cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4704392
title: Annex 3 dataset: Survey for Academic Assessment Systems for Open Science & Research Data (anonymised)

description: <em>The survey served as a reference for the project members to overview current state-of-the-art and identify gaps in responsible academic assessment of research and researchers throughout Europe. This dataset is an appendix to Annex 3 of EOSC Co-creation report "Making FAIReR Assessments Possible" </em>https://doi.org/10.5281/zenodo.4701375.<em> This report is a deliverable of EOSC Co-Creation projects (i) “European overview of career merit systems’’ and (ii) “Vision for research data in research careers”, funded by the EOSC Co-Creation funding. Further information on these projects can be found here: </em>https://avointiede.fi/en/networks/eosc-co-creation.
DOI: 10.5281/zenodo.4704425
title: Annex 4 dataset: OS-CAM Case Studies

description: Purpose of the document is to present case studies of usage of well-known European research eInfrastructures (models and platforms) for responsible academic career assessment based on Open Science outputs, activities and expertise. This dataset is an appendix to Annex 4 of EOSC Co-creation report "Making FAIReR Assessments Possible" https://doi.org/10.5281/zenodo.4701375. This report is a deliverable of EOSC Co-Creation projects (i) “European overview of career merit systems’’ and (ii) “Vision for research data in research careers”, funded by the EOSC Co-Creation funding. Further information on these projects can be found here: https://avointiede.fi/en/networks/eosc-co-creation.
DOI: 10.5281/zenodo.4704424
title: Annex 4 dataset: OS-CAM Case Studies

description: Purpose of the document is to present case studies of usage of well-known European research eInfrastructures (models and platforms) for responsible academic career assessment based on Open Science outputs, activities and expertise. This dataset is an appendix to Annex 4 of EOSC Co-creation report "Making FAIReR Assessments Possible" https://doi.org/10.5281/zenodo.4701375. This report is a deliverable of EOSC Co-Creation projects (i) “European overview of career merit systems’’ and (ii) “Vision for research data in research careers”, funded by the EOSC Co-Creation funding. Further information on these projects can be found here: https://avointiede.fi/en/networks/eosc-co-creation.
DOI: 10.25345/c5781t
title: MassIVE MSV000087255 - Mascot export MGF test test test test test test test test test test
title: test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test test
DOI: 10.6084/m9.figshare.14206034
title: Additional file 6: Table S2

description: Tpm values in MSTRG.494.1, MSTRG.649.1-2 and MSTRG.704.1-3.
DOI: 10.6084/m9.figshare.14206034.v1
title: Additional file 5: Table S1

description: Tpm values in MSTRG.494.1, MSTRG.649.1-2 and MSTRG.704.1-3.
DOI: 10.17632/3223kj9hbt.1
title: Data for: Bayesian subgroup analysis in regression using mixture models

description: This Zip file contains Julia program (version 1.1.1) for implementing the cMFM described in "Bayesian subgroup analysis in regression using mixture models."
DOI: 10.5281/zenodo.4707714
title: In silico voltage-sensitive dye imaging reveals the emergent dynamics of cortical populations: figure data

description: Tabular data corresponding to figures 2 through 5 (and supplementary figures 1 through 6) in the 2021 Nature Communcations publication entitled "In silico voltage-sensitive dye imaging reveals the emergent dynamics of cortical populations". Tabular data are provided for each figure in the form of excel spreadsheets, with individual data sheets for each figure sub-panel, where all axis and units are described in the row and column headings. Additionally, the ipython notebooks used to generate the figure data are provided (figure*.ipynb), together with the necessary raw data files (data.zip), supporting libraries (utils.zip), output folder (figures.zip), and requirements (requirements.txt). See README.rtf for detailed information and usage instructions.
DOI: 10.5517/ccdc.csd.cc1kg2gk
title: CCDC 1443498: Experimental Crystal Structure Determination

description: Related Article: Timothy J. Boyle, Michael L. Neville, Jeremiah M. Sears, Roger Cramer|2016|Chem. Sel.|1|473|doi:10.1002/slct.201600138
DOI: 10.5517/ccdc.csd.cc1zwcks
title: CCDC 1843556: Experimental Crystal Structure Determination

description: Related Article: Wen-Yuan Pei, Jin Yang, Hui Wu, Wei Zhou, Ying-Wei Yang, Jian-Fang Ma|2020|Chem.Commun.|56|2491|doi:10.1039/D0CC00157K
DOI: 10.5517/ccdc.csd.cc26mzlf
title: CCDC 2044995: Experimental Crystal Structure Determination

description: Related Article: Chamila Manankandayalage, Daniel K. Unruh, Clemens Krempner|2021|Chem.-Eur.J.|27|6263|doi:10.1002/chem.202005143
DOI: 10.5517/ccdc.csd.cc26mzpj
title: CCDC 2044998: Experimental Crystal Structure Determination

description: Related Article: Chamila Manankandayalage, Daniel K. Unruh, Clemens Krempner|2021|Chem.-Eur.J.|27|6263|doi:10.1002/chem.202005143
DOI: 10.5517/ccdc.csd.cc26mzqk
title: CCDC 2044999: Experimental Crystal Structure Determination

description: Related Article: Chamila Manankandayalage, Daniel K. Unruh, Clemens Krempner|2021|Chem.-Eur.J.|27|6263|doi:10.1002/chem.202005143
DOI: 10.5517/ccdc.csd.cc26mzrl
title: CCDC 2045000: Experimental Crystal Structure Determination

description: Related Article: Chamila Manankandayalage, Daniel K. Unruh, Clemens Krempner|2021|Chem.-Eur.J.|27|6263|doi:10.1002/chem.202005143
DOI: 10.5517/ccdc.csd.cc26mzsm
title: CCDC 2045001: Experimental Crystal Structure Determination

description: Related Article: Chamila Manankandayalage, Daniel K. Unruh, Clemens Krempner|2021|Chem.-Eur.J.|27|6263|doi:10.1002/chem.202005143
DOI: 10.5517/ccdc.csd.cc26mztn
title: CCDC 2045002: Experimental Crystal Structure Determination

description: Related Article: Chamila Manankandayalage, Daniel K. Unruh, Clemens Krempner|2021|Chem.-Eur.J.|27|6263|doi:10.1002/chem.202005143
DOI: 10.5517/ccdc.csd.cc26mzvp
title: CCDC 2045003: Experimental Crystal Structure Determination

description: Related Article: Chamila Manankandayalage, Daniel K. Unruh, Clemens Krempner|2021|Chem.-Eur.J.|27|6263|doi:10.1002/chem.202005143
DOI: 10.5517/ccdc.csd.cc26mzwq
title: CCDC 2045004: Experimental Crystal Structure Determination

description: Related Article: Chamila Manankandayalage, Daniel K. Unruh, Clemens Krempner|2021|Chem.-Eur.J.|27|6263|doi:10.1002/chem.202005143
DOI: 10.3886/e119601
title: Data and Code: Mobilizing the Masses for Genocide

description: Do political elites use armed groups to foster civilian participation in genocidal violence? Are armed groups employed strategically? How do they mobilize civilians? I investigate these questions using data from the Rwandan Genocide. To establish causality, I exploit exogenous variation in armed groups' transport costs induced by weather ﬂuctuations: the shortest distance of each village to the main road interacted with rainfall along the dirt tracks between main road and village. I ﬁnd: (1) one additional armed-group member resulted in 7.3 more civilian perpetrators, (2) armed-group leaders employed their men strategically, and (3) armed groups invoked civilians' obedience.
description: Administrative Sectors in Rwanda in 1994.
DOI: 10.5517/ccdc.csd.cc26mzxr
title: CCDC 2045005: Experimental Crystal Structure Determination

description: Related Article: Chamila Manankandayalage, Daniel K. Unruh, Clemens Krempner|2021|Chem.-Eur.J.|27|6263|doi:10.1002/chem.202005143
DOI: 10.5517/ccdc.csd.cc26mzys
title: CCDC 2045006: Experimental Crystal Structure Determination

description: Related Article: Chamila Manankandayalage, Daniel K. Unruh, Clemens Krempner|2021|Chem.-Eur.J.|27|6263|doi:10.1002/chem.202005143
DOI: 10.3886/e119601v2
title: Data and Code: Mobilizing the Masses for Genocide

description: Do political elites use armed groups to foster civilian participation in genocidal violence? Are armed groups employed strategically? How do they mobilize civilians? I investigate these questions using data from the Rwandan Genocide. To establish causality, I exploit exogenous variation in armed groups' transport costs induced by weather ﬂuctuations: the shortest distance of each village to the main road interacted with rainfall along the dirt tracks between main road and village. I ﬁnd: (1) one additional armed-group member resulted in 7.3 more civilian perpetrators, (2) armed-group leaders employed their men strategically, and (3) armed groups invoked civilians' obedience.
description: Administrative Sectors in Rwanda in 1994.
DOI: 10.5517/ccdc.csd.cc26n01y
title: CCDC 2045009: Experimental Crystal Structure Determination

description: Related Article: Chamila Manankandayalage, Daniel K. Unruh, Clemens Krempner|2021|Chem.-Eur.J.|27|6263|doi:10.1002/chem.202005143
DOI: 10.5517/ccdc.csd.cc26n02z
title: CCDC 2045010: Experimental Crystal Structure Determination

description: Related Article: Chamila Manankandayalage, Daniel K. Unruh, Clemens Krempner|2021|Chem.-Eur.J.|27|6263|doi:10.1002/chem.202005143
DOI: 10.5517/ccdc.csd.cc26pkn4
title: CCDC 2046516: Experimental Crystal Structure Determination

description: Related Article: Sidney S. Woodhouse, Tyson N. Dais, Emily H. Payne, Mukesh K. Singh, Euan K. Brechin, Paul G. Plieger|2021|Dalton Trans.|50|5318|doi:10.1039/D0DT04286B
DOI: 10.5517/ccdc.csd.cc26pkp5
title: CCDC 2046517: Experimental Crystal Structure Determination

description: Related Article: Sidney S. Woodhouse, Tyson N. Dais, Emily H. Payne, Mukesh K. Singh, Euan K. Brechin, Paul G. Plieger|2021|Dalton Trans.|50|5318|doi:10.1039/D0DT04286B
DOI: 10.5517/ccdc.csd.cc26pkq6
title: CCDC 2046518: Experimental Crystal Structure Determination

description: Related Article: Sidney S. Woodhouse, Tyson N. Dais, Emily H. Payne, Mukesh K. Singh, Euan K. Brechin, Paul G. Plieger|2021|Dalton Trans.|50|5318|doi:10.1039/D0DT04286B
DOI: 10.5517/ccdc.csd.cc26pkr7
title: CCDC 2046519: Experimental Crystal Structure Determination

description: Related Article: Sidney S. Woodhouse, Tyson N. Dais, Emily H. Payne, Mukesh K. Singh, Euan K. Brechin, Paul G. Plieger|2021|Dalton Trans.|50|5318|doi:10.1039/D0DT04286B
DOI: 10.5517/ccdc.csd.cc26r6pw
title: CCDC 2048098: Experimental Crystal Structure Determination

description: Related Article: Christian Schneider, Serhiy Demeshko, Franc Meyer, C. Gunnar Werncke|2021|Chem.-Eur.J.|27|6348|doi:10.1002/chem.202100336
DOI: 10.5517/ccdc.csd.cc26r8t2
title: CCDC 2048164: Experimental Crystal Structure Determination

description: Related Article: Christian Schneider, Serhiy Demeshko, Franc Meyer, C. Gunnar Werncke|2021|Chem.-Eur.J.|27|6348|doi:10.1002/chem.202100336
DOI: 10.5517/ccdc.csd.cc26r8v3
title: CCDC 2048165: Experimental Crystal Structure Determination

description: Related Article: Christian Schneider, Serhiy Demeshko, Franc Meyer, C. Gunnar Werncke|2021|Chem.-Eur.J.|27|6348|doi:10.1002/chem.202100336
DOI: 10.5517/ccdc.csd.cc26r8x5
title: CCDC 2048167: Experimental Crystal Structure Determination

description: Related Article: Christian Schneider, Serhiy Demeshko, Franc Meyer, C. Gunnar Werncke|2021|Chem.-Eur.J.|27|6348|doi:10.1002/chem.202100336
DOI: 10.5517/ccdc.csd.cc26r8w4
title: CCDC 2048166: Experimental Crystal Structure Determination

description: Related Article: Christian Schneider, Serhiy Demeshko, Franc Meyer, C. Gunnar Werncke|2021|Chem.-Eur.J.|27|6348|doi:10.1002/chem.202100336
DOI: 10.5517/ccdc.csd.cc26mzf8
title: CCDC 2044990: Experimental Crystal Structure Determination

description: Related Article: Chamila Manankandayalage, Daniel K. Unruh, Clemens Krempner|2021|Chem.-Eur.J.|27|6263|doi:10.1002/chem.202005143
DOI: 10.5517/ccdc.csd.cc26mzhb
title: CCDC 2044992: Experimental Crystal Structure Determination

description: Related Article: Chamila Manankandayalage, Daniel K. Unruh, Clemens Krempner|2021|Chem.-Eur.J.|27|6263|doi:10.1002/chem.202005143
DOI: 10.5517/ccdc.csd.cc26mzmg
title: CCDC 2044996: Experimental Crystal Structure Determination

description: Related Article: Chamila Manankandayalage, Daniel K. Unruh, Clemens Krempner|2021|Chem.-Eur.J.|27|6263|doi:10.1002/chem.202005143
DOI: 10.5517/ccdc.csd.cc26mznh
title: CCDC 2044997: Experimental Crystal Structure Determination

description: Related Article: Chamila Manankandayalage, Daniel K. Unruh, Clemens Krempner|2021|Chem.-Eur.J.|27|6263|doi:10.1002/chem.202005143
DOI: 10.5521/forestplots.net/2021_3
title: Data from 'Non-structural carbohydrates mediate seasonal water stress across Amazon forests'. Caroline Signori-Müller, Rafael S. Oliveira, [...] David Galbraith et al. 2021. Nature Communications. DOI: 10.1038/s41467-021-22378-8'

description: This package contain the information about non-structural carbohydrates (NSC) in 82 Amazon tree species. There is the mean values of total non-structural carbohydrates (NSCT), starch and soluble sugars (SS) concentrations and the proportion of NSCT in the form of SS (SS:NSCT). Samples are from six sites in the Amazon Basin spanning a broad precipitation gradient. Measurements took place during the wet season in all six sites and during the wet season only in the seasonal sites.
DOI: 10.5281/zenodo.4707896
title: Example dataset

description: Examle record to showcase use of ZENODO
DOI: 10.5281/zenodo.4707895
title: Example dataset

description: Examle record to showcase use of ZENODO
DOI: 10.6084/m9.figshare.13603173.v2
title: Identification of host factors binding to dengue and Zika virus subgenomic RNA by efficient yeast three-hybrid screens of the human ORFeome

description: Flaviviruses such as the dengue (DENV) and the Zika virus (ZIKV) are important human pathogens causing around 100 million symptomatic infections each year. During infection, small subgenomic flavivirus RNAs (sfRNAs) are formed inside the infected host cell as a result of incomplete degradation of the viral RNA genome by cellular exoribonuclease XRN1. Although the full extent of sfRNA functions is to be revealed, these non-coding RNAs are key virulence factors and their detrimental effects on multiple cellular processes seem to consistently involve molecular interactions with RNA-binding proteins (RBPs). Discovery of such sfRNA-binding host-factors has followed established biochemical pull-down approaches skewed towards highly abundant proteins hampering proteome-wide coverage. Yeast three-hybrid (Y3H) systems represent an attractive alternative approach. To facilitate proteome-wide screens for RBP, we revisited and improved existing RNA-Y3H methodology by (1) implementing full-length ORF libraries in combination with (2) efficient yeast mating to increase screening depth and sensitivity, and (3) stringent negative controls to eliminate over-representation of non-specific RNA-binders. These improvements were validated employing the well-characterized interaction between DDX6 (DEAD-box helicase 6) and sfRNA of DENV as paradigm. Our advanced Y3H system was used to screen for human proteins binding to DENV and ZIKV sfRNA, resulting in a list of 69 putative sfRNA-binders, including several previously reported as well as numerous novel RBP host factors. Our methodology requiring no sophisticated infrastructure or analytic pipeline may be employed for the discovery of meaningful RNA–protein interactions at large scale in other fields.
DOI: 10.6084/m9.figshare.13603173
title: Identification of host factors binding to dengue and Zika virus subgenomic RNA by efficient yeast three-hybrid screens of the human ORFeome

description: Flaviviruses such as the dengue (DENV) and the Zika virus (ZIKV) are important human pathogens causing around 100 million symptomatic infections each year. During infection, small subgenomic flavivirus RNAs (sfRNAs) are formed inside the infected host cell as a result of incomplete degradation of the viral RNA genome by cellular exoribonuclease XRN1. Although the full extent of sfRNA functions is to be revealed, these non-coding RNAs are key virulence factors and their detrimental effects on multiple cellular processes seem to consistently involve molecular interactions with RNA-binding proteins (RBPs). Discovery of such sfRNA-binding host-factors has followed established biochemical pull-down approaches skewed towards highly abundant proteins hampering proteome-wide coverage. Yeast three-hybrid (Y3H) systems represent an attractive alternative approach. To facilitate proteome-wide screens for RBP, we revisited and improved existing RNA-Y3H methodology by (1) implementing full-length ORF libraries in combination with (2) efficient yeast mating to increase screening depth and sensitivity, and (3) stringent negative controls to eliminate over-representation of non-specific RNA-binders. These improvements were validated employing the well-characterized interaction between DDX6 (DEAD-box helicase 6) and sfRNA of DENV as paradigm. Our advanced Y3H system was used to screen for human proteins binding to DENV and ZIKV sfRNA, resulting in a list of 69 putative sfRNA-binders, including several previously reported as well as numerous novel RBP host factors. Our methodology requiring no sophisticated infrastructure or analytic pipeline may be employed for the discovery of meaningful RNA–protein interactions at large scale in other fields.
DOI: 10.6084/m9.figshare.13603173.v1
title: Identification of host-factors binding to dengue and Zika virus subgenomic RNA by efficient yeast three-hybrid screens of the human ORFeome

description: Flaviviruses such as the dengue (DENV) and the Zika virus (ZIKV) are important human pathogens causing around 100 million symptomatic infections each year. During infection, small subgenomic flavivirus RNAs (sfRNAs) are formed inside the infected host cell as a result of incomplete degradation of the viral RNA genome by cellular exoribonuclease XRN1. Although the full extent of sfRNA functions is to be revealed, these non-coding RNAs are key virulence factors and their detrimental effects on multiple cellular processes seem to consistently involve molecular interactions with RNA-binding proteins (RBPs). Discovery of such sfRNA-binding host-factors has followed established biochemical pull-down approaches skewed towards highly abundant proteins hampering proteome-wide coverage. Yeast three-hybrid (Y3H) systems represent an attractive alternative approach. To facilitate proteome-wide screens for RBP, we revisited and improved existing RNA-Y3H methodology by (1) implementing full-length ORF libraries in combination with (2) efficient yeast mating to increase screening depth and sensitivity, and (3) stringent negative controls to eliminate over-representation of non-specific RNA-binders. These improvements were validated employing the well-characterized interaction between DDX6 (DEAD-box helicase 6) and sfRNA of DENV as paradigm. Our advanced Y3H system was used to screen for human proteins binding to DENV and ZIKV sfRNA, resulting in a list of 69 putative sfRNA-binders, including several previously reported as well as numerous novel RBP host factors. Our methodology requiring no sophisticated infrastructure or analytic pipeline may be employed for the discovery of meaningful RNA–protein interactions at large scale in other fields.
DOI: 10.5281/zenodo.4695032
title: Deep Mutagenesis of a Transporter for Uptake of a Non-Native Substrate Identifies Conformationally Dynamic Regions

description: Molecular dynamics simulations of the APP+ import mechanism of the human serotonin transporter. <em>Manuscript in review. </em> <em>SeTWT-APP.pdb</em> - sample structure file of SERT embedded in POPC lipid bilayer, solvated with NaCl and TIP3P water molecules. <em>SeTWT-APP-stripped.pdb </em>- stripped (no lipids or water) topology file for SERT APP+ trajectories. <em>MSM_600microstates_100samples.zip</em> contains trajectory files of 100 structures of each microstates (600 total) from the Markov state model in <em>xtc</em> format. <em>SeTWT-APP-600microstates-1sample.dcd - </em>coordinates of 1 sampled structure from each microstate. May be viewed in visualization software such as VMD or PyMOL.
DOI: 10.5281/zenodo.4707904
title: Example file upload

description: An example ZENODO upload
DOI: 10.5281/zenodo.4707903
title: Example file upload

description: An example ZENODO upload
DOI: 10.5281/zenodo.4707744
title: Deep Mutagenesis of a Transporter for Uptake of a Non-Native Substrate Identifies Conformationally Dynamic Regions

description: Molecular dynamics simulations of the APP+ import mechanism of the human serotonin transporter. <em>Manuscript in review. </em> <em>SeTWT-APP.pdb</em> - sample structure file of SERT embedded in POPC lipid bilayer, solvated with NaCl and TIP3P water molecules. <em>SeTWT-APP-stripped.pdb </em>- stripped (no lipids or water) topology file for SERT APP+ trajectories. <em>MSM_600microstates_100samples.zip</em> contains trajectory files of 100 structures of each microstates (600 total) from the Markov state model in <em>xtc</em> format. <em>SeTWT-APP-600microstates-1sample.dcd - </em>coordinates of 1 sampled structure from each microstate. May be viewed in visualization software such as VMD or PyMOL.
description: Version 1.1: Updated pdb files with residue numbering based on the SERT sequence
DOI: 10.6073/pasta/796ef4756a44bd1c15373e8b5a593a9d
title: Repeated synoptic watershed chemistry from three watersheds near Toolik Field Station, Alaska, summer 2016-2018

description: Data file describing repeated sampling of chemistry of distributed river water from the Kuparuk River, Oksrukuyik Creek, and Trevor Creek watersheds near Toolik Field Station, North Slope of Alaska. Data file includes sampling date, season, sampling point, subcatchment area, and resulting concentrations for a suite of solutes.
DOI: 10.25345/c53f8z
title: MassIVE MSV000087256 - Thiol-cleavable Biotin for Chemical and Enzymatic Biotinylation and its Application to Mitochondrial TurboID Proteomics
title: Protein biotinylation via chemical or enzymatic reactions is often coupled with streptavidin-based enrichment and on-beads digestion in numerous biological applications. However, the popular on-beads digestion method faces major challenges of streptavidin contamination, the lost information of biotinylation sites, and limited sequence coverage of enriched proteins. Here, we explored thiol-cleavable biotin as an alternative approach to elute biotinylated proteins from streptavidin-coated beads for both chemical biotinylation and biotin ligase-based proximity labeling. All possible amino acid sites for biotinylation were thoroughly evaluated besides the primary lysine residue. We found that biotinylation at lysine residues notably reduces the trypsin digestion efficiency which can be mitigated by the thiol-cleavable biotinylation method. We then evaluated the applicability of thiol-cleavable biotin as a substrate for proximity labeling in living cells, where TurboID biotin ligase was engineered onto the mitochondrial inner membrane facing the mitochondrial matrix. As a proof-of-principle study, thiol-cleavable biotin-assisted TurboID proteomics achieved remarkable intra-organelle spatial resolution with significantly enriched proteins localized in the mitochondrial inner membrane and mitochondrial matrix.
DOI: 10.5281/zenodo.4707922
title: Supporting data: Vertebrate biodiversity is higher on Canadian private protected areas than government protected areas

description: Supporting data for: <strong>Vertebrate biodiversity is higher on Canadian private protected areas than government protected areas</strong>
DOI: 10.5281/zenodo.4266639
title: Supporting data: Vertebrate biodiversity is higher on Canadian private protected areas than government protected areas

description: Supporting data for: <strong>Vertebrate biodiversity is higher on Canadian private protected areas than government protected areas</strong>