cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25505/fiz.icsd.cc2f8qv9
title: CSD 2242721: Experimental Crystal Structure Determination

description: Related Article: Yang-Ping Zhang, Shao-Min Pei, Xiao-Ming Jiang, Bin-Wen Liu, Guo-Cong Guo|2024|Mater. Chem. Front.|8|2350|doi:10.1039/D3QM01130E
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: 10.15468/dl.he6kyq
title: Occurrence Download

description: A dataset containing 67725 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Patterns of widespread decline in North American bumble bees"
 ]
}

 The dataset includes 67725 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018409-181003121212138/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.cc2g0njp
title: CCDC 2264752: Experimental Crystal Structure Determination

description: Related Article: Raj Kumar Patel, Priyankar Jha, Anil Chauhan±, Ruchir Kant, Ravindra Kumar±|2024|Org.Lett.|26|839|doi:10.1021/acs.orglett.3c03967
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.reeuj5
title: Occurrence Download

description: A dataset containing 55236 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gallus gallus (Linnaeus, 1758)"
 ]
}

 The dataset includes 55236 records from 192 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0190699-200613084148143/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.cc2g6phw
title: CCDC 2270548: Experimental Crystal Structure Determination

description: Related Article: Enfu Wang, Jiangbin Luo, Luoman Zhang, Jian Zhang, Yaojia Jiang|2024|Org.Lett.|26|1249|doi:10.1021/acs.orglett.4c00063
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.hzzrta
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is France",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "Country is Spain"
 ]
 },
 "Year 1960-1969",
 "HasCoordinate is true",
 "TaxonKey is Leucoraja naevus (Müller & Henle, 1841)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018409-181108115102211/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.cc2gmc8r
title: CCDC 2282724: Experimental Crystal Structure Determination

description: Related Article: Ashok Kale, Su Jeong Kwon, Joohan Lee, Jae Kyun Lee, Kyeong Lee|2024|Org.Lett.|26|1196|doi:10.1021/acs.orglett.3c04357
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: 10.25505/fiz.icsd.cc2gmnvm
title: CSD 2283021: Experimental Crystal Structure Determination

description: Related Article: Yang-Ping Zhang, Shao-Min Pei, Xiao-Ming Jiang, Bin-Wen Liu, Guo-Cong Guo|2024|Mater. Chem. Front.|8|2350|doi:10.1039/D3QM01130E
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: 10.5517/ccdc.csd.cc2gmc9s
title: CCDC 2282725: Experimental Crystal Structure Determination

description: Related Article: Ashok Kale, Su Jeong Kwon, Joohan Lee, Jae Kyun Lee, Kyeong Lee|2024|Org.Lett.|26|1196|doi:10.1021/acs.orglett.3c04357
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.r6hdb4
title: Occurrence Download

description: A dataset containing 1221376 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is ESP",
 "Geometry POLYGON((-9.37134 41.64008,-5.96558 41.64008,-5.96558 43.64403,-9.37134 43.64403,-9.37134 41.64008))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1221376 records from 325 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0154385-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18728/igb-fred-883.2
title: Lake Stechlin chemistry data (photometry) 1970-2020

description: Chemical data at Lake Stechlin: total phosphorus, total nitrogen, SRP, nitrite, nitrate, ammonium, chlorophyll a, alkalinity, calcium carbonate, total inorganic carbon, DOC, NPOC, silicate, iron, aluminium, calcium
DOI: 10.5517/ccdc.csd.cc2gphpc
title: CCDC 2284783: Experimental Crystal Structure Determination

description: Related Article: Justyna Kowalska, Beata Łukasik, Sebastian Frankowski, Łukasz Albrecht|2024|Org.Lett.|26|814|doi:10.1021/acs.orglett.3c03911
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.cc2grrvv
title: CCDC 2286958: Experimental Crystal Structure Determination

description: Related Article: Sonbidya Banerjee, Tharmalingam Punniyamurthy|2024|Org.Lett.|26|988|doi:10.1021/acs.orglett.3c03921
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.cc2grrww
title: CCDC 2286959: Experimental Crystal Structure Determination

description: Related Article: Sonbidya Banerjee, Tharmalingam Punniyamurthy|2024|Org.Lett.|26|988|doi:10.1021/acs.orglett.3c03921
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.ghn3yw
title: Occurrence Download

description: A dataset containing 13304 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Pulmonaria longifolia (Bastard) Boreau"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 13304 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018410-180508205500799/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.cc2gtlc8
title: CCDC 2288710: Experimental Crystal Structure Determination

description: Related Article: Muskan, Akhilesh K. Verma|2024|Org.Lett.|26|1238|doi:10.1021/acs.orglett.4c00053
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.cc2gtm86
title: CCDC 2288738: Experimental Crystal Structure Determination

description: Related Article: Yi Tian, Lei Liu, Tu Zeng, Qian Wu, Baosheng Li|2024|Org.Lett.|26|4183|doi:10.1021/acs.orglett.4c00826
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.cc2gxx4g
title: CCDC 2291896: Experimental Crystal Structure Determination

description: Related Article: Rajesh Chakrabortty, Suman Ghosh, Venkataraman Ganesh|2024|Org.Lett.|26|792|doi:10.1021/acs.orglett.3c03863
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.xgshu6
title: Occurrence Download

description: A dataset containing 284 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Acer barbinerve Maxim. ex Miq."
 ]
}

 The dataset includes 284 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0154393-200613084148143/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.cc2gy04l
title: CCDC 2291989: Experimental Crystal Structure Determination

description: Related Article: Paul D. Scesa, Stéphane P. Roche, Lyndon West|2024|Org.Lett.|26|1123|doi:10.1021/acs.orglett.3c03604
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.cc2gy3yh
title: CCDC 2292107: Experimental Crystal Structure Determination

description: Related Article: Daniel Brösamlen, Martin Oestreich|2024|Org.Lett.|26|977|doi:10.1021/acs.orglett.3c03799
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.4lb3yx
title: Occurrence Download

description: A dataset containing 7766 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Loxodonta africana (Blumenbach, 1797)"
 ]
}

 The dataset includes 7766 records from 103 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018410-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qxy663
title: Occurrence Download

description: A dataset containing 44191 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Cynanthus latirostris Swainson, 1827"
 ]
}

 The dataset includes 44191 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0188131-200613084148143/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.cc2h23qf
title: CCDC 2295944: Experimental Crystal Structure Determination

description: Related Article: Zhuang Zhong, Céline Besnard, Jérôme Lacour|2024|Org.Lett.|26|983|doi:10.1021/acs.orglett.3c03929
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.cc2h28lg
title: CCDC 2296095: Experimental Crystal Structure Determination

description: Related Article: Raj Kumar Patel, Priyankar Jha, Anil Chauhan±, Ruchir Kant, Ravindra Kumar±|2024|Org.Lett.|26|839|doi:10.1021/acs.orglett.3c03967
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.6vrnz4
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "ScientificName" : [
 "is one of (Ageratina adenophora)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005685-210819072339941/datasets/export for details.
DOI: 10.15468/dl.gxr2pg
title: Occurrence Download

description: A dataset containing 616 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pyrola americana G.Don",
 "BasisOfRecord is one of (Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (United States of America, Canada)"
 ]
}

 The dataset includes 616 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0270014-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pqs2ag
title: Occurrence Download

description: A dataset containing 5026 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 {
 "or" : [
 "TaxonKey is Pinus pumila (Pall.) Regel",
 "TaxonKey is Pinus albicaulis Engelm.",
 "TaxonKey is Pinus koraiensis Siebold & Zucc.",
 "TaxonKey is Pinus cembra L.",
 "TaxonKey is Pinus sibirica Du Tour",
 "TaxonKey is Pinus parviflora Siebold & Zucc."
 ]
 }
 ]
}

 The dataset includes 5026 records from 209 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0179186-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eyrdw3
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Nocardia terpenica Hoshino et al., 2007"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013217-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bfrc2j
title: Occurrence Download

description: A dataset containing 79079 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "Geometry POLYGON((-119.91456 -22.38478,-28.08544 -22.38478,-28.08544 14.38478,-119.91456 14.38478,-119.91456 -22.38478))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Momotus aequatorialis Gould, 1858",
 "Year 2000-2025"
 ]
}

 The dataset includes 79079 records from 127 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013180-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17294388
title: Comprehensive survey of conserved RNA secondary structures in full-genome alignment of Hepatitis C virus - Supplementary Files

description: This is the repository for all supplementary files of the publication:

Triebel, S., Lamkiewicz, K., Ontiveros, N. et al. Comprehensive survey of conserved RNA secondary structures in full-genome alignment of Hepatitis C virus. Sci Rep 14, 15145 (2024). https://doi.org/10.1038/s41598-024-62897-0

Abstract

Hepatitis C virus (HCV) is a plus-stranded RNA virus that often chronically infects liver hepatocytes and causes liver cirrhosis and cancer. These viruses replicate their genomes employing error-prone replicases. Thereby, they routinely generate a large ‘cloud’ of RNA genomes (quasispecies) which - by trial and error - comprehensively explore the sequence space available for functional RNA genomes that maintain the ability for efficient replication and immune escape. In this context, it is important to identify which RNA secondary structures in the sequence space of the HCV genome are conserved, likely due to functional requirements. Here, we provide the first genome-wide multiple sequence alignment (MSA) with the prediction of RNA secondary structures throughout all representative full-length HCV genomes. We selected 57 representative genomes by clustering all complete HCV genomes from the BV-BRC database based on k-mer distributions and dimension reduction and adding RefSeq sequences. We include annotations of previously recognized features for easy comparison to other studies. Our results indicate that mainly the core coding region, the C-terminal NS5A region, and the NS5B region contain secondary structure elements that are conserved beyond coding sequence requirements, indicating functionality on the RNA level. In contrast, the genome regions in between contain less highly conserved structures. The results provide a complete description of all conserved RNA secondary structures and make clear that functionally important RNA secondary structures are present in certain HCV genome regions but are largely absent from other regions. Full-genome alignments of all branches of Hepacivirus C are provided in the supplement.

The supplementary files include:



F1 - original data set in Fasta (fasta) format

F2 - pre-filtered data set in Fasta (fasta) format

F3 - phylogenetic tree in Newick (treefile) and Nexus (nex) format

F4 - representative genomes in Fasta (fasta) format

F5 - nucleotide alignment in ClustalW (clustal), Fasta (fasta), and Stockholm (stk) format (latterformat with additional annotations such as RNA secondary structures and genes)

F6 - protein alignment in ClustalW (clustal), Fasta (fasta), and Stockholm (stk) format

F7 - nucleotide and protein alignment in Stockholm (stk) format (with additional annotations such as RNAsecondary structures and genes)

F8 - alignment of the 5’ UTR (51 sequences) in Stockholm (stk), ClustalW (clustal), and Fasta (fasta)format

F9 - alignment of the 3’ X-tail (11 sequences) in Stockholm (stk), ClustalW (clustal), and Fasta(fasta) format
DOI: 10.5281/zenodo.17294387
title: Comprehensive survey of conserved RNA secondary structures in full-genome alignment of Hepatitis C virus - Supplementary Files

description: This is the repository for all supplementary files of the publication:

Triebel, S., Lamkiewicz, K., Ontiveros, N. et al. Comprehensive survey of conserved RNA secondary structures in full-genome alignment of Hepatitis C virus. Sci Rep 14, 15145 (2024). https://doi.org/10.1038/s41598-024-62897-0

Abstract

Hepatitis C virus (HCV) is a plus-stranded RNA virus that often chronically infects liver hepatocytes and causes liver cirrhosis and cancer. These viruses replicate their genomes employing error-prone replicases. Thereby, they routinely generate a large ‘cloud’ of RNA genomes (quasispecies) which - by trial and error - comprehensively explore the sequence space available for functional RNA genomes that maintain the ability for efficient replication and immune escape. In this context, it is important to identify which RNA secondary structures in the sequence space of the HCV genome are conserved, likely due to functional requirements. Here, we provide the first genome-wide multiple sequence alignment (MSA) with the prediction of RNA secondary structures throughout all representative full-length HCV genomes. We selected 57 representative genomes by clustering all complete HCV genomes from the BV-BRC database based on k-mer distributions and dimension reduction and adding RefSeq sequences. We include annotations of previously recognized features for easy comparison to other studies. Our results indicate that mainly the core coding region, the C-terminal NS5A region, and the NS5B region contain secondary structure elements that are conserved beyond coding sequence requirements, indicating functionality on the RNA level. In contrast, the genome regions in between contain less highly conserved structures. The results provide a complete description of all conserved RNA secondary structures and make clear that functionally important RNA secondary structures are present in certain HCV genome regions but are largely absent from other regions. Full-genome alignments of all branches of Hepacivirus C are provided in the supplement.

The supplementary files include:



F1 - original data set in Fasta (fasta) format

F2 - pre-filtered data set in Fasta (fasta) format

F3 - phylogenetic tree in Newick (treefile) and Nexus (nex) format

F4 - representative genomes in Fasta (fasta) format

F5 - nucleotide alignment in ClustalW (clustal), Fasta (fasta), and Stockholm (stk) format (latterformat with additional annotations such as RNA secondary structures and genes)

F6 - protein alignment in ClustalW (clustal), Fasta (fasta), and Stockholm (stk) format

F7 - nucleotide and protein alignment in Stockholm (stk) format (with additional annotations such as RNAsecondary structures and genes)

F8 - alignment of the 5’ UTR (51 sequences) in Stockholm (stk), ClustalW (clustal), and Fasta (fasta)format

F9 - alignment of the 3’ X-tail (11 sequences) in Stockholm (stk), ClustalW (clustal), and Fasta(fasta) format