cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10851280
title: Psychological empowerment of politically empowered Saudi women

description: This is data for the study entitled "Psychological empowerment of politically empowered Saudi women". The importance of the research stems from its examination of politically women’s empowerment, especially in a society such as that in Saudi Arabia; it is a country with very few rights granted for women according to The Global Gender Gap Index. Being recently aware of the need of women’s political empowerment, Saudi Arabia launched some of the decisions as the participation of women as voters and candidates for the first time in municipal councils in 2015.
DOI: 10.5517/ccdc.csd.cc2fsq21
title: CCDC 2258073: Experimental Crystal Structure Determination

description: Related Article: Xing Peng, Shaonan Liu, Yuting Zhang, Jun Xu, Qiong Gu|2024|Bioorg.Chem.|145|107253|doi:10.1016/j.bioorg.2024.107253
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.cc2g5bxx
title: CCDC 2269259: Experimental Crystal Structure Determination

description: Related Article: Xing Peng, Shaonan Liu, Yuting Zhang, Jun Xu, Qiong Gu|2024|Bioorg.Chem.|145|107253|doi:10.1016/j.bioorg.2024.107253
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.cc2g5byy
title: CCDC 2269260: Experimental Crystal Structure Determination

description: Related Article: Xing Peng, Shaonan Liu, Yuting Zhang, Jun Xu, Qiong Gu|2024|Bioorg.Chem.|145|107253|doi:10.1016/j.bioorg.2024.107253
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.cc2gq9wd
title: CCDC 2285564: Experimental Crystal Structure Determination

description: Related Article: Haibo Yao, Lige Qiao, Lequn Yuan, Xueyin Luan, Yunjun Shen, Yuzhen Zhang, Liang Zhou, Hedong Bian|2024|J.Mater.Chem.C|12|4473|doi:10.1039/D4TC00081A
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.10851279
title: Psychological empowerment of politically empowered Saudi women

description: This is data for the study entitled "Psychological empowerment of politically empowered Saudi women". The importance of the research stems from its examination of politically women’s empowerment, especially in a society such as that in Saudi Arabia; it is a country with very few rights granted for women according to The Global Gender Gap Index. Being recently aware of the need of women’s political empowerment, Saudi Arabia launched some of the decisions as the participation of women as voters and candidates for the first time in municipal councils in 2015.
DOI: 10.6084/m9.figshare.25183793
title: Reference transcriptome of Leucetta chagosensis

description: De novo transcriptome assembly was carried out using Trinity (Haas, et al. 2013). Transcripts with 90% sequence similarity were clustered and the longest representative contigs (&gt; 300bp) were retained. Isoforms with the highest combined IsoPct or longest length were retained for each transcript to generate a reference transcriptome. Isoforms with zero isoform percentage (IsoPct) were removed.Peptides were predicted using the Transdecoder package in Trinity. Non-redundant set (1 gene = 1 peptide) was generated through peptide selection based on sequence length and type.
DOI: 10.6084/m9.figshare.25183793.v1
title: Reference transcriptome of Leucetta chagosensis

description: De novo transcriptome assembly was carried out using Trinity (Haas, et al. 2013). Transcripts with 90% sequence similarity were clustered and the longest representative contigs (&gt; 300bp) were retained. Isoforms with the highest combined IsoPct or longest length were retained for each transcript to generate a reference transcriptome. Isoforms with zero isoform percentage (IsoPct) were removed.Peptides were predicted using the Transdecoder package in Trinity. Non-redundant set (1 gene = 1 peptide) was generated through peptide selection based on sequence length and type.
DOI: 10.6084/m9.figshare.19521505.v1
title: Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site

description: The internal ribosome entry site (IRES) RNA of bovine viral diarrhoea virus (BVDV), an economically significant <i>Pestivirus</i>, is required for the cap-independent translation of viral genomic RNA. Thus, it is essential for viral replication and pathogenesis. We applied a combination of high-throughput biochemical RNA structure probing (SHAPE-MaP) and <i>in silico</i> modelling approaches to gain insight into the secondary and tertiary structures of BVDV IRES RNA. Our study demonstrated that BVDV IRES RNA in solution forms a modular architecture composed of three distinct structural domains (I–III). Two regions within domain III are represented in tertiary interactions to form an H-type pseudoknot. Computational modelling of the pseudoknot motif provided a fine-grained picture of the tertiary structure and local arrangement of helices in the BVDV IRES. Furthermore, comparative genomics and consensus structure predictions revealed that the pseudoknot is evolutionarily conserved among many <i>Pestivirus</i> species. These studies provide detailed insight into the structural arrangement of BVDV IRES RNA H-type pseudoknot and encompassing motifs that likely contribute to the optimal functionality of viral cap-independent translation element.
DOI: 10.6084/m9.figshare.21603033.v12
title: Inhibition of mitochondrial complex III or dihydroorotate dehydrogenase (DHODH) triggers formation of poly(A)<sup>+</sup> RNA foci adjacent to nuclear speckles following activation of ATM (ataxia telangiectasia mutated)

description: Intracellular and intercellular signalling networks play an essential role in optimizing cellular homoeostasis and are thought to be partly reflected in nuclear mRNA dynamics. However, the regulation of nuclear mRNA dynamics by intracellular and intercellular signals remains largely unexplored, and research tools are lacking. Through an original screening based on the mRNA metabolic mechanism, we discovered that eight well-known inhibitors cause significant nuclear poly(A)<sup>+</sup> RNA accumulation. Among these inhibitors, we discovered a new mRNA metabolic response in which the addition of antimycin A, an inhibitor of mitochondrial respiratory-chain complex III (complex III), resulted in a marked accumulation of poly(A)<sup>+</sup> RNA near the nuclear speckles. Furthermore, dihydroorotate dehydrogenase (DHODH) inhibitors, a rate-limiting enzyme in the intracellular <i>de novo</i> pyrimidine synthesis reaction that specifically exchanges electrons with complex III, also caused a remarkable accumulation of nuclear poly(A)<sup>+</sup> RNA adjacent to the nuclear speckles, which was abolished by extracellular uridine supply, indicating that the depletion of intracellular pyrimidine affects poly(A)<sup>+</sup> RNA metabolism. Further analysis revealed that ataxia telangiectasia mutated (ATM), a serine and threonine kinase and a master regulator of DNA double-strand break (DSB) and nucleolar stress, is required for this poly(A)<sup>+</sup> RNA nuclear accumulation phenomenon. This study reports new insights into novel aspects of nuclear poly(A)<sup>+</sup> RNA metabolism, especially the relationship between mitochondrial respiratory-chain functions, pyrimidine metabolism, and nuclear RNA metabolism.
DOI: 10.6084/m9.figshare.21665289.v8
title: Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics

description: Endothelial cells (ECs) comprise the lumenal lining of all blood vessels and are critical for the functioning of the cardiovascular system. Their phenotypes can be modulated by alternative splicing of RNA to produce distinct protein isoforms. To characterize the RNA and protein isoform landscape within ECs, we applied a long read proteogenomics approach to analyse human umbilical vein endothelial cells (HUVECs). Transcripts delineated from PacBio sequencing serve as the basis for a sample-specific protein database used for downstream mass-spectrometry (MS) analysis to infer protein isoform expression. We detected 53,863 transcript isoforms from 10,426 genes, with 22,195 of those transcripts being novel. Furthermore, the predominant isoform in HUVECs does not correspond with the accepted “reference isoform” 25% of the time, with vascular pathway-related genes among this group. We found 2,597 protein isoforms supported through unique peptides, with an additional 2,280 isoforms nominated upon incorporation of long-read transcript evidence. We characterized a novel alternative acceptor for endothelial-related gene CDH5, suggesting potential changes in its associated signalling pathways. Finally, we identified novel protein isoforms arising from a diversity of RNA splicing mechanisms supported by uniquely mapped novel peptides. Our results represent a high-resolution atlas of known and novel isoforms of potential relevance to endothelial phenotypes and function.
DOI: 10.5281/zenodo.10845700
title: TP-TR Benchmarks from Gen-T: Table Reclamation in Data Lakes

description: This benchmark suite was created and used in experiments of "Gen-T: Table Reclamation in Data Lakes", published in ICDE 2024. These three benchmarks were created to evaluate a new problem we propose called Table Reclamation.
DOI: 10.5281/zenodo.10845701
title: TP-TR Benchmarks from Gen-T: Table Reclamation in Data Lakes

description: This benchmark suite was created and used in experiments of "Gen-T: Table Reclamation in Data Lakes", published in ICDE 2024. These three benchmarks were created to evaluate a new problem we propose called Table Reclamation.
DOI: 10.5281/zenodo.10851336
title: Energy and forces annotated atomic structures of platinum using first-principles calculations

description: Dataset for training machine learning potential of platinum.

Detailed explanation of data generation is described in the preprint. below

Chun, H., Kang, J., Kang, D., Heo, J., Cho, H., Heo, J., … & Han, B. (2022). Tracking the 3d atomic structures during thermal treatment and catalytic activity of individual pt nanoparticles.. https://doi.org/10.21203/rs.3.rs-1441062/v1
DOI: 10.25814/evyj-4926
title: ABARES Fishery Status Reports map data: All Fisheries combined (ALLFSY): fishing intensity and maximum area fished, annual map data for 2010–2022.

description: This dataset presents maps of fishing intensity and maximum area fished of ocean waters of all Australian Government-managed fisheries combined (ALLFSY).

The data were prepared as part of the annual ABARES Fishery Status Reports series, which provides an independent evaluation of the biological and economic status of fish stocks managed solely or jointly by the Australian Government. The data were produced by ABARES from data supplied by the Australian Fisheries Management Authority (AFMA).

The data are presented annually, by calendar year. 

The data are polygon vector format, stored in an ESRI file geodatabase, prepared using ArcGIS Desktop ArcMap version 10.8. 

Fishing intensity is defined as the total catch within a given year, divided by the total area fished in square kilometres. Fishing intensity is presented as classified data in low, medium and high intensity classes. The data attributes include the class, the range of values in the class and the unit of measure. The classification used may vary from year to year, depending on a range of environmental and economic factors. 

Maximum area fished is defined as the maximum area within which fishing occurred during a given fishing season as polygon cells of one degree of longitude by one degree of latitude (approximately 111 kilometres x 111 kilometres). A cell is included if any fishing activity occurred anywhere within that one degree by one degree cell. Note that cells included in this dataset may also partially cover land.

The data supplied by AFMA were filtered to remove activity by fewer than five boats within the area of analysis in order to conform with AFMA’s Information Disclosure Policy (https://www.afma.gov.au/about/fisheries-management-policies/information-disclosure-fisheries-management-paper).
DOI: 10.26179/n2p5-6w03
title: A GIS dataset of bird nests mapped in the Windmill Islands by Frederique Olivier and Drew Lee during the 2002-2003 season
DOI: 10.6084/m9.figshare.25458247
title: Junco hyemalis subspecies analysis of song, genetic, and geographic data

description: The dark-eyed junco (<i>Junco hyemalis</i>) has experienced rapid phenotypic diversification, resulting in subspecies with distinct plumage that reside in partially overlapping regions. The learned songs of these subspecies might gradually accumulate changes, but if song is used for subspecies recognition during mate selection, song differences may facilitate reproductive isolation. Here, we use community-science recordings to explore subspecies-level song variation. We build a machine learning classifier to assess song distinguishability between subspecies. We find that the subspecies have significant song-feature differences. Notably, subspecies pairs with adjacent ranges that do not hybridize have more distinguishable songs and more evidence for genetic differentiation than pairs that do hybridize. Thus, song distinguishability appears to have some predictive power about which subspecies have reported sightings of hybrids, suggesting the possibility that song might reinforce certain subspecies boundaries more than others. Finally, we compare song variation to genetic and geographic data to characterize the evolutionary landscape of the dark-eyed junco. Weak geographic signal in the song and genetic data indicates that individuals who share a range might be more likely to share song characteristics and be genetically similar. Our machine learning analyses of dark-eyed junco songs demonstrates that song differences might be informative about the strength of reproductive boundaries between subspecies, since greater song distinguishability correlates with observed hybridization events and genetic differentiation.
DOI: 10.6084/m9.figshare.25458247.v1
title: Junco hyemalis subspecies analysis of song, genetic, and geographic data

description: The dark-eyed junco (<i>Junco hyemalis</i>) has experienced rapid phenotypic diversification, resulting in subspecies with distinct plumage that reside in partially overlapping regions. The learned songs of these subspecies might gradually accumulate changes, but if song is used for subspecies recognition during mate selection, song differences may facilitate reproductive isolation. Here, we use community-science recordings to explore subspecies-level song variation. We build a machine learning classifier to assess song distinguishability between subspecies. We find that the subspecies have significant song-feature differences. Notably, subspecies pairs with adjacent ranges that do not hybridize have more distinguishable songs and more evidence for genetic differentiation than pairs that do hybridize. Thus, song distinguishability appears to have some predictive power about which subspecies have reported sightings of hybrids, suggesting the possibility that song might reinforce certain subspecies boundaries more than others. Finally, we compare song variation to genetic and geographic data to characterize the evolutionary landscape of the dark-eyed junco. Weak geographic signal in the song and genetic data indicates that individuals who share a range might be more likely to share song characteristics and be genetically similar. Our machine learning analyses of dark-eyed junco songs demonstrates that song differences might be informative about the strength of reproductive boundaries between subspecies, since greater song distinguishability correlates with observed hybridization events and genetic differentiation.
DOI: 10.1594/pangaea.53243
title: Continuous thermosalinograph oceanography along POLARSTERN cruise track ANT-XII/2

description: Version 2, 2016-10-20
DOI: 10.1594/pangaea.326601
title: Continuous meteorological surface measurement during POLARSTERN cruise ANT-XII/2

description: Geocode DATE/TIME has centered values; geocode LATITUDE and LONGITUDE have instantaneous values at end of interval.
DOI: 10.1594/pangaea.56972
title: Relative abundance of diatoms in surface sediments of Lake Lama

description: The patterns of spatial variation of diatom assemblages from surface sediments in Lake Lama were quantified using a combined approach of ordination and geostatistics. The aims were (i) to estimate the amount of variation between diatom assemblages within the lake, (ii) to model the spatial variability of the diatom assemblages and their diversity, and (iii) to map the diatom distributions in the lake. A correspondence analysis (CA) separated the diatom assemblages into a planktonic and a periphytic group. Rheophilic taxa were found within the periphytic group. Variogram analysis showed that only the sample scores of the first CA axis and the Shannon diversity index were spatially structured. The range of spatial correlation was estimated to be 55 km for both variables. The diversity and, to a lesser extent, the sample scores had considerable small-scale variability of about 20 and 3%, respectively. Estimates of the first component of the CA and the Shannon index were derived using block-kriging. The maps of the estimates provided a basis for partitioning Lake Lama according to the spatial structures into an eastern and a western basin, a north–south connection between the basins, and a north–south directed tip at the far eastern end. It was shown that variation in diatom assemblages is mainly spatially structured at the catchment scale and that there is a considerable amount of variation at smaller scales. According to the modeled spatial distribution, the assemblages are most likely affected by the lake size, morphology, and the water and nutrient input introduced by rivers. This has to be taken into account when paleolimnological interpretations are drawn from records of complex lake systems like Lake Lama.
description: Supplement to: Kienel, Ulrike; Kumke, Thomas (2002): Combining ordination techniques and geostatistics to determine the patterns of diatom distributions at Lake Lama, Central Siberia. Journal of Paleolimnology, 28(2), 181-194
DOI: 10.1594/pangaea.56989
title: Plankton analysis from 10 m water depth of Lama Lake
DOI: 10.1594/pangaea.318311
title: Shipboard acoustic doppler current profiling during POLARSTERN cruise ANT-XII/2 (SAC ID 00488)

description: Absolute currents at hourly and 10m intervals. Raw data file can be found under doi:10.1594/PANGAEA.733532
DOI: 10.1594/pangaea.380818
title: Radiosonde PS33/11998 during POLARSTERN cruise ANT-XII/2 on 1994-11-24 10:05h

description: Height of tropopause 12036 m, precipitable water content 1.8417 cm
DOI: 10.1594/pangaea.380819
title: Radiosonde PS33/11999 during POLARSTERN cruise ANT-XII/2 on 1994-11-25 10:04h

description: Height of tropopause 11124 m, precipitable water content 0.6744 cm
DOI: 10.1594/pangaea.380820
title: Radiosonde PS33/12000 during POLARSTERN cruise ANT-XII/2 on 1994-11-26 10:07h

description: Height of tropopause 14959 m, precipitable water content 0.3754 cm
DOI: 10.1594/pangaea.380821
title: Radiosonde PS33/12001 during POLARSTERN cruise ANT-XII/2 on 1994-11-27 10:07h

description: Height of tropopause 12560 m, precipitable water content 0.4912 cm
DOI: 10.1594/pangaea.380822
title: Radiosonde PS33/12002 during POLARSTERN cruise ANT-XII/2 on 1994-11-28 10:04h

description: Height of tropopause 10555 m, precipitable water content 1.1048 cm
DOI: 10.1594/pangaea.380823
title: Radiosonde PS33/12003 during POLARSTERN cruise ANT-XII/2 on 1994-11-29 10:01h

description: Height of tropopause 10626 m, precipitable water content 1.4467 cm
DOI: 10.1594/pangaea.380824
title: Radiosonde PS33/12004 during POLARSTERN cruise ANT-XII/2 on 1994-11-30 09:56h

description: Height of tropopause 9536 m, precipitable water content 0.8668 cm
DOI: 10.1594/pangaea.380825
title: Radiosonde PS33/12005 during POLARSTERN cruise ANT-XII/2 on 1994-11-30 17:04h

description: Height of tropopause 9095 m, precipitable water content 1.1178 cm
DOI: 10.1594/pangaea.380826
title: Radiosonde PS33/12006 during POLARSTERN cruise ANT-XII/2 on 1994-12-01 10:02h

description: Height of tropopause 10580 m, precipitable water content 0.3202 cm
DOI: 10.1594/pangaea.380827
title: Radiosonde PS33/12007 during POLARSTERN cruise ANT-XII/2 on 1994-12-02 09:58h

description: Height of tropopause 10784 m, precipitable water content 0.3608 cm
DOI: 10.1594/pangaea.380828
title: Radiosonde PS33/12008 during POLARSTERN cruise ANT-XII/2 on 1994-12-03 09:58h

description: Height of tropopause 9736 m, precipitable water content 0.7523 cm
DOI: 10.1594/pangaea.380829
title: Radiosonde PS33/12009 during POLARSTERN cruise ANT-XII/2 on 1994-12-04 10:05h

description: Height of tropopause 7966 m, precipitable water content 0.9511 cm
DOI: 10.1594/pangaea.380830
title: Radiosonde PS33/12010 during POLARSTERN cruise ANT-XII/2 on 1994-12-05 10:00h

description: Height of tropopause 9477 m, precipitable water content 1.0376 cm
DOI: 10.1594/pangaea.380831
title: Radiosonde PS33/12011 during POLARSTERN cruise ANT-XII/2 on 1994-12-06 09:58h

description: Height of tropopause 9432 m, precipitable water content 0.8263 cm
DOI: 10.1594/pangaea.380832
title: Radiosonde PS33/12012 during POLARSTERN cruise ANT-XII/2 on 1994-12-07 10:00h

description: Height of tropopause 9852 m, precipitable water content 0.6701 cm
DOI: 10.1594/pangaea.380833
title: Radiosonde PS33/12013 during POLARSTERN cruise ANT-XII/2 on 1994-12-08 09:59h

description: Height of tropopause 9256 m, precipitable water content 0.8638 cm
DOI: 10.1594/pangaea.380834
title: Radiosonde PS33/12014 during POLARSTERN cruise ANT-XII/2 on 1994-12-09 09:58h

description: Height of tropopause 9422 m, precipitable water content 1.2486 cm
DOI: 10.1594/pangaea.380835
title: Radiosonde PS33/12015 during POLARSTERN cruise ANT-XII/2 on 1994-12-10 09:56h

description: Height of tropopause 9742 m, precipitable water content 1.1458 cm
DOI: 10.1594/pangaea.380836
title: Radiosonde PS33/12016 during POLARSTERN cruise ANT-XII/2 on 1994-12-11 09:53h

description: Height of tropopause 8919 m, precipitable water content 0.6206 cm
DOI: 10.1594/pangaea.380837
title: Radiosonde PS33/12017 during POLARSTERN cruise ANT-XII/2 on 1994-12-12 03:35h

description: Height of tropopause 9077 m, precipitable water content 0.7287 cm
DOI: 10.1594/pangaea.380838
title: Radiosonde PS33/12018 during POLARSTERN cruise ANT-XII/2 on 1994-12-13 03:35h

description: Height of tropopause 9044 m, precipitable water content 0.7243 cm
DOI: 10.1594/pangaea.380839
title: Radiosonde PS33/12019 during POLARSTERN cruise ANT-XII/2 on 1994-12-13 10:03h

description: Precipitable water content 0.3708 cm