cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc27f911
title: CCDC 2068352: Experimental Crystal Structure Determination

description: Related Article: Nadezhda B. Tamm, Victor A. Brotsman, Lev N. Sidorov, Sergey I. Troyanov|2021|Inorg.Chem.|60|6991|doi:10.1021/acs.inorgchem.1c00775
DOI: 10.5281/zenodo.4807837
title: Changes in Bacterial and Fungal Soil Communities in Long-Term Organic Cropping Systems

description: In this section you can find the raw sequences and otu table of fungal from the paper: Changes in Bacterial and Fungal Soil Communities in Long-Term Organic Cropping Systems published on 15 May 2021
DOI: 10.5281/zenodo.4807836
title: Changes in Bacterial and Fungal Soil Communities in Long-Term Organic Cropping Systems

description: In this section you can find the raw sequences and otu table of fungal from the paper: Changes in Bacterial and Fungal Soil Communities in Long-Term Organic Cropping Systems published on 15 May 2021
DOI: 10.5281/zenodo.4835786
title: A Longitudinal Analysis of Bloated Java Dependencies

description: A Longitudinal Analysis of Bloated Java Dependencies This repository contains the data and script for the paper "A Longitudinal Analysis of Bloated Java Dependencies" Repository Structure <pre><code>- dataset - projects.csv # list of 500 projects used in the paper - commits.csv # list of commits that are analyzed - project_dependabot.json # dependabot commits for each project - project_releases.json # commits associated to a release for each project - dependency_usage_tree - &lt;project&gt; - &lt;commit&gt; - depclean.json # the dependency usage tree extracted by Deplean - compile.log.zip # Maven compilation log - depClean.log.zip # Deplean log - script - create_dataset.js # ceate projects.csv and commits.csv based on project_releases.json and project_dependabot.json - read_dependency_usage_tree.js # extract the information from dependency_usage_tree and generate a csv file - analysis.py # read dependency_usage_tree.csv and generate the macro and table for the paper</code></pre>
DOI: 10.5281/zenodo.4835785
title: A Longitudinal Analysis of Bloated Java Dependencies

description: A Longitudinal Analysis of Bloated Java Dependencies This repository contains the data and script for the paper "A Longitudinal Analysis of Bloated Java Dependencies" Repository Structure <pre><code>- dataset - projects.csv # list of 500 projects used in the paper - commits.csv # list of commits that are analyzed - project_dependabot.json # dependabot commits for each project - project_releases.json # commits associated to a release for each project - dependency_usage_tree - &lt;project&gt; - &lt;commit&gt; - depclean.json # the dependency usage tree extracted by Deplean - compile.log.zip # Maven compilation log - depClean.log.zip # Deplean log - script - create_dataset.js # ceate projects.csv and commits.csv based on project_releases.json and project_dependabot.json - read_dependency_usage_tree.js # extract the information from dependency_usage_tree and generate a csv file - analysis.py # read dependency_usage_tree.csv and generate the macro and table for the paper</code></pre>
DOI: 10.5281/zenodo.4835784
title: X-ray crystallography and Mass spectrometry raw and processed data for Hahn et al. 2021

description: X-ray diffraction images for PDB 7B1S, 7B2C, 7B2H and raw/processed data for the mass spectrometry experiments regarding the publication: "Crystal structure of a key enzyme for anaerobic ethane activation" from Hahn et al.
description: X-ray diffraction images, data collection parameters (XDS.INP) and integration data (XDS_ASCII.HKL and CORRECT.LP) for: PDB 7B1S: Crystal structure of the ethyl-coenzyme M reductase from Candidatus Ethanoperedens thermophilum at 0.994-A resolution PDB 7B2C: Crystal structure of the ethyl-coenzyme M reductase from Candidatus Ethanoperedens thermophilum gassed with xenon PDB 7B2H: Crystal structure of the methyl-coenzyme M reductase from Methanothermobacter Marburgensis derivatized with xenon Raw and processed (Bionic) mass spectrometry data
description: {"references": ["Crystal structure of a key enzyme for anaerobic ethane activation (2021) Cedric J Hahn, Olivier N Lemaire, J\u00f6rg Kahnt, Sylvain Engilberge, Gunter Wegener, Tristan Wagner"]}
DOI: 10.5281/zenodo.4751127
title: X-ray crystallography and Mass spectrometry raw and processed data for Hahn et al. 2021

description: X-ray diffraction images for PDB 7B1S, 7B2C, 7B2H and raw/processed data for the mass spectrometry experiments regarding the publication: "Crystal structure of a key enzyme for anaerobic ethane activation" from Hahn et al.
description: X-ray diffraction images, data collection parameters (XDS.INP) and integration data (XDS_ASCII.HKL and CORRECT.LP) for: PDB 7B1S: Crystal structure of the ethyl-coenzyme M reductase from Candidatus Ethanoperedens thermophilum at 0.994-A resolution PDB 7B2C: Crystal structure of the ethyl-coenzyme M reductase from Candidatus Ethanoperedens thermophilum gassed with xenon PDB 7B2H: Crystal structure of the methyl-coenzyme M reductase from Methanothermobacter Marburgensis derivatized with xenon Raw and processed (Bionic) mass spectrometry data
description: {"references": ["Crystal structure of a key enzyme for anaerobic ethane activation (2021) Cedric J Hahn, Olivier N Lemaire, J\u00f6rg Kahnt, Sylvain Engilberge, Gunter Wegener, Tristan Wagner"]}
DOI: 10.5281/zenodo.4812785
title: Datasets & utils for paper USING PRE-TRAINED MODELS TO PARTIALLY AUTOMATE CODE REVIEW ACTIVITIES

description: Raw and processed datasets & Configurations files for Pre-training and Fine-Tuning T5 models <strong>Pre-Training dataset </strong>Obtained by mining Stack Overflow and CodeSearchNet data. <strong>Fine-Tuning dataset </strong>We will fine-tune our T5 small model on different datasets obtained by mining code review data from Gerrit and GitHub repositories. <strong>Fine-Tuning dataset v1 (Small)</strong> Same dataset used by Tufano et al., abstracted code and raw comments. <strong>Fine-Tuning dataset v2 (Small)</strong> Same dataset used by Tufano et al., not abstracted code and cleaned comments. <strong>Fine-Tuning dataset (Large) </strong>Our new Large dataset
DOI: 10.18112/openneuro.ds003669.v1.0.0
title: Confidence in Detection and Discrimination
DOI: 10.5281/zenodo.4022573
title: User-centered Usability Analysis of 41 Open Government Data Portals

description: The data were collected during the user-centered analysis of usability of 41 open government data portals including EU27, applying a common methodology to them, considering aspects such as specification of open data set, feedback and requests, further broken down into 14 sub-criteria. Each aspect was assessed using a three-level Likert scale (fulfilled - 3, partially fulfilled - 2, and unfulfilled – 1), that belongs to the acceptability tasks. This dataset summarises a total of 1640 protocols obtained during the analysis of the selected portals carried out by 40 participants, who were selected on a voluntary basis. This is complemented with 4 summaries of these protocols, which include calculated average scores by category, aspect and country. These data allow comparative analysis of the national open data portals, help to find the key challenges that can negatively impact users’ experience, and identifies portals that can be considered as an example for the less successful open data portals.
description: {"references": ["Nikiforova, A., & McBride, K. (2021). Open government data portal usability: A user-centred usability analysis of 41 open government data portals. Telematics and Informatics, 58, 101539, https://doi.org/10.1016/j.tele.2020.101539"]}
DOI: 10.5281/zenodo.4022572
title: User-centered Usability Analysis of 41 Open Government Data Portals

description: The data were collected during the user-centered analysis of usability of 41 open government data portals including EU27, applying a common methodology to them, considering aspects such as specification of open data set, feedback and requests, further broken down into 14 sub-criteria. Each aspect was assessed using a three-level Likert scale (fulfilled - 3, partially fulfilled - 2, and unfulfilled – 1), that belongs to the acceptability tasks. This dataset summarises a total of 1640 protocols obtained during the analysis of the selected portals carried out by 40 participants, who were selected on a voluntary basis. This is complemented with 4 summaries of these protocols, which include calculated average scores by category, aspect and country. These data allow comparative analysis of the national open data portals, help to find the key challenges that can negatively impact users’ experience, and identifies portals that can be considered as an example for the less successful open data portals.
description: {"references": ["Nikiforova, A., & McBride, K. (2021). Open government data portal usability: A user-centred usability analysis of 41 open government data portals. Telematics and Informatics, 58, 101539, https://doi.org/10.1016/j.tele.2020.101539"]}
DOI: 10.6084/m9.figshare.14701935
title: H3K27Ac Ventricle UI rep2

description: For UCSC
DOI: 10.6084/m9.figshare.14701935.v1
title: H3K27Ac Ventricle UI rep2

description: For UCSC
DOI: 10.5281/zenodo.4836136
title: List of wind power projects in Vietnam

description: Historical inventory of wind power projects in Vietnam updated 2021-05-28 The number of records is 508, of which 414 refer to active projects phases, and 158 have investment costs. Each record describes a wind project phase. The table includes projects at all stages of the lifecycle. Some have been mentioned years ago and are now of historical interest only. Some have just a signed exploration MoU. All records are referenced to one or several public sources. Fields: Record status, Project stage, Project name, Owner, Location (hamlet, commune, province, region, longitude*, latitude*), Location type (onshore/nearshore/offshore), Capacity (MWp), Connection plan, Turbines, Investment (VND or USD), Key milestone dates (MoU, Investment Licence, PPA*, Groundbreaking, Expected COD, Actual COD), Note and sources. *Fields added in this release
description: This release only updates the data files.
DOI: 10.5281/zenodo.4817652
title: RoB 2 cribsheets

description: These are the cribsheets related to the Risk of Bias assessment
DOI: 10.5281/zenodo.4836173
title: CEP152 Results from "3D Structure from SMLM images using DeepLearning" Paper

description: <strong>CEP152 Results from "3D Structure from SMLM images using DeepLearning" Paper</strong> This zip file contains 5 subdirectories, each containing data for a single CEP152 experiment from our paper. Inside each directory you will find: The fits and jpg files saved as training progresses The obj and ply files saved as training progresses A montage of input and output images The last.ply file - the structure itself The trained model and checkpoint. The run.conf file used to create this experiment
DOI: 10.5281/zenodo.4836172
title: CEP152 Results from "3D Structure from SMLM images using DeepLearning" Paper

description: <strong>CEP152 Results from "3D Structure from SMLM images using DeepLearning" Paper</strong> This zip file contains 5 subdirectories, each containing data for a single CEP152 experiment from our paper. Inside each directory you will find: The fits and jpg files saved as training progresses The obj and ply files saved as training progresses A montage of input and output images The last.ply file - the structure itself The trained model and checkpoint. The run.conf file used to create this experiment
DOI: 10.5281/zenodo.4585400
title: Dataset supporting "Interpreting extreme climate impacts from large ensemble simulations – are they unseen or unrealistic?"

description: Several datasets that allow reproducing the analysis of the paper "Interpreting extreme climate impacts from large ensemble simulations – are they unseen or unrealistic?" Supporting code available at https://github.com/timokelder/EXPLORE / https://timokelder.github.io/EXPLORE/
DOI: 10.5281/zenodo.4585399
title: Dataset supporting "Interpreting extreme climate impacts from large ensemble simulations – are they unseen or unrealistic?"

description: Several datasets that allow reproducing the analysis of the paper "Interpreting extreme climate impacts from large ensemble simulations – are they unseen or unrealistic?" Supporting code available at https://github.com/timokelder/EXPLORE / https://timokelder.github.io/EXPLORE/
DOI: 10.6084/m9.figshare.14701941
title: Input rep1

description: Input control
DOI: 10.6084/m9.figshare.14701941.v1
title: Input rep1

description: Input control
DOI: 10.5281/zenodo.4836360
title: Supplementary Materials: Forests, Water, and Land Use Change across the Central American Isthmus: Mapping the evidence base for terrestrial Holocene palaeoenvironmental proxies

description: Supplementary Materials for Forests, Water, and Land Use Change across the Central American Isthmus: Mapping the evidence base for terrestrial Holocene palaeoenvironmental proxies: (i) Appendix 1; (ii) Appendix 2; and (iii) Raw Data.
DOI: 10.5281/zenodo.4836359
title: Supplementary Materials: Forests, Water, and Land Use Change across the Central American Isthmus: Mapping the evidence base for terrestrial Holocene palaeoenvironmental proxies

description: Supplementary Materials for Forests, Water, and Land Use Change across the Central American Isthmus: Mapping the evidence base for terrestrial Holocene palaeoenvironmental proxies: (i) Appendix 1; (ii) Appendix 2; and (iii) Raw Data.
DOI: 10.5281/zenodo.4836345
title: ECHAM-HAM simulations of dust-driven droplet freezing

description: The data corresponds to Cloud Top Phase information at different temperature bins for different model configurations with the ECHAM-HAM climate model. CIF_NSTuned:long_name = "Cloud Ice Frequency for simulation CIF_NSTuned" ;<br> CIF_NS10K:long_name = "Cloud Ice Frequency for simulation CIF_NS10K" ;<br> CIF_NS:long_name = "Cloud Ice Frequency for simulation CIF_NS" ;<br> CIF_LD:long_name = "Cloud Ice Frequency for simulation CIF_LD" ;<br> CIF_NoFRZ:long_name = "Cloud Ice Frequency for simulation CIF_NoFRZ" ; The simulations were performed for the period 2007-2010 using 31 vertical model layers converted to 3K temperature bins, and a horizontal resolution of 1.875°(T63). For all simulations, contact freezing and deposition nucleation in the mixed-phase regime are turned off. In the NoFRZ simulation, immersion freezing is turned off, but droplets are converted to ice at −35°C (homogenous freezing). The LD and NS simulations use the LD and NS scheme, respectively, and assume the INP efficiency of the clay mineral montmorillonite. In the NS10K simulation, shifting NB by +10°C causes dust-INP to freeze at temperatures 10°C warmer compared to the NS simulation. The NS-Tuned simulation is based on the NS10K simulation, but only dust number concentrations higher than 10<sup>6</sup> kg<sup>−1</sup> are considered for droplet freezing.
DOI: 10.5281/zenodo.4836344
title: ECHAM-HAM simulations of dust-driven droplet freezing

description: The data corresponds to Cloud Top Phase information at different temperature bins for different model configurations with the ECHAM-HAM climate model. CIF_NSTuned:long_name = "Cloud Ice Frequency for simulation CIF_NSTuned" ;<br> CIF_NS10K:long_name = "Cloud Ice Frequency for simulation CIF_NS10K" ;<br> CIF_NS:long_name = "Cloud Ice Frequency for simulation CIF_NS" ;<br> CIF_LD:long_name = "Cloud Ice Frequency for simulation CIF_LD" ;<br> CIF_NoFRZ:long_name = "Cloud Ice Frequency for simulation CIF_NoFRZ" ; The simulations were performed for the period 2007-2010 using 31 vertical model layers converted to 3K temperature bins, and a horizontal resolution of 1.875°(T63). For all simulations, contact freezing and deposition nucleation in the mixed-phase regime are turned off. In the NoFRZ simulation, immersion freezing is turned off, but droplets are converted to ice at −35°C (homogenous freezing). The LD and NS simulations use the LD and NS scheme, respectively, and assume the INP efficiency of the clay mineral montmorillonite. In the NS10K simulation, shifting NB by +10°C causes dust-INP to freeze at temperatures 10°C warmer compared to the NS simulation. The NS-Tuned simulation is based on the NS10K simulation, but only dust number concentrations higher than 10<sup>6</sup> kg<sup>−1</sup> are considered for droplet freezing.
DOI: 10.5281/zenodo.4836456
title: TBD

description: This folder /final_xyz_structures/ contains the DFT-optimized geometries (in .xyz format together with the gas-phase energy, E) accompanying the paper "Paper Title" Where conformers occur, they are always named from the lowest Gibbs energy to the highest in ascending order from c1, c2, ...
DOI: 10.5281/zenodo.4836274
title: Structural determinants of ligand recognition by the human mitochondrial basic amino acids transporter SLC25A29. Insight from molecular dynamics simulations.

description: Initial coordinates, molecular dynamics trajectories and representative snapshots resulting from the study "Structural determinants of ligand recognition by the human mitochondrial basic amino acids transporter SLC25A29. Insight from molecular dynamics simulations." by Pasquadibisceglie and Polticelli. The folders MD0-MD5 contain the parameter/topology (parm7) and initial coordinates (rst7) for the six molecular dynamics simulations. Moreover, a NetCDF trajectory "prod.nc" of the production phase is also included. The folder PDB_figures contains the PDB files used to produce the figures presented in the manuscript.
DOI: 10.5281/zenodo.4836464
title: Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes

description: This archive contains the data and the R code to reproduce the figures of the manuscript by Sellis et al. (2021): <br> Sellis D, Guérin F, Arnaiz O, Pett W, Lerat E, Boggetto N, Krenek S, Berendonk T, Couloux A, Aury J-M, Labadie K, Malinsky S, Bhullar S, Meyer E, Sperling L, Duret L and Duharcourt S (2021) Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes. bioRxiv: 2020.12.23.424184. https://doi.org/10.1101/2020.12.23.424184
description: {"references": ["Sellis D, Gu\u00e9rin F, Arnaiz O, Pett W, Lerat E, Boggetto N, Krenek S, Berendonk T, Couloux A, Aury J-M, Labadie K, Malinsky S, Bhullar S, Meyer E, Sperling L, Duret L and Duharcourt S (2021) Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes. bioRxiv: 2020.12.23.424184. https://doi.org/10.1101/2020.12.23.424184"]}
DOI: 10.5281/zenodo.4415827
title: Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes

description: This archive contains the data and the R code to reproduce the figures of the manuscript by Sellis et al. (2021): <br> Sellis D, Guérin F, Arnaiz O, Pett W, Lerat E, Boggetto N, Krenek S, Berendonk T, Couloux A, Aury J-M, Labadie K, Malinsky S, Bhullar S, Meyer E, Sperling L, Duret L and Duharcourt S (2021) Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes. bioRxiv: 2020.12.23.424184. https://doi.org/10.1101/2020.12.23.424184
description: {"references": ["Sellis D, Gu\u00e9rin F, Arnaiz O, Pett W, Lerat E, Boggetto N, Krenek S, Berendonk T, Couloux A, Aury J-M, Labadie K, Malinsky S, Bhullar S, Meyer E, Sperling L, Duret L and Duharcourt S (2021) Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes. bioRxiv: 2020.12.23.424184. https://doi.org/10.1101/2020.12.23.424184"]}
DOI: 10.5281/zenodo.3784963
title: Supplementary Data to Dual clumped isotope thermometry resolves kinetic biases in carbonate formation temperatures

description: In this dataset, we provide analytical and model data to <em>Dual clumped isotope thermometry resolves kinetic biases in carbonate formation temperatures</em> by Bajnai et al. (2020). Also deposited here is the R code that we used to calculate the equations and generate the figures in the manuscript.
description: Surface temperature is a fundamental parameter of Earth's climate. Its evolution through time is commonly reconstructed using the oxygen isotope and the clumped isotope compositions of carbonate archives. However, reaction kinetics involved in the precipitation of carbonates can introduce inaccuracies in the derived temperatures. Here, we show that dual clumped isotope analyses, ie simultaneous ∆47 and ∆48 measurements on the single carbonate phase, can identify the origin and quantify the extent of these kinetic biases. Our results verify theoretical predictions and evidence that the isotopic disequilibrium commonly observed in speleothems and scleractinian coral skeletons is inherited from the dissolved inorganic carbon pool of their parent solutions. Further, we show that dual clumped isotope thermometry can achieve reliable palaeotemperature reconstructions, devoid of kinetic bias. Analysis of a belemnite rostrum implies that it precipitated near isotopic equilibrium and confirms the warmer-than-present temperatures during the Early Cretaceous at southern high latitudes.
DOI: 10.5281/zenodo.3784962
title: Supplementary Data to Dual clumped isotope thermometry resolves kinetic biases in carbonate formation temperatures

description: In this dataset, we provide analytical and model data to <em>Dual clumped isotope thermometry resolves kinetic biases in carbonate formation temperatures</em> by Bajnai et al. (2020). Also deposited here is the R code that we used to calculate the equations and generate the figures in the manuscript.
description: Surface temperature is a fundamental parameter of Earth's climate. Its evolution through time is commonly reconstructed using the oxygen isotope and the clumped isotope compositions of carbonate archives. However, reaction kinetics involved in the precipitation of carbonates can introduce inaccuracies in the derived temperatures. Here, we show that dual clumped isotope analyses, ie simultaneous ∆47 and ∆48 measurements on the single carbonate phase, can identify the origin and quantify the extent of these kinetic biases. Our results verify theoretical predictions and evidence that the isotopic disequilibrium commonly observed in speleothems and scleractinian coral skeletons is inherited from the dissolved inorganic carbon pool of their parent solutions. Further, we show that dual clumped isotope thermometry can achieve reliable palaeotemperature reconstructions, devoid of kinetic bias. Analysis of a belemnite rostrum implies that it precipitated near isotopic equilibrium and confirms the warmer-than-present temperatures during the Early Cretaceous at southern high latitudes.
DOI: 10.5281/zenodo.4836470
title: List of articles - Global Adaptation Mapping Initiative

description: This file contains the bibliographic list of 1682 documents screened and coded by the The Global Adaptation Mapping Initiative (https://globaladaptation.github.io/index.html). Coded data are not included. Abstracts are excluded due to copyright restrictions.
DOI: 10.5281/zenodo.4836469
title: List of articles - Global Adaptation Mapping Initiative

description: This file contains the bibliographic list of 1682 documents screened and coded by the The Global Adaptation Mapping Initiative (https://globaladaptation.github.io/index.html). Coded data are not included. Abstracts are excluded due to copyright restrictions.