cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3886/e176401v1
title: Code for: Public and Private Options in Practice: The Military Health System

description: This project is to share the code for "Public and Private Options in Practice: The Military Health System"<br><br>Abstract: Recent debates over health care reform, including in the context of the Military Health System (MHS) and Veterans Administration, highlight the dispute between public and private provision of health care services. Using novel data on childbirth claims from the MHS and drawing on the combination of plausibly exogenous patient moves and heterogeneity across bases in the availability of base hospitals, we identify the impact of receiving obstetrical care on versus off military bases. We find evidence that off-base care is associated with slightly greater resource intensity, but also notably better outcomes, suggesting marginal efficiency gains from care privatization.
description: Dependents of active duty United States military personnel.
DOI: 10.5281/zenodo.10019444
title: Yamada et al Zylazine Usage Survey Data
DOI: 10.5281/zenodo.10019443
title: Yamada et al Zylazine Usage Survey Data
DOI: 10.14469/hpc/13086
title: Swern, initial proton abstraction by NMe3 in the presence of Cl(-), TS, Def2-TZVPP, G = -1458.941651 DG = +7.1 kcal/mol, IRC

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/13068
title: Swern, TS for exo S-inversion, Def2-QZVPP, superfine, G = -823.604044, ΔG = 30.2 (G = -823.652146 for pericyclic TS) ==&gt; IRC

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/13085
title: Swern, initial reactant prior to proton abstraction by NMe3 in the presence of Cl(-) (next to S), Def2-TZVPP, G = -1458.965242

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/13087
title: Swern, initial reactant prior to proton abstraction by NMe3 in the presence of Cl(-) (next to NMe3), Def2-TZVPP,G = -1458.953205

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/13090
title: Cl(-)NHMe3(+), Def2-TZVPP, iso position for Cl(-) G -635.345558 = (+ TS1 endo = -823.61242) == -1,458.957978 (Supermolecule TS -1458.953030)

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/13353
title: PT mechanism for inversion/endo-exo isomerisation via proton transfer to trimethylamine, B3LYP+GD+BJ/Def2-TZVPP/IEFPCM. G = -1458.946171

description: Gaussian 16 (C01) calculation
DOI: 10.6084/m9.figshare.25153358.v4
title: Case Studies on IPN-NFID - Mahalanobis

description: Describe los archivos
DOI: 10.5281/zenodo.10642569
title: Supporting Data for "Quantifying Methane Emissions from United States Landfills"

description: Supporting plume data for "Quantifying Methane Emissions from United States Landfills" by Cusworth et al.

Dataset includes plume concentrations "[Plume metadata]..tile.tif" and delineated plume masks "[Plume metadata]..quantification-mask.tif" for plumes listed in the spreadsheet "Landfill_plume_detections.csv." Concentrations are reported in units of CH4 column enhancement (ppm-m). Two subdirectories exist: "ppmm_1000" and "ppmm_1500" which indicates which concentration threshold was used to delineate plume quantification masks.
DOI: 10.5281/zenodo.10642570
title: Supporting Data for "Quantifying Methane Emissions from United States Landfills"

description: Supporting plume data for "Quantifying Methane Emissions from United States Landfills" by Cusworth et al.

Dataset includes plume concentrations "[Plume metadata]..tile.tif" and delineated plume masks "[Plume metadata]..quantification-mask.tif" for plumes listed in the spreadsheet "Landfill_plume_detections.csv." Concentrations are reported in units of CH4 column enhancement (ppm-m). Two subdirectories exist: "ppmm_1000" and "ppmm_1500" which indicates which concentration threshold was used to delineate plume quantification masks.
DOI: 10.34740/kaggle/dsv/7598552
title: WallStreetBets 2022
DOI: 10.5517/ccdc.csd.cc2g4tv9
title: CCDC 2268761: Experimental Crystal Structure Determination

description: Related Article: Ashraf A. Aly, Elham M. Abdallah, Salwa A. Ahmed, Mai M. Rabee, Olaf Fuhr, Mahmoud A.A. Ibrahim, Hayat Ali Alzahrani, Bahaa G.M. Youssif|2024|Polyhedron|251|116851|doi:10.1016/j.poly.2024.116851
description: Related Article: Olaf Fuhr|2023|CSD Communication|||
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.cc2gk6x5
title: CCDC 2280667: Experimental Crystal Structure Determination

description: Related Article: Bo Tao, Yongqi Li, Yulin Duan, Zhengyi Shi, Jie Li, Yi Guo, Xinye Huang, Yeting Zhang, Weiguang Sun, Changxing Qi, Yonghui Zhang|2024|Bioorg.Chem.|144|107145|doi:10.1016/j.bioorg.2024.107145
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.cc2gm9l0
title: CCDC 2282672: Experimental Crystal Structure Determination

description: Related Article: Tao Jiang, Ji-Hong Lu, Chao Huang, Dong-Mei Chen, Bi-Xue Zhu|2024|Dyes Pigm.|223|111972|doi:10.1016/j.dyepig.2024.111972
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.cc2gm9m1
title: CCDC 2282673: Experimental Crystal Structure Determination

description: Related Article: Tao Jiang, Ji-Hong Lu, Chao Huang, Dong-Mei Chen, Bi-Xue Zhu|2024|Dyes Pigm.|223|111972|doi:10.1016/j.dyepig.2024.111972
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.cc2gm9n2
title: CCDC 2282674: Experimental Crystal Structure Determination

description: Related Article: Tao Jiang, Ji-Hong Lu, Chao Huang, Dong-Mei Chen, Bi-Xue Zhu|2024|Dyes Pigm.|223|111972|doi:10.1016/j.dyepig.2024.111972
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.cc2gm9p3
title: CCDC 2282675: Experimental Crystal Structure Determination

description: Related Article: Tao Jiang, Ji-Hong Lu, Chao Huang, Dong-Mei Chen, Bi-Xue Zhu|2024|Dyes Pigm.|223|111972|doi:10.1016/j.dyepig.2024.111972
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.cc2gnl7z
title: CCDC 2283901: Experimental Crystal Structure Determination

description: Related Article: Bo Tao, Yongqi Li, Yulin Duan, Zhengyi Shi, Jie Li, Yi Guo, Xinye Huang, Yeting Zhang, Weiguang Sun, Changxing Qi, Yonghui Zhang|2024|Bioorg.Chem.|144|107145|doi:10.1016/j.bioorg.2024.107145
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.cc2gnl80
title: CCDC 2283902: Experimental Crystal Structure Determination

description: Related Article: Bo Tao, Yongqi Li, Yulin Duan, Zhengyi Shi, Jie Li, Yi Guo, Xinye Huang, Yeting Zhang, Weiguang Sun, Changxing Qi, Yonghui Zhang|2024|Bioorg.Chem.|144|107145|doi:10.1016/j.bioorg.2024.107145
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.cc2gnld4
title: CCDC 2283906: Experimental Crystal Structure Determination

description: Related Article: Bo Tao, Yongqi Li, Yulin Duan, Zhengyi Shi, Jie Li, Yi Guo, Xinye Huang, Yeting Zhang, Weiguang Sun, Changxing Qi, Yonghui Zhang|2024|Bioorg.Chem.|144|107145|doi:10.1016/j.bioorg.2024.107145
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.cc2gwz0c
title: CCDC 2290993: Experimental Crystal Structure Determination

description: Related Article: Qin Ouyang, Yun-Xuan He, Yi-Liang Zhang, Jin-Qiu You, Mei-Hua Yu, Chun Lei, Ai-Jun Hou|2024|Phytochemistry|219|113990|doi:10.1016/j.phytochem.2024.113990
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.cc2gwz1d
title: CCDC 2290994: Experimental Crystal Structure Determination

description: Related Article: Qin Ouyang, Yun-Xuan He, Yi-Liang Zhang, Jin-Qiu You, Mei-Hua Yu, Chun Lei, Ai-Jun Hou|2024|Phytochemistry|219|113990|doi:10.1016/j.phytochem.2024.113990
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.10523297
title: Unified Human Gastrointestinal Proteome clustering results by DPCfam

description: This dataset contains the result of clustering the Unified Human Gastrointestinal Proteome using the DPCfam algorithm. 

More details on the DPCfam clustering algorithm can be found in the original publication:

Russo, Elena Tea, et al. "DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets." PLOS Computational Biology 18.10 (2022): e1010610. https://doi.org/10.1371/journal.pcbi.1010610

All of the putative protein families obtained through DPCfam (including previous results) can be browsed online at our dedicated webserver: https://dpcfam.areasciencepark.it/uhgp

The original protein dataset is version 1.0 of the UHGP-50 dataset, available for download from MGnify at https://www.ebi.ac.uk/metagenomics/.

FILES DESCRIPTION:

Only MCs with seeds with 1) more than 50 elements and 2) average length larger than 50 aminoacids are reported.

metaclusters_xml.tar.gz:



dpcfam_uhgp_metaclusters.xml: Metaclusters' seeds. Metaclusters entries include also some statistical information about each MC (such as size, average length, low complexity fraction, etc.) and Pfam comparison (Dominant Architecture).

dpcfam_metaclusters.xsd: XML schema file for the data. 

MCxml_to_tables.awk: Awk script to convert from XML to tabular text files. Use through the parse.sh script.

parse.sh: XML parser. 

README.md


uhgp_xml.tar.gz: 



uhgp_seed_match.xml: XML file containing all of UHGP-50 proteins and its corresponding sequences, annotated with Pfam and DPCfam metacluster data.  Annotations comprise the membership of a protein as a seed or matches found though the profile-hmms of the DPCfam-UHGP and the DPCfam-Uniref clusterings. 

uhgp_matches.xsd: XML schema file for the data. 

xml_to_list.awk: Awk script to convert from XML to tabular text files. Use through the parse.sh script.

xml_to_list_mcfiles.awk: Awk script to convert from XML to tabular text files (including individual files for metaclusters' seeds). Use through the parse.sh script.

parse.sh: XML parser. 

README.md


Metacluster Files:



seeds.zip: Metaclusters' seed sequences. A fasta file for each metacluster before filtering.

filtered_seeds.zip: Metaclusters' seed sequences after clustering at 60 percent identity. 

metaclusters_hmms.tar.gz: Metaclusters' profile-hmms. A ".hmm" file for each metacluser. 

metaclusters_msas.tar.gz: Metaclusters' multiple sequence alignments, in fasta format.
DOI: 10.5281/zenodo.7335147
title: Unified Human Gastrointestinal Proteome clustering results by DPCfam

description: This dataset contains the result of clustering the Unified Human Gastrointestinal Proteome using the DPCfam algorithm. More details on the DPCfam clustering algorithm can be found in the original publication: Russo, Elena Tea, et al. "DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets." <em>PLOS Computational Biology</em> 18.10 (2022): e1010610. https://doi.org/10.1371/journal.pcbi.1010610 All of the putative protein families obtained through DPCfam (including previous results) can be browsed online at our dedicated webserver: https://dpcfam.areasciencepark.it/uhgp The original protein dataset is version 1.0 of the UHGP-50 dataset, available for download from MGnify at https://www.ebi.ac.uk/metagenomics/. <strong>FILES DESCRIPTION:</strong> Only MCs with seeds with 1) more than 50 elements and 2) average length larger than 50 aminoacids are reported. <strong>metaclusters_xml.tar.gz:</strong> <strong>dpcfam_uhgp_metaclusters.xml</strong>: Metaclusters' seeds. Metaclusters entries include also some statistical information about each MC (such as size, average length, low complexity fraction, etc.) and Pfam comparison (Dominant Architecture). <strong>dpcfam_metaclusters.xsd</strong>: XML schema file for the data. <strong>MCxml_to_tables.awk:</strong> Awk script to convert from XML to tabular text files. Use through the parse.sh script. <strong>parse.sh</strong>: XML parser. <strong>README.md</strong> <strong>uhgp_xml.tar.gz: </strong> <strong>uhgp_proteins.xml</strong>: XML file containing all of UHGP-50 proteins and its corresponding sequences, annotated with Pfam and DPCfam metacluster data. Annotations comprise the membership of a protein as a seed or matches found though the profile-hmms of the DPCfam-UHGP and the DPCfam-Uniref clusterings. <strong>uhgp_matches.xsd</strong>: XML schema file for the data. <strong>xml_to_list.awk:</strong> Awk script to convert from XML to tabular text files. Use through the parse.sh script. <strong>xml_to_list_mcfiles.awk:</strong> Awk script to convert from XML to tabular text files (including individual files for metaclusters' seeds). Use through the parse.sh script. <strong>parse.sh</strong>: XML parser. <strong>README.md</strong> <strong>Metacluster Files:</strong> <strong>seeds.zip: </strong>Metaclusters' seed sequences. A fasta file for each metacluster before filtering. <strong>filtered_seeds.zip: </strong>Metaclusters' seed sequences after clustering at 60 percent identity. <strong>metaclusters_hmms.tar.gz: </strong>Metaclusters' profile-hmms. A ".hmm" file for each metacluser. <strong>metaclusters_msas.tar.gz: </strong>Metaclusters' multiple sequence alignments, in fasta format.
description: {"references": ["Russo, E. T., Barone, F., Bateman, A., Cozzini, S., Punta, M., & Laio, A. (2022). DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets. PLoS computational biology, 18(10), e1010610."]}
DOI: 10.5281/zenodo.10611777
title: Unified Human Gastrointestinal Proteome clustering results by DPCfam

description: This dataset contains the result of clustering the Unified Human Gastrointestinal Proteome (UHGP) using the DPCfam algorithm. 

More details on the DPCfam clustering algorithm can be found in the original publication:

Russo, Elena Tea, et al. "DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets." PLOS Computational Biology 18.10 (2022): e1010610. https://doi.org/10.1371/journal.pcbi.1010610

All of the putative protein families obtained through DPCfam (including previous results) can be browsed online at our dedicated webserver: https://dpcfam.areasciencepark.it/uhgp

The original protein dataset is version 1.0 of the UHGP-50 dataset, available for download from MGnify at https://www.ebi.ac.uk/metagenomics/.

FILES DESCRIPTION:

Only MCs with seeds with 1) more than 50 elements and 2) average length larger than 50 aminoacids are reported.

metaclusters_xml.tar.gz:



dpcfam_uhgp_metaclusters.xml: Metaclusters' seeds. Metaclusters entries include also some statistical information about each MC (such as size, average length, low complexity fraction, etc.) and Pfam comparison (Dominant Architecture).

dpcfam_metaclusters.xsd: XML schema file for the data. 

MCxml_to_tables.awk: Awk script to convert from XML to tabular text files. Use through the parse.sh script.

parse.sh: XML parser. 

README.md


uhgp_xml.tar.gz: 



uhgp_seed_match.xml: XML file containing all of UHGP-50 proteins and its corresponding sequences, annotated with Pfam and DPCfam metacluster data.  Annotations comprise the membership of a protein as a seed or matches found though the profile-hmms of the DPCfam-UHGP and the DPCfam-Uniref clusterings. 

uhgp_matches.xsd: XML schema file for the data. 

xml_to_list.awk: Awk script to convert from XML to tabular text files. Use through the parse.sh script.

xml_to_list_mcfiles.awk: Awk script to convert from XML to tabular text files (including individual files for metaclusters' seeds). Use through the parse.sh script.

parse.sh: XML parser. 

README.md


Metacluster Files:



seeds.zip: Metaclusters' seed sequences. A fasta file for each metacluster before filtering.

filtered_seeds.zip: Metaclusters' seed sequences after clustering at 60 percent identity. 

metaclusters_hmms.tar.gz: Metaclusters' profile-hmms. A ".hmm" file for each metacluser. 

metaclusters_msas.tar.gz: Metaclusters' multiple sequence alignments, in fasta format. 


uhgp_protein_mapping.txt:



Contains a mapping between the identifiers of versions 1.0 and 2.0.2 of UHGP. The first column corresponds to the ID in UHGP-50 1.0 (representatives for the clustering at 50% protein identity), the second column to the ID in version 2.0.2 and the third column to the ID of the representative of the protein for clustering at 100% sequence identity, for which the protein sequence can be found in UHGP-100.
DOI: 10.5281/zenodo.7335146
title: Unified Human Gastrointestinal Proteome clustering results by DPCfam

description: This dataset contains the result of clustering the Unified Human Gastrointestinal Proteome (UHGP) using the DPCfam algorithm. 

More details on the DPCfam clustering algorithm can be found in the original publication:

Russo, Elena Tea, et al. "DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets." PLOS Computational Biology 18.10 (2022): e1010610. https://doi.org/10.1371/journal.pcbi.1010610

All of the putative protein families obtained through DPCfam (including previous results) can be browsed online at our dedicated webserver: https://dpcfam.areasciencepark.it/uhgp

The original protein dataset is version 1.0 of the UHGP-50 dataset, available for download from MGnify at https://www.ebi.ac.uk/metagenomics/.

FILES DESCRIPTION:

Only MCs with seeds with 1) more than 50 elements and 2) average length larger than 50 aminoacids are reported.

metaclusters_xml.tar.gz:



dpcfam_uhgp_metaclusters.xml: Metaclusters' seeds. Metaclusters entries include also some statistical information about each MC (such as size, average length, low complexity fraction, etc.) and Pfam comparison (Dominant Architecture).

dpcfam_metaclusters.xsd: XML schema file for the data. 

MCxml_to_tables.awk: Awk script to convert from XML to tabular text files. Use through the parse.sh script.

parse.sh: XML parser. 

README.md


uhgp_xml.tar.gz: 



uhgp_seed_match.xml: XML file containing all of UHGP-50 proteins and its corresponding sequences, annotated with Pfam and DPCfam metacluster data.  Annotations comprise the membership of a protein as a seed or matches found though the profile-hmms of the DPCfam-UHGP and the DPCfam-Uniref clusterings. 

uhgp_matches.xsd: XML schema file for the data. 

xml_to_list.awk: Awk script to convert from XML to tabular text files. Use through the parse.sh script.

xml_to_list_mcfiles.awk: Awk script to convert from XML to tabular text files (including individual files for metaclusters' seeds). Use through the parse.sh script.

parse.sh: XML parser. 

README.md


Metacluster Files:



seeds.zip: Metaclusters' seed sequences. A fasta file for each metacluster before filtering.

filtered_seeds.zip: Metaclusters' seed sequences after clustering at 60 percent identity. 

metaclusters_hmms.tar.gz: Metaclusters' profile-hmms. A ".hmm" file for each metacluser. 

metaclusters_msas.tar.gz: Metaclusters' multiple sequence alignments, in fasta format. 


uhgp_protein_mapping.txt:



Contains a mapping between the identifiers of versions 1.0 and 2.0.2 of UHGP. The first column corresponds to the ID in UHGP-50 1.0 (representatives for the clustering at 50% protein identity), the second column to the ID in version 2.0.2 and the third column to the ID of the representative of the protein for clustering at 100% sequence identity, for which the protein sequence can be found in UHGP-100.
DOI: 10.5281/zenodo.10639507
title: MetaClean3.0: Robust and accurate removal of low-quality event measurements in cytometry.

description: This data set contains a set of positive control FCS files used to validate the MetaClean3.0 method. MetaClean3.0 is a method that cleans FCS files by removing low-quality measurements and is the fastest and most accurate of its kind to date.
DOI: 10.5281/zenodo.10639508
title: MetaClean3.0: Robust and accurate removal of low-quality event measurements in cytometry.

description: This data set contains a set of positive control FCS files used to validate the MetaClean3.0 method. MetaClean3.0 is a method that cleans FCS files by removing low-quality measurements and is the fastest and most accurate of its kind to date.
DOI: 10.5281/zenodo.10640608
title: Structure-Informed Protein Language Model

description: These are datasets and model weights for Structure-Informed Protein Language Model (https://arxiv.org/abs/2402.05856). Datasets can also be downloaded from https://github.com/hehefan/Continuous-Discrete-Convolution.
DOI: 10.5281/zenodo.10640609
title: Structure-Informed Protein Language Model

description: These are datasets and model weights for Structure-Informed Protein Language Model (https://arxiv.org/abs/2402.05856). Datasets can also be downloaded from https://github.com/hehefan/Continuous-Discrete-Convolution.