cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc21mtp6
title: CCDC 1895888: Experimental Crystal Structure Determination

description: Related Article: Brian W. Skelton, Effendy, Allan H. White|2019|CSD Communication|||
description: Related Article: Effendy, Corrado Di Nicola, Peter C. Healy, Fabio Marchetti, Claudio Pettinari, Brian W. Skelton, Alessia Tombesi, Allan H. White|2022|Inorg.Chim.Acta|536|120895|doi:10.1016/j.ica.2022.120895
DOI: 10.5517/ccdc.csd.cc28jh6j
title: CCDC 2101217: Experimental Crystal Structure Determination

description: Related Article: Devin J. Angevine, Kristine Joy Camacho, Javid Rzayev, Jason B. Benedict|2022|Cryst.Growth Des.|22|1594|doi:10.1021/acs.cgd.1c01110
DOI: 10.15784/601533
title: Raw gastropod collection data from Amsler et al. 2022 Antarctic Science

description: This file represents the raw gastropod count data used for the analyses in Amsler et al. 2022, Antarctic Science. See the methods there in the main text and supplementary material for specifics on collections and exact coordinates of the collection sites.
DOI: 10.15785/sbgrid/675
title: X-Ray Diffraction data from horse liver alcohol dehydrogenase E with NAD, pentafluorobenzyl alcohol, source of 4DWV structure

description: Wild type alcohol dehydrogenase with data to 1.1 A, High and low resolution passes. Publication used data to 1.14. Basis for other structures with S48T, L57F, F93W, and V203A substitutions.
description: High resolution data "PFB1-100K-high_1.????" image says detector distance is 130 mm, but integration refines at 133 mm. Used known cell dimensions to index.
DOI: 10.21223/lnj6hk/6boyxq
title: 01-Encuestas-medios-vida-caracteristicas-del-hogar.tab

description: :unav
DOI: 10.5281/zenodo.6360725
title: Supplementary Data for the manuscript 'The Rad9-Rad1-Hus1 DNA repair clamp is found in Microsporidia'

description: This dataset contains the supplementary data files for the manuscript titled 'The Rad9-Rad1-Hus1 DNA repair clamp is found in Microsporidia'.
description: This versions includes .md5 checksum files and fixes the broken archives from version 1.0 (due to a faulty SSD). Also includes models 1 to 5 from AlphaFold.
DOI: 10.5281/zenodo.5639615
title: Supplementary Data for the manuscript 'The Rad9-Rad1-Hus1 DNA repair clamp is found in Microsporidia'

description: This dataset contains the supplementary data files for the manuscript titled 'The Rad9-Rad1-Hus1 DNA repair clamp is found in Microsporidia'.
description: This versions includes .md5 checksum files and fixes the broken archives from version 1.0 (due to a faulty SSD). Also includes models 1 to 5 from AlphaFold.
DOI: 10.6084/m9.figshare.19119698
title: transcript counts_GBM T cells_scRNAseq.xlsx

description: Raw transcript counts of GBM T cells from 3 patient GBM tissue samples (BT20, BT23 and BT26).<br>Using R version 3.6.3 and Seurat version 3.1.5, cells with (i) fewer than 200 genes, (ii) gene numbers outside ±2 standard deviations from the mean, or (iii) a mitochondrial gene fraction greater than 10% were excluded. Remaining cells were log normalised by total expression and scaled to 10,000 transcripts/cell with the NormalizeData function in Seurat. Using the FindIntegrationAnchors (dims = 1:30, k.filter = 200) and IntegrateData (dims = 1:30) functions, cells from different libraries were combined by assessing the pairwise correspondence between a set of representative genes (anchors). The FindVariableGenes function was used to identify variable genes returning 2000 features using vst as the selection method. The data were then scaled and principal component analysis applied using the ScaleData and RunPCA functions respectively. Cells were clustered based on gene expression profiles using the FindNeighbors and FindClusters functions with resolution set to 0.5. <br>
DOI: 10.6084/m9.figshare.19119698.v1
title: transcript counts_GBM T cells_scRNAseq.xlsx

description: Raw transcript counts of GBM T cells from 3 patient GBM tissue samples (BT20, BT23 and BT26).<br>Using R version 3.6.3 and Seurat version 3.1.5, cells with (i) fewer than 200 genes, (ii) gene numbers outside ±2 standard deviations from the mean, or (iii) a mitochondrial gene fraction greater than 10% were excluded. Remaining cells were log normalised by total expression and scaled to 10,000 transcripts/cell with the NormalizeData function in Seurat. Using the FindIntegrationAnchors (dims = 1:30, k.filter = 200) and IntegrateData (dims = 1:30) functions, cells from different libraries were combined by assessing the pairwise correspondence between a set of representative genes (anchors). The FindVariableGenes function was used to identify variable genes returning 2000 features using vst as the selection method. The data were then scaled and principal component analysis applied using the ScaleData and RunPCA functions respectively. Cells were clustered based on gene expression profiles using the FindNeighbors and FindClusters functions with resolution set to 0.5. <br>
DOI: 10.5517/ccdc.csd.cc297bjf
title: CCDC 2122214: Experimental Crystal Structure Determination

description: Related Article: Zeli Song|2021|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2976h8
title: CCDC 2122089: Experimental Crystal Structure Determination

description: Related Article: yang shuo|2021|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc28jh7k
title: CCDC 2101218: Experimental Crystal Structure Determination

description: Related Article: Devin J. Angevine, Kristine Joy Camacho, Javid Rzayev, Jason B. Benedict|2022|Cryst.Growth Des.|22|1594|doi:10.1021/acs.cgd.1c01110
DOI: 10.5517/ccdc.csd.cc28jh8l
title: CCDC 2101219: Experimental Crystal Structure Determination

description: Related Article: Devin J. Angevine, Kristine Joy Camacho, Javid Rzayev, Jason B. Benedict|2022|Cryst.Growth Des.|22|1594|doi:10.1021/acs.cgd.1c01110
DOI: 10.5281/zenodo.6358847
title: Digging deeper into colonial palaeontological practices in modern day Mexico and Brazil

description: Scientific practices stemming from colonialism, whereby middle- and low-income countries supply data for high-income countries and the contributions of local expertise are devalued, are still prevalent today in the field of palaeontology. In response to these unjust practices, countries such as Mexico and Brazil adopted protective laws and regulations during the twentieth century to preserve their palaeontological heritage. However, scientific colonialism is still reflected in many publications describing fossil specimens recovered from these countries. Here, we present examples of ‘palaeontological colonialism’ from publications on Jurassic–Cretaceous fossils from NE Mexico and NE Brazil spanning the last three decades. Common issues that we identified in these publications are the absence of both fieldwork and export permit declarations and the lack of local experts among authorships. In Mexico, access to many fossil specimens is restricted on account of these specimens being housed in private collections, whereas a high number of studies on Brazilian fossils are based on specimens illegally reposited in foreign collections, particularly in Germany and Japan. Finally, we outline and discuss the wider academic and social impacts of these research practices, and propose exhaustive recommendations to scientists, journals, museums, research institutions and government and funding agencies in order to overcome these practices. <strong>Files included:</strong> <strong>Table S1.</strong> Sabinas, La Popa and Parras basins fossil publications by foreign authors <strong>Table S2.</strong> Araripe fossil publications by foreign authors (vertebrates and plants) <strong>Table S3.</strong> Preliminary list of Araripe fossil arthropod publications <strong>Table S4.</strong> List of palaeontology museums and postgraduate courses in Brazil with palaeontology advisors <strong>Table S5.</strong> List of palaeontology museums and postgraduate courses in Mexico with palaeontology advisors <strong>Translation S1.</strong> Complete article in Portuguese <strong>Translation S2.</strong> Complete article in Spanish <strong>Appendix A.</strong> Laws in Brazil (includes English translations) <strong>Appendix B.</strong> Laws in Mexico (includes English translations)
DOI: 10.5281/zenodo.6358846
title: Digging deeper into colonial palaeontological practices in modern day Mexico and Brazil

description: Scientific practices stemming from colonialism, whereby middle- and low-income countries supply data for high-income countries and the contributions of local expertise are devalued, are still prevalent today in the field of palaeontology. In response to these unjust practices, countries such as Mexico and Brazil adopted protective laws and regulations during the twentieth century to preserve their palaeontological heritage. However, scientific colonialism is still reflected in many publications describing fossil specimens recovered from these countries. Here, we present examples of ‘palaeontological colonialism’ from publications on Jurassic–Cretaceous fossils from NE Mexico and NE Brazil spanning the last three decades. Common issues that we identified in these publications are the absence of both fieldwork and export permit declarations and the lack of local experts among authorships. In Mexico, access to many fossil specimens is restricted on account of these specimens being housed in private collections, whereas a high number of studies on Brazilian fossils are based on specimens illegally reposited in foreign collections, particularly in Germany and Japan. Finally, we outline and discuss the wider academic and social impacts of these research practices, and propose exhaustive recommendations to scientists, journals, museums, research institutions and government and funding agencies in order to overcome these practices. <strong>Files included:</strong> <strong>Table S1.</strong> Sabinas, La Popa and Parras basins fossil publications by foreign authors <strong>Table S2.</strong> Araripe fossil publications by foreign authors (vertebrates and plants) <strong>Table S3.</strong> Preliminary list of Araripe fossil arthropod publications <strong>Table S4.</strong> List of palaeontology museums and postgraduate courses in Brazil with palaeontology advisors <strong>Table S5.</strong> List of palaeontology museums and postgraduate courses in Mexico with palaeontology advisors <strong>Translation S1.</strong> Complete article in Portuguese <strong>Translation S2.</strong> Complete article in Spanish <strong>Appendix A.</strong> Laws in Brazil (includes English translations) <strong>Appendix B.</strong> Laws in Mexico (includes English translations)
DOI: 10.5281/zenodo.6360755
title: SciExpeM - 10.5281/zenodo.6360755

description: Cai, Liming; Uygun, Yasar; Togbé, Casimir; Pitsch, Heinz; Olivier, Herbert; Dagaut, Philippe; Sarathy, S. Mani - Proceedings Of The Combustion Institute, 2015, (35), 419-427
DOI: 10.5281/zenodo.6360754
title: SciExpeM - 10.5281/zenodo.6360755

description: Cai, Liming; Uygun, Yasar; Togbé, Casimir; Pitsch, Heinz; Olivier, Herbert; Dagaut, Philippe; Sarathy, S. Mani - Proceedings Of The Combustion Institute, 2015, (35), 419-427
DOI: 10.5281/zenodo.6360757
title: SciExpeM - 10.5281/zenodo.6360757

description: Cai, Liming; Uygun, Yasar; Togbé, Casimir; Pitsch, Heinz; Olivier, Herbert; Dagaut, Philippe; Sarathy, S. Mani - Proceedings Of The Combustion Institute, 2015, (35), 419-427
DOI: 10.5281/zenodo.6360756
title: SciExpeM - 10.5281/zenodo.6360757

description: Cai, Liming; Uygun, Yasar; Togbé, Casimir; Pitsch, Heinz; Olivier, Herbert; Dagaut, Philippe; Sarathy, S. Mani - Proceedings Of The Combustion Institute, 2015, (35), 419-427
DOI: 10.5281/zenodo.6360760
title: SciExpeM - 10.5281/zenodo.6360760

description: Cai, Liming; Uygun, Yasar; Togbé, Casimir; Pitsch, Heinz; Olivier, Herbert; Dagaut, Philippe; Sarathy, S. Mani - Proceedings Of The Combustion Institute, 2015, (35), 419-427
DOI: 10.5281/zenodo.6360759
title: SciExpeM - 10.5281/zenodo.6360760

description: Cai, Liming; Uygun, Yasar; Togbé, Casimir; Pitsch, Heinz; Olivier, Herbert; Dagaut, Philippe; Sarathy, S. Mani - Proceedings Of The Combustion Institute, 2015, (35), 419-427
DOI: 10.5281/zenodo.6360764
title: SciExpeM - 10.5281/zenodo.6360764

description: Cai, Liming; Uygun, Yasar; Togbé, Casimir; Pitsch, Heinz; Olivier, Herbert; Dagaut, Philippe; Sarathy, S. Mani - Proceedings Of The Combustion Institute, 2015, (35), 419-427
DOI: 10.5281/zenodo.6360763
title: SciExpeM - 10.5281/zenodo.6360764

description: Cai, Liming; Uygun, Yasar; Togbé, Casimir; Pitsch, Heinz; Olivier, Herbert; Dagaut, Philippe; Sarathy, S. Mani - Proceedings Of The Combustion Institute, 2015, (35), 419-427
DOI: 10.5281/zenodo.6360766
title: SciExpeM - 10.5281/zenodo.6360766

description: Cai, Liming; Uygun, Yasar; Togbé, Casimir; Pitsch, Heinz; Olivier, Herbert; Dagaut, Philippe; Sarathy, S. Mani - Proceedings Of The Combustion Institute, 2015, (35), 419-427
DOI: 10.5281/zenodo.6360765
title: SciExpeM - 10.5281/zenodo.6360766

description: Cai, Liming; Uygun, Yasar; Togbé, Casimir; Pitsch, Heinz; Olivier, Herbert; Dagaut, Philippe; Sarathy, S. Mani - Proceedings Of The Combustion Institute, 2015, (35), 419-427
DOI: 10.17632/s86vm9x66w.1
title: Interaction between Pace-of-life type, Pesticide exposure and Autotomy

description: Data used in 'The pace-of life explains whether gills improve or exacerbate pesticide sensitivity in a damselfly larva' in Environmental Pollution. (Authors: Lizanne Janssens, Wilco Verberk & Robby Stoks)
DOI: 10.17632/y8dndzn3mg.1
title: Genome-scale CRISPR screen identifies TMEM41B as a critical host factor required for coronavirus replication

description: These data are part of the Supplemental Items associated with the manuscript entitled "Genome-scale CRISPR screen identifies TMEM41B as a critical host factor required for coronavirus replication". These files include Supplementary Data file 1-4.
DOI: 10.17632/gw9xc4z8rm.1
title: Temporal changes of fecal carbohydrates relative to perturbations in gut microbiome of neonatal calves: emerging of diarrhea induced by extended-spectrum β-lactamase producing enteroaggregative Escherichia coli 

description: Metabolomics preprocessed data, the data set is related to figure 4, figure 5, Extended Data figure S2.
DOI: 10.5281/zenodo.6360062
title: 1km-res FESOM2 data for Nares Strait

description: The temperature, salinity, current velocity and sea ice data subsets from the high-resolution FESOM2 model run. The outputs represent the data from Nares Strait for 2006-2010 used in the author's manuscript entitled "The role of oceanic heat flux in reducing thermodynamic ice growth in Nares Strait and promoting earlier collapse of the ice bridge".
DOI: 10.5517/ccdc.csd.cc25wqng
title: CCDC 2022646: Experimental Crystal Structure Determination

description: Related Article: Neha Manav, Mohsin Y. Lone, Md Kausar Raza, Jaydeepsinh Chavda, Shigeki Mori, Iti Gupta|2022|Dalton Trans.|51|3849|doi:10.1039/D1DT04218A
DOI: 10.5517/ccdc.csd.cc25wqqj
title: CCDC 2022648: Experimental Crystal Structure Determination

description: Related Article: Neha Manav, Mohsin Y. Lone, Md Kausar Raza, Jaydeepsinh Chavda, Shigeki Mori, Iti Gupta|2022|Dalton Trans.|51|3849|doi:10.1039/D1DT04218A
DOI: 10.5517/ccdc.csd.cc2741s7
title: CCDC 2059478: Experimental Crystal Structure Determination

description: Related Article: Wei Wei, Xiaodan Zhao|2022|Org.Lett.|24|1780|doi:10.1021/acs.orglett.2c00117
DOI: 10.5517/ccdc.csd.cc27427q
title: CCDC 2059492: Experimental Crystal Structure Determination

description: Related Article: Wei Wei, Xiaodan Zhao|2022|Org.Lett.|24|1780|doi:10.1021/acs.orglett.2c00117
DOI: 10.5517/ccdc.csd.cc27429s
title: CCDC 2059494: Experimental Crystal Structure Determination

description: Related Article: Wei Wei, Xiaodan Zhao|2022|Org.Lett.|24|1780|doi:10.1021/acs.orglett.2c00117
DOI: 10.5517/ccdc.csd.cc2742bt
title: CCDC 2059495: Experimental Crystal Structure Determination

description: Related Article: Wei Wei, Xiaodan Zhao|2022|Org.Lett.|24|1780|doi:10.1021/acs.orglett.2c00117
DOI: 10.5517/ccdc.csd.cc27zn30
title: CCDC 2085032: Experimental Crystal Structure Determination

description: Related Article: Guang Yang, Zhicheng Xiong, Hongsheng Nie, Meiqin He, Qiong Feng, Xuan Li, Huabin Huang, Shoucai Wang, Fanghua Ji, Guangbin Jiang|2022|Org.Lett.|24|1859|doi:10.1021/acs.orglett.2c00454
DOI: 10.5517/ccdc.csd.cc287r2c
title: CCDC 2092812: Experimental Crystal Structure Determination

description: Related Article: Ming-Feng Xiong, Bao-Hui Ye|2022|Organometallics|41|617|doi:10.1021/acs.organomet.1c00683
DOI: 10.5517/ccdc.csd.cc287r4f
title: CCDC 2092814: Experimental Crystal Structure Determination

description: Related Article: Ming-Feng Xiong, Bao-Hui Ye|2022|Organometallics|41|617|doi:10.1021/acs.organomet.1c00683
DOI: 10.5517/ccdc.csd.cc287r5g
title: CCDC 2092815: Experimental Crystal Structure Determination

description: Related Article: Ming-Feng Xiong, Bao-Hui Ye|2022|Organometallics|41|617|doi:10.1021/acs.organomet.1c00683
DOI: 10.15468/ucuadj
title: PELD - RLaC | Ambientes de restinga sob a ótica da ecologia funcional: definição de atributos funcionais e seu papel na estruturação de formações vegetais especializadas das restingas do Estado do Rio de Janeiro

description: A pesquisa teve como objetivo descrever a estrutura da vegetação da Formação Arbustiva Aberta de Clusia em nível taxonômico, filogenético e funcional, ao longo de um gradiente latitudinal no Parque Nacional da Restinga de Jurubatiba.
DOI: 10.26188/19351607
title: UniMelb Thylacine Genomics Repository

description: <br><br>This FigShare repository contains genomic datasets for the Thylacine Genomics Project at the University of Melbourne (VIC, Australia). Currently 4 files arising from 2 publications are hosted on this repository. All assemblies arise from NCBI BioSample SAMN06049672<br><br>1). Feigin et al. 2018: Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore [https://www.nature.com/articles/s41559-017-0417-y]<br><br>a) ThyCyn1.0: This assembly is the first de novo whole-genome assembly for the thylacine. It is a contig-level assembly and thus contains no scaffolds. It was generated from short insert paired-end reads (https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=354646). Sequencing and data pre-processing strategy are discussed in the methods of Feigin et al. 2018. This assembly was used exclusively to estimate genome size and G+C content of the thylacine genome.<br><br>b) UniMelb_Thylacine_Refassem_1/GCA_007646695.1: Because of the highly-fragmentary nature (low N50) of ThyCyn1.0, UniMelb_Thylacine_Refassem_1 was generated to perform all evolutionary analyses detailed in Feigin et al. 2018. UniMelb_Thylacine_Refassem_1 was generated by mapping thylacine reads against the repeatmasked version of the previous Tasmanian devil draft genome Devil_ref v7.0 and generating reference-guided scaffolds. This is not a complete genome assembly, as it is composed only of non-repetitive genomic regions and does not include indel differences between Thylacine and devil. This was done to preserve the coordinate systems between thylacine and devil, permitting the use of the already-existing Tasmanian devil gene annotations. See methods of Feigin et al. 2018 for details. Assembly is hosted on NCBI under BioProject PRJNA354646.<br><br> 2) Feigin et al. 2022: A chromosome-scale hybrid genome assembly of the extinct Tasmanian tiger (Thylacinus cynocephalus) [https://www.biorxiv.org/content/10.1101/2022.03.02.482690v1.full]<br><br>a) ThyCyn2.0: This assembly is a chromosome-scale hybrid genome for the thylacine. It was generated by producing improved de novo contigs and short read-based scaffolds, which were then aligned to the Tasmanian devil reference genome mSarHar1.11. This assembly represents a substantial improvement in contiguity and completeness over both ThyCyn1.0 and UniMelb_Thylacine_Refassem_1. Assembly is hosted on NCBI under BioProject PRJNA354646.<br><br>b) ThyCyn2.0 annotation: Associated with ThyCyn2.0, we have produced a set of homology-based gene annotations using a gene model liftover procedure (see Feigin et al. 2022 for details). Briefly, exons from the Tasmanian devil genome RefSeq annotation were aligned to the thylacine assembly and gene models were created by linking exons together, filtering for those with preserved the intron-exon structure of the reference devil annotation (with an allowable distance scaling factor of 4).<br><br>
DOI: 10.26188/19351607.v3
title: UniMelb Thylacine Genomics Repository

description: <br><br>This FigShare repository contains genomic datasets for the Thylacine Genomics Project at the University of Melbourne (VIC, Australia). Currently 4 files arising from 2 publications are hosted on this repository. All assemblies arise from NCBI BioSample SAMN06049672<br><br>1). Feigin et al. 2018: Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore [https://www.nature.com/articles/s41559-017-0417-y]<br><br>a) ThyCyn1.0: This assembly is the first de novo whole-genome assembly for the thylacine. It is a contig-level assembly and thus contains no scaffolds. It was generated from short insert paired-end reads (https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=354646). Sequencing and data pre-processing strategy are discussed in the methods of Feigin et al. 2018. This assembly was used exclusively to estimate genome size and G+C content of the thylacine genome.<br><br>b) UniMelb_Thylacine_Refassem_1/GCA_007646695.1: Because of the highly-fragmentary nature (low N50) of ThyCyn1.0, UniMelb_Thylacine_Refassem_1 was generated to perform all evolutionary analyses detailed in Feigin et al. 2018. UniMelb_Thylacine_Refassem_1 was generated by mapping thylacine reads against the repeatmasked version of the previous Tasmanian devil draft genome Devil_ref v7.0 and generating reference-guided scaffolds. This is not a complete genome assembly, as it is composed only of non-repetitive genomic regions and does not include indel differences between Thylacine and devil. This was done to preserve the coordinate systems between thylacine and devil, permitting the use of the already-existing Tasmanian devil gene annotations. See methods of Feigin et al. 2018 for details. Assembly is hosted on NCBI under BioProject PRJNA354646.<br><br> 2) Feigin et al. 2022: A chromosome-scale hybrid genome assembly of the extinct Tasmanian tiger (Thylacinus cynocephalus) [https://www.biorxiv.org/content/10.1101/2022.03.02.482690v1.full]<br><br>a) ThyCyn2.0: This assembly is a chromosome-scale hybrid genome for the thylacine. It was generated by producing improved de novo contigs and short read-based scaffolds, which were then aligned to the Tasmanian devil reference genome mSarHar1.11. This assembly represents a substantial improvement in contiguity and completeness over both ThyCyn1.0 and UniMelb_Thylacine_Refassem_1. Assembly is hosted on NCBI under BioProject PRJNA354646.<br><br>b) ThyCyn2.0 annotation: Associated with ThyCyn2.0, we have produced a set of homology-based gene annotations using a gene model liftover procedure (see Feigin et al. 2022 for details). Briefly, exons from the Tasmanian devil genome RefSeq annotation were aligned to the thylacine assembly and gene models were created by linking exons together, filtering for those with preserved the intron-exon structure of the reference devil annotation (with an allowable distance scaling factor of 4).<br><br>