cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22002665
title: Genetic architecture for skeletal muscle glycolytic potential in Chinese Erhualian pigs revealed by a genome-wide association study using 1.4M SNP array

description: Muscle glycolytic potential (GP) is a key factor affecting multiple meat quality traits. It is calculated based on the contents of residual glycogen and glucose (RG), glucose-6-phosphate (G6P), and lactate (LAT) contents in muscle. However, the genetic basis of glycolytic metabolism in skeletal muscle of pigs remains poorly understood. With a history of more than 400 years and some unique characteristics, the Erhualian pig is called the "giant panda" in the world's pig species by Chinese animal husbandry. Here, we performed a genome-wide association study (GWAS) using 1.4M single nucleotide polymorphisms (SNPs) chips for longissimus RG, G6P, LAT, and GP levels in 301 purebred Erhualian pigs. We found that the average GP value of Erhualian was unusually low (68.09 µmol/g), but the variation was large (10.4–112.7 µmol/g). The heritability estimates for the four traits ranged from 0.16-0.32. In total, our GWAS revealed 31 quantitative trait loci (QTLs), including 8 for RG, 9 for G6P, 9 for LAT, 5 for GP. Of these loci, 8 were genome-wide significant (<em>P</em> &lt; 3.8×10-7), and 6 loci were common to two or three traits. Multiple promising candidate genes such as <em>FTO</em>, <em>MINPP1</em>, <em>RIPOR2</em>,<em> SCL8A3</em>, <em>LIFR</em> and <em>SRGAP1</em> were identified. The genotype combinations of the 5 GP-associated SNPs also showed significant effect on other meat quality traits. These results not only provide insights into the genetic architecture of GP related traits in Erhualian, but also are useful for pig breeding programs involving this breed.
DOI: 10.6084/m9.figshare.22002665.v1
title: Genetic architecture for skeletal muscle glycolytic potential in Chinese Erhualian pigs revealed by a genome-wide association study using 1.4M SNP array

description: Muscle glycolytic potential (GP) is a key factor affecting multiple meat quality traits. It is calculated based on the contents of residual glycogen and glucose (RG), glucose-6-phosphate (G6P), and lactate (LAT) contents in muscle. However, the genetic basis of glycolytic metabolism in skeletal muscle of pigs remains poorly understood. With a history of more than 400 years and some unique characteristics, the Erhualian pig is called the "giant panda" in the world's pig species by Chinese animal husbandry. Here, we performed a genome-wide association study (GWAS) using 1.4M single nucleotide polymorphisms (SNPs) chips for longissimus RG, G6P, LAT, and GP levels in 301 purebred Erhualian pigs. We found that the average GP value of Erhualian was unusually low (68.09 µmol/g), but the variation was large (10.4–112.7 µmol/g). The heritability estimates for the four traits ranged from 0.16-0.32. In total, our GWAS revealed 31 quantitative trait loci (QTLs), including 8 for RG, 9 for G6P, 9 for LAT, 5 for GP. Of these loci, 8 were genome-wide significant (<em>P</em> &lt; 3.8×10-7), and 6 loci were common to two or three traits. Multiple promising candidate genes such as <em>FTO</em>, <em>MINPP1</em>, <em>RIPOR2</em>,<em> SCL8A3</em>, <em>LIFR</em> and <em>SRGAP1</em> were identified. The genotype combinations of the 5 GP-associated SNPs also showed significant effect on other meat quality traits. These results not only provide insights into the genetic architecture of GP related traits in Erhualian, but also are useful for pig breeding programs involving this breed.
DOI: 10.5517/ccdc.csd.cc2br35d
title: CCDC 2167153: Experimental Crystal Structure Determination

description: Related Article: Saravanan Kandasamy, George F.S. Whitehead, Iñigo J. Vitórica-Yrezábal, John M. Gardiner|2023|Carbohydr.Res.|524|108744|doi:10.1016/j.carres.2023.108744
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.cc2b7st6
title: CCDC 2152448: Experimental Crystal Structure Determination

description: Related Article: Neha U. Parsekar,  Venkatesha R. Hathwar,  Kedar U. Narvekar,  Bikshandarkoil R. Srinivasan|2022|J.Coord.Chem.|75|1396|doi:10.1080/00958972.2022.2100989
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.cc2b7sx9
title: CCDC 2152451: Experimental Crystal Structure Determination

description: Related Article: Neha U. Parsekar,  Venkatesha R. Hathwar,  Kedar U. Narvekar,  Bikshandarkoil R. Srinivasan|2022|J.Coord.Chem.|75|1396|doi:10.1080/00958972.2022.2100989
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.cc2b7sv7
title: CCDC 2152449: Experimental Crystal Structure Determination

description: Related Article: Neha U. Parsekar,  Venkatesha R. Hathwar,  Kedar U. Narvekar,  Bikshandarkoil R. Srinivasan|2022|J.Coord.Chem.|75|1396|doi:10.1080/00958972.2022.2100989
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.cc2b7syb
title: CCDC 2152452: Experimental Crystal Structure Determination

description: Related Article: Neha U. Parsekar,  Venkatesha R. Hathwar,  Kedar U. Narvekar,  Bikshandarkoil R. Srinivasan|2022|J.Coord.Chem.|75|1396|doi:10.1080/00958972.2022.2100989
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.cc2btlc4
title: CCDC 2169546: Experimental Crystal Structure Determination

description: Related Article: Zhi‐Chao Hu, Jing‐Jing Cui, Zhi‐Bing Dong|2022|Eur.J.Org.Chem.|2022|e202201075|doi:10.1002/ejoc.202201075
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.cc2bttrr
title: CCDC 2169775: Experimental Crystal Structure Determination

description: Related Article: Kriti Pathak, Shivankan Mishra, Subhash Bairagi, B. Rajeshwaree, Arnab Dutta, Sundargopal Ghosh|2023|Organometallics|42|133|doi:10.1021/acs.organomet.2c00421
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.cc29cq0f
title: CCDC 2126414: Experimental Crystal Structure Determination

description: Related Article: Yan-Ping Jiao,  Wen-Yan Zhou,  Hao-Yu Shi,  Ai-Quan Jia,  Qian-Feng Zhang|2022|J.Coord.Chem.|75|764|doi:10.1080/00958972.2022.2081079
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.cc29cq1g
title: CCDC 2126415: Experimental Crystal Structure Determination

description: Related Article: Yan-Ping Jiao,  Wen-Yan Zhou,  Hao-Yu Shi,  Ai-Quan Jia,  Qian-Feng Zhang|2022|J.Coord.Chem.|75|764|doi:10.1080/00958972.2022.2081079
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.cc29cq2h
title: CCDC 2126416: Experimental Crystal Structure Determination

description: Related Article: Yan-Ping Jiao,  Wen-Yan Zhou,  Hao-Yu Shi,  Ai-Quan Jia,  Qian-Feng Zhang|2022|J.Coord.Chem.|75|764|doi:10.1080/00958972.2022.2081079
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.cc29cq3j
title: CCDC 2126417: Experimental Crystal Structure Determination

description: Related Article: Yan-Ping Jiao,  Wen-Yan Zhou,  Hao-Yu Shi,  Ai-Quan Jia,  Qian-Feng Zhang|2022|J.Coord.Chem.|75|764|doi:10.1080/00958972.2022.2081079
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.cc29cq4k
title: CCDC 2126418: Experimental Crystal Structure Determination

description: Related Article: Yan-Ping Jiao,  Wen-Yan Zhou,  Hao-Yu Shi,  Ai-Quan Jia,  Qian-Feng Zhang|2022|J.Coord.Chem.|75|764|doi:10.1080/00958972.2022.2081079
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.cc29cq6m
title: CCDC 2126420: Experimental Crystal Structure Determination

description: Related Article: Yan-Ping Jiao,  Wen-Yan Zhou,  Hao-Yu Shi,  Ai-Quan Jia,  Qian-Feng Zhang|2022|J.Coord.Chem.|75|764|doi:10.1080/00958972.2022.2081079
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.cc2b7qkw
title: CCDC 2152378: Experimental Crystal Structure Determination

description: Related Article: Yan-Ping Jiao,  Wen-Yan Zhou,  Hao-Yu Shi,  Ai-Quan Jia,  Qian-Feng Zhang|2022|J.Coord.Chem.|75|764|doi:10.1080/00958972.2022.2081079
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.cc29cq9q
title: CCDC 2126423: Experimental Crystal Structure Determination

description: Related Article: Yan-Ping Jiao,  Wen-Yan Zhou,  Hao-Yu Shi,  Ai-Quan Jia,  Qian-Feng Zhang|2022|J.Coord.Chem.|75|764|doi:10.1080/00958972.2022.2081079
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: 10.6084/m9.figshare.21971945.v2
title: material_fse23.zip

description: anonymous dataset
DOI: 10.5281/zenodo.7600250
title: Dataset - In-situ amplification of spin echoes within a kinetic inductance parametric amplifier

description: Raw data and analysis for arXiv:2211.11333
DOI: 10.5281/zenodo.7596979
title: Dataset - In-situ amplification of spin echoes within a kinetic inductance parametric amplifier

description: Raw data and analysis for arXiv:2211.11333
DOI: 10.6084/m9.figshare.21995438.v1
title: LncRNA of Chinese sturgeon

description: The LncRNAs identified in Chinese sturgeon
DOI: 10.5281/zenodo.6774693
title: miR-126 promotes M1 to M2 macrophage phenotype switching via VEGFA and KLF4

description: <strong>Background. </strong>Macrophage polarization and microRNA play crucial roles in the development of atherosclerosis (AS). The M1 macrophage phenotype contributes to the formation of plaques, while the M2 macrophage phenotype resolves inflammation and promotes tissue repair. MiR-126 has been found to play a role in regulating macrophage polarization in the context of AS. However, the exact mechanism of miR-126 requires further research. <strong>Methods.</strong> The foam cell model was established by stimulating THP-1 with oxidized low-density lipoprotein (ox-LDL). We transfected foam cells with miR-126 mimic and its negative control. The transfection of miR-126 was implemented by riboFECT CP transfection kit. The levels of miR-126 and M1/M2 associated genes in foam cells were quantified using reverse transcription-quantitative PCR (RT-qPCR). Additionally, the expressions of CD86<sup>+</sup> and CD206<sup>+</sup> cells in foam cells were determined by flow cytometry. Western blotting and RT-qPCR were used to determine the protein and mRNA levels of the vascular endothelial growth factor A (VEGFA) and the transcriptional regulator Krüppel-like factor 4 (KLF4), respectively. Additionally, we detected endothelial cell migration after co-culturing endothelial cells and macrophages. MG-132 was used to indirectly activate the expression of VEGFA, and the expression of KLF4 was also evaluated. <strong>Results. </strong>The activation of apoptosis and production of foam cells were boosted by the addition of ox-LDL. We transfected foam cells with miR-126 mimic and its negative control and observed that miR-126 greatly suppressed foam cell development and inhibited phagocytosis. Moreover, it caused pro-inflammatory M1 macrophages to switch to the anti-inflammatory M2 phenotype. This was reflected by the increase in anti-inflammatory gene expression and the decrease in pro-inflammatory gene expression. Additionally, miR-126 dramatically decreased the expressions of VEGFA and KLF4. The protein-protein interaction network analysis showed a significantly high correlation between miR-126, VEGFA, and KLF4. MiR-126 may also promote EC migration by activating macrophage PPAR γ expression and effectively suppressing macrophage inflammation. MG-132 indirectly activated the expression of VEGFA, and the expression of KLF4 also significantly increased, which indicates a direct or indirect relationship between VEGFA and KLF4. <strong>Conclusion.</strong> Our study shows that miR-126 can reverse ox-LDL-mediated phagocytosis and apoptosis in macrophages. Consequently, the potential role of miR-126 was manifested in regulating macrophage function and promoting vascular endothelial migration.
DOI: 10.5281/zenodo.6730211
title: miR-126 promotes M1 to M2 macrophage phenotype switching via VEGFA and KLF4

description: <strong>Background. </strong>Macrophage polarization and microRNA play crucial roles in the development of atherosclerosis (AS). The M1 macrophage phenotype contributes to the formation of plaques, while the M2 macrophage phenotype resolves inflammation and promotes tissue repair. MiR-126 has been found to play a role in regulating macrophage polarization in the context of AS. However, the exact mechanism of miR-126 requires further research. <strong>Methods.</strong> The foam cell model was established by stimulating THP-1 with oxidized low-density lipoprotein (ox-LDL). We transfected foam cells with miR-126 mimic and its negative control. The transfection of miR-126 was implemented by riboFECT CP transfection kit. The levels of miR-126 and M1/M2 associated genes in foam cells were quantified using reverse transcription-quantitative PCR (RT-qPCR). Additionally, the expressions of CD86<sup>+</sup> and CD206<sup>+</sup> cells in foam cells were determined by flow cytometry. Western blotting and RT-qPCR were used to determine the protein and mRNA levels of the vascular endothelial growth factor A (VEGFA) and the transcriptional regulator Krüppel-like factor 4 (KLF4), respectively. Additionally, we detected endothelial cell migration after co-culturing endothelial cells and macrophages. MG-132 was used to indirectly activate the expression of VEGFA, and the expression of KLF4 was also evaluated. <strong>Results. </strong>The activation of apoptosis and production of foam cells were boosted by the addition of ox-LDL. We transfected foam cells with miR-126 mimic and its negative control and observed that miR-126 greatly suppressed foam cell development and inhibited phagocytosis. Moreover, it caused pro-inflammatory M1 macrophages to switch to the anti-inflammatory M2 phenotype. This was reflected by the increase in anti-inflammatory gene expression and the decrease in pro-inflammatory gene expression. Additionally, miR-126 dramatically decreased the expressions of VEGFA and KLF4. The protein-protein interaction network analysis showed a significantly high correlation between miR-126, VEGFA, and KLF4. MiR-126 may also promote EC migration by activating macrophage PPAR γ expression and effectively suppressing macrophage inflammation. MG-132 indirectly activated the expression of VEGFA, and the expression of KLF4 also significantly increased, which indicates a direct or indirect relationship between VEGFA and KLF4. <strong>Conclusion.</strong> Our study shows that miR-126 can reverse ox-LDL-mediated phagocytosis and apoptosis in macrophages. Consequently, the potential role of miR-126 was manifested in regulating macrophage function and promoting vascular endothelial migration.
DOI: 10.5281/zenodo.7601487
title: Energy Consumption Due To Test Quality: State of Affairs, Impacts, and Ways Forward

description: This replication package contains data and scripts used in <strong>"Energy Consumption Due To Test Quality: State of Affairs, Impacts, and Ways Forward"</strong> For details, please read README
DOI: 10.6084/m9.figshare.21995438.v2
title: LncRNA prediction of Chinese sturgeon

description: The LncRNAs identified in Chinese sturgeon
DOI: 10.6084/m9.figshare.21995438.v3
title: LncRNA prediction of Chinese sturgeon

description: The LncRNAs identified in Chinese sturgeon
DOI: 10.6084/m9.figshare.21995213.v1
title: Files for Main Figure 5

description: Files for generating main figure 5 <br> 1. 3_UTR: locations of 3'UTR of genes 2. 5_UTR: locations of 5'UTR of genes 3. Sensing_gene_TE_cor_GSVA_lasTEq: Correlation results between DNA-RNA sensing genes and TE quantified by lasTEq 4. Sensing_gene_TE_cor_GSVA_telescope: Correlation results between DNA-RNA sensing genes and TE quantified by telescope 5. GSVA_TCGA_COAD_sensing_gene: GSVA scores calculated for DNA-RNA sensing genes 6. HM450_hg38_CpG_probes: Information about HM450 CpG probes in hg38 7. intergenic_TE_gene_5kb: Correlation results between intergenic TEs and +/- 5kb genes 8. lasTEq_TPM_paired: TE TPM counts quantified by lasTEq for 26 paired TCGA-COAD samples 9. telescope_TPM_paired: TE TPM counts quantified by telescope for 26 paired TCGA-COAD samples 10. TCGA_COAD_four_endpoint_survival: Survival data in four endpoints for TCGA-COAD patients 11. TCGA_COAD_gene: Gene TPM expression for TCGA-COAD patients 12: TCGA_COAD_methylation450: Methylation data in HM450 CpG probes represented as beta values for TCGA-COAD 13: TCGA_COAD_paired_samples: Information about paired samples in TCGA-COAD cohort 14: trinucleotide_mutational_profile: Summary of mutational profile in trinucleotide context in TCGA-COAD patients 15: TCGA_COAD_TE_exp_lasTEq: TE expression of full TCGA-COAD cohort using lasTEq 16: TCGA_COAD_TE_exp_telescope: TE expression of full TCGA-COAD cohort using telescope
DOI: 10.6084/m9.figshare.21995438.v4
title: LncRNA prediction of Chinese sturgeon

description: The LncRNAs identified in Chinese sturgeon
DOI: 10.48505/nims.3857
title: A material dictionary database to extract information on permanent magnets from scientific articles

description: In this study, we developed a new information extraction method using a material dictionary database (MDDB), which parses scientific articles and collects related phrases from various ex-pressions. We used magnetic properties as an illustrative case to analyze the working of the proposed system. Structured terms comprising sub-phrases, tagged words, and their relationships enabled automatic annotation and information extraction. The MDDB was constructed on a pre-built knowledge base that includes information categories and related keywords. These cat-egories can be hierarchically structured and flexibly updated to extract a wide range of information on the associations between magnetic materials and properties along with the measurement systems used, structural analyses performed, and theoretical foundations. Herein, we propose preliminary rule-based phrase collection methods and label pattern extraction for phrases that can easily add new structured terms. We found 1,136 new phrases by label pattern-matching that enabled more related expressions to be retrieved from the text and enhanced the information extraction’s accuracy. Approximately 350 relationships among the material types, properties, and values were extracted from the manually modified annotations of 40 articles on permanent magnets. Our method can be applied to other research domains and can be used by such disciplines to build knowledge bases for any topic in their field.
DOI: 10.6084/m9.figshare.21995438.v5
title: LncRNA prediction of Chinese sturgeon

description: The LncRNAs identified in Chinese sturgeon
DOI: 10.6084/m9.figshare.21995438.v6
title: LncRNA prediction of Chinese sturgeon

description: The LncRNAs identified in Chinese sturgeon
DOI: 10.3886/e178821
title: Arrhythmia spontaneous reporting system database analysis

description: Database analysis on arrhythmia and antidementia drugs.
DOI: 10.3886/e178821v1
title: Arrhythmia spontaneous reporting system database analysis

description: Database analysis on arrhythmia and antidementia drugs.
DOI: 10.6084/m9.figshare.22002797.v1
title: Early Neoarchean metavolcanic rocks from Jiaobei terrane, North China Craton

description: Zircon U-Pb isotopic dating data of early Neoarchean metavolcanic rocks from Jiaobei terrane, North China Craton