cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7321904
title: Development of a spectral library for the discovery of altered genomic events in Mycobacterium avium associated with virulence using mass spectrometry-based proteogenomic analysis

description: <em>Mycobacterium avium</em> is one of the prominent disease-causing bacteria in humans. It causes lymphadenitis, chronic and extrapulmonary, and disseminated infections in adults, children, and immunocompromised patients. <em>M. avium</em> has ~4,500 predicted protein-coding regions on an average, which can be helpful in discovering several variants at the proteome level. Many of them are potentially associated with virulence, thus identifying such proteins can be a helpful feature in the development of panel-based theranostics. In line with such a long-term goal, we carried out an in-depth proteomic analysis of <em>M. avium</em> with both data-dependent and data-independent acquisition methods. Further, a set of proteogenomic investigations were carried out using the protein database for <em>Mycobacterium tuberculosis,</em> and a genome six-frame translated database and a variant protein database of <em>M. avium</em>. A search of mass spectrometry data analysis against <em>M. avium</em> protein database resulted in the identification of 2,954 proteins. Further, proteogenomic analyses aided in the identification of 1,301 novel peptide sequences and correction of translation start sites for 15 proteins. At the end, we created a spectral library of <em>M. avium</em> proteins including novel genome search-specific peptides and variant peptides detected in this study. We validated the spectral library by a data-independent acquisition of the <em>M. avium</em> proteome. Thus, we present a <em>M. avium </em>spectral library of 29,033 peptide precursors supported by 0.4 million fragment ions for further use by the biomedical community.
description: For easy access and reproducibility of the pipeline, this dataset repository consists of final search outputs such as i) Genome alignment percentage from BWA analysis, ii) M. avium proteins annotated variants (SnpEff output), iii) Summary of annotated variants from SnpEff, iv) AutoRT model and outputs from retention time (RT) prediction analysis, v) Proteome database search results in different spectral library formats (BLIB - Skyline, DLIB - EncyclopeDIA, TSV - OpenSWATH and Spectronaut) and vi) Annotated Peptide Spectra for pseudogenes, novel gene, N-terminal extensions and variant peptides. The raw LC-MS/MS files, database search, and spectral library search results are available in the PRoteomics IDEntifications (PRIDE) repository under the ID PXD032067.
DOI: 10.5281/zenodo.7321903
title: Development of a spectral library for the discovery of altered genomic events in Mycobacterium avium associated with virulence using mass spectrometry-based proteogenomic analysis

description: <em>Mycobacterium avium</em> is one of the prominent disease-causing bacteria in humans. It causes lymphadenitis, chronic and extrapulmonary, and disseminated infections in adults, children, and immunocompromised patients. <em>M. avium</em> has ~4,500 predicted protein-coding regions on an average, which can be helpful in discovering several variants at the proteome level. Many of them are potentially associated with virulence, thus identifying such proteins can be a helpful feature in the development of panel-based theranostics. In line with such a long-term goal, we carried out an in-depth proteomic analysis of <em>M. avium</em> with both data-dependent and data-independent acquisition methods. Further, a set of proteogenomic investigations were carried out using the protein database for <em>Mycobacterium tuberculosis,</em> and a genome six-frame translated database and a variant protein database of <em>M. avium</em>. A search of mass spectrometry data analysis against <em>M. avium</em> protein database resulted in the identification of 2,954 proteins. Further, proteogenomic analyses aided in the identification of 1,301 novel peptide sequences and correction of translation start sites for 15 proteins. At the end, we created a spectral library of <em>M. avium</em> proteins including novel genome search-specific peptides and variant peptides detected in this study. We validated the spectral library by a data-independent acquisition of the <em>M. avium</em> proteome. Thus, we present a <em>M. avium </em>spectral library of 29,033 peptide precursors supported by 0.4 million fragment ions for further use by the biomedical community.
description: For easy access and reproducibility of the pipeline, this dataset repository consists of final search outputs such as i) Genome alignment percentage from BWA analysis, ii) M. avium proteins annotated variants (SnpEff output), iii) Summary of annotated variants from SnpEff, iv) AutoRT model and outputs from retention time (RT) prediction analysis, v) Proteome database search results in different spectral library formats (BLIB - Skyline, DLIB - EncyclopeDIA, TSV - OpenSWATH and Spectronaut) and vi) Annotated Peptide Spectra for pseudogenes, novel gene, N-terminal extensions and variant peptides. The raw LC-MS/MS files, database search, and spectral library search results are available in the PRoteomics IDEntifications (PRIDE) repository under the ID PXD032067.
DOI: 10.5281/zenodo.7594850
title: ESTIMATIVAS DA DISTRIBUIÇÃO DE RADIAÇÃO ULTRAVIOLETA EM DIFERENTES PARTES DO CORPO

description: Resultados simulados a partir de um modelo geométrico aperfeiçoado para estimativa de doses eritêmicas em superfícies inclinadas.
DOI: 10.5281/zenodo.7594849
title: ESTIMATIVAS DA DISTRIBUIÇÃO DE RADIAÇÃO ULTRAVIOLETA EM DIFERENTES PARTES DO CORPO

description: Resultados simulados a partir de um modelo geométrico aperfeiçoado para estimativa de doses eritêmicas em superfícies inclinadas.
DOI: 10.5281/zenodo.7583241
title: Mass spectrometry- based biomarkers to detect prostate cancer: A multicentric study based on non- invasive urine collection without prior intervention

description: These are datasets related to mass spectrometry proteomics analysis, in particular Capillary Electrophoresis coupled to Mass Spectrometery (CE-MS). CE-MS was employed to acquire proteomics profiles from 970 patients from two different clinical centers. with the aim to develop a biomarker model to detect Prostate Cancer.
DOI: 10.5281/zenodo.7437643
title: Mass spectrometry- based biomarkers to detect prostate cancer: A multicentric study based on non- invasive urine collection without prior intervention

description: These are datasets related to mass spectrometry proteomics analysis, in particular Capillary Electrophoresis coupled to Mass Spectrometery (CE-MS). CE-MS was employed to acquire proteomics profiles from 970 patients from two different clinical centers. with the aim to develop a biomarker model to detect Prostate Cancer.
DOI: 10.5281/zenodo.7594838
title: TFOM: Generic Facilitation Template

description: This spreadsheet is based on one created initially to manage "The Future of Meetings" symposium in 2020. It was developed from scratch to help track the various tasks and deadlines associated with managing an online meeting, though it would be useful in hybrid and in-person contexts too. Since then, it has been used in other events TFOM has been associated with, including ICWIP2021, SP21, S4PGxTFOM and the A4E symposium. It has also been improved over time, based on experience with later events. We are uploading it here in case it might be useful to others in terms of tracking your own conferences, meetings and events. We note that this spreadsheet is only indicative in terms of appropriate categories and items to track and expect that people will need to customise or improve it to match their own context better. We have always used it in an online cloud form (since this is the easiest way to manage multiple editors), and so we also make available the original Google sheet version here: https://docs.google.com/spreadsheets/d/1QwST-ETBYEw4llWZjtcv8za2hziweFIB8K84b4HKUYE/edit?usp=sharing We welcome feedback on the spreadsheet and any possible suggestions for improvement: https://twitter.com/futuremeetings
DOI: 10.5281/zenodo.7594837
title: TFOM: Generic Facilitation Template

description: This spreadsheet is based on one created initially to manage "The Future of Meetings" symposium in 2020. It was developed from scratch to help track the various tasks and deadlines associated with managing an online meeting, though it would be useful in hybrid and in-person contexts too. Since then, it has been used in other events TFOM has been associated with, including ICWIP2021, SP21, S4PGxTFOM and the A4E symposium. It has also been improved over time, based on experience with later events. We are uploading it here in case it might be useful to others in terms of tracking your own conferences, meetings and events. We note that this spreadsheet is only indicative in terms of appropriate categories and items to track and expect that people will need to customise or improve it to match their own context better. We have always used it in an online cloud form (since this is the easiest way to manage multiple editors), and so we also make available the original Google sheet version here: https://docs.google.com/spreadsheets/d/1QwST-ETBYEw4llWZjtcv8za2hziweFIB8K84b4HKUYE/edit?usp=sharing We welcome feedback on the spreadsheet and any possible suggestions for improvement: https://twitter.com/futuremeetings
DOI: 10.5517/ccdc.csd.ccq070y
title: CCDC 655619: Experimental Crystal Structure Determination

description: Related Article: Perumal Venkatesan, Subbiah Thamotharan, M. Judith Percino, Andivelu Ilangovan|2021|Cryst.Growth Des.|21|779|doi:10.1021/acs.cgd.0c01010
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.ccqsd84
title: CCDC 678846: Experimental Crystal Structure Determination

description: Related Article: Perumal Venkatesan, Subbiah Thamotharan, M. Judith Percino, Andivelu Ilangovan|2021|Cryst.Growth Des.|21|779|doi:10.1021/acs.cgd.0c01010
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.cc23js4l
title: CCDC 1952539: Experimental Crystal Structure Determination

description: Related Article: Kai Li, Huang Ye, Xiaoqi Li, Xinqiang Wang, Junhua Luo, Xitao Liu|2023|Inorg.Chem.Front.|10|435|doi:10.1039/D2QI02149H
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.ccqbx64
title: CCDC 665886: Experimental Crystal Structure Determination

description: Related Article: Perumal Venkatesan, Subbiah Thamotharan, M. Judith Percino, Andivelu Ilangovan|2021|Cryst.Growth Des.|21|779|doi:10.1021/acs.cgd.0c01010
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.ccw0hbp
title: CCDC 804832: Experimental Crystal Structure Determination

description: Related Article: Perumal Venkatesan, Subbiah Thamotharan, M. Judith Percino, Andivelu Ilangovan|2021|Cryst.Growth Des.|21|779|doi:10.1021/acs.cgd.0c01010
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.ccw0lbs
title: CCDC 804925: Experimental Crystal Structure Determination

description: Related Article: Perumal Venkatesan, Subbiah Thamotharan, M. Judith Percino, Andivelu Ilangovan|2021|Cryst.Growth Des.|21|779|doi:10.1021/acs.cgd.0c01010
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.ccq9zb9
title: CCDC 664991: Experimental Crystal Structure Determination

description: Related Article: Perumal Venkatesan, Subbiah Thamotharan, M. Judith Percino, Andivelu Ilangovan|2021|Cryst.Growth Des.|21|779|doi:10.1021/acs.cgd.0c01010
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.ccqbx53
title: CCDC 665885: Experimental Crystal Structure Determination

description: Related Article: Perumal Venkatesan, Subbiah Thamotharan, M. Judith Percino, Andivelu Ilangovan|2021|Cryst.Growth Des.|21|779|doi:10.1021/acs.cgd.0c01010
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.ccw0hcq
title: CCDC 804833: Experimental Crystal Structure Determination

description: Related Article: Perumal Venkatesan, Subbiah Thamotharan, M. Judith Percino, Andivelu Ilangovan|2021|Cryst.Growth Des.|21|779|doi:10.1021/acs.cgd.0c01010
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.cc25sr2t
title: CCDC 2019776: Experimental Crystal Structure Determination

description: Related Article: M. R. Godyn, D. Larowska, E. Bartoszak-Adamska|2021|Cryst.Growth Des.|21|396|doi:10.1021/acs.cgd.0c01242
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.cc25sr3v
title: CCDC 2019777: Experimental Crystal Structure Determination

description: Related Article: M. R. Godyn, D. Larowska, E. Bartoszak-Adamska|2021|Cryst.Growth Des.|21|396|doi:10.1021/acs.cgd.0c01242
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.cc25sr4w
title: CCDC 2019778: Experimental Crystal Structure Determination

description: Related Article: M. R. Godyn, D. Larowska, E. Bartoszak-Adamska|2021|Cryst.Growth Des.|21|396|doi:10.1021/acs.cgd.0c01242
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.cc25sr5x
title: CCDC 2019779: Experimental Crystal Structure Determination

description: Related Article: M. R. Godyn, D. Larowska, E. Bartoszak-Adamska|2021|Cryst.Growth Des.|21|396|doi:10.1021/acs.cgd.0c01242
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.cc25sr6y
title: CCDC 2019780: Experimental Crystal Structure Determination

description: Related Article: M. R. Godyn, D. Larowska, E. Bartoszak-Adamska|2021|Cryst.Growth Des.|21|396|doi:10.1021/acs.cgd.0c01242
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.cc25sr7z
title: CCDC 2019781: Experimental Crystal Structure Determination

description: Related Article: M. R. Godyn, D. Larowska, E. Bartoszak-Adamska|2021|Cryst.Growth Des.|21|396|doi:10.1021/acs.cgd.0c01242
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.cc25sr91
title: CCDC 2019783: Experimental Crystal Structure Determination

description: Related Article: M. R. Godyn, D. Larowska, E. Bartoszak-Adamska|2021|Cryst.Growth Des.|21|396|doi:10.1021/acs.cgd.0c01242
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.cc25sr80
title: CCDC 2019782: Experimental Crystal Structure Determination

description: Related Article: M. R. Godyn, D. Larowska, E. Bartoszak-Adamska|2021|Cryst.Growth Des.|21|396|doi:10.1021/acs.cgd.0c01242
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.cc26lkky
title: CCDC 2043630: Experimental Crystal Structure Determination

description: Related Article: Yusheng Zhang, Wuhua Duan, Yuning Yang, Tian Jian, Yusen Qiao, Guoxi Ren, Nian Zhang, Lei Zheng, Wensheng Yan, Jianchen Wang, Jing Chen, Stefan G. Minasian, Taoxiang Sun|2022|Inorg.Chem.|61|92|doi:10.1021/acs.inorgchem.1c02236
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.cc26lklz
title: CCDC 2043631: Experimental Crystal Structure Determination

description: Related Article: Yusheng Zhang, Wuhua Duan, Yuning Yang, Tian Jian, Yusen Qiao, Guoxi Ren, Nian Zhang, Lei Zheng, Wensheng Yan, Jianchen Wang, Jing Chen, Stefan G. Minasian, Taoxiang Sun|2022|Inorg.Chem.|61|92|doi:10.1021/acs.inorgchem.1c02236
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.cc26lkm0
title: CCDC 2043632: Experimental Crystal Structure Determination

description: Related Article: Yusheng Zhang, Wuhua Duan, Yuning Yang, Tian Jian, Yusen Qiao, Guoxi Ren, Nian Zhang, Lei Zheng, Wensheng Yan, Jianchen Wang, Jing Chen, Stefan G. Minasian, Taoxiang Sun|2022|Inorg.Chem.|61|92|doi:10.1021/acs.inorgchem.1c02236
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.cc26lkn1
title: CCDC 2043633: Experimental Crystal Structure Determination

description: Related Article: Yusheng Zhang, Wuhua Duan, Yuning Yang, Tian Jian, Yusen Qiao, Guoxi Ren, Nian Zhang, Lei Zheng, Wensheng Yan, Jianchen Wang, Jing Chen, Stefan G. Minasian, Taoxiang Sun|2022|Inorg.Chem.|61|92|doi:10.1021/acs.inorgchem.1c02236
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.cc26lkp2
title: CCDC 2043634: Experimental Crystal Structure Determination

description: Related Article: Yusheng Zhang, Wuhua Duan, Yuning Yang, Tian Jian, Yusen Qiao, Guoxi Ren, Nian Zhang, Lei Zheng, Wensheng Yan, Jianchen Wang, Jing Chen, Stefan G. Minasian, Taoxiang Sun|2022|Inorg.Chem.|61|92|doi:10.1021/acs.inorgchem.1c02236
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.