cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2f7g05
title: CCDC 2241486: Experimental Crystal Structure Determination

description: Related Article: Yassin H. Andaloussi, Andrey A. Bezrukov, Debobroto Sensharma, Michael J. Zaworotko|2023|CrystEngComm|25|4175|doi:10.1039/D3CE00557G
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.cc2f7g16
title: CCDC 2241487: Experimental Crystal Structure Determination

description: Related Article: Yassin H. Andaloussi, Andrey A. Bezrukov, Debobroto Sensharma, Michael J. Zaworotko|2023|CrystEngComm|25|4175|doi:10.1039/D3CE00557G
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.cc2f7g27
title: CCDC 2241488: Experimental Crystal Structure Determination

description: Related Article: Yassin H. Andaloussi, Andrey A. Bezrukov, Debobroto Sensharma, Michael J. Zaworotko|2023|CrystEngComm|25|4175|doi:10.1039/D3CE00557G
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.cc2f7g38
title: CCDC 2241489: Experimental Crystal Structure Determination

description: Related Article: Yassin H. Andaloussi, Andrey A. Bezrukov, Debobroto Sensharma, Michael J. Zaworotko|2023|CrystEngComm|25|4175|doi:10.1039/D3CE00557G
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.cc2fkpl9
title: CCDC 2251331: Experimental Crystal Structure Determination

description: Related Article: Wei Bai, Lei Li, Yukang Fu, Junping Tang, Yue Zhao, Yilun Wang, Yang Li|2023|Dalton Trans.|52|9731|doi:10.1039/D3DT01558K
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.7802728
title: The OHEJP BeONE Project – Escherichia coli genome assembly dataset

description: <strong>Dataset</strong> This dataset comprises the genome assemblies of 308 <em>Escherichia coli</em> samples collected by the BeONE Consortium on behalf of the One Health European Joint Programme “BeONE: Building Integrative Tools for One Health Surveillance” (https://onehealthejp.eu/jrp-beone/). Additionally, a complementary dataset is also made available (https://zenodo.org/record/7120057), comprising genome assemblies of 1,999 <em>E. coli</em> samples selected among the Whole-Genome Sequencing (WGS) data publicly available in the European Nucleotide Archive (ENA) or in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). File “<strong>BeONE_Ec_metadata.xlsx</strong>” contains the genome assembly statistics for each isolate, including European Nucleotide Archive accession numbers, in-silico Multi Locus Sequence Type and Serotype, and information regarding year of sampling, country and source. The archive “<strong>BeONE_Ec_assemblies.zip</strong>” contains all the genome assemblies (.fasta format) of each isolate presented in the metadata file. <strong>Dataset selection and curation</strong> This anonymized dataset of <em>E. coli</em> genome assemblies was generated using Next Generation Sequencing data collected within the BeONE Consortium available at the European Nucleotide Archive under BioProject Accession Number PRJEB57098. Read quality control, trimming and assembly were performed with Aquamis v1.3.9 (Deneke et al. 2021) using default parameters. Assembly quality control (QC), including contamination assessment, as well as MLST ST determination were performed with the same pipeline. All genome assemblies passing the QC were included in the final dataset. Among the others, we noticed that a considerable proportion of assemblies was flagged as “QC fail” exclusively due to the “NumContamSNVs” parameter, suggesting that this setting might have been too strict. After manual inspection of a random subset, assemblies for which the percentage of reads corresponding to the correct species was &gt;98% were recovered and integrated in the final dataset (those samples are labeled in the Metadata file). In total, 308 isolates passed the dataset curation step and were included in the final dataset. In-silico serotyping was performed with seq_typing v2.2. <strong>Funding</strong> This work was supported by funding from the European Union’s Horizon 2020 Research and Innovation programme under grant agreement No 773830: One Health European Joint Programme. <strong>Acknowledgements</strong> We thank the National Distributed Computing Infrastructure of Portugal (INCD) for providing the necessary resources to run the genome assemblies. INCD was funded by FCT and FEDER under the project 22153-01/SAICT/2016.
DOI: 10.5281/zenodo.7802717
title: The OHEJP BeONE Project – Campylobacter jejuni genome assembly dataset

description: <strong>Dataset</strong> This dataset comprises the genome assemblies of 610 <em>Campylobacter jejuni </em>samples collected by the BeONE Consortium on behalf of the One Health European Joint Programme “BeONE: Building Integrative Tools for One Health Surveillance” (https://onehealthejp.eu/jrp-beone/). Additionally, a complementary dataset is also made available (https://zenodo.org/record/7120166), comprising genome assemblies of 3,076 <em>C. jejuni</em> samples selected among the Whole-Genome Sequencing (WGS) data publicly available in the European Nucleotide Archive (ENA) or in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). File “<strong>BeONE_Cj_metadata.xlsx</strong>” contains the genome assembly statistics for each isolate, including European Nucleotide Archive accession numbers and <em>in-silico</em> Multi Locus Sequence Type, and information regarding year of sampling, country and source. The archive “<strong>BeONE_Cj_assemblies.zip</strong>” contains all the genome assemblies (.fasta format) of each isolate presented in the metadata file. <strong>Dataset selection and curation</strong> This anonymized dataset of <em>C. jejuni</em> genome assemblies was generated using Next Generation Sequencing data collected within the BeONE Consortium available at the European Nucleotide Archive under BioProject Accession Number PRJEB57119. Read quality control, trimming and assembly were performed with Aquamis v1.3.9 (Deneke et al. 2021) using default parameters. Assembly quality control (QC), including contamination assessment, as well as MLST ST determination were performed with the same pipeline. All genome assemblies passing the QC were included in the final dataset. Among the others, we noticed that a considerable proportion of assemblies was flagged as “QC fail” exclusively due to the “NumContamSNVs” parameter, suggesting that this setting might have been too strict. After manual inspection of a random subset, assemblies for which the percentage of reads corresponding to the correct species was &gt;98% were recovered and integrated in the final dataset (those samples are labeled in the Metadata file). In total, 610 isolates passed the dataset curation step and were included in the final dataset. <strong>Funding</strong> This work was supported by funding from the European Union’s Horizon 2020 Research and Innovation programme under grant agreement No 773830: One Health European Joint Programme. <strong>Acknowledgements</strong> We thank the National Distributed Computing Infrastructure of Portugal (INCD) for providing the necessary resources to run the genome assemblies. INCD was funded by FCT and FEDER under the project 22153-01/SAICT/2016.
DOI: 10.6084/m9.figshare.22060433
title: CanaryClim - Topographic variables

description: Topographic variables were generated using Digital Elevation Maps (DEM) of the Canary Islands at 2m resolution from the IGN (https://martingonzalez.net/ign-dem-grabber/) and Saga-GIS v. 7.9.1 ("Slope,Aspect, and Curvature" and "TWI" modules). Maps were then aggregated applying a mean at 100m resolution. These maps are described in the paper entitled "<strong>Spatial resolution determines projected plant responses to climate change on topographically complex islands</strong>" which has been accepted in Diversity and Distributions. If you are using these datasets, please cite us: Patiño, J. & Collart, F., Vanderpoorten, V., Martin-Esquivel, J.L., Naranjo-Cigala, A., Mirolo, S., Karger, D.N. Spatial resolution determines projected plant responses to climate change on topographically complex islands. <em>Diversitity and Distributions. </em>(doi: 10.1111/ddi.13757 ).
DOI: 10.6084/m9.figshare.22060433.v1
title: CanaryClim - Topographic variables

description: Topographic variables were generated using Digital Elevation Maps (DEM) of the Canary Islands at 2m resolution from the IGN (https://martingonzalez.net/ign-dem-grabber/) and Saga-GIS v. 7.9.1 ("Slope,Aspect, and Curvature" and "TWI" modules). Maps were then aggregated applying a mean at 100m resolution. These maps are described in the paper entitled "<strong>Spatial resolution determines projected plant responses to climate change on topographically complex islands</strong>" which has been accepted in Diversity and Distributions. If you are using these datasets, please cite us: Patiño, J. & Collart, F., Vanderpoorten, V., Esquivel, J., Naranjo-Cigala, A., Mirolo, S., Karger, D.N. Spatial resolution determines projected plant responses to climate change on topographically complex islands. <em>Diversitity and Distributions. </em>(doi: 10.1111/ddi.13757 ).
DOI: 10.5281/zenodo.7802702
title: The OHEJP BeONE Project – Listeria monocytogenes genome assembly dataset

description: <strong>Dataset</strong> This dataset comprises the genome assemblies of 1,426 <em>Listeria monocytogenes</em> samples collected by the BeONE Consortium on behalf of the One Health European Joint Programme “BeONE: Building Integrative Tools for One Health Surveillance” (https://onehealthejp.eu/jrp-beone/). Additionally, a complementary dataset is also made available (https://zenodo.org/record/7116878), comprising genome assemblies of 1,874 <em>L. monocytogenes</em> samples selected among the Whole-Genome Sequencing (WGS) data publicly available in the European Nucleotide Archive (ENA) or in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). File “<strong>BeONE_Lm_metadata.xlsx</strong>” contains the genome assembly statistics for each isolate, including European Nucleotide Archive accession numbers and <em>in-silico</em> Multi Locus Sequence Type, and information regarding year of sampling, country and source. The archive “<strong>BeONE_Lm_assemblies.zip</strong>” contains all the genome assemblies (.fasta format) of each isolate presented in the metadata file. <strong>Dataset selection and curation</strong> This anonymized dataset of <em>L. monocytogenes </em>genome assemblies was generated using Next Generation Sequencing data collected within the BeONE Consortium available at the European Nucleotide Archive under BioProject Accession Number PRJEB57166. Read quality control, trimming and assembly were performed with Aquamis v1.3.9 (Deneke et al. 2021) using default parameters. Assembly quality control (QC), including contamination assessment, as well as MLST ST determination were performed with the same pipeline. All genome assemblies passing the QC were included in the final dataset. Among the others, we noticed that a considerable proportion of assemblies was flagged as “QC fail” exclusively due to the “NumContamSNVs” parameter, suggesting that this setting might have been too strict. After manual inspection of a random subset, assemblies for which the percentage of reads corresponding to the correct species was &gt;98% were recovered and integrated in the final dataset (those samples are labeled in the Metadata file). In total, 1,426 isolates passed the dataset curation step and were included in the final dataset. <strong>Funding</strong> This work was supported by funding from the European Union’s Horizon 2020 Research and Innovation programme under grant agreement No 773830: One Health European Joint Programme. <strong>Acknowledgements</strong> We thank the National Distributed Computing Infrastructure of Portugal (INCD) for providing the necessary resources to run the genome assemblies. INCD was funded by FCT and FEDER under the project 22153-01/SAICT/2016.
DOI: 10.6084/m9.figshare.22060340
title: CanaryClim - Climatic maps

description: Monthly precipitation, minimal and maximal temperature and bioclimatic variables at 100m resolution at present time (1979-2013), and in the future (2071-2100) under 5 Global Circulation Models and 3 shared socio-economic pathways These climatic datasets are described in the paper entitled "<strong>Spatial resolution determines projected plant responses to climate change on topographically complex islands</strong>" which has been accepted in Diversity and Distributions. If you are using these datasets, please cite us: Patiño, J. & Collart, F., Vanderpoorten, V., Martin-Esquivel, J.L., Naranjo-Cigala, A., Mirolo, S., Karger, D.N. Spatial resolution determines projected plant responses to climate change on topographically complex islands. <em>Diversitity and Distributions. </em>(doi: 10.1111/ddi.13757).
DOI: 10.6084/m9.figshare.22060340.v1
title: CanaryClim - Climatic maps

description: Monthly precipitation, minimal and maximal temperature and bioclimatic variables at 100m resolution at present time (1979-2013), and in the future (2071-2100) under 5 Global Circulation Models and 3 shared socio-economic pathways These climatic datasets are described in the paper entitled "<strong>Spatial resolution determines projected plant responses to climate change on topographically complex islands</strong>" which has been accepted in Diversity and Distributions. If you are using these datasets, please cite us: Patiño, J. & Collart, F., Vanderpoorten, V., Esquivel, J., Naranjo-Cigala, A., Mirolo, S., Karger, D.N. Spatial resolution determines projected plant responses to climate change on topographically complex islands. <em>Diversitity and Distributions. </em>(doi: 10.1111/ddi.13757).
DOI: 10.5281/zenodo.6008488
title: Orientation-dependent propulsion of active Brownian spheres: from self-advection to programmable cluster shapes

description: Supplemental data for the following manuscript: Stephan Bröker, Jens Bickmann, Michael te Vrugt, Michael E. Cates, Raphael Wittkowski, "Orientation-dependent propulsion of active Brownian spheres: from self-advection to programmable cluster shapes".
description: M.t.V. thanks the Studienstiftung des deutschen Volkes for financial support. M.E.C. is funded by the Royal Society. R.W. is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 283183152 (WI 4170/3-2). The simulations for this work were performed on the computer cluster PALMA II of the University of Münster.
DOI: 10.5281/zenodo.8154359
title: Orientation-dependent propulsion of active Brownian spheres: from self-advection to programmable cluster shapes

description: Supplemental data for the following manuscript: Stephan Bröker, Jens Bickmann, Michael te Vrugt, Michael E. Cates, Raphael Wittkowski, "Orientation-dependent propulsion of active Brownian spheres: from self-advection to programmable cluster shapes".
description: M.t.V. thanks the Studienstiftung des deutschen Volkes for financial support. M.E.C. is funded by the Royal Society. R.W. is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 283183152 (WI 4170/3-2). The simulations for this work were performed on the computer cluster PALMA II of the University of Münster.
DOI: 10.6084/m9.figshare.23737641
title: Seasonal Sea Ice Concentration Best Fit, 1905-2020

description: Best Fit members for Seasonal Antarctic sea ice concentration reconstructions, 1905-2020. Data are gridded on the 25x25km polar stereographic projection, like sea ice data from NSIDC. All four seasons are contained in this file.
DOI: 10.6084/m9.figshare.23737641.v1
title: Seasonal Sea Ice Concentration Best Fit, 1905-2020

description: Best Fit members for Seasonal Antarctic sea ice concentration reconstructions, 1905-2020. Data are gridded on the 25x25km polar stereographic projection, like sea ice data from NSIDC. All four seasons are contained in this file.
DOI: 10.6084/m9.figshare.21717907
title: X-ray-induced bio-acoustic emissions from cultured cells

description: We characterize for the first time the emission of acoustic waves from cultured cells irradiated with X-ray photon radiation. Human cancer cell lines (MCF-7, HL-60) and control cell-free media were exposed to 1 Gy X-ray photons while recording the sound generated before, during and after irradiation using custom large-bandwidth ultrasound transducer. The effects of dose rate and cell viability were investigated. We report the first recorded acoustic signals captured from a collective pressure wave response to ionizing irradiation in cell culture. The acoustic signal was co-terminous with the radiation pulse, its magnitude was dependent on radiation dose rate, and live and dead cells showed qualitatively and quantitatively different acoustic signal characteristics. The signature of the collective acoustic peaks was temporally wider and with higher acoustic power for irradiated HL-60 than for irradiated MCF-7. We show that X-ray irradiation induces two cultured cancer cell types to emit a characteristic acoustic signal for the duration of the radiation pulse. The rapid decay of the signal excludes acoustic emissions themselves from contributing to the inter-organism bystander signal previously reported in intact animals, but they remain a potential component of the bystander process in tissues and cell cultures. This preliminary study suggests that further work on the potential role of radiation-induced acoustic emission (RIAE) in the inter-cellular bystander effect is merited.
DOI: 10.6084/m9.figshare.21717907.v2
title: X-ray-induced bio-acoustic emissions from cultured cells

description: We characterize for the first time the emission of acoustic waves from cultured cells irradiated with X-ray photon radiation. Human cancer cell lines (MCF-7, HL-60) and control cell-free media were exposed to 1 Gy X-ray photons while recording the sound generated before, during and after irradiation using custom large-bandwidth ultrasound transducer. The effects of dose rate and cell viability were investigated. We report the first recorded acoustic signals captured from a collective pressure wave response to ionizing irradiation in cell culture. The acoustic signal was co-terminous with the radiation pulse, its magnitude was dependent on radiation dose rate, and live and dead cells showed qualitatively and quantitatively different acoustic signal characteristics. The signature of the collective acoustic peaks was temporally wider and with higher acoustic power for irradiated HL-60 than for irradiated MCF-7. We show that X-ray irradiation induces two cultured cancer cell types to emit a characteristic acoustic signal for the duration of the radiation pulse. The rapid decay of the signal excludes acoustic emissions themselves from contributing to the inter-organism bystander signal previously reported in intact animals, but they remain a potential component of the bystander process in tissues and cell cultures. This preliminary study suggests that further work on the potential role of radiation-induced acoustic emission (RIAE) in the inter-cellular bystander effect is merited.
DOI: 10.5281/zenodo.7802723
title: The OHEJP BeONE Project – Salmonella enterica genome assembly dataset

description: <strong>Dataset</strong> This dataset comprises the genome assemblies of 1,540 <em>Salmonella enterica</em> samples collected by the BeONE Consortium on behalf of the One Health European Joint Programme “BeONE: Building Integrative Tools for One Health Surveillance” (https://onehealthejp.eu/jrp-beone/). Additionally, a complementary dataset is also made available (https://zenodo.org/record/7119735), comprising genome assemblies of 1,434 <em>S. enterica</em> samples selected among the Whole-Genome Sequencing (WGS) data publicly available in the European Nucleotide Archive (ENA) or in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). File “<strong>BeONE_Se_metadata.xls</strong>x” contains the genome assembly statistics for each isolate, including European Nucleotide Archive accession numbers, in-silico Multi Locus Sequence Type and Serotype, and information regarding year of sampling, country and source. The archive “<strong>BeONE_Se_assemblies.zi</strong>p” contains all the genome assemblies (.fasta format) of each isolate presented in the metadata file. <strong>Dataset selection and curation</strong> This anonymized dataset of <em>S. enterica</em> genome assemblies was generated using Next Generation Sequencing data collected within the BeONE Consortium available at the European Nucleotide Archive under BioProject Accession Number PRJEB57179. Read quality control, trimming and assembly were performed with Aquamis v1.3.9 (Deneke et al. 2021) using default parameters. Assembly quality control (QC), including contamination assessment, as well as MLST ST determination were performed with the same pipeline. All genome assemblies passing the QC were included in the final dataset. Among the others, we noticed that a considerable proportion of assemblies was flagged as “QC fail” exclusively due to the “NumContamSNVs” parameter, suggesting that this setting might have been too strict. After manual inspection of a random subset, assemblies for which the percentage of reads corresponding to the correct species was &gt;98% were recovered and integrated in the final dataset (those samples are labeled in the Metadata file). In total, 1,540 isolates passed the dataset curation step and were included in the final dataset. In-silico serotyping was performed with SeqSero2 v1.2.1 (Zhang et al. 2019). <strong>Funding</strong> This work was supported by funding from the European Union’s Horizon 2020 Research and Innovation programme under grant agreement No 773830: One Health European Joint Programme. <strong>Acknowledgements</strong> We thank the National Distributed Computing Infrastructure of Portugal (INCD) for providing the necessary resources to run the genome assemblies. INCD was funded by FCT and FEDER under the project 22153-01/SAICT/2016.