cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8169289
title: FireProtDB + PDB Structural Protein Stability Dataset

description: Dataset compiled and curated for use in the ThermoMPNN paper: https://doi.org/10.1073/pnas.2314853121: 

Dataset for training models for prediction of thermodynamic stability changes (ddG) of protein point mutations given a wildtype protein structure (PDB) file. Data was assembled by matching sequence-based ddG measurements in FireProtDB to structures from the RCSB Protein Data Bank (PDB). For details, see the Methods section of our manuscript.

Citing this work: If you choose to use this dataset for your own research, please cite this repository and the ThermoMPNN paper: https://doi.org/10.1073/pnas.2314853121.

 

Contents:

pdbs/ directory contains all PDB files

csvs/ directory contains all CSVs with mutation data

csvs/4_fireprotDB_bestpH.csv is the main (full) dataset file with 3,438 mutations across 100 proteins.

csvs/fireprot_splits.pkl contains the dataset splits (train/val/test) used in our study

csvs/splits/ contains csvs for each of the splits (train/val/test/homologue-free) indexed from the full dataset csv.

Important CSV columns:



pdb_id_corrected: corresponds to the PDB in the pdbs/ directory (after curation and disambiguation)

ddG: ddG value for mutation (mutant - WT)

wild_type: wild-type amino acid (1-letter code)

mutation: mutant amino acid (1-letter code)

pdb_position: 0-based index of the mutated residue in the PDB file (may be different from position in  the original FireProtDB sequence entry)
DOI: 10.5281/zenodo.8277285
title: Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer

description: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% GLACIER METEOROLOGICAL DATA    SWISS ALPS -2022%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%Data gathered and structured by Thomas Shaw (WSL, Switzerland (until Oct 2022)).
On and off-glacier meteorological data were gathered and analysed as part of a Marie-Curie project 'TEMPEST' (tempestglacier.com).The dataset consists of hourly low-cost AWS (Davis Vantage Pro2) and simple temperature ('T-')logger (Onset TidBitv2) sensor records on three glaciers in the Swiss Alps (Canton Valais).
The glaciers are:Haut Glacier d'Arolla (45.967°N, 7.526°E)Glacier d'Otemma (45.956°N, 7.454°E)Glacier du Corbassière (45.975°N, 7.303°E)
Data are provided in individual Excel files per glacier that contain all hourly data for the sub-period of comparison (11 August-18 September, 2022).Data are quality controlled and checked for obvious errors. Any uncertain values are set to NaN.Air temperature data at 'T-Logger' stations were corrected for heating errors using the comparison of measurements in artificially (AWS) and naturally ventilated (T-Logger) radiation shields on Arolla and Corbassiere glaciers.A multiple linear regression model was applied to estimate these differences at all T-Loggers on all glaciers as a function of incoming shortwave radiation (MeteoSwiss station-derived) and wind speed (measured at AWS).
Each Excel file contains a 'META' tab for simple metadata related to station locations (latitude 'LAT' (°), longitude 'LON' (°), elevation 'ELE' (m a.s.l.) and flowpath length 'FPL' (m)) and a 'DATA' tab for the hourly data. Suffixes to the station names in each column provide the variable measured at that site:'TA' - 2m air temperature (°C)'TA_Hi' - Maximum air temperature for timestep (°C)'TA_Lo' - Minimum air temperature for timestep (°C)'RH' - 2m relative humiditiy (%)'FF' - Wind speed (m s^-1)'FF_Hi' - Maximum wind speed for timestep (m s^-1)'FF_Lo' - Minimum wind speed for timestep (m s^-1)'DIR' - Wind direction (°)'DEW' - Dewpoint temperature (°C)'PRESS' - Air pressure (mbar)'CHILL' - Calculated wind chill temperature (°C)'Heat_idx' - Calculated heat index (°C)'THSW' - A calculated index that uses humidity and temperature like for the Heat Index, but also includes the heating effects of sunshine and the cooling effects of wind (like Wind Chill) to calculate an apparent temperature of what it "feels" like out in the shade
Wind speeds and direction measured at off-glacier sites 'OG' are for the lower off-glacier station ('OG_Low'). 
-------------------------
 
This work was funded by the EU Horizon 2020 Marie Skłodowska-Curie Actions Grant 101026058.
DOI: 10.17189/1520332
title: ODYSSEY THEMIS IR RDR V1.0
DOI: 10.18128/d071.v1.1
title: IPUMS Health Surveys: Medical Expenditure Panel Survey: Version 1.1

description: IPUMS MEPS is an NICHD-funded project designed to make Medical Expenditure Panel Survey Household Component (MEPS-HC) data easier for researchers to use. MEPS-HC is an ongoing panel survey, started in 1996, that is produced by the Agency for Healthcare Research and Quality (AHRQ). IPUMS MEPS Version 1.1 contains data and documentation for more than 1,000 annual person-level variables from the 1996-2017 full-year consolidated files. These variables are consistently named and coded over time within MEPS, and where possible, they are named and coded consistently with comparable variables from the National Health Interview Survey. Version 1.1 also includes technical documentation on topics such as sample sizes, appropriate variance estimation in analyses of MEPS data, and explanations of expenditure data collection and definition in MEPS.
DOI: 10.5281/zenodo.10019700
title: Model simulations
DOI: 10.5281/zenodo.10393508
title: Additional data and models for the article "Role of metasomatism in the development of the East African Rift at the Northern Tanzanian Divergence: Insights from 3D magnetotelluric modelling."

description: Additional data and models for the article "Role of metasomatism in the development of the East African Rift at the Northern Tanzanian Divergence: Insights from 3D magnetotelluric modelling."

This data package includes:

1-ModEM rho and dat format files of the final preferred model.

2-vtk version of this model

3-Scripts to plot the MT models

4-Water content models calculated with MATE

5-Scripts to plot the water content models

6-Parameter files used in water calculation with MATE

7- EDI files used in the model.
DOI: 10.5281/zenodo.10409519
title: Dynamics of macrophage polarization in Salmonella infection : Raw data

description: Experimental raw data of the paper "Dynamics of macrophage polarization support Salmonella persistence in a whole living organism", Leiba et al.
DOI: 10.5281/zenodo.10555911
title: The EFSA Excel mapping tool to be used to report 2023 zoonoses data and sample-based results of Echinococcus multilocularis under the Commission Delegated Regulation (EU) 2018/772

description: The main objective of the mapping tools is to provide a simple and useable platform for Member states and other reporting countries to map their country-specific standard terminology to that used by EFSA and to enable the production of an XML file for the submission of sample or aggregated-based zoonoses monitoring data via the Data Collection Framework (DCF).

The catalogues and the specific hierarchy of each data model (AMR, ESBL, PRV, FBO, AP, DS and SSD2 for Echinococcus multilocularis) are already inserted into each of the specific mapping tool. Specific Excel mapping tools corresponding to each of the five data models are available.

Dynamic or manual version of the tool can be chosen for the first six data models.

The Emulti_SSD2_tool can be used to report sample-based results of Echinococcus multilocularis under the Commission Delegated Regulation (EU) 2018/772.
description: EU; xlsx; zoonoses.support@efsa.europa.eu;
DOI: 10.5281/zenodo.7501563
title: Focused mantle upwelling beneath the Southeastern Asian Basalt Province revealed by seismic surface wave tomography

description: This dataset contains the earthquake waveforms, the manually picked surface wave dispersion data, and the final inverted 3-D Vs model data for our research paper "Focused mantle upwelling beneath the Southeastern Asian Basalt Province revealed by seismic surface wave tomography", which has been published in Geophysical Research Letters (https://doi.org/10.1029/2023GL104336).
DOI: 10.5281/zenodo.8406445
title: 5-stack data

description: Flux data used to measure the transmission and energy selection characteristics of a 5-layer energy analyzer
DOI: 10.6084/m9.figshare.24916566
title: Gilotti-et-al_Tectonics_2023_Supplementary Information

description: Supporting Information for manuscript published in <i>Tectonics</i> entitled “Exhumation of an ultrahigh-pressure slice from the upper plate of the Caledonian orogen – a record from titanite in North-East Greenland” by Jane A. Gilotti, William C. McClelland, Wentao Cao &<sup> </sup>Matthew A. Coble. (Tectonics, 43, e2023TC007810. https://doi.org/10.1029/2023TC007810)
DOI: 10.5281/zenodo.8319570
title: Reactive Multiphase Flow in Porous Media at the Darcy Scale: a Benchmark proposal

description: Description and data files for a "Reactive Two-phase flow Benchmark" Modeling reactive multiphase multicomponent flow in porous media leads to a highly nonlinear coupled system of degenerate partial differential equations and algebraic and/or ordinary differential equations, requiring special numerical treatment. The Benchmark consists of five test problems in total (both in 1D and in 2D), with varying degrees of difficulty, designed to verify the algorithms and<br> the codes dedicated to simulate coupled isothermal Hydro-Chemical processes during injection and storage of CO2 in the subsurface. It is intended to be used as a basis for comparing codes in order to better understand different couplings such as chemical reactions with two-phase flow, phase behavior with equilibrium reactions, dissolution and precipitation
DOI: 10.5281/zenodo.8357267
title: Patterns of Alluviation in Mixed Bedrock-Alluvial Channels

description: <strong>morph2d</strong> Filename: morph2D.f90<br> 2-Dimensional Morphodynamic Model<br> Written by Jongseok Cho and Peter A. Nelson<br> Department of Civil and Environmental Engineering<br> Colorado State University, Fort Collins, Colorado<br> <br> Filename: P1505.mat<br> Results from the simulation of bar formation in a straight flume.<br> <br> Filename: BRtopo.txt<br> Randomly abraded bedrock topography is used to simulate the mixed bedrock-alluvial channels.<br> <br> Filename: XYZ.mat<br> The x- and y-coordinates and bedrock elevation are used in the simulations of mixed bedrock-alluvial channels.<br> <br> Filename: 2-Ax.mat, 2-Bx.mat, and 2-Dx.mat<br> Time evolution of alluvial thickness and the fraction of exposed bedrock surface for the simulations starting from the bare bedrock bed channel.<br> <br> Filename: 2-A.mat and 2-B.mat<br> Time evolution of alluvial thickness and the fraction of exposed bedrock surface for the simulations starting from the alluvial bed channel.<br> <br> Filename: 2-B2-z.mat<br> Time evolution of alluvial thickness and the fraction of exposed bedrock surface for the simulations starting from the alluvial bed channel with different sediment layer thickness.<br> <br> Filename: 2-B2-k.mat<br> Time evolution of total, bed surface, sediment transport, and bedform roughnesses for the simulations starting from the alluvial bed channel with different sediment layer thickness.<br> <br> Filename: 2-B2-x.mat<br> Time evolution of alluvial thickness and the fraction of exposed bedrock surface for the simulations starting from the alluvial bed channel without the effects of bedform and sediment transport roughnesses and shear stress correction for bedload transport.
DOI: 10.26022/ieda/113038
title: Oxygen fugacity of global ocean island basalts

description: This dataset contains oxygen fugacity data (FMQ and NNO) for global ocean island basalts. The oxygen fugacity was determined using the empirical relationship between fO2 and the vanadium partition coefficient between olivine and melt. Olivine and basaltic matrix compositions used to calculate fO2 are also provided.
DOI: 10.3886/icpsr00017.v1
title: Census of Governments, 1962 and 1967
title: Version 1

description: This study contains economic and employment data at the county level for states and local governments in the United States in 1962 and 1967. Data are provided on total population, land area, general revenues, number of municipalities and local governments of all types, number of public school districts, and number of employees of local governments. Information is also provided on educational payrolls of local governments, average earnings of full-time teachers, water supply revenues and expenditures of local governments, local government general expenditures on public welfare, highways, health and hospitals, police and fire protection, natural resources, and urban renewal, long-term general debt outstanding of local schools and local governments, and per capita intergovernmental revenues and expenditures.
description: 1962: 132 variables; 3173 cases; 
1967: 57 variables; 3471 cases;
description: ICPSR data undergo a confidentiality review and are altered when necessary to limit the risk of 
				disclosure. ICPSR also routinely creates ready-to-go data files along with setups in the major 
				statistical software formats as well as standard codebooks to accompany the data. In addition to 
				these procedures, ICPSR performed the following processing steps for this data collection:
			   		Created variable labels and/or value labels.; Standardized missing values..
description: Response Rates: 
					Not provided.
description: Datasets: 
					
						DS0: Study-Level Files
						DS1: 1962
						DS2: 1967
description: Census of Governments Series
description: States, county, and local governments in the United States in 1962 and 1967.
				   		Smallest Geographic Unit: State
DOI: 10.5067/40l92g8144iv
title: OMPS-NPP L2 NM Aerosol Index swath orbital
DOI: 10.5281/zenodo.10015316
title: Consequences of drought for grassland songbird reproduction - R code and data files

description: R code and data files for a submitted manuscript on the effects of a severe drought in NE Kansas on grassland songbird reproduction
DOI: 10.5281/zenodo.10448042
title: Dataset for "Spatial variations in the degree of upper-mantle depletion in a mid-ocean ridge-transform fault system" by M. Morishige

description: This is the dataset for "Spatial variations in the degree of upper-mantle depletion in a mid-ocean ridge-transform fault system" by M. Morishige.
DOI: 10.5281/zenodo.10555887
title: The EFSA catalogues applied for the 2023 zoonoses data reporting

description: The EFSA catalogues applied for the 2023 zoonoses data reporting are made available in Excel format for easier use and reference.
description: EU; xlsx; zoonoses.support@efsa.europa.eu;
DOI: 10.5281/zenodo.8056934
title: Time/frequency-domain characterization of a mid-IR DFG frequency comb via two-photon and heterodyne detection: datasets

description: This archive contains the datasets used for generating the plots shown in the paper entitled "Time/frequency-domain characterization of a mid-IR DFG frequency comb via two-photon and heterodyne detection", authored by Tecla Gabbrielli, Giacomo Insero, Michele De Regis, Nicola Corrias, Iacopo Galli, Davide Mazzotti, Paolo Bartolini, Jeong Hyun Huh, Carsten Cleff, Alexander Kastner, Ronald Holzwarth, Simone Borri, Luigi Consolino, Paolo De Natale, and Francesco Cappelli. 


A README file describing the contained data and how to elaborate them is also provided. 


 
description: The authors also acknowledge financial support by the European Union's NextGenerationEU Programme with the I-PHOQS Infrastructure [IR0000016, ID D2B8D520, CUP B53C22001750006] "Integrated infrastructure initiative in Photonic and Quantum Sciences", by the European Union's QuantERA II [G.A. n. 101017733] – QATACOMB Project "Quantum correlations in terahertz QCL combs", and by the Italian ESFRI Roadmap (Extreme Light Infrastructure – ELI Project).
DOI: 10.22000/1724
title: FrancoDiazACP2023
title: Convective gravity wave events during summer near 54°N present in both AIRS and RMR Lidar observations

description: Data to reproduce the figures in publication.
DOI: 10.6084/m9.figshare.25125272
title: Supplementary Material for: Predictors and prognosis of early neurological outcomes on patients with Vertebrobasilar artery occlusion undergoing endovascular treatment

description: Background: This research explored the factors influencing early neurological outcomes (ENO) in patients who had vertebrobasilar artery occlusion (VBAO) and received endovascular treatment (EVT), as well as examining the causal influence of ENO on the prognosis of VBAO patients.
Methods: A retrospective review was carried out on patients from 65 Chinese stroke centers, all within 24 hours of the estimated occlusion time. ENO includes early neurological improvement (ENI) and early neurological deterioration (END), defined as a decrease or an increase of at least 4 points in NIHSS score between baseline and 24 hours after EVT. Death within 24 hours after EVT also consider as END. END was further divided into explainable END and unexplainable END (unEND). Independent predictors of ENO and the association between ENO and outcomes in patients with VBAO were determined using center-adjusted analyses. The study developed a multivariate logistic regression model to examine the comparative risk of unEND versus explainable END on the clinical outcomes in VBAO patients.
Results: A total of 2257 patients were included. Glasgow Coma Scale (GCS) (OR 1.16, 95% CI 1.03-1.30) and successful reperfusion (OR 1.15, 95% CI 1.02-1.30) were associated with ENI. Baseline NIHSS (OR 0.60, 95% CI 0.53-0.68), successful reperfusion (OR 0.79, 95% CI 0.71-0.89) and puncture to reperfusion time (OR 1.17, 95% CI 1.03-1.33) were associated with END. When examining three-month prognostic indexes, both END and ENI were found to be linked to the three-month outcomes, but in opposite directions. A subgroup analysis of END suggested that unexplained END typically demonstrated a more favorable prognosis compared to explained END, although the prognosis remained generally unfavorable.
Conclusions: ENO, whether they manifested as early improvement or deterioration, were linked to the prognosis of VBAO patients undergoing EVT. The outcomes after unEND were more favorable than those following explained END.
DOI: 10.25592/uhhfdm.13914
title: Catalogue data and loan statistics for 24 German-Jewish Archives at the National Library of Israel

description: Research data created in the context of UWA project RFE10 "Wandering Artefacts. The Materialistic History of German-Jewish Archives". The data served as a basis for the article "A Guide for the Perplexed. Exploring the German-Jewish Archives at the National Library of Israel" by Sebastian Schirrmeister, <em>Jewish Culture and History</em> 25,1 (2024), 1-27, https://doi.org/10.1080/1462169X.2024.2306005.

The spreadsheet contains: a) catalogue data for all 19,489 file records from 24 German-Jewish archives digitized as part of a cooperation between CSMC and the National Library of Israel (NLI) in 2021/2022 and b) loan statistics of the files between November 2019 and April 2023.
description: The creation of this research data was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy – EXC 2176 'Understanding Written Artefacts: Material, Interaction and Transmission in Manuscript Cultures', project no. 390893796. The research was conducted within the scope of the Centre for the Study of Manuscript Cultures (CSMC) at Universität Hamburg.
DOI: 10.25592/uhhfdm.13913
title: Catalogue data and loan statistics for 24 German-Jewish Archives at the National Library of Israel

description: Research data created in the context of UWA project RFE10 "Wandering Artefacts. The Materialistic History of German-Jewish Archives". The data served as a basis for the article "A Guide for the Perplexed. Exploring the German-Jewish Archives at the National Library of Israel" by Sebastian Schirrmeister, <em>Jewish Culture and History</em> 25,1 (2024), 1-27, https://doi.org/10.1080/1462169X.2024.2306005.

The spreadsheet contains: a) catalogue data for all 19,489 file records from 24 German-Jewish archives digitized as part of a cooperation between CSMC and the National Library of Israel (NLI) in 2021/2022 and b) loan statistics of the files between November 2019 and April 2023.
description: The creation of this research data was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy – EXC 2176 'Understanding Written Artefacts: Material, Interaction and Transmission in Manuscript Cultures', project no. 390893796. The research was conducted within the scope of the Centre for the Study of Manuscript Cultures (CSMC) at Universität Hamburg.
DOI: 10.5281/zenodo.7500743
title: The computation results of coupled hydrological and hydrodynamic modelling application for the Nemunas River watershed – Curonian Lagoon – South-Eastern Baltic Sea continuum

description: 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:




Abbreviation in datasets
Model
Institution




ICHEC
EC-Earth
Irish Centre for High-End Computing


IPSL
IPSL-CM 5A-MR
The Institut Pierre-Simon Laplace


MOHC
HadGEM2-ES
Met Office Hadley Centre


MPI
MPI-ESM-LR
Max Planck Institute for Meteorology




 

Climate change scenarios and periods:



Historical/reference (1970-2005);

RCP4.5 (2005-2100);

RCP8.5 (2005-2100).


The datasets consist of time series for the parameters of:



Ice thickness - average ice thickness in the Curonian Lagoon;

Meteorological data - bias-corrected temperature and precipitation data for the marine and terrestrial areas;

Nemunas River discharge - simulated average daily values for the discharge and water temperature;

Salinity - selected points in the south-eastern Baltic Sea and one point next to Juodkrantė (in the Curonian Lagoon);

Water fluxes - through four predefined cross-sections in the Curonian Lagoon;

Water level - in 10 preselected points in the Curonian Lagoon and South-eastern Baltic Sea;

Water residence time - in the total Curonian Lagoon area, as well as its northern and southern parts;

Water temperature - in 10 preselected points in the Curonian Lagoon and South-eastern Baltic Sea.


Some of the datasets (zip files) have additional information (coordinates, data column explanations, units, etc.) in READ_ME.txt files.
description: This project has received funding from the Research Council of Lithuania (LMTLT), agreement No S-MIP-21-24.