Find research datasets worth reusing

Model outputs and species-level data for "Functional traits and climate drive interspecific differences in disturbance-induced tree mortality"

This repository is divided in three sub-directories:  <ul> <li>sensitivity contains the posterior of each parameter estimated by the bayesian mortality model in a rdata file. This file was generated by the script https://github.com/jbarrere3/SalvageModel/tree/withFinland</li> <li>climate contains for each tree species the climatic variables (mean annual temperature, minimum annual temperature and annual precipitation) extracted from CHELSA and the disturbance-related climatic indices (Fire Weather Index, Snow Water Equivalent and Gust Wind Speed)</li> <li>traits contains the traits calculated directly with NFI data (bark thickness, height to dbh ratio, maximum growth), and a text file with the Species and Trait ID to request to TRY database. </li> </ul> The content of this repository can be used to reproduce the analyses of the paper, with the script stored in  in https://github.com/jbarrere3/DisturbancePaper Edit (19/09/2023): A minor coding error was found in the pre-formatted data of the paper, which did not affect the main results but led to minor change in the value of the posterior estimates. An updated version of the posterior estimates of this dataset was made available at https://zenodo.org/record/8358921.

opencc-zeroFeb 2023View details →

dryad36/100

Data from: Computational model of the full-length TSH receptor

The receptor for thyroid stimulating hormone (TSHR), a GPCR, is of particular interest as the primary antigen in autoimmune hyperthyroidism (Graves' disease) caused by stimulating TSHR antibodies. To date, only one domain of the extracellular region of the TSHR has been crystallized. We have run a 1000ns Molecular Dynamic simulation on a model of the entire TSHR generated by merging the extracellular region of the receptor, obtained using artificial intelligence, with our recent homology model of the transmembrane domain, embedded it in a lipid membrane solvated it with water and counterions. The simulations showed that the structure of the transmembrane and leucine-rich domains were remarkably constant while the linking region (LR), known more commonly as the "hinge region", showed significant flexibility, forming several transient secondary structural elements. Furthermore, the relative orientation of the leucine-rich domain with the rest of the receptor was also seen to be variable. These data suggest that this linker region is an intrinsically disordered protein (IDP). Furthermore, preliminary data simulating the full TSHR model complexed with its ligand (TSH) showed that (a) there is a strong affinity between the linker region and TSH ligand and (b) the association of the linker region and the TSH ligand reduces the structural fluctuations in the linker region. This full-length model illustrates the importance of the linker region in responding to ligand binding and lays the foundation for studies of pathologic TSHR autoantibodies complexed with the TSHR to give further insight into their interaction with the flexible linker region. The dataset represents the coordinates of a model of the Thyroid Stimulating Hormone Recpetor (TSHR) built from the AI-based alphafold2 model of the TSHR ectodomain and the MD geverated model of the transmembrane domain (TMD) of TSHR.

opencc-by-4.0Dec 2022View details →

Data for "Diabatic Quantum Annealing for the Frustrated Ring Model"

This repository contains data for the paper "Diabatic Quantum Annealing for the Frustrated Ring Model". In particular, the Jupyter notebook within the repository reproduces the figures that contain data in our paper. We also include a Qiskit implementation of our algorithm and the associated code for the population levels.

Raw Data for the article: Impact of the Organizational Model Adopted during the COVID-19 Pandemic on the Perceived Safety of Intensive Care Unit Staff

Background: The SARS-CoV-2 pandemic had a devastating health, social, and economic effect on the population. Organizational, technical and structural operations aimed at protecting staff, outpatients and inpatients were implemented in an Italian hospital with a COVID-19 dedicated intensive care unit. The impact of the organizational model adopted on the perceived safety among staff was evaluated. Methods: Descriptive, structured and voluntary, anonymous, non-funded, self-administered cross-sectional surveys on the impact of the organizational model adopted during COVID-19 on the perceived safety among staff. Results: Response rate to the survey was 67.4% (153 completed surveys). A total of 91 (59%) of respondents had more than three years of ICU experience, while 16 (10%) were employed for less than one year. Group stratification according to profession: 74 nurses (48%); 12 medical-doctors (7%); 11 physiotherapists (7%); 35 nurses-aides (22%); 5 radiology-technicians (3%); 3 housekeeping (1%); 13 other (8%). The organizational model implemented at ISMETT made them feel safe during their workday. A total of 113 (84%) agreed or strongly agreed with the sense of security resulting from the implemented measures. A vast majority of respondents perceived COVID-19 as a dangerous and deadly disease (94%) not only for themselves but even more as vectors towards their families (79%). A total of 55% of staff took isolation measures and moved away from their home by changing personal habits. The organizational model was perceived overall as appropriate (91%) to guarantee their health. Conclusion: The vast majority of respondents perceived the overall model applied during an unexpected, emergency situation as appropriate.

Raw Data for the article: Mortality after transjugular intrahepatic portosystemic shunt in older adult patients with cirrhosis: A validated prediction model

Background and aims: Implantation of a transjugular intrahepatic portosystemic shunt (TIPS) improves survival in patients with cirrhosis with refractory ascites and portal hypertensive bleeding. However, the indication for TIPS in older adult patients (greater than or equal to 70 years) is debated, and a specific prediction model developed in this particular setting is lacking. The aim of this study was to develop and validate a multivariable model for an accurate prediction of mortality in older adults. Approach and results: We prospectively enrolled 411 consecutive patients observed at four referral centers with de novo TIPS implantation for refractory ascites or secondary prophylaxis of variceal bleeding (derivation cohort) and an external cohort of 415 patients with similar indications for TIPS (validation cohort). Older adult patients in the two cohorts were 99 and 76, respectively. A cause-specific Cox competing risks model was used to predict liver-related mortality, with orthotopic liver transplant and death for extrahepatic causes as competing events. Age, alcoholic etiology, creatinine levels, and international normalized ratio in the overall cohort, and creatinine and sodium levels in older adults were independent risk factors for liver-related death by multivariable analysis. Conclusions: After TIPS implantation, mortality is increased by aging, but TIPS placement should not be precluded in patients older than 70 years. In older adults, creatinine and sodium levels are useful predictors for decision making. Further efforts to update the prediction model with larger sample size are warranted.

Surface hourly measurement data of O3, NO2 and PM2.5 for "Large modeling uncertainty in projecting decadal surface ozone changes over urban and industrial regions of China"

Surface hourly measurement data of O3, NO2 and PM2.5 during summer of 2017. In the .csv files, the first column contains the ID for each measurement site. "lon", "lat" are longitude and latitude, respectively. Date format is "YYYYMMDD_hour".

Effect of Hydrophobicity of Fluorescent Carbon Nanoparticles on Transport in Porous Media: Column Experiment Data and Modeling

The data contained here are derived from sand column experiments and modeling which investigate the effects of hydrophobicity on the transport of fluorescent carbon nanoparticles (FCN) in porous media. The data consist of outlet concentrations (relative to the inlet concentrations) of FCN for a suite of experiments testing the recovery of FCN synthesized using four different pyrolysis temperatures(190C, 210C, 230C, and 250C), as well as the recovery of FCN when passed through three different sand types (Fine, Medium, and Coarse). Column experiments were tested under both saturated and unsaturated conditions to investigate the role of pore water content on FCN retention. Finally, results from tests using an inert bromide tracer are also included (File: May_et_al_Column_Experiment_Outlet_Concentrations.xlsx). Additionally, the results from modeling the observed breakthrough curves of FCN are included for three different transport models, as well as modelling results for an inert bromide tracer (File: May_et_al_Breakthrough_Curve_Modeling.xlsx). The raw output files for the two-kinetic sites model that was determined to best reproduce the observed breakthrough curves are also provided (File: May_et_al_Two_Kinetic_Sites_Model_Raw_Output.zip) Finally, the results of sand surface characterization for three sands using a scanning electron microscope are included (File: May_et_al_Sand_Surface_Characterization_SEM-DATA.zip). Please see the following paper for more details: May, D.F., B. Hassanpour, L. Sinclair, T.S. Steenhuis, and L.M. Cathles, (2023, pending), Effect of Hydrophobicity of Fluorescent Carbon Nanoparticles on Transport in Porous Media: Column Experiments and Modeling, Water Resources Research, Manuscript Submitted for Review.

opencc-by-4.0Jun 2022View details →

Supplementary Data: Global fits of vector-mediated s-channel simplified models for scalar and fermionic dark matter with GAMBIT

This record contains the YAML files, data files, and some of the plotting scripts for: "Global fits of vector-mediated s-channel simplified models for scalar and fermionic dark matter with GAMBIT". The paper can be found at https://arxiv.org/abs/2209.13266. Samples have been created using GAMBIT and figures can be reproduced with pippi.

MJO-QBO Model Inter-comparison Data

Data in support of the paper "The Lack of a QBO-MJO Connection in Climate Models with a Nudged Stratosphere" by Zane K. Martin, Isla R. Simpson, Pu Lin, Clara Orbe, Qi Tang, Julie M. Caron, Chih-Chieh Chen, Hyemi Kim, L. Ruby Leung, Jadwiga H. Richter, and Shaocheng Xie, currently in preparation for submission. Data is organized by model, then ensemble member, then the temporal data resolution. Daily data are daily model OLR (olr/) and precipitation (precip/) in lat/lon/time format, over at least the tropical region spanning all longitudes and 20N to 20S. Daily data also include the Real-time Multivariate MJO index (RMM; RMM_index/) value from each model and ensemble members. OLR and precip files are provided on a 2.5 x 2.5 degree similar grid, rather than the models' native grid. Monthly data are temperature (temp/, at all vertical levels and all longitudes, from at least 20N to 20S, and the 100 hPa temperature file, as described more in the paper) zonal wind (at all vertical levels, and the 50 hPa wind file; wind/), and TEM vertical velocity (wtem/).

opencc-by-4.0Jan 2023View details →

Harmonising the land-use flux estimates of global models and national inventories for 2000-2020: background data

This online repository includes all the relevant data used in the paper "Harmonizing the land-use flux estimates of global models and national inventories for 2000-2020" (Grassi et al. 2023), plus some additional methodological information, organised in the following files: 1)  "Global models land CO2 data 2000-2020" (MS Excel Format), including for each country data for: a.  Land-use CO2 fluxes from each of three Bookkeeping Models (BMs) used, and for different categories (net LULUCF, deforestation, forest, other transitions, organic soils).  b. The ensemble mean of the ‘natural terrestrial sink’ estimated by 16 Dynamic Global Vegetation Models (DGVMs), filtered with maps of intact/non-intact forest. The global model data included here are consistent with those included in the Global Carbon Budget 2022 (Friedlingstein et al., 2022). 2) “National inventories LULUCF data 2000-2020” (version Dec 2022, MS Excel Format), including a  comprehensive collection of LULUCF CO2 data based on countries' submissions to the United Nations Framework Convention on Climate Change (UNFCCC). The data here represent a slight update of the dataset included in Grassi et al. (2022). 3) “Processing steps for DGVM results”, describing the protocol used to filter the results of DGVMs with maps of intact/non-intact forest and further details on the maps (PDF Format).   4) “Intact and non-intact forest maps”, available in two files with different resolutions (0.5 and 0.05 degrees) in NetCDF format. Grassi et al. (2023) used the 0.5 degree resolution. 5) "IntactAndNonIntactForest_0.5deg_script.js", the Google Earth Engine Java script to produce the forest maps (.js/text format) For further details, please refer to: Grassi et al. (2023) Harmonising the land-use flux estimates of global models and national inventories for 2000-2020. Earth Syst. Sci. Data. Other references: Friedlingstein et al. (2022) Global Carbon Budget 2022, Earth Syst. Sci. Data, 14, 4811–4900. Grassi et al (2022) Carbon fluxes from land 2000–2020: bringing clarity to countries' reporting. Earth Syst. Sci. Data, 14, 4643-4666.

Model data for region 1

This is the model data that was used to run the hydrological model for region 1. The model code that was used for running the model has been given as a .zip file named 'fortran_code.zip'

Data for Narragansett Bay (RI, USA) Modeling

Observed data and simulation data for three-dimensional mechanistic modeling for Narragansett Bay, RI, USA. Five folders. Folders include text files for five locations in Narragansett Bay: Phillipsdale, Bullock Reach, Conimicut Point, North Prudence, and Quonset Point Observed data are presented as Depth Profile Data and Sonde Data Simulations provide Dissolved Oxygen output (WASP Output DO) and Phytoplankton Output (chl a, WASP Ouput Chl a) and the Load Scenarios.

Data supplement for PhD thesis "Pattern Formation with Mass Conservation - From Passive to Active Models"

Here, we provide Mathematica files that provide the details of the weakly nonlinear analysis employed in the PhD thesis "Pattern Formation with Mass Conservation - From Passive to Active Models" submitted by Tobias Frohoff-Hülsmann.

Model output data for 3D Climate modelling of LP 890-9 c with a modern Venus-like atmosphere

We make available the output data from 3D climate modelling of LP 890-9 c with a modern Venus-like atmosphere. The data here has been produced for the publication submitted to Monthly Notices of the Royal Astronomical Society: Letters under the title: «3D Global Climate Model of an Exo-Venus: a modern Venus-like Atmosphere for the Nearby Super-Earth LP 890-9 c». The data includes the temperature profiles, emission (thermal) phase curves and transmission spectra files calculated for JWST/NIRSpec Prism. We also make available larger versions of the synthetic observable figures. Proper credit should be given to the authors. For further information, please get in touch with the corresponding author (Diogo Quirino) at: dfquirino@fc.ul.pt

Data for Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in the antibiotic response

Data from simulations used to generate the figures in the paper Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in the antibiotic response. To reproduce analyses, extract colony_data.zip in the data folder after cloning the vivarium-ecoli repository. The extracted folder contains the following items: <ul> <li>sim_dfs: a folder containing the CSV files that represent a subset of the raw simulation data used for downstream analyses.</li> <li>glc_10000_fluxome.csv: Each row represents a reaction in central carbon metabolism (in same order as listed in validation/ecoli/flat/toya_2010_central_carbon_fluxes.tsv). Each column represents a single time point for a single cell in a baseline glucose simulation (seed 10000). Each value is a flux (mmol/L/hr). Provided as input to ecoli/analysis/centralCarbonMetabolism.py script to reproduce fluxome validation plot.</li> <li>glc_10000_proteome_avgs.csv: Each row represents a protein monomer (in same order as sim_data.translation.monomer_data["id"] where sim_data is reconstruction/sim_data/kb/validationData.cPickle). Each column represents a cell in a baseline glucose simulation (seed 10000). Each row represents a protein monomer. Each value represents the average count of a given protein monomer for a given cell. Provided as input to ecoli/analysis/proteinCountsValidation.py script to reproduce proteome validation plot.</li> <li>glc_10000_expressome.csv: Each column represents a gene (with the exception of the final two metadata columns: "Time" and "Agent ID"). Each row represents a specific cell (agent) at a specific time in a baseline glucose simulation (seed 10000). Each value represents the number of new RNA transcripts for a given gene in a given cell at a given time. Provided as input to ecoli/analysis/antibiotics_colony/subgen_gene_plots/count_subgen.py script to calculate number of sub-generational genes among all genes and antibiotic response genes.</li> <li>glc_10000_total_mrna.json: Mapping of agent IDs for all cells in a baseline glucose simulation (seed 10000) to their average total mRNA count. Used by ecoli/analysis/antibiotics_colony/plot.py to generate Fig. 2C,D.</li> <li>jenner_2013.csv: Data extracted from Fig. 2C of <a href="https://doi.org/10.1073/pnas.1216691110">10.1073/pnas.1216691110</a>. Used by ecoli/analysis/antibiotics_colony/plot.py to generate Fig. S6A.</li> <li>olson_2006.csv: Data extracted from Fig. 2D of <a href="https://doi.org/10.1128%2FAAC.01499-05">10.1128/AAC.01499-05</a>. Used by ecoli/analysis/antibiotics_colony/plot.py to generate Fig. S6A.</li> <li>lysis_ratios.csv: Data extracted from Fig. 2 of <a href="https://doi.org/10.1099/00221287-31-3-339">10.1099/00221287-31-3-339</a>. Used by ecoli/analysis/antibiotics_colony/plot.py to generate Fig. 4N.</li> </ul>

Preliminary data of drifting snow mass flux from the lower SPC at MOSAiC (2020-01-26 to 2020-02-04) for the submitted paper "Towards a fully physical representation of snow on Arctic sea ice using a 3D snow-atmosphere model"

Preliminary data of lower SPC massflux from MOSAiC, for the time period 2020-01-26 -- 2020-02-04. 1-h averaged time series of mass flux (kg/m²/h) to compare with the ALPINE3D simulation results. Will soon be replaced with a DOI / Repositiry at the Arctic Data Centre from BAS.

Data used to create figures and tables in the GMD manuscript "Inter-comparison of multiple two-way coupled meteorology and air quality models (WRF v4.1.1-CMAQ v5.3.1, WRF-Chem v4.1.1 and WRF v3.7.1-CHIMERE v2020r1) in eastern China"

This dataset contains all simulation output and observational data of ground-based/satellite-retrieved meteorological and air quality for computing statistical metrics in the GMD manuscript "Inter-comparison of multiple two-way coupled meteorology and air quality models (WRF v4.1.1-CMAQ v5.3.1, WRF-Chem v4.1.1 and WRF v3.7.1-CHIMERE v2020r1) in eastern China", as follows: 1. Simulation and observational results of meteorological and air quality including four folders:      Day_PBLH: Daily PBLH data      Hour_air: Hourly air quality data regarding PM2.5, O3, SO2, NO2 and CO      Hour_met: Hourly meteorological data regarding T2, Q2, RH2, WS10 and precipitation      Hour_radiation: Hourly surface radiation data 2. Simulation and satellite-retrieved results of meteorological and air quality including nine folders:     AOD: Yearly and seasonal AOD data     CF: Yearly and seasonal CF data     CO: Yearly and seasonal CO data     LWP: Yearly and seasonal LWP data     NO2: Yearly and seasonal NO2 data     O3: Yearly and seasonal O3 data     Precipitation: Yearly and seasonal precipitation data     Radiation: Yearly and seasonal radiation data     SO2: Yearly and seasonal SO2 data

Experimental data set for the article entitled "Mathematical Model of Steam Reforming in the Anode Channel of a Molten Carbonate Fuel Cell"

Experimental data for the article: Szablowski, L.; Dybinski, O.; Szczesniak, A.; Milewski, J. Mathematical Model of Steam Reforming in the Anode Channel of a Molten Carbonate Fuel Cell. Energies 2022, 15, 608. The experiments were performed by the first two authors. These data set refer to experiments carried out on a stand used to test high-temperature fuel cells. The subject of the study was a molten carbonate fuel cell fueled with a mixture of methane and steam with steam to carbon ratio of 2.0, 2.5, 3.0 and 3.5 and at the cell operating temperature of 550°C and 650°C. Additionally, in the anode channel of the cell, there was a catalyst in the amount of 2 g. The active area of the cell was 20.25 cm2. The article that uses these research results is published in an open access journal with a CC-BY license. This research was funded by the National Science Center, Poland (Grant number 2020/39/D/ST8/02021).

Data files for "Ground state and spectral properties of the doped one-dimensional optical Hubbard-Su-Schrieffer-Heeger model"

This repo contains the relevant data files for the paper D. Banerjee et al., "Ground state and spectral properties of the doped one-dimensional optical Hubbard-Su-Schrieffer-Heeger model". (2023) Preprint: arXiv:2303.10193