 2023 | Input dataset
<p>This upload contains the supplementary data for the EFECT modelling mission 2023.</p> <p> </p>
Benchmark denoising strategies on fMRIPrep output - input data
<p>All inputs required to build the figures and statistics in the jupyter book.<br> Including: summary statistics for the figures and average connectomes per dataset.<br> Untar the file and put it under the `inputs/` directory.</p> <p>Repository: https://github.com/SIMEXP/fmriprep-denoise-benchmark</p> <p>Book: https://simexp.github.io/fmriprep-denoise-benchmark/</p> <p> </p>
LOTOS code inputs for local earthquake tomography of the Irazú-Turrialba volcanic complex, Costa Rica
<p>Local earthquake seismic tomography model for Jiwani-Brown, E., Koulakov, I., Muñoz-Burbano, F., Pacheco, J., Mora, M., & Lupi, M. (2023). Comparing local and ambient seismic tomographic methods to infer the plumbing system of the Irazú-Turrialba volcanic complex, Costa Rica. </p> <p>The tomography model presented in the paper are obtained using the LOTOS code by Koulakov (2009). Input files for running of LOTOS code adapted for Windows OS. More details on the LOTOS code can be found at<a href="http://www.ivan-art.com/science/LOTOS">www.ivan-art.com/science/LOTOS</a></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.