cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.24416/uu01-q25gd7
title: Proteome and phospholipidome interrelationship of synovial fluid-derived extracellular vesicles in equine osteoarthritis:  An exploratory ‘multi-omics’ study towards combined biomarkers

description: Osteoarthritis causes progressing joint deterioration, severe morbidity, and reduced mobility in both humans and horses. Extracellular vesicles (EVs) are complex structures that play a key role in cell-to-cell communication and are potential sources for highly specific composite biomarker panel discovery. We used a multi-omics strategy combining proteomics and lipidomics in an integral approach to biomarker discovery by identifying EV-based combined biomarkers in synovial fluid (SF) from healthy and mildly and severely osteoarthritic equine joints.
Extracellular vesicles were isolated by differential ultracentrifugation and density gradients.  Single extracellular vesicle-based flow cytometry unveiled that the number of extracellular vesicles was unaffected by osteoarthritis. The proteome and phospholipidome were quantified using mass spectrometry. Multi-omic integration utilised an unsupervised sparse partial least squares strategy. Analysis of variance of the proteome identified 40 differentially expressed proteins (p<0.05). In both mild and severe osteoarthritis groups, significant canonical pathways identified included signalling by Rho family GTPases (p=1.24x10-19), integrins (p=2.72x10-24), the actin cytoskeleton (p=3.88x10-32), and clathrin-mediated endocytosis (p=1.30 x10-24). Multi-omics data integration revealed a highly positive correlation between the proteome and the phospholipidome, allowing for the identification of possible candidate biomarkers like phosphatidylcholine O-32:3, sphingomyelin 36:0;2 coupled with the cell surface markers CD90 and CD109. Our findings suggest that the composition of the lipid membrane, transmembrane proteins and the protein cargo of SF-derived EVs concertedly respond to osteoarthritis pathology and hence could be used as combined diagnostic biomarkers of disease. This study provides a basis and framework for future research, such as studies in larger equine and human cohorts.

The data found in this repository contains only the mass spectrometry lipidomics dataset. The mass spectrometry proteomics data were deposited to the ProteomeXchange Consortium via PRIDE proteome exchange (identifier PXD042765) (E.J. Clarke, J.R. Anderson, M.J. Peffers, Nuclear magnetic resonance spectroscopy of biofluids for osteoarthritis, Br. Med. Bull. 137 (2021) 28–41. https://doi.org/10.1093/bmb/ldaa037.)
DOI: 10.5517/ccdc.csd.cc1n8806
title: CCDC 1527277: Experimental Crystal Structure Determination

description: Related Article: Lars H. Finger, Alexander Venker, Fabian G. Schröder, Jörg Sundermeyer|2017|Dalton Trans.|46|3014|doi:10.1039/C7DT00308K
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.cc1n8817
title: CCDC 1527278: Experimental Crystal Structure Determination

description: Related Article: Lars H. Finger, Alexander Venker, Fabian G. Schröder, Jörg Sundermeyer|2017|Dalton Trans.|46|3014|doi:10.1039/C7DT00308K
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.cc1n8828
title: CCDC 1527279: Experimental Crystal Structure Determination

description: Related Article: Lars H. Finger, Alexander Venker, Fabian G. Schröder, Jörg Sundermeyer|2017|Dalton Trans.|46|3014|doi:10.1039/C7DT00308K
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.cc1n886d
title: CCDC 1527283: Experimental Crystal Structure Determination

description: Related Article: V.A.Vasin, V.A.Kalyasin, P.S.Petrov, N.V.Somov|2019|Zh.Org.Khim.|55|426|doi:10.1134/S107042801904002X
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.cc1n1540
title: CCDC 1520461: Experimental Crystal Structure Determination

description: Related Article: Wan-Zhen Qiao, Hang Xu, Peng Cheng, Bin Zhao|2017|Cryst.Growth Des.|17|3128|doi:10.1021/acs.cgd.7b00063
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.cc1n888g
title: CCDC 1527285: Experimental Crystal Structure Determination

description: Related Article: V.A.Vasin, V.A.Kalyasin, P.S.Petrov, N.V.Somov|2019|Zh.Org.Khim.|55|426|doi:10.1134/S107042801904002X
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.cc1n899j
title: CCDC 1527317: Experimental Crystal Structure Determination

description: Related Article: Anthony B. Carter,  Robert J. Laverick,  Dominic J. Wales,  Sarah O. Akponasa,  Aaron J. Scott,  Tony D. Keene,  and Jonathan A. Kitchen|2017|Cryst.Growth Des.|17|5129|doi:10.1021/acs.cgd.7b00534
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.cc1n89cl
title: CCDC 1527319: Experimental Crystal Structure Determination

description: Related Article: Anthony B. Carter,  Robert J. Laverick,  Dominic J. Wales,  Sarah O. Akponasa,  Aaron J. Scott,  Tony D. Keene,  and Jonathan A. Kitchen|2017|Cryst.Growth Des.|17|5129|doi:10.1021/acs.cgd.7b00534
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.cc1n89dm
title: CCDC 1527320: Experimental Crystal Structure Determination

description: Related Article: Anthony B. Carter,  Robert J. Laverick,  Dominic J. Wales,  Sarah O. Akponasa,  Aaron J. Scott,  Tony D. Keene,  and Jonathan A. Kitchen|2017|Cryst.Growth Des.|17|5129|doi:10.1021/acs.cgd.7b00534
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.cc1n89fn
title: CCDC 1527321: Experimental Crystal Structure Determination

description: Related Article: Anthony B. Carter,  Robert J. Laverick,  Dominic J. Wales,  Sarah O. Akponasa,  Aaron J. Scott,  Tony D. Keene,  and Jonathan A. Kitchen|2017|Cryst.Growth Des.|17|5129|doi:10.1021/acs.cgd.7b00534
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.cc1n89gp
title: CCDC 1527322: Experimental Crystal Structure Determination

description: Related Article: Anthony B. Carter,  Robert J. Laverick,  Dominic J. Wales,  Sarah O. Akponasa,  Aaron J. Scott,  Tony D. Keene,  and Jonathan A. Kitchen|2017|Cryst.Growth Des.|17|5129|doi:10.1021/acs.cgd.7b00534
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.cc1n89hq
title: CCDC 1527323: Experimental Crystal Structure Determination

description: Related Article: Anthony B. Carter,  Robert J. Laverick,  Dominic J. Wales,  Sarah O. Akponasa,  Aaron J. Scott,  Tony D. Keene,  and Jonathan A. Kitchen|2017|Cryst.Growth Des.|17|5129|doi:10.1021/acs.cgd.7b00534
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.cc1n89jr
title: CCDC 1527324: Experimental Crystal Structure Determination

description: Related Article: Anthony B. Carter,  Robert J. Laverick,  Dominic J. Wales,  Sarah O. Akponasa,  Aaron J. Scott,  Tony D. Keene,  and Jonathan A. Kitchen|2017|Cryst.Growth Des.|17|5129|doi:10.1021/acs.cgd.7b00534
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.cc1n488b
title: CCDC 1523441: Experimental Crystal Structure Determination

description: Related Article: Suguru Ito, Tomohiro Taguchi, Takeshi Yamada, Takashi Ubukata, Yoshitaka Yamaguchi, Masatoshi Asami|2017|RSC Advances|7|16953|doi:10.1039/C7RA01006K
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.cc1n88v1
title: CCDC 1527303: Experimental Crystal Structure Determination

description: Related Article: Matthew W. Logan, Suliman Ayad, Jeremy D. Adamson, Tristan Dilbeck, Kenneth Hanson, Fernando J. Uribe-Romo|2017|J.Mater.Chem.A|5|11854|doi:10.1039/C7TA00437K
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.cc1n88w2
title: CCDC 1527304: Experimental Crystal Structure Determination

description: Related Article: Matthew W. Logan, Suliman Ayad, Jeremy D. Adamson, Tristan Dilbeck, Kenneth Hanson, Fernando J. Uribe-Romo|2017|J.Mater.Chem.A|5|11854|doi:10.1039/C7TA00437K
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.cc1n8907
title: CCDC 1527308: Experimental Crystal Structure Determination

description: Related Article: Matthew W. Logan, Suliman Ayad, Jeremy D. Adamson, Tristan Dilbeck, Kenneth Hanson, Fernando J. Uribe-Romo|2017|J.Mater.Chem.A|5|11854|doi:10.1039/C7TA00437K
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: 10.15468/dl.3ud52x
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Hedysarum minjanense"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054598-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc1n88y4
title: CCDC 1527306: Experimental Crystal Structure Determination

description: Related Article: Matthew W. Logan, Suliman Ayad, Jeremy D. Adamson, Tristan Dilbeck, Kenneth Hanson, Fernando J. Uribe-Romo|2017|J.Mater.Chem.A|5|11854|doi:10.1039/C7TA00437K
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.cc1n88z5
title: CCDC 1527307: Experimental Crystal Structure Determination

description: Related Article: Matthew W. Logan, Suliman Ayad, Jeremy D. Adamson, Tristan Dilbeck, Kenneth Hanson, Fernando J. Uribe-Romo|2017|J.Mater.Chem.A|5|11854|doi:10.1039/C7TA00437K
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.cc1n88x3
title: CCDC 1527305: Experimental Crystal Structure Determination

description: Related Article: Matthew W. Logan, Suliman Ayad, Jeremy D. Adamson, Tristan Dilbeck, Kenneth Hanson, Fernando J. Uribe-Romo|2017|J.Mater.Chem.A|5|11854|doi:10.1039/C7TA00437K
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.cc1n89qy
title: CCDC 1527330: Experimental Crystal Structure Determination

description: Related Article: Alebel N. Belay, Johan A. Venter, Andreas Roodt|2017|Z.Kristallogr.-New Cryst.Struct.|232|163|doi:10.1515/ncrs-2016-0064
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.cc1n89t1
title: CCDC 1527333: Experimental Crystal Structure Determination

description: Related Article: Gamal A. El-Hiti, Keith Smith, Amany S. Hegazy, Benson M. Kariuki|2017|Z.Kristallogr.-New Cryst.Struct.|232|329|doi:10.1515/ncrs-2016-0290
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.cc1n89w3
title: CCDC 1527335: Experimental Crystal Structure Determination

description: Related Article: Jidapa Noinart, Suradet Buttachon, Tida Dethoup, Luís Gales, José A. Pereira, Ralph Urbatzka, Sara Freitas, Michael Lee, Artur M. S. Silva, Madalena M. M. Pinto, Vítor Vasconcelos, Anake Kijjoa|2017|Marine Drugs|15|139|doi:10.3390/md15050139
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.cc1n89x4
title: CCDC 1527336: Experimental Crystal Structure Determination

description: Related Article: K. Reuter, R. G. M. Maas, A. Reuter, F. Kilgenstein, Y. Asfaha, C. von Hänisch|2017|Dalton Trans.|46|4530|doi:10.1039/C7DT00321H
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: 10.24416/uu01-2s9fa0
title: Monitoring of Antibiotic Resistance in Veterinary Pathogens by re-use of data? Validation of existing databases

description: The emergence and spread of antimicrobial resistance (AMR) is considered a serious public health threat with use of antimicrobials in animals considered as one of the potential risk factors. In the Netherlands, veterinary use of antimicrobials (AMU) has been decreased substantially in the last decade and gradually the focus shifts to ‘prudent use’: reduction and refinement of AMU. To achieve 'prudent use' in practice, among others evidence-based treatment guidelines are required and therefore knowledge on prevalences of AMR in animal pathogens is pivotal.  One of the aims of this project was to aggregate existing antimicrobial susceptibility testing (AST) results for different animal species/bacterial species combinations in the time period from 2016 up to (including) 2020 in MIC distributions. Additional analyses, to evaluate representativeness and reliability of the aggregrated AST results are not shown here but are reported seperately in the final ZonMw report.

To obtain aggregated AST results (MIC (Minimal Inhibitory Concentration) distributions) for different, pathogenic bacterial species from pigs, poultry, veal calves, dogs and cats were extracted from the Laboratory Information Management Systems (LIMS) of GD (pigs, poultry, veal calves) and of VMDC/UU (dogs and cats), from January 2016 to January 2021. Actual bacteriological culture and AST of bacterial isolates were not part of this project.

Upon extraction of MIC values from the LIMS of Royal GD and VMDC/UU, datasets of MIC values were validated and next, STATA 15.1 (StataCorp, 2017) was used for calculation of MIC50 (the lowest concentration that inhibits growth of 50% of the isolates) and MIC90 (the lowest concentration that inhibits growth of 90% of the isolates) values, calculation of percentages susceptible isolates and percentages resistant isolates and the resistance confidence interval, creation of MIC distributions for each bacterial species/animal species combination.

This data package contains MIC distributions over time period 2016 - 2019 and 2020 (separately) from:
- Actinobacillus Pleuropneumoniae, Escherichia coli and Streptococcus suis isolates originating from pig (samples) 
- Escherichia coli isolates originating from poultry (broilers)
- Salmonella dublin and Salmonella Typhimurium isolates originating from veal calves
- Escherichia coli, Staphylococcus spp. and Pseudomonas aeruginosa isolates originating from dogs
- Escherichia coli and Staphylococcus spp. originating from cats
DOI: 10.5517/ccdc.csd.cc1n89y5
title: CCDC 1527337: Experimental Crystal Structure Determination

description: Related Article: K. Reuter, R. G. M. Maas, A. Reuter, F. Kilgenstein, Y. Asfaha, C. von Hänisch|2017|Dalton Trans.|46|4530|doi:10.1039/C7DT00321H
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.cc1n89z6
title: CCDC 1527338: Experimental Crystal Structure Determination

description: Related Article: K. Reuter, R. G. M. Maas, A. Reuter, F. Kilgenstein, Y. Asfaha, C. von Hänisch|2017|Dalton Trans.|46|4530|doi:10.1039/C7DT00321H
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.cc1n8b08
title: CCDC 1527339: Experimental Crystal Structure Determination

description: Related Article: K. Reuter, R. G. M. Maas, A. Reuter, F. Kilgenstein, Y. Asfaha, C. von Hänisch|2017|Dalton Trans.|46|4530|doi:10.1039/C7DT00321H
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.cc1n8b19
title: CCDC 1527340: Experimental Crystal Structure Determination

description: Related Article: K. Reuter, R. G. M. Maas, A. Reuter, F. Kilgenstein, Y. Asfaha, C. von Hänisch|2017|Dalton Trans.|46|4530|doi:10.1039/C7DT00321H
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.