cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25505/fiz.icsd.cc1xk1n5
title: CSD 1774057: Experimental Crystal Structure Determination

description: Related Article: R.V. Shpanchenko, V.V. Chernaya, A.M. Abakumov, E.V. Antipov, J. Hadermann, G. van Tendeloo, E.E. Kaul, C. Geibel, D. Sheptyakov, A.M. Balagurov|2001|Z.Anorg.Allg.Chem.|627|2143|doi:10.1002/1521-3749(200109)627:9&lt;2143::AID-ZAAC2143&gt;3.0.CO;2-R
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25505/fiz.icsd.cc1xk1p6
title: CSD 1774058: Experimental Crystal Structure Determination

description: Related Article: R.V. Shpanchenko, V.V. Chernaya, E.V. Antipov, J. Hadermann, E.E. Kaul, C. Geibel|2003|J.Solid State Chem.|173|244|doi:10.1016/S0022-4596(03)00039-2
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25505/fiz.icsd.cc1xtzxm
title: CSD 1782652: Experimental Crystal Structure Determination

description: Related Article: Qing Hua Hao, Zhan Gang Han, Jing Jing Wu, Yan Na Wang|2010|Jiegou Huaxue|29|1425|
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25505/fiz.icsd.cc1xv0xp
title: CSD 1782683: Experimental Crystal Structure Determination

description: Related Article: Kong Fang, Xu Xiang, Mao Jiang Gao|2010|Inorg.Chem.|49|11573|doi:10.1021/ic101843g
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25505/fiz.icsd.cc1xv1ld
title: CSD 1782704: Experimental Crystal Structure Determination

description: Related Article: L.I. Gongorova, B.G. Bazarov, O.D. Chimitova, A.G. Anshits, T.A. Vereschagina, R.F. Klevtsova, L.A. Glinskaya, Zh.G. Bazarova|2012|J.Struct.Chem.|53|329|doi:10.1134/S0022476612020175
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25505/fiz.icsd.cc1y2xrp
title: CSD 1790273: Experimental Crystal Structure Determination

description: Related Article: Piotr A. Gunka, Kamil F. Dziubek, Andrzej Gladysiak, Maciej Dranka, Jacek Piechota, Michael Hanfland, Andrzej Katrusiak, Janusz Zachara|2015|Cryst.Growth Des.|15|3740|doi:10.1021/acs.cgd.5b00390
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25505/fiz.icsd.cc1y2xsq
title: CSD 1790274: Experimental Crystal Structure Determination

description: Related Article: Piotr A. Gunka, Kamil F. Dziubek, Andrzej Gladysiak, Maciej Dranka, Jacek Piechota, Michael Hanfland, Andrzej Katrusiak, Janusz Zachara|2015|Cryst.Growth Des.|15|3740|doi:10.1021/acs.cgd.5b00390
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.6987336
title: Supporting data and analysis for, "An atlas of healthy and injured cell states and niches in the human kidney"

description: Online repository for contents associated with kidney cell state atlas: This combines the image datasets used for the manuscript describing an approach for the integrated tissue cytometry analysis of mesoscale confocal imaging datasets. Linked deposits: Zenodo Extended Data figures 10.5281/zenodo.7120908 3D Cytometry and neighborhood analysis 10.5281/zenodo.7120941 Github repository, "Cell-State-Atlas_2022" https://github.com/KPMP/Cell-State-Atlas-2022
DOI: 10.57745/n45ejm
title: 2014_notice cartographie OSCR_VF.pdf

description: :unav
DOI: 10.57745/qmyt8m
title: OSCR_zones_livraison_v2_L93.gpkg

description: :unav
DOI: 10.5517/ccdc.csd.cc2bqlsg
title: CCDC 2166676: Experimental Crystal Structure Determination

description: Related Article: Alexander S. Mikherdov, Roman A. Popov, Andrey S. Smirnov, Anastasiya A. Eliseeva, Alexander S. Novikov, Vadim P. Boyarskiy, Rosa M. Gomila, Antonio Frontera, Vadim Yu. Kukushkin, Nadezhda A. Bokach|2022|Cryst.Growth Des.|22|6079|doi:10.1021/acs.cgd.2c00686
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.cc2bqlth
title: CCDC 2166677: Experimental Crystal Structure Determination

description: Related Article: Alexander S. Mikherdov, Roman A. Popov, Andrey S. Smirnov, Anastasiya A. Eliseeva, Alexander S. Novikov, Vadim P. Boyarskiy, Rosa M. Gomila, Antonio Frontera, Vadim Yu. Kukushkin, Nadezhda A. Bokach|2022|Cryst.Growth Des.|22|6079|doi:10.1021/acs.cgd.2c00686
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.20263974
title: Genome assemblies, gene models, gene annotations, taxonomy classifications, clusters, and counts tables

description: <strong>File description:</strong> * .fa.gz - Metagenome-assembled genomes * .faa.gz - Proteins (Amino-acid space) * .ffn.gz - ORFs (DNA space) * .gff.gz - Gene models (GFF3) * clusters.tsv.gz - [MAG, SLC] identifier mapping (No header) * taxonomy_classification.tsv.gz - Taxonomy classifications for MAG * taxonomy_classification.clusters.tsv.gz - Taxonomy classifications for SLC * genome_quality.tsv.gz - Genome quality assessment * genome_statistics.tsv.gz - Genome assembly statistics * identifier_mapping.tsv.gz - [ORF, contig, MAG] identifier mapping (No header, tab-separated) * identifier_mapping.orthogroups.tsv.gz - [ORF, contig, MAG, SLC, SSO] identifier mapping (Includes header, tab-separated) <br> <strong>Abbreviations:</strong> ORF - Open reading frame MAG - Metagenome-assembled genome SLC - Species-level cluster SSO - SLC-specific orthogroup <br> <strong>Citation:</strong> * Espinoza, J.L., Dupont, C.L. VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes. <em>BMC Bioinformatics</em> <strong>23</strong>, 419 (2022). https://doi.org/10.1186/s12859-022-04973-8 * Espinoza, Josh (2022): Genome assemblies, gene models, gene annotations, taxonomy classifications, clusters, and counts tables. figshare. Dataset. https://doi.org/10.6084/m9.figshare.20263974.v1
DOI: 10.6084/m9.figshare.19616016
title: Profile HMM marker sets

description: Archaea_76.hmm - (Anvi'o) Lee, https://doi.org/10.1093/bioinformatics/btz188 (https://github.com/merenlab/anvio/tree/master/anvio/data/hmm/Archaea_76) Bacteria_71.hmm - (Anvi'o) Lee modified, https://doi.org/10.1093/bioinformatics/btz188 (https://github.com/merenlab/anvio/tree/master/anvio/data/hmm/Bacteria_71) Protista_83.hmm - (Anvi'o) Delmont, http://merenlab.org/delmont-euk-scgs (https://github.com/merenlab/anvio/tree/master/anvio/data/hmm/Protista_83) Fungi_593.hmm - (FGMP) https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2782-9 CPR_43.hmm - (CheckM) https://github.com/Ecogenomics/CheckM/tree/master/custom_marker_sets eukaryota_odb10 - (BUSCO) https://busco-data.ezlab.org/v5/data/lineages/eukaryota_odb10.2020-09-10.tar.gz <strong>Citation:</strong> * Espinoza, J.L., Dupont, C.L. VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes. BMC Bioinformatics 23, 419 (2022). https://doi.org/10.1186/s12859-022-04973-8 * Espinoza, Josh (2022): Profile HMM marker sets. figshare. Dataset. https://doi.org/10.6084/m9.figshare.19616016.v1 * Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO. 2015. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ 3:e1319 https://doi.org/10.7717/peerj.1319 * Cissé, O.H., Stajich, J.E. FGMP: assessing fungal genome completeness. BMC Bioinformatics 20, 184 (2019). https://doi.org/10.1186/s12859-019-2782-9 * Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015 Jul;25(7):1043-55. doi: 10.1101/gr.186072.114. * Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Mol Biol Evol. 2021 Sep 27;38(10):4647-4654. doi: 10.1093/molbev/msab199.
DOI: 10.6084/m9.figshare.19616016.v1
title: Profile HMM marker sets

description: Archaea_76.hmm - (Anvi'o) Lee, https://doi.org/10.1093/bioinformatics/btz188 (https://github.com/merenlab/anvio/tree/master/anvio/data/hmm/Archaea_76) Bacteria_71.hmm - (Anvi'o) Lee modified, https://doi.org/10.1093/bioinformatics/btz188 (https://github.com/merenlab/anvio/tree/master/anvio/data/hmm/Bacteria_71) Protista_83.hmm - (Anvi'o) Delmont, http://merenlab.org/delmont-euk-scgs (https://github.com/merenlab/anvio/tree/master/anvio/data/hmm/Protista_83) Fungi_593.hmm - (FGMP) https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2782-9 CPR_43.hmm - (CheckM) https://github.com/Ecogenomics/CheckM/tree/master/custom_marker_sets eukaryota_odb10 - (BUSCO) https://busco-data.ezlab.org/v5/data/lineages/eukaryota_odb10.2020-09-10.tar.gz <strong>Citation:</strong> * Espinoza, J.L., Dupont, C.L. VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes. BMC Bioinformatics 23, 419 (2022). https://doi.org/10.1186/s12859-022-04973-8 * Espinoza, Josh (2022): Profile HMM marker sets. figshare. Dataset. https://doi.org/10.6084/m9.figshare.19616016.v1 * Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO. 2015. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ 3:e1319 https://doi.org/10.7717/peerj.1319 * Cissé, O.H., Stajich, J.E. FGMP: assessing fungal genome completeness. BMC Bioinformatics 20, 184 (2019). https://doi.org/10.1186/s12859-019-2782-9 * Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015 Jul;25(7):1043-55. doi: 10.1101/gr.186072.114. * Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Mol Biol Evol. 2021 Sep 27;38(10):4647-4654. doi: 10.1093/molbev/msab199.
DOI: 10.6084/m9.figshare.21340092
title: Phosphosites matrix

description: For phosphosite localization, phosphosite confidence was determined using ptmRS and a phosphosite probability &gt; 0.75 was used for further analysis.
DOI: 10.6084/m9.figshare.21340092.v1
title: Phosphosites matrix

description: For phosphosite localization, phosphosite confidence was determined using ptmRS and a phosphosite probability &gt; 0.75 was used for further analysis.
DOI: 10.6084/m9.figshare.21339999
title: Protein abundances matrix

description: Protein abundance was then estimated using a traditional label-free, intensity-based absolute quantification (iBAQ) algorithm, which divided the protein abundance (derived from intensities of the identified peptides) by the number of theoretically observable peptides. Fraction of total (FOT) is a relative quantification value defined as a protein’s iBAQ divided by the sum of the iBAQ of all proteins identified in an experiment, calculated as the normalized abundance of a particular protein in the experiment. Finally, for the ease of presentation, the FOT was further multiplied by 1e5.
DOI: 10.6084/m9.figshare.21340089
title: WES data

description: Paired-end sequencing is performed using an Illumina NovaSeq6000 system according to Illumina’s 2x150 paired-end sequencing protocol. WES was conducted with a mean coverage depth of 297X (range: 250‒412X) for tumor samples and 156X (range: 120‒208X) for paired blood samples.
DOI: 10.6084/m9.figshare.21340089.v1
title: WES data

description: Paired-end sequencing is performed using an Illumina NovaSeq6000 system according to Illumina’s 2x150 paired-end sequencing protocol. WES was conducted with a mean coverage depth of 297X (range: 250‒412X) for tumor samples and 156X (range: 120‒208X) for paired blood samples.
DOI: 10.5517/ccdc.csd.cc2cq3y5
title: CCDC 2196007: Experimental Crystal Structure Determination

description: Related Article: Suman Mondal, Calvin Samuel, Viswanathan Baskar|2023|J.Mol.Struct.|1273|134274|doi:10.1016/j.molstruc.2022.134274
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.cc2cq3z6
title: CCDC 2196008: Experimental Crystal Structure Determination

description: Related Article: Suman Mondal, Calvin Samuel, Viswanathan Baskar|2023|J.Mol.Struct.|1273|134274|doi:10.1016/j.molstruc.2022.134274
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.cc2cq408
title: CCDC 2196009: Experimental Crystal Structure Determination

description: Related Article: Suman Mondal, Calvin Samuel, Viswanathan Baskar|2023|J.Mol.Struct.|1273|134274|doi:10.1016/j.molstruc.2022.134274
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.cc2cq419
title: CCDC 2196010: Experimental Crystal Structure Determination

description: Related Article: Suman Mondal, Calvin Samuel, Viswanathan Baskar|2023|J.Mol.Struct.|1273|134274|doi:10.1016/j.molstruc.2022.134274
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.21334563
title: dataset_clean.sav- Parents between family and work: the role of motivation and basic psychological needs satisfaction

description: The dataset includes demographic variables, items and total scores of the constructs object of this study.
DOI: 10.6084/m9.figshare.21334563.v2
title: dataset_clean.sav- Parents between family and work: the role of motivation and basic psychological needs satisfaction

description: The dataset includes demographic variables, items and total scores of the constructs object of this study.
DOI: 10.6084/m9.figshare.21334563.v1
title: dataset_clean.sav- Parents between family and work: the role of motivation and basic psychological needs satisfaction

description: The dataset includes demographic variables, items and total scores of the constructs object of this study.
DOI: 10.5281/zenodo.7199989
title: Cytoplasmic components of the machinery mediating telomere-led rapid chromosome movements in mouse meiosis

description: Telomere-led rapid chromosome movements (RPMs) are a prominent characteristic of chromosome dynamics during meiosis. Although of crucial importance in maintaining germ cell integrity, the extranuclear portion of the machinery supporting RPMs in mammals is poorly understood. Using an unbiased proteomic approach to identify motor proteins associated to microtubules in mouse meiotic cells, complemented with co-immunoprecipitation confirmation, we uncovered kinesins as candidate of the machinery mediating RPMs in mouse spermatocytes. Further biochemical, microscopy, and functional analysis shows that KIF5B and KIF2B interact with KASH5 and act as motor proteins mediating the LINC complex-microtubule interactions. Our results show that member of the kinesin family of molecular motors act as novel critical modules of the machinery promoting complex dynamic chromosomes in mammals.
description: These are the raw data file for experiment carried out on a Thermo Scientific Q-Exactive Plus system. The program Mascot was used to search the human protein sequence database to identify the proteins in each sample.
DOI: 10.5281/zenodo.7199988
title: Cytoplasmic components of the machinery mediating telomere-led rapid chromosome movements in mouse meiosis

description: Telomere-led rapid chromosome movements (RPMs) are a prominent characteristic of chromosome dynamics during meiosis. Although of crucial importance in maintaining germ cell integrity, the extranuclear portion of the machinery supporting RPMs in mammals is poorly understood. Using an unbiased proteomic approach to identify motor proteins associated to microtubules in mouse meiotic cells, complemented with co-immunoprecipitation confirmation, we uncovered kinesins as candidate of the machinery mediating RPMs in mouse spermatocytes. Further biochemical, microscopy, and functional analysis shows that KIF5B and KIF2B interact with KASH5 and act as motor proteins mediating the LINC complex-microtubule interactions. Our results show that member of the kinesin family of molecular motors act as novel critical modules of the machinery promoting complex dynamic chromosomes in mammals.
description: These are the raw data file for experiment carried out on a Thermo Scientific Q-Exactive Plus system. The program Mascot was used to search the human protein sequence database to identify the proteins in each sample.
DOI: 10.6084/m9.figshare.21340161.v1
title: Integrated Proteogenomic Characterization across Major Histological Types of Pituitary Neuroendocrine Tumors

description: Pituitary neuroendocrine tumor (PitNET) is one of the most common intracranial tumors. Due to its extensive tumor heterogeneity and the lack of high-quality tissues for biomarker discovery, the causative molecular mechanisms are far from being fully defined. Therefore, more studies are needed to improve the current clinicopathological classification system, and advanced treatment strategies such as targeted therapy and immunotherapy are yet to be explored. Here, we performed the largest integrative genomics, transcriptomics, proteomics, and phosphoproteomics analysis reported to date for a cohort of 200 PitNET patients. Genomics data indicate that <em>GNAS</em> copy number gain can serve as a reliable diagnostic marker for hyperproliferation of the PIT1 lineage. Proteomics-based classification of PitNETs identified 7 clusters, among which, tumors overexpressing epithelial-mesenchymal transition (EMT) markers clustered into a more invasive subgroup. Further analysis identified potential therapeutic targets, including CDK6, TWIST1, EGFR, and VEGFR2, for different clusters. Immune subtyping to explore the potential for application of immunotherapy in PitNET identified an association between alterations in the JAK1-STAT1-PDL1 axis and immune exhaustion, and between changes in the JAK3-STAT6-FOS/JUN axis and immune infiltration. These identified molecular markers and alternations in various clusters/subtypes were further confirmed in an independent cohort of 750 PitNET patients. This proteogenomic analysis across traditional histological boundaries improves our current understanding of PitNET pathophysiology and suggests novel therapeutic targets and strategies.
DOI: 10.6084/m9.figshare.21340176
title: Supplementary Material to Leuzinger et al. - Latest Maastrichtian middle- and high-latitude mosasaurs and fish isotopic composition: carbon source, thermoregulation strategy and thermal latitudinal gradient

description: Supplementary Figures: photographs of the fossil material. Supplementary Table 1: minor element and REE concentrations of our fossil material. Supplementary Table 2: stable isotopes data from the literature used in Fig. 4