cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23497564.v1
title: Association analysis of PMEL gene expression and single nucleotide polymorphism with plumage color in quail

description: To explore the relationship between PMEL gene and quail plumage color, to provide a reference for subsequent quail plumage color breeding. In this experiment, RT-qPCR technology was used to analyze the relative mRNA expression levels of Korean quail (maroon) and Beijing white quail embryos at different developmental stages. Two SNPs in PMEL gene were screened based on the RNA-Seq data of skin tissues of Korean quail and Beijing white quail during embryonic stage. The KASP technology was used for genotyping in the resource population and correlation analysis was carried out with the plumage color traits of quail. Finally, the bioinformatics technology was used to predict the effects of these two SNPs on the structure and function of the encoded protein. The results showed that the expression levels of PMEL gene during the embryonic development of Beijing white quail were extremely significantly higher than that of Korean quail (<i>p</i> &lt; 0.01). The frequency distribution of the three genotypes (AA, AB, and BB) of the Beijing white quail at the c. 1030C &gt; T and c. 1374A &gt; G mutation sites were extremely significantly different from that of the Korean quail (<i>p</i> &lt; 0.01). And there was a significant correlation between the c. 1374A &gt; G mutation site with white plumage phenotype. Bioinformatics analysis showed that SNP1 (c. c1030t) located in exon 6 was a harmful mutation site, and SNP2 (c. a1374g) located in exon 7 was a neutral mutation site. Protein conservation prediction showed that the coding protein P344S site caused by SNP1 (c. c1030t) site and the coding protein I458M site caused by SNP2 (c. g2129a) site were non-conservative sites. The results of this experiment showed that the PMEL gene was associated with the plumage color traits of quail and could be used as a candidate gene for studying the plumage color of quail.
DOI: 10.6084/m9.figshare.16681831
title: Results of area distortion for 1M sample points on projection planes

description: Root link of the proposed FWD-GCA-based metric: 10.6084/m9.figshare.15020151.<br><br>Results of area distortions of traditional differential-based (10.6084/m9.figshare.15022074), GCA and the proposed FWD-GCA (10.6084/m9.figshare.15022092) metrics for 1 million sample points (10.6084/m9.figshare.15035457).<br>These results are generated by 'eval_1M.jl' in 10.6084/m9.figshare.15022095, and compressed as ZIP files.<br>Unzip all files to a folder named 'img_data_area', and use 'plot_1M.py' and unzipped CSV format for further plotting (results of plots: 10.6084/m9.figshare.16681909).
DOI: 10.6084/m9.figshare.21400362.v1
title: Additional file 1 of Multi-omics reveals the key and specific miRNA-mRNA modules underlying salt tolerance in wild emmer wheat (Triticum dicoccoides L.)

description: Additional file 1: Table S1. Details of identified miRNAs (conserved/known and novel). Table S2. Differentially expressed miRNAs of two genotypes at each treatment time point. Table S3. Details of target genes of differentially expressed miRNAs. Table S4. Differentially expressed mRNAs of two genotypes at each treatment time point. Table S5. Coherent miRNA-mRNA pairs of two genotypes at each treatment time point. Table S6. Salt tolerance-related miRNA-mRNA pairs. Table S7. Summary of co-expression network. Table S8. GO enrichment of genes co-expressed with salt tolerance-related target genes. Table S9. Primers used in this study.
DOI: 10.6084/m9.figshare.23497589
title: iso- and OH-GDGTs data in 74 surface sediment from 65 West China lakes

description:  iso- and OH-GDGTs data in 74 surface sediment from 65 West China lakes.
DOI: 10.6084/m9.figshare.12487472.v1
title: Additional file 1 of Computational identification and characterization of glioma candidate biomarkers through multi-omics integrative profiling

description: Additional file 1: Table S1. 15,176 genes’ RNA expression levels across 30 normal human tissues. Table S2. Tissue specificity τ values and maximum expression levels of the top 100 brain-specific protein-coding genes. Table S3.PRKCG-like genes and their annotations.
DOI: 10.6084/m9.figshare.21400332
title: Additional file 1 of NOVA1 promotes NSCLC proliferation and invasion by activating Wnt/β-catenin signaling

description: Additional file 1: Supplementary material. Original images of WB-1. Original images of WB-2.
DOI: 10.6084/m9.figshare.16681864
title: Results of angular distortion for 200k sample points

description: Root link of the proposed FWD-GCA-based metric: 10.6084/m9.figshare.15020151.<br><br>Results of angular distortions of traditional differential-based (10.6084/m9.figshare.15022074), GCA and the proposed FWD-GCA (10.6084/m9.figshare.15022092) metrics for 200k sample points (10.6084/m9.figshare.15022071) on unit sphere.<br>Results of area distortions are also provided at 10.6084/m9.figshare.16681867.
DOI: 10.6084/m9.figshare.16681867
title: Results of area distortion for 200k sample points

description: Root link of the proposed FWD-GCA-based metric: 10.6084/m9.figshare.15020151.<br><br>Results of area distortions of traditional differential-based (10.6084/m9.figshare.15022074), GCA and the proposed FWD-GCA (10.6084/m9.figshare.15022092) metrics for 200k sample points (10.6084/m9.figshare.15022071) on unit sphere.<br>Results of angular distortions are also provided at 10.6084/m9.figshare.16681864.
DOI: 10.11588/data/muxyry
title: Spatial resolution of HIV-1 post-entry steps in resting CD4 T cells [data]

description: #enter description, e.g. paper abstract
DOI: 10.6084/m9.figshare.16681745
title: Additional file 2 of Screening for differentially expressed circRNAs in ischemic stroke by RNA sequencing

description: Additional file 2.
DOI: 10.6084/m9.figshare.12487472
title: Additional file 1 of Computational identification and characterization of glioma candidate biomarkers through multi-omics integrative profiling

description: Additional file 1: Table S1. 15,176 genes’ RNA expression levels across 30 normal human tissues. Table S2. Tissue specificity τ values and maximum expression levels of the top 100 brain-specific protein-coding genes. Table S3.PRKCG-like genes and their annotations.
DOI: 10.6084/m9.figshare.21400362
title: Additional file 1 of Multi-omics reveals the key and specific miRNA-mRNA modules underlying salt tolerance in wild emmer wheat (Triticum dicoccoides L.)

description: Additional file 1: Table S1. Details of identified miRNAs (conserved/known and novel). Table S2. Differentially expressed miRNAs of two genotypes at each treatment time point. Table S3. Details of target genes of differentially expressed miRNAs. Table S4. Differentially expressed mRNAs of two genotypes at each treatment time point. Table S5. Coherent miRNA-mRNA pairs of two genotypes at each treatment time point. Table S6. Salt tolerance-related miRNA-mRNA pairs. Table S7. Summary of co-expression network. Table S8. GO enrichment of genes co-expressed with salt tolerance-related target genes. Table S9. Primers used in this study.
DOI: 10.5281/zenodo.10705460
title: Conformational defects DB PRMen
DOI: 10.5281/zenodo.10705461
title: Conformational defects DB PRMen
DOI: 10.6084/m9.figshare.21400332.v1
title: Additional file 1 of NOVA1 promotes NSCLC proliferation and invasion by activating Wnt/β-catenin signaling

description: Additional file 1: Supplementary material. Original images of WB-1. Original images of WB-2.
DOI: 10.6084/m9.figshare.25287916
title: Data Yield and Climate

description: <b>Early coupling of vapour pressure deficit and chilling temperatures extreme in mid-autumn leads to phenology and yield changes in food crops</b>
DOI: 10.6084/m9.figshare.25287916.v1
title: Data Yield and Climate

description: <b>Early coupling of vapour pressure deficit and chilling temperatures extreme in mid-autumn leads to phenology and yield changes in food crops</b>
DOI: 10.6084/m9.figshare.11439030
title: BST2 suppresses porcine epidemic diarrhea virus replication by targeting and degrading virus nucleocapsid protein with selective autophagy

description: Interferon-induced BST2 (bone marrow stromal cell antigen 2) inhibits viral replication by tethering enveloped virions to the cell surface to restrict viral release and by inducing the NFKB-dependent antiviral immune response. However, the mechanism by which BST2 uses the selective autophagy pathway to inhibit viral replication is poorly understood. In this study, we showed that BST2 expression was significantly increased during porcine epidemic diarrhea virus (PEDV) infection of Vero cells by IRF1 targeting its promoter. We also showed that BST2 suppressed PEDV replication by binding and degrading the PEDV-encoded nucleocapsid (N) protein. The downregulation of N protein was blocked by macroautophagy/autophagy inhibitors but not a proteasome inhibitor, implying that the N protein was degraded via the selective autophagy pathway. Both the BST2 and N protein interacted with the E3 ubiquitin ligase MARCHF8/MARCH8 and the cargo receptor CALCOCO2/NDP52, and the ubiquitination of N protein was necessary for the degradation of N mediated by the BST2-MARCHF8 axis. The knockdown of MARCHF8 or ATG5 with small interfering RNAs blocked the selective autophagy pathway, rescued the protein abundance of PEDV N in 293T cells, and prevented the inhibition of PEDV replication by BST2 in Vero cells. Together, our data demonstrate the novel mechanism of BST2-mediated virus restriction, in which BST2 recruits MARCHF8 to catalyze the ubiquitination of the PEDV N protein. The ubiquitinated N protein is then recognized by CALCOCO2/NDP52, which delivers it to autolysosome for degradation through the selective autophagy pathway. <b>Abbreviations</b>: 3MA: 3-methyladenine; ATG: autophagy-related; Baf A1: bafilomycin A<sub>1</sub>; BST2: bone marrow stromal cell antigen 2; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CC: coiled-coil; ChIP: chromatin immunoprecipitation; Co-IP: co-immunoprecipitation; CQ: chloroquine; CT: cytoplasmic tail; DAPI: 4′,6-diamidino-2-phenylindole; GPI: glycosyl-phosphatidylinositol; hpi: hours post infection; IRF1: interferon regulatory factor 1; ISG: IFN-stimulated gene; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MARCHF8/MARCH8: membrane-associated ring-CH-type finger 8; MOI: multiplicity of infection; N protein: nucleocapsid protein; PED: porcine epidemic diarrhea; PEDV: porcine epidemic diarrhea virus; RT: room temperature; siRNA: small interfering RNA; STAT: signal transducer and activator of transcription; TCID<sub>50</sub>: 50% tissue culture infectious doses; TM: transmembrane.
DOI: 10.6084/m9.figshare.11439030.v1
title: BST2 suppresses porcine epidemic diarrhea virus replication by targeting and degrading virus nucleocapsid protein with selective autophagy

description: Interferon-induced BST2 (bone marrow stromal cell antigen 2) inhibits viral replication by tethering enveloped virions to the cell surface to restrict viral release and by inducing the NFKB-dependent antiviral immune response. However, the mechanism by which BST2 uses the selective autophagy pathway to inhibit viral replication is poorly understood. In this study, we showed that BST2 expression was significantly increased during porcine epidemic diarrhea virus (PEDV) infection of Vero cells by IRF1 targeting its promoter. We also showed that BST2 suppressed PEDV replication by binding and degrading the PEDV-encoded nucleocapsid (N) protein. The downregulation of N protein was blocked by macroautophagy/autophagy inhibitors but not a proteasome inhibitor, implying that the N protein was degraded via the selective autophagy pathway. Both the BST2 and N protein interacted with the E3 ubiquitin ligase MARCHF8/MARCH8 and the cargo receptor CALCOCO2/NDP52, and the ubiquitination of N protein was necessary for the degradation of N mediated by the BST2-MARCHF8 axis. The knockdown of MARCHF8 or ATG5 with small interfering RNAs blocked the selective autophagy pathway, rescued the protein abundance of PEDV N in 293T cells, and prevented the inhibition of PEDV replication by BST2 in Vero cells. Together, our data demonstrate the novel mechanism of BST2-mediated virus restriction, in which BST2 recruits MARCHF8 to catalyze the ubiquitination of the PEDV N protein. The ubiquitinated N protein is then recognized by CALCOCO2/NDP52, which delivers it to autolysosome for degradation through the selective autophagy pathway. <b>Abbreviations</b>: 3MA: 3-methyladenine; ATG: autophagy-related; Baf A1: bafilomycin A<sub>1</sub>; BST2: bone marrow stromal cell antigen 2; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CC: coiled-coil; ChIP: chromatin immunoprecipitation; Co-IP: co-immunoprecipitation; CQ: chloroquine; CT: cytoplasmic tail; DAPI: 4′,6-diamidino-2-phenylindole; GPI: glycosyl-phosphatidylinositol; hpi: hours post infection; IRF1: interferon regulatory factor 1; ISG: IFN-stimulated gene; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MARCHF8/MARCH8: membrane-associated ring-CH-type finger 8; MOI: multiplicity of infection; N protein: nucleocapsid protein; PED: porcine epidemic diarrhea; PEDV: porcine epidemic diarrhea virus; RT: room temperature; siRNA: small interfering RNA; STAT: signal transducer and activator of transcription; TCID<sub>50</sub>: 50% tissue culture infectious doses; TM: transmembrane.
DOI: 10.6084/m9.figshare.7244630.v1
title: Preparation of Microcapsules of Slow-Release NPK Compound Fertilizer and the Release Characteristics

description: In this study, a novel type of slow-release fertilizer (SRF) was synthesized through lignin-based microcapsules. K2HPO4 and urea were coated by lignin and formaldehyde to prepare microcapsules of NPK compound SRF. The slow-release performance was measured by determining the NPK contents in water solution and soil column leaching. The release amounts of N, P and K after 5 days were 95.39, 95.28 and 96.75% in water, and 83.35, 96.62 and 90.75% in soil, respectively. The properties of SRF were analyzed by Fourier transform infrared spectroscopy, thermogravimetry and scanning electron microscopy. NPK release from the SRF was promoted by higher temperature and acid environment, but inhibited by alkaline environment. The first order kinetics equation provides the best correlation to describe nutrient release characteristics. The results indicated that SRF have good slow-release properties and are cost-saving and environment-friendly, and thus can efficiently improve the utilization efficiency of fertilizers in agricultural production.
DOI: 10.6084/m9.figshare.21400412
title: Additional file 6 of An asparagine metabolism-based classification reveals the metabolic and immune heterogeneity of hepatocellular carcinoma

description: Additional file 6. Table S3: Six established gene sets for predicting the patients' response to ICI therapy.
DOI: 10.5281/zenodo.8309135
title: Madrid Regional Elections Data Sets

description: This resource presents the data used in the construction of a Knowledge Graph following the SPEECH ontology (Social media Published Entities Exploitable aCross cHannels).
description: This work has been funded by the project SIGTRANS-UPM: Sistema de Información Geográfica interoperable y semánticamente enriquecido para el análisis y la gestión del TRANSporte público funded by MCIN/AEI/10.13039/501100011033 and by the European Union Next GenerationEU/PRTR.
DOI: 10.5281/zenodo.8309136
title: Madrid Regional Elections Data Sets

description: This resource presents the data used in the construction of a Knowledge Graph following the SPEECH ontology (Social media Published Entities Exploitable aCross cHannels).
description: This work has been funded by the project SIGTRANS-UPM: Sistema de Información Geográfica interoperable y semánticamente enriquecido para el análisis y la gestión del TRANSporte público funded by MCIN/AEI/10.13039/501100011033 and by the European Union Next GenerationEU/PRTR.
DOI: 10.6084/m9.figshare.11439033
title: LncRNA ANCR promotes hepatocellular carcinoma metastasis through upregulating HNRNPA1 expression

description: LncRNA ANCR plays important roles in the modulation of epithelial mesenchymal transition (EMT) and tumour metastasis in many tumours. However, the role of ANCR in regulating hepatocellular carcinoma (HCC) metastasis is still not known. The current study aims to investigate the underlying mechanism for tumour oncogenesis of ANCR in HCC metastasis. HCC cell proliferation and migration/invasion were measured by MTT and Transwell assays. Xenograft model was established to determine the effect of ANCR on HCC growth and metastasis. ChIP assay was used to detect the H3 and H4 histone acetylation levels at the ANCR promoter region. RNA pull-down and RIP assay was performed to analyse the relationship between ANCR and heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1). Dual-luciferase reporter gene assay was conducted to determine the interaction between ANCR and miR-140-3p. The results indicated that ANCR was highly expressed in HCC tissues and cells, which promoted the proliferation and migration/invasion of HCC cells. <i>In vivo</i> experiments showed interfering ANCR suppressed the growth and metastasis of HCC. H3/H4 histone acetylation levels at the ANCR promoter region were elevated in HCC tissues and cells, and interfering histone deacetylases 3 (HDAC3) significantly up-regulated ANCR expression. ANCR could bind to HNRNPA1, and promoted the expression of HNRNPA1 through regulating its degradation. In addition, ANCR upregulated the expression of HNRNPA1 through sponging miR-140-3p. Finally, we found that ANCR promoted the EMT and invasion/migration of HCC cells through regulating HNRNPA1. In conclusion, ANCR promoted HCC metastasis by upregulating HNRNPA1, inhibiting HNRNPA1 degradation and sponging miR-140-3p.
DOI: 10.6084/m9.figshare.16681723.v1
title: Additional file 4 of Elucidation of ligninolysis mechanism of a newly isolated white-rot basidiomycete Trametes hirsuta X-13

description: Additional file 4: The identified proteins from secretome of T. hirsuta X-13 in lignin-containing medium.
DOI: 10.6084/m9.figshare.16681726.v1
title: Additional file 5 of Elucidation of ligninolysis mechanism of a newly isolated white-rot basidiomycete Trametes hirsuta X-13

description: Additional file 5: Functional classification of identified proteins from secretome of T. hirsuta X-13.
DOI: 10.6084/m9.figshare.11439033.v1
title: LncRNA ANCR promotes hepatocellular carcinoma metastasis through upregulating HNRNPA1 expression

description: LncRNA ANCR plays important roles in the modulation of epithelial mesenchymal transition (EMT) and tumour metastasis in many tumours. However, the role of ANCR in regulating hepatocellular carcinoma (HCC) metastasis is still not known. The current study aims to investigate the underlying mechanism for tumour oncogenesis of ANCR in HCC metastasis. HCC cell proliferation and migration/invasion were measured by MTT and Transwell assays. Xenograft model was established to determine the effect of ANCR on HCC growth and metastasis. ChIP assay was used to detect the H3 and H4 histone acetylation levels at the ANCR promoter region. RNA pull-down and RIP assay was performed to analyse the relationship between ANCR and heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1). Dual-luciferase reporter gene assay was conducted to determine the interaction between ANCR and miR-140-3p. The results indicated that ANCR was highly expressed in HCC tissues and cells, which promoted the proliferation and migration/invasion of HCC cells. <i>In vivo</i> experiments showed interfering ANCR suppressed the growth and metastasis of HCC. H3/H4 histone acetylation levels at the ANCR promoter region were elevated in HCC tissues and cells, and interfering histone deacetylases 3 (HDAC3) significantly up-regulated ANCR expression. ANCR could bind to HNRNPA1, and promoted the expression of HNRNPA1 through regulating its degradation. In addition, ANCR upregulated the expression of HNRNPA1 through sponging miR-140-3p. Finally, we found that ANCR promoted the EMT and invasion/migration of HCC cells through regulating HNRNPA1. In conclusion, ANCR promoted HCC metastasis by upregulating HNRNPA1, inhibiting HNRNPA1 degradation and sponging miR-140-3p.
DOI: 10.6084/m9.figshare.7244630
title: Preparation of Microcapsules of Slow-Release NPK Compound Fertilizer and the Release Characteristics

description: In this study, a novel type of slow-release fertilizer (SRF) was synthesized through lignin-based microcapsules. K2HPO4 and urea were coated by lignin and formaldehyde to prepare microcapsules of NPK compound SRF. The slow-release performance was measured by determining the NPK contents in water solution and soil column leaching. The release amounts of N, P and K after 5 days were 95.39, 95.28 and 96.75% in water, and 83.35, 96.62 and 90.75% in soil, respectively. The properties of SRF were analyzed by Fourier transform infrared spectroscopy, thermogravimetry and scanning electron microscopy. NPK release from the SRF was promoted by higher temperature and acid environment, but inhibited by alkaline environment. The first order kinetics equation provides the best correlation to describe nutrient release characteristics. The results indicated that SRF have good slow-release properties and are cost-saving and environment-friendly, and thus can efficiently improve the utilization efficiency of fertilizers in agricultural production.
DOI: 10.6084/m9.figshare.16681726
title: Additional file 5 of Elucidation of ligninolysis mechanism of a newly isolated white-rot basidiomycete Trametes hirsuta X-13

description: Additional file 5: Functional classification of identified proteins from secretome of T. hirsuta X-13.
DOI: 10.6084/m9.figshare.16681723
title: Additional file 4 of Elucidation of ligninolysis mechanism of a newly isolated white-rot basidiomycete Trametes hirsuta X-13

description: Additional file 4: The identified proteins from secretome of T. hirsuta X-13 in lignin-containing medium.
DOI: 10.6084/m9.figshare.21400412.v1
title: Additional file 6 of An asparagine metabolism-based classification reveals the metabolic and immune heterogeneity of hepatocellular carcinoma

description: Additional file 6. Table S3: Six established gene sets for predicting the patients' response to ICI therapy.
DOI: 10.6084/m9.figshare.23497661
title: Extended data for the manuscript 'Self-Assembled Soft Alloy with Frank-Kasper Phases beyond Metals'

description:  Extended data for the manuscript 'Self-Assembled Soft Alloy with Frank-Kasper Phases beyond Metals'