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27,923 results for “model”
Dataset Nucleation Patterns of Polymer Crystals Analyzed by Machine Learning Models
<p>This dataset contains the raw data (01_raw_data), processed data (02_processed_data), and plotting scripts (03_figures) related to the paper:</p> <p>"Nucleation Patterns of Polymer Crystals Analyzed by Machine Learning Models"<br>Atmika Bhardwaj, Jens-Uwe Sommer, Marco Werner</p> <p>Macromolecules <strong>2024</strong>; DOI: <a href="10.1021/acs.macromol.4c00920">10.1021/acs.macromol.4c00920</a></p> <p>Please refer to the README.md files in their respective folders.</p>
Pre-trained models for segmentation and tracking of Coronal Bright Fronts from SDO AIA Base Difference images
<p>Here we present pretrained U-NET-based models followed by SDO AIA Base Difference(BD) validation set after intensity tresholding [-50;150] with predicted feature masks samples. <br>We provide a command-line Python utility for image segmentation using our CNNs designed to process images of solar eruptive phenomena. The https://gitlab.com/iahelio/helios_cnn repository includes regularly updated and newly published models. </p> <p>First model we present is designed to predict the likelihood of each pixel belonging to a certain class or feature in the solar image. A probabilistic output allows for a more nuanced interpretation of ambiguous region. The output can be converted into binary masks through thresholding. The range of values also gives insights into the model's confidence</p> <p>We also present sample segmentation results and the second model designed to produce binary masks.</p>
Data used in "BIOPERIANT12: a mesoscale resolving coupled physics-biogeochemical model for the Southern Ocean"
<div> <p>This repository contains the data used to generate the figures for the submitted manuscript "BIOPERIANT12: a mesoscale resolving coupled physics-biogeochemical model for the Southern Ocean".</p> </div> <h3>Contents</h3> <div> <ul> <li> <p>Model input:</p> <ul> <li> <p>INPUTS: ocean model input/grid files</p> </li> <li> <p>PISCES_INPUTS: BGC input files</p> </li> <li> <p>OBC: open boundary forcing </p> </li> <li> <p>WEIGHTS: weight files for ERA interim forcing</p> </li> </ul> </li> </ul> </div> <div> <ul> <li> <p>Manuscript files:</p> <ul> <li> <p>data: files used to generate manuscript images</p> </li> <li> <p>config, src, notebooks: Python code and Jupyter notebooks used to generate images</p> </li> <li> <p>figures, supplementary: manuscript figures and supplementary figures</p> </li> </ul> </li> </ul> </div> <div> </div> <div><strong>Abstract: </strong>"We present BIOPERIANT12, a regional model configuration of the Southern Ocean (SO) at a mesoscale-resolving 1/12 degree. This is a stable, ocean–ice–biogeochemical configuration derived from the Nucleus for European Modelling of the Ocean (NEMO) modelling platform. It is specifically designed to investigate questions related to the mean state, seasonal cycle variability and mesoscale processes in the mixed layer and within the upper ocean (<1000 m). In particular, the focus is on understanding processes behind carbon and heat exchange, systematic errors in biogeochemistry and assumptions underlying the parameters chosen to represent these SO processes. The dynamics of the ocean model play a large role in driving ocean biogeochemistry and we show that over the chosen period of analysis 2000–2009 that the simulated dynamics in the upper ocean provide a stable mean state, as compared to observation-based datasets (themselves subject to biases such as sparsity of data, cloud cover, etc.), and through which the characteristics of variability can be described. Using ocean biomes to delineate the major regions of the SO, the model demonstrates a useful representation of ocean biogeochemistry and partial pressure of carbon dioxide (pCO2). In addition to a reasonable model mean state performance, through model–data metrics BIOPERIANT12 highlights several pathways for improving Southern Ocean model simulations such as the representation of temporal variability and the overestimation of biological biomass."</div>
Hail Event on 2022-06-28 in Locarno-Monti (TI), Switzerland: Drone Photogrammetry Imagery, Mask R-CNN Model and Analysis Data of Hailstones
<p>This hail data collection belongs to a drone hail survey performed on 2022-06-28 in Locarno-Monti (TI, Switzerland). The supercell reached the location around 07:50 UTC in the morning. Only one photogrammetry flight could be performed and thus no estimation of the hail melting process is available. The orthophoto is masked to ignore parts where detection of hail is unwanted.</p> <p> </p> <p>Expert 1 (lai, mlainer), Expert 2 (jtm), Expert 3 (por, jportmann)</p>
Model simulation data used in "The global impact of the transport sectors on atmospheric aerosol in 2030 – Part 2: Aviation" (Righi et al., Atmos. Chem. Phys., 2016)
<p>This dataset contains the output of the EMAC global model simulations analysed and discussed in Righi et al. (<i>Atmos. Chem. Phys.</i>, 2016). For details see the README.md file.</p>
Model simulation data used in "The global impact of the transport sectors on atmospheric aerosol in 2030 – Part 1: Land transport and shipping" (Righi et al., Atmos. Chem. Phys., 2015)
<p>This dataset contains the output of the EMAC global model simulations analysed and discussed in Righi et al. (<i>Atmos. Chem. Phys.</i>, 2015). For details see the README.md file.</p>
AN OPEN-SOURCE, THREE-DIMENSIONAL GROWTH MODEL OF THE MANDIBLE
<p>This repository contains all geometrical data and metadata belonging to the paper AN OPEN-SOURCE, THREE-DIMENSIONAL GROWTH MODEL OF THE MANDIBLE by the MAGIC Amsterdam research consortium. The following contents are uploaded:</p><p><strong>shapeVectors_original.csv</strong> | shape vectors of the original data<br><strong>shapeVectors_rescaled.csv</strong> | shape vectors of the rescaled data<br>678 x 62589 matrices where the rows are samples and the columns are shape vectors. The shape vectors are formatted<i> [x1, x2, x3, ..., y1, y2, y3, ..., z1, z2, z3, ...].</i></p><p><strong>PCA_coeff_original.csv</strong> | principal component coefficients of the original data<br><strong>PCA_coeff_rescaled.csv</strong> | principal component coefficients of the rescaled data<br>62589 x 677 matrices where each row of these matrices is a variable (x-, y-, or z-coordinate of a vertex) and each column is a principal component.</p><p><strong>PCA_score_original.csv</strong> | principal component scores of the original data<br><strong>PCA_score_rescaled.csv</strong> | principal component scores of the rescaled data<br>678 x 677 matrices where rows correspond to samples and columns correspond to principal components.</p><p><strong>PCA_latent_original.csv</strong> | principal component variances of the original data<br><strong>PCA_latent_rescaled.csv</strong> | principal component variances of the rescaled data<br>677 x 1 vectors where each element is an eigenvalue of a principal component.</p><p><strong>PCA_mu_original.csv</strong> | mean of the original data<br><strong>PCA_mu_rescaled.csv</strong> | mean of the rescaled data<br>1 x 62589 vectors that represent the average shape vector. All (centered) data can be reconstructed as follows: <i>shapeVectors = PCA_score * PCA_coeff' + PCA_mu.</i></p><p><strong>PCA_standardDeviations_original.csv</strong> | standard deviations of each sample for each principal component of the original data.<br><strong>PCA_standardDeviations_rescaled.csv</strong> | standard deviations of each sample for each principal component of the rescaled data.<br>677 x 678 matrices where the rows are principal components and the columns are samples. The standard deviations were calculated as follows: <i>PCA_standardDeviations = PCA_score' ./ sqrt(PCA_latent).</i></p><p><strong>metadata.csv</strong> | This matrix contains the age in years (first column) and biological sex (second column, 1 = male and 2 = female) for all samples (rows).</p><p><strong>connectivityList.csv</strong> | This matrix defines the mesh of the 3D model of the mandible. The vector in each row represents which vertices define a triangle. Indexing starts at 0, so for use in e.g. Matlab, add 1 to all elements.</p>
Numerical weather simulation using COSMOiso in June 2019 during L-WAIVE field campaign: selected model output and post-processed data.
<p>This dataset consists of extracts from a simulation with the isotope-enabled regional numerical weather prediction model COSMOiso, which covers the timespan of 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 simulation has a horizontal resolution of 0.1° (~10km) and 40 vertical levels.</p><p>This COSMOiso simulation is used in Thurnherr et al. (submitted) to compare stable water isotope measurements from various platforms. Here, we provide selected model outputs and post-processed data used in this comparison study. The post-processed data contain:</p><ol><li>COSMOiso output files for time steps 20190612_12, 20190613_12, 20190615_13, 20190616_13, 20190617_12, 20190622_12.</li><li>Pressure weighted total and subcolumn averages for time steps 20190612_12, 20190613_12, 20190615_13, 20190616_13, 20190617_12, 20190622_12.</li><li>Vertical cross section of selected variables at Annecy, the location of the L-WAIVE field campaign, for the simulation time window.</li><li>Interpolated time series of subcolumn and total column averages at Annecy, the location of the L-WAIVE field campaign, for the simulation time window.</li><li>Interpolated variables along the flight tracks from the L-WAIVE campaign (see Sodemann and Seidl, 2023).</li></ol><p>See also README files for more details on the provided data.</p><p>To access further model output and post-processed data, please contact the dataset authors.</p>
Supplementary data for the article: Future environmental impacts of metals: a systematic review of impact trends, modelling approaches, and challenges
<p>This repository provides the supplementary data to the paper titled <a href="https://doi.org/10.1016/j.resconrec.2024.107572" target="_blank" rel="noopener"><em>"Future environmental impacts of metals: a systematic review of impact trends, modelling approaches, and challenges"</em></a>, published 2024 in <em>Resources, Conservation and Recycling</em>.</p> <h4><strong>Contents</strong></h4> <p>The repository is split in 3 parts and comprises the following files (more details are provided in the <em>README.md</em>):</p> <p><strong>A_Database of reviewed studies:</strong></p> <ul> <li>contains the detailed review data, meant for readers to use as an overview file to gather studies relevant to them. It also includes an overview of all data sources that the reviewed studies used.</li> </ul> <p><strong>B_Scientific supplement to paper:</strong></p> <ul> <li>Contains all data relevant to the related publication Harpprecht et al. (2024), such as studies screened , FAIR data analysis, or analyzed impact trends.</li> </ul> <p><strong>C_Data for figures in paper:</strong></p> <ul> <li>This file contains all the data for Figures 3, 4 and 5 in tabular form, representing impact trends, scenario variables, scenario modelling approaches and data sources used.</li> </ul> <h4><strong>Summary</strong></h4> <p>These files allow to reproduce the results of our study. In this work, we systematically reviewed studies which assessed future environmental impacts of metal supply chains. Our review yielded 40 publications covering 15 metals: copper, iron, aluminium, nickel, zinc, lead, cobalt, lithium, gold, manganese, neodymium, dysprosium, praseodymium, terbium, and titanium. We evaluated their results regarding future impact trends, and their methods, i.e., modelling approaches, scenario variables, and data sources of scenario variables. We identified 15 scenario variables. The most common variables are background electricity mix, ore grade, recycling shares, demand, and energy efficiency. We identified 229 unique data sources for the reviewed scenario variables.</p> <h4><strong>Related publication</strong></h4> <p>More details on the data and its interpretation as well as the scientific context are provided in the publication itself:</p> <p><a href="https://doi.org/10.1016/j.resconrec.2024.107572" target="_blank" rel="noopener">Harpprecht, C., Miranda Xicotencatl, B., van Nielen, S., van der Meide, M., Li, C. , Li, Z., Tukker, A., Steubing, B. (2024). <em>Future environmental impacts of metals: a systematic review of impact trends, modelling approaches, and challenges.</em> Resources, Conservation and Recycling.</a></p> <h4><strong>Funding </strong></h4> <p>Carina Harpprecht received funding from the Energy Program of the German Aerospace Center in 2022. Zhijie Li received funding from the European Institute of Innovation and Technology (EIT) under the project Valomag (Project No. 14049).</p> <h4><strong>License</strong></h4> <p>CC-BY 4.0 license for DLR (German Aerospace Center)</p>
Dataset: An Analytic Hierarchy Process-Based Multicriteria Model for Component Selection in a Computational Numerical Control (CNC) Machine
<p><i><strong>"An Analytic Hierarchy Process-Based Multicriteria Model for Component Selection in a Computational Numerical Control (CNC) Machine"</strong></i></p><p><i>CHILECON 2023 - </i><a href="https://site.ieee.org/chilesur/ieee-chilecon-2023/"><i>https://site.ieee.org/chilesur/ieee-chilecon-2023/</i></a><i> </i></p><p>---</p><p>En el marco del trabajo de referencia, los autores ponemos a disposición de los lectores la base de datos utilizada para el proceso de toma de decisión multicriterio para la selección del software y del MCU de una maquina CNC. </p><p>En el repositorio podrán encontrar los datos referentes a los criterios, subcriterios, indicadores, datos, fuentes de los datos extraídos, política de decisión, cálculos de las evaluaciones de los modelos AHP aplicados y el análisis de sensibilidad de estos. Además, podrán encontrar las gráficas utilizadas en el estudio en la mejor calidad posible. </p><p>El material fue puesto a disposición de todos los interesados para fines académicos y científicos. </p><p>Atte. </p><p>Los autores. </p><p>---</p>
Processing of 3-D Polygon Mesh Model and Radio Propagation Simulations in a Cave: Surface Reconstruction from Point Cloud, Simplification of the Mesh, and Ray Tracing
<p><strong>ABOUT</strong></p><p>This repository includes mesh data from cave geometry scanning and processing, and radio propagation data from ray tracing simulations.</p><p>The geometry data is obtained with laser scanning in a cave in Slovenija. </p><p>The geometry processing includes (i) 3-D shape reconstruction - surface reconstruction from point cloud data and (ii) simplification - reduction of the geometric complexity of the 3-D mesh model. </p><p>The radio propagation data is obtained using CloudRT [1] ray-tracing simulator. </p><p>The obtained propagation-related quantities include information about the propagation mechanism, interactions with the geometry, received power, delay, azimuth and elevation angles of arrival and departure, and path loss. </p><p> </p><p><strong>AUTHORS</strong></p><p>Teodora Kocevska, Andrej Hrovat, Tomaž Javornik</p><p>Department of Communication Systems</p><p>Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia</p><p>teodora.kocevska@ijs.si</p><p> </p><p><strong>GEOMETRY PROCESSING</strong></p><p>The cave segment used for the propagation calculations is selected from a point cloud obtained in a cave in Litia, Slovenia. The point cloud is obtained with 3-D laser scanning of the environment. The selected segment is approx. 58 m long. Several parameter configurations were considered for 3-D shape reconstruction, including Poisson surface reconstruction with octree depths of 8, 10, and 12. Geometries that represent the cave shape and have different levels of complexity were created and studied. In the simplification process, one and two-stage simplification was explored using the Quadric Edge Collapse Decimation approach. </p><p> </p><p><strong>RADIO SETUP</strong></p><p>The transmitter (Tx) is fixed at the entrance of the cave and the receiver (Rx) is moved along the cave in 40 positions with a step of 1 m.</p><p>Omnidirectional antennas at the Tx and Rx sites and vertical polarization are considered. The antenna is mounted 1.5 m above the ground.</p><p>The start frequency is 3.5 GHz, the end frequency is 3.6 GHz and the step is 10 MHz. Direct propagation and first-order reflection are considered. </p><p>The cave geometry is represented by a triangular mesh, and the material of the cave is wet earth. The material electromagnetic properties are selected according to the specifications presented in [2].</p><p> </p><p><strong>FOLDER STRUCTURE</strong></p><p>The folder structure is:</p><p> - Polygon_Mesh_Models</p><p> <i># 3-D environment models with varying </i>levels<i> of geometry complexity</i></p><p> - Reconstruction_Segmen1_Poisson_Surface_Reconstruction</p><p> - Simplification_Segment1_Quadric_Edge_Collapse_Decimation</p><p> - Propagation_Data</p><p> <i># Propagation quantities of all rays between a transmitter and receiver</i></p><p> - AllRay_PropData</p><p> - PathLoss</p><p> - readme.txt</p><p> - RayTracing_EnvironmentModel</p><p> <i> # Final environment model used for ray tracing simulations</i></p><p> - Cave_MeshModel.json</p><p> - Cave_MeshModel.skb</p><p> - Cave_MeshModel.skp</p><p> - RayTracing_MaterialProperties</p><p> <i># Properties of the materials in the environment</i></p><p> - materials.json</p><p> - materials.mtl</p><p> - readme.txt</p><p> - Cave_Length.txt</p><p> <i># Length between selected locations in the environment</i></p><p> - Cave_Segment1_visual.png</p><p> <i> # Visualization of the environment segment used for propagation calculation</i></p><p> - readme.txt</p><p> <i># Overall description </i></p><p><strong>REFERENCES</strong></p><p>[1] D. He, B. Ai, K. Guan, L. Wang, Z. Zhong, and T. Kürner, "The Design and Applications of High-Performance Ray-Tracing Simulation Platform for 5G and Beyond Wireless Communications: A Tutorial," in IEEE Communications Surveys & Tutorials, vol. 21, no. 1, pp. 10-27, First quarter 2019, doi: 10.1109/COMST.2018.2865724.</p><p>[2] R. sector of International Telecommunication Union (ITU-R), "Effects of building materials and structures on radio wave propagation above about 100 MHz," International Telecommunication Union, ITU-R Recommendation P.2040-2, 2021.</p><p> </p><p><strong>ACKNOWLEDGEMENT</strong></p><p>This work was supported by the Slovenian Research Agency under grant <strong>J2-3048</strong>.</p><p> </p>
Higher orders for cosmological phase transitions: a global study in a Yukawa model
<p>Data used in the article with preprint title: <a href="https://arxiv.org/abs/2310.02308">Higher orders for cosmological phase transitions: a global study in a Yukawa model by Oliver Gould and Cheng Xie</a></p><p>Contains file: dataPublishedExport.csv, which consists of the variable used in, and evaluations from the global parameter scan. More details of the content are specified in README.txt.</p>
A dataset to model Levantine landcover and land-use change connected to climate change, the Arab Spring and COVID-19
<p><strong>Overview</strong></p> <p>This dataset is the repository for the following paper submitted to <em>Data in Brief</em>:</p> <p>Kempf, M. A dataset to model Levantine landcover and land-use change connected to climate change, the Arab Spring and COVID-19. <em>Data in Brief</em> (submitted: December 2023).</p> <p>The <em>Data in Brief</em> article contains the supplement information and is the related data paper to:</p> <p>Kempf, M. Climate change, the Arab Spring, and COVID-19 - Impacts on landcover transformations in the Levant. <em>Journal of Arid Environments</em> (revision submitted: December 2023).</p> <p><strong>Description/abstract</strong></p> <p>The Levant region is highly vulnerable to climate change, experiencing prolonged heat waves that have led to societal crises and population displacement. Since 2010, the area has been marked by socio-political turmoil, including the Syrian civil war and currently the escalation of the so-called Israeli-Palestinian Conflict, which strained neighbouring countries like Jordan due to the influx of Syrian refugees and increases population vulnerability to governmental decision-making. Jordan, in particular, has seen rapid population growth and significant changes in land-use and infrastructure, leading to over-exploitation of the landscape through irrigation and construction. This dataset uses climate data, satellite imagery, and land cover information to illustrate the substantial increase in construction activity and highlights the intricate relationship between climate change predictions and current socio-political developments in the Levant. </p> <p><strong>Folder structure</strong></p> <p>The main folder after download contains all data, in which the following subfolders are stored are stored as zipped files: </p> <p>“code” stores the above described 9 code chunks to read, extract, process, analyse, and visualize the data.</p> <p>“MODIS_merged” contains the 16-days, 250 m resolution NDVI imagery merged from three tiles (h20v05, h21v05, h21v06) and cropped to the study area, n=510, covering January 2001 to December 2022 and including January and February 2023.</p> <p>“mask” contains a single shapefile, which is the merged product of administrative boundaries, including Jordan, Lebanon, Israel, Syria, and Palestine (“MERGED_LEVANT.shp”).</p> <p>“yield_productivity” contains .csv files of yield information for all countries listed above.</p> <p>“population” contains two files with the same name but different format. The .csv file is for processing and plotting in R. The .ods file is for enhanced visualization of population dynamics in the Levant (Socio_cultural_political_development_database_FAO2023.ods).</p> <p>“GLDAS” stores the raw data of the NASA Global Land Data Assimilation System datasets that can be read, extracted (variable name), and processed using code “8_GLDAS_read_extract_trend” from the respective folder. One folder contains data from 1975-2022 and a second the additional January and February 2023 data.</p> <p>“built_up” contains the landcover and built-up change data from 1975 to 2022. This folder is subdivided into two subfolder which contain the raw data and the already processed data. “raw_data” contains the unprocessed datasets and “derived_data” stores the cropped built_up datasets at 5 year intervals, e.g., “Levant_built_up_1975.tif”. </p> <p><strong>Code structure</strong></p> <p>1_MODIS_NDVI_hdf_file_extraction.R </p> <p><br>This is the first code chunk that refers to the extraction of MODIS data from .hdf file format. The following packages must be installed and the raw data must be downloaded using a simple mass downloader, e.g., from google chrome. Packages: terra. Download MODIS data from after registration from: https://lpdaac.usgs.gov/products/mod13q1v061/ or https://search.earthdata.nasa.gov/search (MODIS/Terra Vegetation Indices 16-Day L3 Global 250m SIN Grid V061, last accessed, 09th of October 2023). The code reads a list of files, extracts the NDVI, and saves each file to a single .tif-file with the indication “NDVI”. Because the study area is quite large, we have to load three different (spatially) time series and merge them later. Note that the time series are temporally consistent.</p> <p><br>2_MERGE_MODIS_tiles.R</p> <p><br>In this code, we load and merge the three different stacks to produce large and consistent time series of NDVI imagery across the study area. We further use the package gtools to load the files in (1, 2, 3, 4, 5, 6, etc.). Here, we have three stacks from which we merge the first two (stack 1, stack 2) and store them. We then merge this stack with stack 3. We produce single files named NDVI_final_*consecutivenumber*.tif. Before saving the final output of single merged files, create a folder called “merged” and set the working directory to this folder, e.g., setwd("your directory__MODIS/merged").</p> <p><br>3_CROP_MODIS_merged_tiles.R</p> <p><br>Now we want to crop the derived MODIS tiles to our study area. We are using a mask, which is provided as .shp file in the repository, named "MERGED_LEVANT.shp". We load the merged .tif files and crop the stack with the vector. Saving to individual files, we name them “NDVI_merged_clip_*consecutivenumber*.tif. We now produced single cropped NDVI time series data from MODIS. <br>The repository provides the already clipped and merged NDVI datasets.</p> <p><br>4_TREND_analysis_NDVI.R</p> <p><br>Now, we want to perform trend analysis from the derived data. The data we load is tricky as it contains 16-days return period across a year for the period of 22 years. Growing season sums contain MAM (March-May), JJA (June-August), and SON (September-November). December is represented as a single file, which means that the period DJF (December-February) is represented by 5 images instead of 6. For the last DJF period (December 2022), the data from January and February 2023 can be added. The code selects the respective images from the stack, depending on which period is under consideration. From these stacks, individual annually resolved growing season sums are generated and the slope is calculated. We can then extract the p-values of the trend and characterize all values with high confidence level (0.05). Using the ggplot2 package and the melt function from reshape2 package, we can create a plot of the reclassified NDVI trends together with a local smoother (LOESS) of value 0.3.<br>To increase comparability and understand the amplitude of the trends, z-scores were calculated and plotted, which show the deviation of the values from the mean. This has been done for the NDVI values as well as the GLDAS climate variables as a normalization technique. </p> <p><br>5_BUILT_UP_change_raster.R</p> <p><br>Let us look at the landcover changes now. We are working with the terra package and get raster data from here: https://ghsl.jrc.ec.europa.eu/download.php?ds=bu (last accessed 03. March 2023, 100 m resolution, global coverage). Here, one can download the temporal coverage that is aimed for and reclassify it using the code after cropping to the individual study area. Here, I summed up different raster to characterize the built-up change in continuous values between 1975 and 2022. </p> <p><br>6_POPULATION_numbers_plot.R</p> <p><br>For this plot, one needs to load the .csv-file “Socio_cultural_political_development_database_FAO2023.csv” from the repository. The ggplot script provided produces the desired plot with all countries under consideration. </p> <p><br>7_YIELD_plot.R</p> <p><br>In this section, we are using the country productivity from the supplement in the repository “yield_productivity” (e.g., "Jordan_yield.csv". Each of the single country yield datasets is plotted in a ggplot and combined using the patchwork package in R. </p> <p><br>8_GLDAS_read_extract_trend</p> <p><br>The last code provides the basis for the trend analysis of the climate variables used in the paper. The raw data can be accessed https://disc.gsfc.nasa.gov/datasets?keywords=GLDAS%20Noah%20Land%20Surface%20Model%20L4%20monthly&page=1 (last accessed 9th of October 2023). The raw data comes in .nc file format and various variables can be extracted using the [“^a variable name”] command from the spatraster collection. Each time you run the code, this variable name must be adjusted to meet the requirements for the variables (see this link for abbreviations: https://disc.gsfc.nasa.gov/datasets/GLDAS_CLSM025_D_2.0/summary, last accessed 09th of October 2023; or the respective code chunk when reading a .nc file with the ncdf4 package in R) or run print(nc) from the code or use names(the spatraster collection). <br>Choosing one variable, the code uses the MERGED_LEVANT.shp mask from the repository to crop and mask the data to the outline of the study area.<br>From the processed data, trend analysis are conducted and z-scores were calculated following the code described above. However, annual trends require the frequency of the time series analysis to be set to value = 12. Regarding, e.g., rainfall, which is measured as annual sums and not means, the chunk r.sum=r.sum/12 has to be removed or set to r.sum=r.sum/1 to avoid calculating annual mean values (see other variables). Seasonal subset can be calculated as described in the code. Here, 3-month subsets were chosen for growing seasons, e.g. March-May (MAM), June-July (JJA), September-November (SON), and DJF (December-February, including Jan/Feb of the consecutive year).<br>From the data, mean values of 48 consecutive years are calculated and trend analysis are performed as describe above. In the same way, p-values are extracted and 95 % confidence level values are marked with dots on the raster plot. This analysis can be performed with a much longer time series, other variables, ad different spatial extent across the globe due to the availability of the GLDAS variables. </p> <p><br>(9_workflow_diagramme) this simple code can be used to plot a workflow diagram and is detached from the actual analysis.</p> <p>___</p> <p>Conceptualization, Methodology, Software, Validation, Formal analysis, Investigation, Resources, Data Curation, Writing - Original Draft, Writing - Review & Editing, Visualization, Supervision, Project administration, and Funding acquisition: Michael Kempf</p> <p>___</p> <p><strong>Acknowledgements</strong></p> <p><span><span><span><span>I would like to thank three </span></span></span></span><span><span><span><span><span>anonymous</span></span></span></span></span><span><span><span><span> reviewers for their constructive comments and suggestions that sharpened the paper in the Journal of Arid Environments. I am particularly grateful to the Swiss National Science Foundation (SNSF/SNF) to fund my research project </span></span></span></span><span><span><span><span><em><span>EXOCHAINS - Exploring Holocene Climate Change and Human Innovations across Eurasia</span></em></span></span></span></span><span><span><span><span> at the University of Basel under grant number </span></span></span></span><span><span><span><span>TMPFP2_217358.</span></span></span></span></p> <p> </p> <p><span><span><span><span>__</span></span></span></span></p> <p><br>All data underlying the results of this article are publicly available on the internet:</p> <p>GLDAS Noah Land Surface Model L4 data: NASA's Earth Science Data Systems (ESDS) Program, https://disc.gsfc.nasa.gov/datasets?keywords=GLDAS%20Noah%20Land%20Surface%20Model%20L4%20monthly&page=1 (last accessed 09th December 2023); </p> <p><br>Country borders: https://www.geoboundaries.org (last accessed 7th of March 2023) and Natural Earth https://www.naturalearthdata.com/ (last accessed 5th of December 2023);</p> <p><br>FAOstats (Food and Agriculture Organisation of the United Nations: https://www.fao.org/faostat/en/#data/QCL (last accessed 7th of March 2023);</p> <p><br>Global Human Settlement Layer datasets (GHSL): https://ghsl.jrc.ec.europa.eu/download.php?ds=bu (last accessed 7th of March 2023);</p> <p><br>Population development: <br>FAO, https://www.fao.org/countryprofiles/index/en/?iso3=JOR (last accessed 4th of March 2023); <br>the Worldbank, https://www.worldbank.org/en/home (last accessed: 04th of March 2023); <br>Worlddata.info, https://www.worlddata.info/asia/palestine/populationgrowth.php (last accessed 4th of March 2023);</p> <p><br>Water demand and population numbers (Tab. 1): https://www.fao.org/faostat/en/#data/OA; https://databank.worldbank.org/reports.aspx?source=world-development-indicators# (last accessed 13th of December 2023);</p> <p><br>MODIS: Earthdata server of the United States Geological Survey (USGS), MODIS/Terra Vegetation Indices 16-Day L3 Global 250m SIN Grid V006, https://lpdaac.usgs.gov/products/mod13q1v061/ (last accessed 7th of March 2023).</p> <p><br>Competing interests statement:<br>The author declares no conflict of interest.<br>The author has no relevant financial or non-financial interests to disclose.<br>Data availability: All data underlying the analyses are freely available on the internet and where applicable, sources are cited in the text.<br>Ethical approval: This article does not contain any studies with human participants performed by any of the authors.<br>Informed consent: This article does not contain any studies with human participants performed by any of the authors.</p>
Wind measurement data from the publication: "Development of a load model validation framework applied to synthetic turbulent wind field evaluation"
<h3>Dataset description:</h3> <p>This datasat represents supplementary material used in the contribution "Development of a load model validation framework applied to<br>synthetic turbulent wind field evaluation" by Meyer, Huhn and Gottschall.</p> <p>Wind measurements from the Testfeld BHV are made available. For installation details, see the mentioned reference.</p> <p> </p> <h3>File description:</h3> <ul> <li>Lidar_HWS.nc - Horizontal wind speed measurements (10 min averages) from a WindCube V2 vertical profiler for one day with a low-level jet occurrence ( <div> <div>2021-04-20)</div> </div> </li> <li>Cups_HWS.nc - Horizontal wind speed measurements (10 min averages) from cup anemometer installed on a met mast for the same day</li> <li>Ensemble_averaged_Spectra.nc - Ensemble averaged spectra for neutral and near neutral situations from a Gill Windmaster at 110m above ground level, used to fit the Mann and KSEC model parameters</li> </ul> <h3> </h3> <h3>Referencing:</h3> <p>When used, please cite like the following:</p> <p>Meyer, Paul J., Matthias L. Huhn, and Julia Gottschall. 2024. "Development of a Load Model Validation Framework Applied to Synthetic Turbulent Wind Field Evaluation" <em>Energies</em> 17, no. 4: 797. https://doi.org/10.3390/en17040797</p> <p> </p> <p> </p>
Evaluation datasets and results for the paper "Enhancing Business Process Simulation Models with Extraneous Activity Delays"
<p>Event-logs and Business Process Simulation Models used in the experimentation of the paper "Enhancing Business Process Simulation Models with Extraneous Activity Delays", where the '<em>inputs</em>' folder contains all the files used as input, and the '<em>output</em>' folder the results of the evaluation.</p> <p> </p> <p><em><strong>Inputs</strong></em>: event-logs, BPS models, and simulation parameters used as input in the experimentation.</p> <ul> <li><em><strong>Real-life</strong></em>: real-life event logs, corresponding to two disjoint subsets of traces from an Academic Credentials' process, and the BPIC 2012 and BPIC 2017 event logs (filtered as explained in the paper), and the BPS model (plus simulation parameters) used as input for each dataset in the presented approach.</li> <li><em><strong>Synthetic</strong></em>: simulated event-logs and corresponding BPS models (plus simulation parameters) for four different processes with 0, 1, 3 and 5 timer events.</li> </ul> <p><em><strong>Outputs</strong></em>: results of the experimentation.</p> <ul> <li><em><strong>Real-life</strong></em>: results corresponding to the evaluation with real-life event logs. Each of the folders is composed by the original and the enhanced BPS models, 10 event logs simulated with each of them, two folders with the best iteration of the two hyperparameter optimization processes, and the values for the injected timers in each case. In addition, a CSV file with the EMD metrics (cycle time and absolute hour event distribution) for each dataset is provided.</li> <li><em><strong>Synthetic</strong></em>: results corresponding to the simulated event-logs. <ul> <li>Before-After: BPS models and discovered timer events for the four synthetic processes, with five timers placed before and after different activity instances.</li> <li>Complete: BPS models and quality measures (precision, recall, and SMAPE of the discovered timers) for the four synthetic processes with zero, one, three, and five timer events.</li> <li>Individual: event logs enhanced with the discovered extraneous delay for each activity instance, for the four synthetic processes with zero, one, three, and five timer events; and SMAPE of the estimations.</li> </ul> </li> </ul>
A Missing Piece of the E-Region Puzzle: High-Resolution Photoionization Cross Sections and Solar Irradiances in Models
<p>Dataset corresponding to the associated publication, "A Missing Piece of the E-Region Puzzle: High-Resolution Photoionization Cross Sections and Solar Irradiances in Models." The dataset includes high-resolution photoionization and photoabsorption cross section for O and N<sub>2</sub> as well as high-resolution solar spectrum. Photoionization rates from model runs obtained from AURIC and the Meier photoionization code are also included. Please refer to the readme for information on the data structure.</p> <p><strong>***Please note that the paper is under review and has not been accepted yet.***</strong></p>
CPD model and data for CPD inversion
<div>This file includes the Curie Point Depth (CPD) model and related data files for the manuscript 'A continental model of Curie Point Depth for China and surroundings based on Equivalent Source Method'</div> <div>This work is fulfilled by Lei, Y., Jiao, L., Huang, Q., and Tu, J.</div> <div>For any questions, please contact us by Email: lgjiao@cea-igp.ac.cn; leiyu@cea-igp.ac.cn</div> <div> </div> <div>The files *.mat are data complied in Matlab, and the codes and data files should be placed in the same directory.</div> <div> </div> <div>The file cpd_result.xyz is the result of the inverted CPD in mainland China, which is shown in Figure 3. </div> <div> </div> <div>The file d_obs.mat is the observed lithospheric magnetic data from EMM2017 model, and magnetic responses generated by global oceanic remanent magnetization have been removed due to the assumption of induced magnetization. The spherical harmonic coefficients of the EMM2017 model can be download from https://www.ngdc.noaa.gov/geomag/EMM/. The global ocean remanent magnetization model is proposed by Masterton et al. (2013), https://doi.org/ 10.1093/gji/ggs063</div> <div> </div> <div>The file ini_cpd.mat is the initial CPD model proposed by Sun et al., 2022, which can be found in https://doi.org/10.5381/zenodo.6459746</div> <div> </div> <div>Outside the study area, the magnetization is refered to the global vertical integral susceptibility model proposed by Hemant & Maus, (2005). The magnetic responses base on their model are saved as mag_out.mat. </div> <div> </div> <div>The core field used in this study for the inducing field calculation is from the IGRF13 model. The model provide the spherical harmonic coefficients to the degree of 13 (stored in IGRF13.txt), can be download from https://www.ngdc.noaa.gov/IAGA/vmod/igrf.html</div> <div> </div> <div>The global topography data are from ETOPO global relief model, which can be found at https://www.ncei.noaa.gov/products/etopo-global-relief-model. The topography data in the study areas is stored in etopo30_6_66_62_146.mat</div> <div> </div> <div>The Crust1.0 model (crust1.bnds) used for establishing the susceptibility model are from https://igppweb.ucsd.edu/~gabi/crust1.html. </div> <div> </div> <div>The geoid topography comes from EGM2008 gravity model, and can be obtained from http://icgem.gfz-potsdam.de/calcgrid</div> <div> </div> <div>The surface heat flow data (HF_China.xlsx) are download from Jiang et al., 2019.</div> <div>Reference:</div> <div>Alken, P., Thébault, E., Beggan, C.D. et al. (2021). International Geomagnetic Reference Field: the thirteenth generation. Earth Planets Space 73, 49 . https://doi.org/10.1186/s40623-020-01288-x</div> <div>Hemant, K., Maus, S. (2005). Geological modeling of the new CHAMP magnetic anomaly maps using a geographical information system technique. Journal Geophysical Research Solid Earth 110, B12103, https://doi.org/10.1029/2005JB003837</div> <div>Jiang, G., Hu, S., Shi, Y., Zhang, C., Wang, Z., Hu, D. (2019). Terrestrial heat flow of continent China: Updated dataset and tectonic implications. Tectonophysics, 753, 36-48. https://doi.org/ 10.1016/j.tecto.2019.01.006 </div> <div>Laske, G., Masters, G., Ma, Z., Pasyanos, M. (2013). Update on Crust1.0 - A 1-degree global model of earth’s crust. Geophysical Research Abstracts, 15, Abstract EGU2013-2658. http://igppweb. ucsd.edu/~gabi/rem.html </div> <div>Sun, Y., Dong, S., Wang, X., Liu, Mian., Zhang, H., Shi, Y., (2022). Three-dimensional thermal structure of East Asian continental lithosphere. Journal Geophysical Research: Solid Earth, 127, e2021JB023432. https://doi.org/10.1029/2021JB023432</div> <div> </div> <div> </div> <div> </div>
Data for: 3D in vitro modeling of the exocrine pancreatic unit using tomographic volumetric bioprinting
<p><strong>Abstract</strong></p> <div> <div> <p><span><span>Pancreatic ductal adenocarcinoma (PDAC) is the most frequent type of pancreatic cancer, one of the leading causes of cancer-related deaths worldwide. The first lesions associated with PDAC occur within the functional units of exocrine pancreas</span><span>. T</span><span>he crosstalk between PDAC cells and stromal cells plays a key role in tumor progression.</span><span> Thus,</span> <span>i</span></span><span><span>n vitro</span></span><span><span>, fully human models of the pancreatic cancer microenvironment are needed to foster the development of new, more effective therapies</span><span>.</span> <span>However,</span><span> it is challenging to make these models anatomically and functionally relevant. Here, we used tomographic volumetric bioprinting, a novel method to fabricate </span><span>three-dimensional </span><span>cell-laden constructs</span><span>,</span><span> to produce a </span><span>portion</span><span> of the </span><span>complex convoluted </span><span>exocrine pancreas</span> </span><span><span>in vitro</span></span><span><span>.</span><span> Human fibroblast-laden gelatin methacrylate-based pancreatic models were processed to reassemble the </span><span>tubuloacinar</span><span> structures of the exocrine pancreas and, then human pancreatic ductal epithelial (HPDE) cells overexpressing the KRAS oncogene (HPDE-KRAS) were seeded in the acinar lumen to reproduce the pathological exocrine pancreatic tissue. The growth and organization of HPDE cells within the structure was evaluated and the formation of a thin epithelium which covered the acini inner surfaces in a physiological way inside the 3D model was</span> <span>successfully</span> <span>demonstrated</span><span>. Interestingly, immunofluorescence assays revealed a significantly higher expressions of alpha smooth muscle </span><span>actin</span><span> (α-SMA) vs. </span><span>actin</span><span> in the fibroblasts co-cultured with cancerous than with wild-type HPDE cells. Moreover, α-SMA expression increased with time, and it was found to be higher in fibroblasts that laid closer to HPDE cells than in those </span><span>laying </span><span>deeper into the model. Increased levels of interleukin (IL)-6 were also quantified in supernatants from co-cultures of stromal and HPDE-KRAS cells. These findings correlate with inflamed tumor-associated fibroblast behavior, thus being relevant biomarkers to </span><span>monitor</span><span> the early progression of the disease and to target drug efficacy. </span></span><span> </span></p> </div> <div> <p><span><span>To our knowledge, this is the first</span> <span>demonstration of a </span><span>3D </span><span>bioprinted</span> <span>portion</span><span> of </span><span>pancreas that</span> <span>rec</span><span>apit</span><span>ulates</span> <span>its</span> <span>true 3-dimensional </span><span>microanatomy</span><span>,</span><span> and which shows </span><span>tumor triggered </span><span>inflammation</span><span>. </span></span><span> </span></p> </div> </div> <p> </p> <p><strong>Contents</strong></p> <p>This repository contains the raw data, materials list, protocols, and code necessary to reproduce the work in the namesake preprint.</p> <p> </p>
Atrial Models with Personalized Effective Refractory Period
<h1>Impact of Effective Refractory Period Personalization on Prediction of Atrial Fibrillation Vulnerability</h1> <div> </div> <div> <div><strong>Authors:</strong> Patricia Martínez Díaz, Christian Goetz, Albert Dasi, Laura Anna Unger, Annika Haas, Olaf Dössel, Armin Luik, Axel Loewe</div> <div>patricia.martinez@kit.edu / publications@ibt.kit.edu</div> <div><a href="https://doi.org/10.1093/europace/euad122.542">doi:10.1093/europace/euad122.542</a></div> <div> </div> <div>This dataset contains 7 atrial meshes, 6 left atria and 1 right atrium, derived from electroanatomical mapping and measurements of the effective refractory period (ERP), bipolar voltage (bi) and local activation times (lat). The meshes include annotations and fibers and are ready for simulations in the cardiac electrophysiology simulator <a href="https://doi.org/10.1016/j.cmpb.2021.106223">openCARP</a>. We also provide the code to reproduce 272 reentries by reading the selected parameters.par and state.roe files. The meshes were generated using <a href="https://github.com/KIT-IBT/AugmentA">AugmentA code</a> and the simulated reentries were induced following the <a href="https://doi.org/10.3389/fphys.2021.656411">PEERP protocol</a> by Azzolin et al. </div> <div> </div> <h2>Folder structure</h2> <div>The code is located in the `src` folder, the meshes in the `data` folder and the reentries in the `results` folder. </div> <div>```</div> <div>src/</div> <div> |-- run.py</div> <div> |-- induceReentry.py</div> <div> |-- getStimPoints.py</div> <div> |-- element_tag.csv</div> <div> |-- al_mk_H.par</div> <div> |-- requirements.txt</div> <div> |-- reproduceReentry.py</div> <div>data/</div> <div> |-- meshes/</div> <div> |-- P1/ </div> <div> |-- P1_with_erp_lat_bi.vtk </div> <div> |-- ERP.pts</div> <div> |-- ERP_values.txt</div> <div> |-- ablation.pts</div> <div> |-- LA_stim_points_2cm.pts</div> <div> |-- bilayer/</div> <div> <div> |-- nodal_adjustment/</div> <div> |--PARAMETER_SCENARIO.adj (e.g. Gto_continuous.adj)</div> </div> <div>.</div> <div>.</div> <div>.</div> <div> |-- P7 </div> <div>results/</div> <div> |-- MESH_SCENARIO_CV/ (e.g P1_continuous_0.3) </div> <div> |-- point_X_beat_Y</div> <div> |-- MESH_SCENARIO_CV_PERTURBATION_SET/ (e.g P1_continuous_0.7_2_1) </div> <div> |-- point_X_beat_Y </div> <div>README.md</div> <div>```</div> <div> <ul> <li>`src`: contains the source files needed to run PEERP protocol <ul> <li>`run.py` This is the main function to run the pacing protocol (not needed to run if reentries are only reproduced, check reproduceReentry.py)</li> <li>`induceReentry.py` Contains a list of pacing protocols. The PEERP protocol is included here</li> <li>`getStimPoints.py` Extract the stimulation points</li> <li>`element_tag.csv` Region tag numbering</li> <li>`al_mk_H.par` Par file with ionic scaling factors for three states; H:Healthy, M:Mild, S:Severe</li> <li>`requirements.txt` Packages to create the virtual enviroment. (This was my output of ```pip3 list> requirements.txt```)</li> <li>`reproduceReentry.py` Reentries can be reproduced given a selected folder where the .par and .roe files are stored.</li> </ul> </li> <li>`data`: contains the `meshes` folder with the bilayer meshes in openCARP (.elem, .lon and .pts) and .vtk format. Synthetic fibrotic distributions are included in the the .regele files. <ul> <li>`meshes/P1/P1_with_erp_lat_bi.vtk` Mesh with ERP, LAT and bipolar voltage data</li> <li>`meshes/P1/ERP_values.txt/` measured ERP data</li> <li>`meshes/P1/ERP.pts/` electrode coordinates where ERP data was measured</li> <li>`meshes/P1/ablation.pts/` electrode coordinates where tissue was ablated</li> <li>`meshes/P1/LA_stim_points_2cm.pts` Stimulation points for the PEERP protocol</li> <li> `meshes/P1/bilayer/LA_bilayer_with_fiber_slow_conductive.regele` Element ids corresponding to regions of low voltage (< 0.5mV)</li> <li>`meshes/P1/bilayer/LA_bilayer_with_fiber_scar.regele` Element ids corresponding to regions of low voltage (< 0.1mV)</li> <li>`meshes/P1/bilayer/LA_bilayer_with_erp_regions_um.vtk` Bilayer mesh with a discrete split where each region has a single ERP value</li> <li>`meshes/P1/bilayer/LA_bilayer_with_fiber_with_fibrosis.vtk` Bilayer mesh with fibrosis informed by low voltage areas</li> <li>`meshes/P1/bilayer/LA_bilayer_with_erp_continuous_um.vtk` Bilayer mesh with a continuous ERP distribution by interpolation of measured ERP data</li> <li>`meshes/P1/bilayer/LA_bilayer_with_erp_continuous_2ms_um.vtk` Bilayer mesh with a continuous ERP distribution by interpolation of measured ERP data with +- 2ms perturbation</li> </ul> </li> </ul> <p>We studied 7 different scenarios: </p> </div> <ol> <li>Monoregion scenario with no ERP personalization, where all nodes had the same ERP</li> <li>Control scenario with no ERP personalization, where ERP nodes of certain defined anatomical regions where modified as reported in Loewe et al. 2015 </li> <li>Regional scenario with ERP personalization, where each region had a single ERP value derived from clinical measurement</li> <li>Continuous scenario with ERP personalization, where the ERP distribution was generated by interpolation of measured ERP data</li> <li>Control scenario with fibrosis, where elements corresponding to regions of low voltage (bi<0.5 mV) where set as slow or non conducing elements</li> <li>Continuous scenario with fibrosis, where elements corresponding to regions of low voltage (bi<0.5 mV) where set as slow or non conducing elements</li> <li>Continuous scenario where ERP measurements with additional perturbation draw from a uniform distribution. The perturbations were 2,5,10 and 20 ms, and we repeated this set 5 times for P6</li> </ol> <p>In summary, we provide the following data: </p> <div> <ul> <li>7 meshes for openCARP simulations</li> <li>7 meshes in vtk format with continuous ERP distribution</li> <li>27 meshes in vtk format with continuous ERP distribution with perturbed ERP with 2,5,10 and 20ms from a random uniform distribution</li> <li>7 meshes in vtk format with regional ERP</li> <li>7 meshes in vtk format with ERP, LAT and bipolar voltage</li> <li>7 ablation set points</li> <li>7 ERP set points with their corresponding values</li> <li>209 reentries generated under 4 ERP scenarios (monoregion, control,regional,continuous) run with a conduction velocity of 0.7 0.5 and 0.3 m/s</li> <li>26 reentries generated under 2 scenarios ERP+Fibrosis (control + continuous) run with a conduction velocity 0.3 m/s</li> <li>37 reentries induced with continuous ERP for patient P3 @CV 0.3 for the sensitivity analysis </li> </ul> </div> <h2>Create a dynamic Courtemanche model</h2> <p>As we will modify the ionic parameters on a nodel basis you will need to create a dynamic Courtemanche model and then declare the variables (ionic conductances) you need to modify. In your openCARP installation folder, go to the `limpet` copy the Courtemanche.model file</p> <p>```<br>cd openCARP/physics/model/limpet<br>cp Courtemanche.model Courtemanche_nodal.model<br>vim Courtemanche_nodal.model<br>```</p> <p>Then add on top the parameters that need to be modified on a nodal-basis:</p> <p>```<br>group {<br> GK1 ;<br> Gto ;<br> GKr ;<br> GKs ;<br> GCaL ;<br> factorGKur ;<br> maxINaCa ;<br> maxIpCa ;<br>} .nodal();</p> <p>```</p> <p>Then you would need to recompile openCARP. In the terminal, go to your openCARP's top level folder:<br>```<br>cd openCARP/ <br>```</p> <p>Configure CMake with updated imp_list.txt via:<br>```<br>cmake -S. -B_build -DUPDATE_IMPLIST=ON</p> <p>```<br>Run the CMake building process:<br>```<br> cmake --build _build<br>```<br> This will generate the `.h` and `.cc` files for your dynamic model inside `physics/limpet/src/imps_src`</p> <p>**Note:** If you want to add or modify a model file after openCARP was compiled, it is possible to first clean the previous generated files during compilation by running `make clean` before recompiling openCARP.</p> <p>If you compile your own version of openCARP, then you can modify the settings.yaml file, to point to your openCARP version with the dynamic model.<br>```<br>cd .config/carputils<br>subl settings.yaml <br>```<br>Add the build name:</p> <p>```<br>CARP_EXE_DIR:<br> CPU: /Users/lm104/Documents/OpenCARP/opencarp/_build/bin<br> NODAL: /Users/lm104/Documents/OpenCARP/openCARP_nodal_adj/_build/bin<br>```<br>You can check that the new dynamic model is there by calling bench<br>```<br>bench -—list-imps<br>bench —-imp Courtemanche_nodal --imp-info<br>```</p> <p>You can find additional information about dynamic models <a href="https://opencarp.org/documentation/examples/01_ep_single_cell/04_limpet_fe">here</a>.</p> <h2>Reproduce the reentries </h2> <div>You can generate the .igb file of a specific reentry by selecting the corresponding folder in the results directory. An example is given to reproduce the reentry in P1_bi_M_LA/point_0_beat_2/reproduce_reentry.igb. Select the folder `--par_file_directory`and set `--tend` to define the duration of the simulation in miliseconds.</div> <div>_HINT: We recommend keeping the folder structure so that the other parameters, such as: mesh, scenario, state and chamber, can be read from the --par_file_directory. Otherwise, the meshes and results directories need to be modified._</div> <div>```</div> <div>cd src/</div> <div>reproduceReentry.py --par_file_directory ../results/P1_bi_M_LA/point_0_beat_2 --tend 1500</div> <div> </div> <div>```</div> <div> </div> <h3>Preparation before running the PEERP pacing protocol</h3> <div>Follow the next steps if you want to run the PEERP pacing protocol, either for the provided meshes or for your own meshes. To run the PEERP protocol in a controlled environment, it is recommended, before running the run.py, to create a virtual environment. Go to your terminal and type: </div> <div>```</div> <div>cd src/</div> <div>python3 -m venv ./myEnv</div> <div>source ./myEnv/bin/activate</div> <div>pip3 install -r requirements.txt</div> <div>```</div> <div> </div> <div>You need to add carputils to your `PATH`. You can run the code in the terminal or use and IDE to debug the code. </div> <div>Note: I am using PyCharm 2020.3. and in Settings --> Python interpreter --> show all and then in the (+) symbol, add the path to carputils there:</div> <div> </div> <div>Otherwise you can add this extra lines at the beginning of `run.py``:</div> <div>```</div> <div># Replace '/path/to/carputils' with the actual path to your carputils package</div> <div>carputils_path = '/path/to/carputils'</div> <div> </div> <div># Add the carputils path to sys.path</div> <div>sys.path.append(carputils_path)</div> <div>```</div> <h3>Run the PEERP protocol</h3> <div> </div> <div>The following example runs the PEERP from a single stimulation point. If you want to run PEERP over all the points, simply add the flag --run_all_points 1 </div> <div>```</div> <div>cd src/</div> <div>python3 run.py --giL 0.4166 --geL 1.458 --cv 0.8 --mesh monoatrial --protocol PEERP --pacing 122718 --stim_file LA_stim_points.txt --geometry LA_bilayer_with_fiber_um --cell_bcl 500 --model Courtemanche --ionic_prop_file al_mk_S.par --max_n_beats_PEERP 1 --overwrite-behaviour overwrite</div> <div>```</div> <div> </div> <h3>Running your own experiment and making your own changes</h3> <div>Extract the stimulation points on your mesh, where the PEERP protocol will be run: </div> <div>```</div> <div>python3 getStimPoints.py --mesh monoatrial --tolerance 20000 --stim_file LA_stim_points.txt --chamber LA</div> <div>```</div> <div> </div> <div>Tune conduction velocity (CV) and conductivites. The code expects the intracellular end extracellular longitudinal conductivity values as an input. We used `tuneCV` to fit CV=0.7m/s with dx=0.4mm and dt=20us</div> <div>If you want to adjust the values, run in the terminal:</div> <div>```</div> <div>tuneCV --resolution 400 --model Courtemanche --velocity 0.7 --converge True --sourceModel monodomain --surf True --dt 20</div> <div>```</div> <div>You can provide the location of the start of the activation by selecting the desired point ID:</div> <div>- Load the mesh in Paraview (or Meshalyzer)</div> <div>- click on the ? symbol</div> <div>- save the ID and change the `--pacing` argument </div> <div> </div> <div>Call `run.py` with a new mesh. The protocol starts by prepacing the mesh and then using the last beat as initial condition tu run the PEERP.</div> <div>Be aware that for a monoatrial mesh you might need to give the new id for the location of the earliest activation. Change `12345` to your desired point ID.</div> <div>```</div> <div>python3 run.py --mesh newMesh --pacing 12345 --protocol prepace --stim_file LA_stim_points.txt</div> <div>```</div> <div> </div> <div>Run the protocol with different electrical remodelling stage. You can change the .par file or select one file from the three provided: </div> <div>```</div> <div>python3 run.py --mesh newMesh --pacing 12345 --protocol PEERP --stim_file LA_stim_points.txt --args.ionic_prop 'l_mk_M.par'</div> <div>```</div> <div> </div> <div>You can also try to run a biatrial example. The biatrial mesh is also provided. You need to extract the points on the RA surface using `getStimPoints.py`, to run the RA experiment: </div> <div>```</div> <div>cd src</div> <div>python3 getStimPoints.py --mesh biatrial --tolerance 20000 --stim_file RA_stim_points.txt --chamber RA</div> <div>```</div> <div>Then run PEERP twice, one per each chamber:</div> <div> </div> <div>```</div> <div>python3 run.py --mesh biatrial --geometry LA_RA_bilayer_with_fiber --pacing 12345 --stim_file LA_endo_2cm.txt --args.ionic_prop 'l_mk_M.par'</div> <div>python3 run.py --mesh biatrial --geometry LA_RA_bilayer_with_fiber --stim_file LA_stim_points.txt --args.ionic_prop 'l_mk_M.par'</div> <p> </p> </div> <p> </p>
Deflections of the s-FKLP model for validation purposes
<p>The test data included are for plate deflections obtained according to the s-FKLP model produced for model validation. The methodology and analysis of the obtained data is included in the Open Access article:</p> <p>Stempin, P.; Pawlak, T. P. & Sumelka, W.<br>Formulation of non-local space-fractional plate model and validation for composite micro-plates <br><em>International Journal of Engineering Science, </em><em>Elsevier BV, </em><strong>2023</strong><em>, 192</em>, 103932.</p> <p>DOI: https://doi.org/10.1016/j.ijengsci.2023.103932</p> <p> </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.