cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25425721.v1
title: Raw data used to calculate means, standard deviations and create graphs

description: Peptidoglycan (PG) is the main component of the bacterial cell wall; it maintains cell shape while protecting the cell from internal osmotic pressure and external environmental challenges. PG synthesis is essential for bacterial growth and survival, and a series of PG modifications are required to allow expansion of the sacculus. Endopeptidases (EPs), for example, cleave the crosslinks between adjacent PG strands to allow the incorporation of newly synthesized PG. EPs are collectively essential for bacterial growth and must likely be carefully regulated to prevent sacculus degradation and cell death. However, EP regulation mechanisms are poorly understood. Here, we used TnSeq to uncover novel EP regulators in <i>Vibrio cholerae</i>. This screen revealed that the carboxypeptidase DacA1 (PBP5) alleviates EP toxicity. <i>dacA1</i> is essential for viability on LB medium, and this essentiality was suppressed by EP overexpression, revealing that EP toxicity both mitigates, and is mitigated by, a defect in <i>dacA1</i>. A subsequent suppressor screen to restore viability of <i>∆dacA1</i> in LB medium identified hypomorphic mutants in the PG synthesis pathway, as well as mutations that promote EP activation. Our data thus reveal a more complex role of DacA1 in maintaining PG homeostasis than previously assumed.
DOI: 10.5281/zenodo.10827916
title: Input and enriched files for the pf1600 dataset - ENPKG

description: Input files (.mgf spectra and .tsv metadata) and enriched files (metabolite annotation, molecular networks and taxonomical resolution results) for the pf1600 dataset described at https://doi.org/10.1093/gigascience/giac124 and used prior to their semantic enrichment and conversion to knowledge graphs as described in https://doi.org/10.1021/acscentsci.3c00800.

 

A typical directory looks like :

 

├── neg│   ├── isdb   │   │   ├── config.yaml│   │   ├── VGF159_A02_isdb_neg.tsv│   │   ├── VGF159_A02_isdb_reweighted_flat_neg.tsv│   │   ├── VGF159_A02_isdb_reweighted_neg.tsv│   │   ├── VGF159_A02_treemap_chemo_counted_neg.html│   │   └── VGF159_A02_treemap_chemo_intensity_neg.html│   ├── molecular_network│   │   ├── config.yaml│   │   ├── VGF159_A02_mn_metadata_neg.tsv│   │   └── VGF159_A02_mn_neg.graphml│   ├── VGF159_A02_features_ms2_neg.mgf│   ├── VGF159_A02_features_quant_neg.csv│   ├── VGF159_A02_lcms_method_params_neg.txt│   ├── VGF159_A02_lcms_processing_params_neg.xml│   ├── VGF159_A02_sirius_neg.mgf│   └── VGF159_A02_WORKSPACE_SIRIUS│       ├── canopus_compound_summary.tsv│       ├── canopus_formula_summary_adducts.tsv│       ├── canopus_formula_summary.tsv│       ├── canopus_neg.tsv│       ├── canopus_npc_neg.tsv│       ├── canopus_npc.tsv│       ├── canopus.tsv│       ├── compound_identifications_adducts.tsv│       ├── compound_identifications.tsv│       ├── csi_fingerid_neg.tsv│       ├── csi_fingerid.tsv│       ├── formula_identifications_adducts.tsv│       ├── formula_identifications.tsv│       ├── params.yml│       └── report.mztab├── pos│   ├── isdb│   │   ├── config.yaml│   │   ├── VGF159_A02_isdb_pos.tsv│   │   ├── VGF159_A02_isdb_reweighted_flat_pos.tsv│   │   ├── VGF159_A02_isdb_reweighted_pos.tsv│   │   ├── VGF159_A02_treemap_chemo_counted_pos.html│   │   └── VGF159_A02_treemap_chemo_intensity_pos.html│   ├── molecular_network│   │   ├── config.yaml│   │   ├── VGF159_A02_mn_metadata_pos.tsv│   │   └── VGF159_A02_mn_pos.graphml│   ├── VGF159_A02_features_ms2_pos.mgf│   ├── VGF159_A02_features_quant_pos.csv│   ├── VGF159_A02_lcms_method_params_pos.txt│   ├── VGF159_A02_lcms_processing_params_pos.xml│   ├── VGF159_A02_sirius_pos.mgf│   └── VGF159_A02_WORKSPACE_SIRIUS│       ├── canopus_neg.tsv│       ├── canopus_summary_adducts.tsv│       ├── canopus_summary.tsv│       ├── canopus.tsv│       ├── compound_identifications_adducts.tsv│       ├── compound_identifications.tsv│       ├── csi_fingerid_neg.tsv│       ├── csi_fingerid.tsv│       ├── formula_identifications_adducts.tsv│       ├── formula_identifications.tsv│       ├── npc_summary.csv│       ├── params.yml│       └── report.mztab├── rdf│   └── graph_params.yaml├── taxo_output│   ├── params.yaml│   ├── VGF159_A02_species.json│   ├── VGF159_A02_taxo_metadata.tsv│   └── VGF159_A02_taxon_info.json└── VGF159_A02_metadata.tsv
DOI: 10.5281/zenodo.10827917
title: Input and enriched files for the pf1600 dataset - ENPKG

description: Input files (.mgf spectra and .tsv metadata) and enriched files (metabolite annotation, molecular networks and taxonomical resolution results) for the pf1600 dataset described at https://doi.org/10.1093/gigascience/giac124 and used prior to their semantic enrichment and conversion to knowledge graphs as described in https://doi.org/10.1021/acscentsci.3c00800.

 

A typical directory looks like :

 

├── neg│   ├── isdb   │   │   ├── config.yaml│   │   ├── VGF159_A02_isdb_neg.tsv│   │   ├── VGF159_A02_isdb_reweighted_flat_neg.tsv│   │   ├── VGF159_A02_isdb_reweighted_neg.tsv│   │   ├── VGF159_A02_treemap_chemo_counted_neg.html│   │   └── VGF159_A02_treemap_chemo_intensity_neg.html│   ├── molecular_network│   │   ├── config.yaml│   │   ├── VGF159_A02_mn_metadata_neg.tsv│   │   └── VGF159_A02_mn_neg.graphml│   ├── VGF159_A02_features_ms2_neg.mgf│   ├── VGF159_A02_features_quant_neg.csv│   ├── VGF159_A02_lcms_method_params_neg.txt│   ├── VGF159_A02_lcms_processing_params_neg.xml│   ├── VGF159_A02_sirius_neg.mgf│   └── VGF159_A02_WORKSPACE_SIRIUS│       ├── canopus_compound_summary.tsv│       ├── canopus_formula_summary_adducts.tsv│       ├── canopus_formula_summary.tsv│       ├── canopus_neg.tsv│       ├── canopus_npc_neg.tsv│       ├── canopus_npc.tsv│       ├── canopus.tsv│       ├── compound_identifications_adducts.tsv│       ├── compound_identifications.tsv│       ├── csi_fingerid_neg.tsv│       ├── csi_fingerid.tsv│       ├── formula_identifications_adducts.tsv│       ├── formula_identifications.tsv│       ├── params.yml│       └── report.mztab├── pos│   ├── isdb│   │   ├── config.yaml│   │   ├── VGF159_A02_isdb_pos.tsv│   │   ├── VGF159_A02_isdb_reweighted_flat_pos.tsv│   │   ├── VGF159_A02_isdb_reweighted_pos.tsv│   │   ├── VGF159_A02_treemap_chemo_counted_pos.html│   │   └── VGF159_A02_treemap_chemo_intensity_pos.html│   ├── molecular_network│   │   ├── config.yaml│   │   ├── VGF159_A02_mn_metadata_pos.tsv│   │   └── VGF159_A02_mn_pos.graphml│   ├── VGF159_A02_features_ms2_pos.mgf│   ├── VGF159_A02_features_quant_pos.csv│   ├── VGF159_A02_lcms_method_params_pos.txt│   ├── VGF159_A02_lcms_processing_params_pos.xml│   ├── VGF159_A02_sirius_pos.mgf│   └── VGF159_A02_WORKSPACE_SIRIUS│       ├── canopus_neg.tsv│       ├── canopus_summary_adducts.tsv│       ├── canopus_summary.tsv│       ├── canopus.tsv│       ├── compound_identifications_adducts.tsv│       ├── compound_identifications.tsv│       ├── csi_fingerid_neg.tsv│       ├── csi_fingerid.tsv│       ├── formula_identifications_adducts.tsv│       ├── formula_identifications.tsv│       ├── npc_summary.csv│       ├── params.yml│       └── report.mztab├── rdf│   └── graph_params.yaml├── taxo_output│   ├── params.yaml│   ├── VGF159_A02_species.json│   ├── VGF159_A02_taxo_metadata.tsv│   └── VGF159_A02_taxon_info.json└── VGF159_A02_metadata.tsv
DOI: 10.5281/zenodo.10827907
title: Text data for keyboard layout evaluation

description: Text data





Text source
Information




"Alice in Wonderland"
Alice in Wonderland (Ch.1)


"Romeo and Juliet"
Romeo and Juliet


"Bhagavad Gita"
Bhagavad Gita


"Memento screenplay"
Memento screenplay


"100K tweets"
100,000 tweets from: Sentiment140 dataset training data


"20K tweets"
20,000 tweets from Gender Classifier Data


"MASC tweets"
MASC tweets (cleaned of html markup)


"MASC spoken"
MASC spoken transcripts (phone and face-to-face: 25,783 words)


"COCA blogs"
Corpus of Contemporary American English blog samples


"Google website"
Google homepage (accessed 10/20/2020)


"Software languages"
"Tower of Hanoi" (programming languages A-Z from Rosetta Code)


"Monkey text"
Ian Douglas's English-generated monkey0-7.txt corpus


"Coder text"
Ian Douglas's software-generated coder0-7.txt corpus


"iweb cleaned corpus"
First 150,000 lines of Shai Coleman's iweb-corpus-samples-cleaned.txt




Reference for Monkey and Coder texts: Douglas, Ian. (2021, March 28). Keyboard Layout Analysis: Creating the Corpus, Bigram Chains, and Shakespeare's Monkeys (Version 1.0.0). Zenodo. http://doi.org/10.5281/zenodo.4642460
DOI: 10.5281/zenodo.10827908
title: Text data for keyboard layout evaluation

description: Text data





Text source
Information




"Alice in Wonderland"
Alice in Wonderland (Ch.1)


"Romeo and Juliet"
Romeo and Juliet


"Bhagavad Gita"
Bhagavad Gita


"Memento screenplay"
Memento screenplay


"100K tweets"
100,000 tweets from: Sentiment140 dataset training data


"20K tweets"
20,000 tweets from Gender Classifier Data


"MASC tweets"
MASC tweets (cleaned of html markup)


"MASC spoken"
MASC spoken transcripts (phone and face-to-face: 25,783 words)


"COCA blogs"
Corpus of Contemporary American English blog samples


"Google website"
Google homepage (accessed 10/20/2020)


"Software languages"
"Tower of Hanoi" (programming languages A-Z from Rosetta Code)


"Monkey text"
Ian Douglas's English-generated monkey0-7.txt corpus


"Coder text"
Ian Douglas's software-generated coder0-7.txt corpus


"iweb cleaned corpus"
First 150,000 lines of Shai Coleman's iweb-corpus-samples-cleaned.txt




Reference for Monkey and Coder texts: Douglas, Ian. (2021, March 28). Keyboard Layout Analysis: Creating the Corpus, Bigram Chains, and Shakespeare's Monkeys (Version 1.0.0). Zenodo. http://doi.org/10.5281/zenodo.4642460
DOI: 10.34740/kaggle/dsv/7869462
title: Forex Exchange Rates Since 2004 (Updated Daily)
DOI: 10.34740/kaggle/dsv/7869534
title: Full TMDB Movies Dataset 2024 (1M Movies)
DOI: 10.34740/kaggle/dsv/7869505
title: UHPC Direct Tension Database
DOI: 10.34740/kaggle/dsv/7869571
title: Trending Youtube Video Statistics (113 Countries)
DOI: 10.34740/kaggle/dsv/7869590
title: Top Spotify Songs in 73 Countries (Daily Updated)
DOI: 10.5281/zenodo.10040654
title: Data for: The thermo-optical coefficient as an alternative probe for the structural arrest of polymeric glass formers
title: Data for: Experimental determination of the glass transition temperature in a very narrow temperature range by Temperature Modulated Optical Refractometry

description: The data is supplementary to the publication "The thermo-optical coefficient as an alternative probe for the structural arrest of polymeric glass formers", DOI: 10.1016/j.polymer.2024.126868, and contains processed raw data.

Key words: Temperature-modulated optical refractometry, Solidification, Glass transition temperature, Thermo-optical coefficient, Structural arrest

The data sets contain measured data on Temperature-modulated optical refractometry (TMOR) of a model epoxy polymer from the viscoelastic temperature range, through the glass transition to the glassy state. The data sets were collected via the temperature-jump method.

Material details:



Bisphenol A Diglycidyl ether (DGEBA, DER332, CAS 1675-54-3) + Difunctional and trifunctional carbocylic acids (Pripol1040, Croda) +1,5,7-triazabicyclo[4.4.0]dec-5-en (TBD, CAS 5807-14-7, 10 mol-% relative to carboxylic acid functions)


Funding received from:



German Research Foundation (DFG), project number: 521902629
DOI: 10.5517/ccdc.csd.cc29g475
title: CCDC 2128746: Experimental Crystal Structure Determination

description: Related Article: Zhiyuan Peng, Shoujun Sun, Meng-Meng Zheng, Yangyang Li, Xixi Li, Suhua Li, Xiao-Song Xue, Jiajia Dong, Bing Gao |2024|Nature Chemistry|16|353|doi:10.1038/s41557-024-01452-w
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2f903w
title: CCDC 2242977: Experimental Crystal Structure Determination

description: Related Article: Zhiyuan Peng, Shoujun Sun, Meng-Meng Zheng, Yangyang Li, Xixi Li, Suhua Li, Xiao-Song Xue, Jiajia Dong, Bing Gao |2024|Nature Chemistry|16|353|doi:10.1038/s41557-024-01452-w
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.25410019
title: VR--two-way (final)

description: Dataset that contains all the experiments done with zebrafish where we had them swim in VR and interact with a virtual conspecific. Here we had two-way interactions (i.e. the virtual fish was responding to the real fish). Experiments conducted in 2024.
DOI: 10.6084/m9.figshare.25410019.v1
title: VR--two-way (final)

description: Dataset that contains all the experiments done with zebrafish where we had them swim in VR and interact with a virtual conspecific. Here we had two-way interactions (i.e. the virtual fish was responding to the real fish). Experiments conducted in 2024.
DOI: 10.5281/zenodo.10827399
title: CodeUltraFeedback - Dataset and Benchmark
DOI: 10.5281/zenodo.10827400
title: CodeUltraFeedback - Dataset and Benchmark
DOI: 10.5281/zenodo.10827492
title: CodeUltraFeedback - Dataset and Benchmark
DOI: 10.34740/kaggle/dsv/7869717
title: Daily Public Opinion on Israel-Palestine War
DOI: 10.34740/kaggle/dsv/7869745
title: Public Opinion on Climate Change (Updated Daily)
DOI: 10.5281/zenodo.10828016
title: AAR_Bahia Vera-Cabo Raso, Camarones, Argentina

description: Amino acid racemization data from Ameghinomya antiqua shells found in Pleistocene beach ridges in the Patagonia Argentina
DOI: 10.5281/zenodo.10828017
title: AAR_Bahia Vera-Cabo Raso, Camarones, Argentina

description: Amino acid racemization data from Ameghinomya antiqua shells found in Pleistocene beach ridges in the Patagonia Argentina
DOI: 10.6084/m9.figshare.25425760
title: QOL Dataset

description: A study of the Quality of Life outcomes after breast surgery using EORTC QLQ-C30 and EORTC QLQ-BR23
DOI: 10.5281/zenodo.10828086
title: Cure4Aqua WP6 - MicroFluid_v1

description: Selection of the markers for Integrated microfluidics (IMF) platforms
DOI: 10.5281/zenodo.10828087
title: Cure4Aqua WP6 - MicroFluid_v1

description: Selection of the markers for Integrated microfluidics (IMF) platforms
DOI: 10.5517/ccdc.csd.cc2hn7yc
title: CCDC 2313373: Experimental Crystal Structure Determination

description: Related Article: Anton Bannykh, Petri M. Pihko|2024|Org.Lett.|26|1991|doi:10.1021/acs.orglett.3c04213
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2hn85m
title: CCDC 2313380: Experimental Crystal Structure Determination

description: Related Article: Anton Bannykh, Petri M. Pihko|2024|Org.Lett.|26|1991|doi:10.1021/acs.orglett.3c04213
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.7251098
title: Dataset for Assessing Multi-Dimensional Impacts of Achieving Sustainability Goals by Projecting the Sustainable Agriculture Matrix into the Future

description: This data repository feeds into the meta-repository setup for post-processing of GCAM-SAM outputs. GitHub link of meta-repository is: https://github.com/JGCRI/Kyle-etal_2022_EF 

Folders: 
model/ is the static version of the model used to simulate 8 scenarios. See the GitHub GCAM-SAM repository to follow active development of this model. 
inputs/ folder contains input datasets and scripts used to prepare files while postprocessing. This is to be used with GitHub post-processing meta-repository. 
outdata/ contains GCAM-SAM output and post-processed output files used to plot figures. 

Key files: 
SAM-matrix.dat is the consolidated GCAM-SAM output. Use proj_load.R in the metarepo to read the file. 
region_vals.csv has all 8 indicators in all 8 scenarios for years 2020 till 2100 on a 10 year time step. 

Short introduction to the study:


In this paper sustainable agriculture matrix (SAM) is estimated to 2100 using Global Change Analysis Model (GCAM). We model combinatorial variations of yield intensification, dietary shift, and greenhouse gas mitigation scenarios. Findings include scenarios having significant tradeoffs across multiple environmental, economic, and social dimensions. Assessment of these multi-dimensional tradeoffs in a consistent framework improves the quality of information for decision-making.

Should you have any questions, feel free to reach out Page Kyle at pkyle@pnnl.gov.
DOI: 10.5281/zenodo.7251099
title: Dataset for Assessing Multi-Dimensional Impacts of Achieving Sustainability Goals by Projecting the Sustainable Agriculture Matrix into the Future

description: This data repository feeds into the meta-repository setup for post-processing of GCAM-SAM outputs. GitHub link of meta-repository is: https://github.com/JGCRI/Kyle-etal_2022_EF 

Folders: 
model/ is the static version of the model used to simulate 8 scenarios. See the GitHub GCAM-SAM repository to follow active development of this model. 
inputs/ folder contains input datasets and scripts used to prepare files while postprocessing. This is to be used with GitHub post-processing meta-repository. 
outdata/ contains GCAM-SAM output and post-processed output files used to plot figures. 

Key files: 
SAM-matrix.dat is the consolidated GCAM-SAM output. Use proj_load.R in the metarepo to read the file. 
region_vals.csv has all 8 indicators in all 8 scenarios for years 2020 till 2100 on a 10 year time step. 

Short introduction to the study:


In this paper sustainable agriculture matrix (SAM) is estimated to 2100 using Global Change Analysis Model (GCAM). We model combinatorial variations of yield intensification, dietary shift, and greenhouse gas mitigation scenarios. Findings include scenarios having significant tradeoffs across multiple environmental, economic, and social dimensions. Assessment of these multi-dimensional tradeoffs in a consistent framework improves the quality of information for decision-making.

Should you have any questions, feel free to reach out Page Kyle at pkyle@pnnl.gov.
DOI: 10.5281/zenodo.10828099
title: RADCURE_radiomic_MAE

description: RADCURE_radiomic_MAE_v2 data object generated by ORCESTRA.
DOI: 10.5281/zenodo.10828100
title: RADCURE_radiomic_MAE

description: RADCURE_radiomic_MAE_v2 data object generated by ORCESTRA.
DOI: 10.3886/e171801
title: Draft pick data (NBA, NFL, NHL) from 1988-2017

description: NBA, NFL, and NHL draft pick data from 1988-2017. Used in the paper, "The Endowment Effect and the Trading of Draft Picks in Major Professional U.S. Sports."
DOI: 10.3886/e171801v2-147085
title: ECIN Replication Package for "The endowment effect and the trading of draft picks in major professional U.S. sports"

description: NBA, NFL, and NHL draft pick data from 1988-2017. Used in the paper, "The Endowment Effect and the Trading of Draft Picks in Major Professional U.S. Sports."
DOI: 10.5281/zenodo.10828107
title: Viabundus map of premodern European transport and mobility

description: Viabundus.eu is a freely accessible online street map of late medieval and early modern northern Europe (1350-1650). Originally conceived as the digitisation of Friedrich Bruns and Hugo Weczerka's Hansische Handelsstraßen (1962) atlas of land roads in the Hanseatic area, the Viabundus map moves beyond that. It includes among others: a database with information about settlements, towns, tolls, staple markets and other information relevant for the pre-modern traveller; a route calculator; a calendar of fairs; and additional land routes as well as water ways.

Viabundus is a work in progress. Version 1.3, released on 17 March 2024, contains a rough digitisation of the land routes from Hansische Handelsstraßen, as well as a thoroughly researched road network for the current-day Netherlands, Denmark, the German states of Lower Saxony, Schleswig-Holstein, Thuringia, Saxony-Anhalt, Brandenburg, Mecklenburg-Vorpommern, Hesse and North Rhine-Westfalia, and parts of Poland (Pomerania, Royal Prussia, Greater Poland). The inclusion of other regions is currently being planned. Additions to the dataset will be released as new versions in the future.

The project's homepage viabundus.eu contains a web map application to explore the data. To allow for more advanced spatial and historical analyses, the underlying dataset is available for download under the CC-BY-SA license.

The dataset is designed as a network model and therefore consists of two main elements: 1) a relational database of nodes, i.e. geographical places, with historical information about settlements, towns, tolls, staple markets, fairs, bridges, ferries, harbours and shipping locks; 2) a database with edges, i.e. the geospatial representations of the land and water routes that connected these nodes. The entire database is available in CSV format (with geospatial geometry as WKT); the edges and the outlines of towns in the 16th century are also separately available as geojson and GML files. For more information about the structure of the dataset, theoretical considerations and sources, please consult the enclosed documentation file.
description: Viabundus was made possible by Niedersächsisches Ministerium für Wissenschaft und Kultur (Pro*Niedersachsen), Kulturministeriets Forskningsudvalg (DK), Friedrich-Christian-Lesser-Stiftung, Radboud Institute for Culture and History (RICH), Kone Foundation.