Find research datasets worth reusing

The computation results of coupled hydrological and hydrodynamic modelling application for the Nemunas River watershed – Curonian Lagoon – South-Eastern Baltic Sea continuum

The datasets provided here were used to analyse the cumulative impacts of climate change in a Nemunas River watershed – Curonian Lagoon – South‑Eastern Baltic Sea continuum by applying a state-of-the-art coupled modelling system, which consists of hydrological and hydrodynamic models. Meteorological data used for running the models were acquired from CORDEX (Coordinated Regional Downscaling Experiment) scenarios for Europe from the Rossby Centre high-resolution regional atmospheric climate model (RCA4), which consisted of four sets of simulations (downscaling) driven by four global climate models: <table> <tbody> <tr> <th>Abbreviation in datasets</th> <th>Model</th> <th>Institution</th> </tr> </tbody> <tbody> <tr> <td>ICHEC</td> <td>EC-Earth</td> <td>Irish Centre for High-End Computing</td> </tr> <tr> <td>IPSL</td> <td>IPSL-CM 5A-MR</td> <td>The Institut Pierre-Simon Laplace</td> </tr> <tr> <td>MOHC</td> <td>HadGEM2-ES</td> <td>Met Office Hadley Centre</td> </tr> <tr> <td>MPI</td> <td>MPI-ESM-LR</td> <td>Max Planck Institute for Meteorology</td> </tr> </tbody> </table>   Climate change scenarios and periods: <ul> <li>Historical/reference (1970-2005);</li> <li>RCP4.5 (2005-2100);</li> <li>RCP8.5 (2005-2100).</li> </ul> The datasets consist of time series for the parameters of: <ul> <li>Ice thickness - average ice thickness in the Curonian Lagoon;</li> <li>Meteorological data - bias-corrected temperature and precipitation data for the marine and terrestrial areas;</li> <li>Nemunas River discharge - simulated average daily values for the discharge and water temperature;</li> <li>Salinity - selected points in the south-eastern Baltic Sea and one point next to Juodkrantė (in the Curonian Lagoon);</li> <li>Water fluxes - through four predefined cross-sections in the Curonian Lagoon;</li> <li>Water level - in 10 preselected points in the Curonian Lagoon and South-eastern Baltic Sea;</li> <li>Water residence time - in the total Curonian Lagoon area, as well as its northern and southern parts;</li> <li>Water temperature - in 10 preselected points in the Curonian Lagoon and South-eastern Baltic Sea.</li> </ul> Some of the datasets (zip files) have additional information (coordinates, data column explanations, units, etc.) in READ_ME.txt files.

Supplementary videos for the "Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocytes in co-culture" manuscript

Supplementary videos for preprint manuscript:  Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocytes in co-culture Liuba Dvinskikh, Hugh Sparks, Liliana Brito, Kenneth T MacLeod, Sian E Harding, Christopher Dunsby bioRxiv 2023.01.28.526043; doi: https://doi.org/10.1101/2023.01.28.526043 All videos have been rendered with JPEG compression. Shortened video captions (Please see supplementary information document for full caption) Video 1: 3D LSFM timelapse of hiPSC-CM undergoing spontaneous calcium transients.   Video 2: Widefield transillumination timelapse of hiPSC-CM and adult-CM  Video 3: Widefield fluorescence timelapse of hiPSC-CM and adult CM with synchronized spontaneous calcium transients.  Video 4a: 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture undergoing synchronized spontaneous transients.  Video 4b: Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture undergoing synchronized spontaneous transients.  Video 5a: 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture undergoing synchronized spontaneous transients in a sample without NBleb.  Video 5b: Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture without NBleb undergoing synchronized spontaneous transients.  Video 6a: 3D LSFM timelapse of hiPSC-CM and adult-CM co-culture undergoing synchronized spontaneous transients in a sample treated with NBleb.  Video 6b: Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture with NBleb undergoing synchronized spontaneous transients.  Video 7a: 3D LSFM timelapse of hiPSC-CM and adult-CM day 0 co-culture undergoing synchronized spontaneous transients in a sample without NBleb.  Video 7b: Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 0 co-culture without NBleb.

Dataset of electron-phonon coupling calculations for graphene using DFTBephy

This dataset accompanies the publication titled "DFTBephy: A DFTB-based Approach for Electron-Phonon Coupling Calculations". The ZIP file contains results for graphene obtained with <a href="https://github.com/CoMeT4MatSci/dftbephy">DFTBephy</a> for different parametrizations (matsci, mio and 3ob) and one SCC calculation (matsci-scc). The corresponding directories contain the optimized unit-cell (geo_end.gen), the electronic band-structure and phonon dispersion along a band-path (path_el_bandstructure.json and path_ph_bandstructure.json), the (square of the) electron-phonon coupling matrix close to the K-point (el-ph-Nq200-K.hdf5), and the electronic life-times on a k-mesh (relaxation-times-fine.hdf5).

Dataset for "Binary-coupling sparse Sachdev-Ye-Kitaev model: an improved model of quantum chaos and holography"

Spectral data for binary, unary and Gaussian-coupling, sparse and dense Sachdev-Ye-Kitaev model used for the publication. Directories are named by the number of Majorana fermions, and the coupling type (binary, Gaussian, unary) and the number of non-zero couplings are indicated in the file name. In each file, the computed eigenenergies are given in little-endian double-precision floating numbers, eight bytes for each eigenstate, in ascending order for each parity sector (even followed by odd) for each generated sample. Except for N = 32 and 34 where a single sample is given, each file contains 2^{24-(N/2)} samples, 131 072 for N = 14, 65 536 for N = 16, ..., and 512 for N = 30.

opencc-by-4.0Feb 2023View details →

Dataset: Core excitations and ionizations of uranyl in Cs2UO2Cl4 from relativistic embedded damped response time-dependent density functional theory and equation of motion coupled cluster calculations

This dataset collects the unprocessed (= outputs from calculations) results discussed in the paper titled "Core excitations and ionizations of uranyl in  Cs2UO2Cl4  from relativistic embedded damped response time-dependent density functional theory and equation of motion coupled cluster calculations", by Wilken Aldair Misael and Andre Severo Pereira Gomes. It also contains the figures used in the manuscript.

opencc-by-4.0Feb 2023View details →

Cavity-waveguide coupling gap

Extrinsic coupling loss of a microring coupled to a waveguide as a function of the gap between the structures. Data simulated with Comsol.

opencc-by-4.0Feb 2023View details →

Ring-ring coupling gap

Coupling coefficients of two coupled microrings as a function of the gap between the structures. Data simulated with Comsol.

opencc-by-4.0Apr 2023View details →

Dataset: GNSS PPP-RTK Tightly Coupled with Low-cost Visual Inertial Odometry aiming at Urban Canyons

GNSS can provide high-precision positioning worldwide and is the preferred positioning method in autonomous driving and intelligent transportation etc. However, in complex urban environments, due to serious signal occlusion, the positioning performance of GNSS deteriorates sharply, and it even provides incorrect positioning information. To obtain robust navigation, GNSS is usually integrated with inertial measurement unit (IMU) to form a GNSS/INS integrated system. But in complex scenarios, the performance of GNSS/INS is closely related to IMU. For low-cost MEMS IMU, though it can facilitate GNSS positioning to a certain extent, it still cannot stably provide reliable positioning information. Visual sensors and IMUs can be combined to form a VINS system, which can obtain accurate local pose estimation. Therefore, adding visual information to MEMS IMU-based GNSS/INS systems can effectively suppress the divergence of MEMS IMU errors, and provide precise and reliable positioning services in GNSS-challenging environments.

opencc-by-4.0Mar 2022View details →

Oncogenic signalling is coupled to colorectal cancer cell differentiation state

Mass cytometry and single-cell RNA-sequencing data as well as R Markdown reports to reproduce the figures of our publication. Raw MC data were saved post de-convolution, spillover-compensation, and removal of calibration bead events. Gates for singlets and non-dead cells (low_Pt) are included as logical columns and should be applied prior to usage. As we performed random sampling to equalise cell numbers across conditions, batch normalisation, and used non-linear dimensionality reduction techniques (UMAP and Diffusion Maps), resulting plots may differ slightly from the published figures, yet still support the drawn conclusions. Already normalised and/or sampled data as well as pre-computed UMAP and Diffusion Map coordinates are included in this data set to reproduce the manuscript figures exactly, as shown in the included report “figures_only”. For all details on the batch normalisation and data analysis steps performed, please consult the report “data_analysis” instead.

dryad40/100

Food webs coupled in space: Consumer foraging movement affects both stocks and fluxes

The exchange of material and individuals between neighbouring food webs is ubiquitous and affects ecosystem functioning. Here, we explore animal foraging movement between adjacent, heterogeneous habitats and its effect on a suite of interconnected ecosystem functions. Combining dynamic food-web models with nutrient-recycling models, we study foraging across habitats that differ in fertility and plant diversity. We found that net foraging movement flowed from high to low fertility or high to low diversity and boosted stocks and flows across the whole loop of ecosystem functions including biomass, detritus, and nutrients in the recipient habitat. Contrary to common assumptions, however, the largest flows were often between the highest and intermediate fertility habitats rather than highest and lowest. The effect of consumer influx on ecosystem functions was similar to the effect of increasing fertility. Unlike fertility, however, consumer influx caused a shift towards highly predator-dominated biomass distributions, especially in habitats that were unable to support predators in the absence of consumer foraging. This shift resulted from both direct and indirect effects propagated through the interconnected ecosystem functions. Only by considering both stocks and fluxes across the whole loop of ecosystem functions do we uncover the mechanisms driving our results. In conclusion, the outcome of animal foraging movements will differ from that of dispersal and diffusion. Together we show how considering active types of animal movement and the interconnectedness of ecosystem functions can aid our understanding of the patchy landscapes of the Anthropocene.

opencc-zeroApr 2023View details →

opencc-by-4.0Apr 2023View details →

Data for Coupling Covariance Matrix Adaptation with Continuum Modeling for Determination of Kinetic Parameters Associated with Electrochemical CO2 Reduction

This data set contains digitized and tagged polarization and partial current density data for 18 datasets of CO2 reduction to H2 and CO over Ag catalysts, as well as 8 datasets of CO2 reduction to HCOO-, CO, and H2 over Sn catalysts. We analyze this data using a coupled continuum modeling and covariance matrix adaptation approach for which the codebase is provided in DOI: 10.5281/zenodo.7866195.

opencc-by-4.0Apr 2023View details →

Virtual Coupling in Railways: A Comprehensive Review. Support data files

Support files for VOSviewer maps and Scopus statistics

Tip of the Red Giant Branch Bounds on the Axion-Electron Coupling Revisited

# Reproduction package for the Paper "Tip of the Red Giant Branch Bounds on the Axion-Electron Coupling Revisited" ## Authors Mitchell T. Dennis (mtde226@hawaii.edu) Jeremy Sakstein (sakstein@hawaii.edu) ## Software MESA version 12778 (http://mesa.sourceforge.net/)   MESASDK version 20200325 (http://www.astro.wisc.edu/~townsend/static.php?ref=mesasdk)   GFORTRAN GCC version 9.2.0 Python 3.8.10 TensorFlow 2.4.1 ## Citation Policy If you use any part of this reproduction package for independent work, we recommend you cite: * This paper If you use any of the MESA outputs found in the LOGS folder, we recommend you cite the MESA papers * Astrophys. J. Suppl. 192, 3 (2011) * Astrophys. J. Suppl. 208, 4 (2013) * Astrophys. J. Suppl. 234, 34 (2018) * Astrophys. J. Suppl. 243, 10 (2019)   For more information, see the Readme.md

MESMAR v1: A new regional coupled climate model for downscaling, predictability, and data assimilation studies in the Mediterranean region. Article data

Regional coupled and Earth System models are fundamental numerical tools for climate investigations, downscaling of predictions and projections, process-oriented understanding of regional extreme events, and many more applications. Here we introduce a newly developed coupled regional modeling framework for the Mediterranean region, called MESMAR (Mediterranean Earth System model at ISMAR) version 1, which is composed of the WRF atmospheric model, the NEMO oceanic 15 model, and the HD hydrological discharge model, coupled via the OASIS coupler. The model is implemented at moderate resolution (about 1/12° for the ocean and river routing, while twice coarser for the atmosphere) for long-term investigations. The gzipped tarball contains data files contained in the manuscript associated with the MESMARv1 description and submitted to Geoscientific Model Developments: MESMAR v1: A new regional coupled climate model for downscaling, predictability, and data assimilation studies in the Mediterranean region by Andrea Storto, Yassmin Hesham Essa, Vincenzo de Toma, Alessandro Anav, Gianmaria Sannino, Rosalia Santoleri, Chunxue Yang

Data and code associated with the paper 'Mode-Specific Coupling of Nanoparticle-on-Mirror Cavities with Cylindrical Vector Beams'

Data and code associated with the following paper: <a href="https://doi.org/10.1021/acs.nanolett.3c00561">V. Vento et al, Nano Lett. 2023</a> A thorough explanation of the experiment performed is available there. The name of each sub-folder and file in Maps_data_code.zip indicates the corresponding figure number ("FIG #") and the type of content ("raw_data", "data", "plot", "analysis", "calculation", "simulation"). The Raman maps data are analyzed through the script Raman_maps_analysis.m. The photoluminescence maps data in the supplementary information are analyzed through the script PL_maps_analysis.m.  Used softwares: Matlab R2021a, Python 3.9, Comsol Multiphysics 5.6

Deformation simulation results of Capriccio method coupled systems for conducting comparative one- and multidimensional studies on the coupling of the finite element method with particle-based techniques

readme_3Dresults.txt Description: This readme explains the content and path structure of the results obtained from a deformation test conducted on slightly different MD-FE coupled systems performing the Capriccio method in a three-dimensional space within the associated project thesis [1], published on the following dataset: <a href="https://doi.org/10.5281/zenodo.7924367">https://doi.org/10.5281/zenodo.7924367</a> Furthermore, input files and parameters as well as potential tables required to reproduce the obtained data are provided as well. The molecular dynamics (MD) part is executed in LAMMPS and the finite element (FE) method part by a MATLAB script as described in Section 4.1 of [1]. The whole setup of the 3D models is elaborated in Section 4.2 of [1]. A discussion of some results is given in Chapter 6 of [1] in the context of assessing their comparability with the corresponding 1D model. Context: [1] L. Laubert, "Establishing a framework for conducting comparative one- and multidimensional studies on the coupling of the finite element method with particle-based techniques", Project Thesis, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 2023. Contact: Lukas Laubert Institute of Applied Mechanics Friedrich-Alexander-Universiät Erlangen-Nürnberg Egerlandstraße 5 91058 Erlangen License: Creative Commons Attribution Non Commercial 4.0 International Path structure and files: - The ZIP compressed files each contain a folder containing all simulation files as well as   postprocessing variables: * /FE_data/ contains all output files after each FE simulation in each iteration step * /MD_data/ contains all output files after each MD simulation in each iteration step * /input_files/ contains the input FE model "cgps_dpd_c_1_2000.inp", the MD particle   configurations "cgps_dpd_c_1_2000.data", the AP particle coordinates    "cgps_dpd_c_1_2000.ac" as well as further Abaqus CAE FE files that   can be used to adapt the present FE model * /input_parameters/ contains the parameter dataset; "Capriccio.prm" is the main parameter   dataset, whose adaptations lead to similar adjustments in the other parameter files * "Capriccio_FEMD_main_meggie_WZ.sh" is a shell script for executing simulations * "job.out" is an output protocol that documents the progress of the simulations * "Job.err" is an error protocol that documents detected errors during the simulations * "log.lammps" logs MD parameter sets * "meta.info" provides version information of used softwares among few other information * "next_job.info" documents the next load step and iteration step that is to be executed   when simulation jobs are restarted on the used computation cluser * **_workspace_vars.mat comprises a set of postprocessing variables obtained by executing a   postprocessing script provided by Capriccio group - "md_dpd_main-CBpot-writeobs-sandw.in" is an input script that further defines and loads   MD simulation parameter - ***_table are potential tables applied during the MD simulations * "Angle_table" lists the angle bending potential * "Bond_table" lists the bond potentials * "Nonbond_table" lists the non-bonded interaction potential

Interaction of genital microbiota in infertile couples

Bacteria colonise most of the human body and the genital tract is not an exception. While it has been known for decades that a vaginal microbiota exists, other genital sites have traditionally been viewed as sterile environments, with bacterial presence associated only with pathological conditions. However, recent studies identified specific patterns of bacterial colonisation in most genital sites. Shifts in the bacterial colonisation of the female genital tract have been linked to impairment of reproduction and adverse pregnancy outcomes, such as preterm birth. The goal of this project is to understand the association between the genital microbiota of couples seeking assisted procreation aid and the outcome of this treatment. Male and female partners will be studied as a unit (“couple microbiota”) and the interaction between their microbiota will be evaluated. We have characterized microbial samples coming from vaginal and penile swabs, as well as follicular fluid and semen, using next generation sequencing (16S rRNA profiling). The results were linked to clinical data of the patients included in the study and particularly to the results of the fertility treatment process. With this project, we aim to gain a better understanding of how the male genital microbiota could influence the lower (vagina) and upper (follicular fluid) female genital tracts. Github repository link: <a href="https://github.com/dfmemicrobiota/infertile_couples">https://github.com/dfmemicrobiota/infertile_couples</a>

opencc-by-4.0Jun 2023View details →

Rock magnetic data sets for Coupled detachment faulting and hydrothermal circulation at 49.7°E Southwest Indian Ridge revealed by seafloor magnetism

The rock magnetic data sets in "Coupled detachment faulting and hydrothermal circulation at 49.7°E Southwest Indian Ridge revealed by seafloor magnetism" was studied, including the density, magnetic susceptibility, NRM, Q ratio and other parameters of rock samples , as well as the thermomagnetic curves, hysteresis loops, FORCs, AF and TD demagnetization.

dryad40/100

Data for: Coupling dynamic energy budget and population dynamic models to inform stock enhancement in fisheries management

Extensive applications of fishery stock enhancement worldwide bring up broad concerns about its negative effects, creating a pivotal need for science-based assessment and planning of enhancement strategies. However, the lack of mechanistic understanding of enhanced population dynamics, particularly the density-dependent processes, leads to compromise in model development and limits the capacity in predicting enhancement effects. Here, we developed an individual-based model based on dynamic energy budget theory and full life history processes, to understand the mechanism of density dependence in population dynamics that emerge from individual-level processes. We demonstrated the utility of the model framework by applying it to an extensively enhanced species, Chinese prawn (Fenneropenaeus chinensis, Penaeidae). The model could yield projections reflecting the observed trajectory of population biomass and yields. The model also delineated the key effects of density dependence on the vital rates of growth, fecundity, and starvation mortality. Regarding the manifold effects of stock enhancement, we demonstrated a dampened shape in population biomass and yields with increasing magnitude of enhancement, and trade-offs between the ecological and economic objectives, i.e., pursuing high benefit might compromise the wild population without proper management. Furthermore, we illustrated the possibility of combining stock enhancement and harvest regulation in promoting population recovery while maintaining fisheries yields. We highlight the potential of the proposed model for understanding density dependence in enhancement program, and for designing integrated management strategies. The approach developed herein may serve as a general approach to assess the population dynamics in stock enhancement and inform enhancement management.

opencc-zeroJun 2023View details →