cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13516318
title: A host-based whole genome sequencing study reveals novel risk loci associated with severity of influenza A(H1N1)pdm09 infection

description: Influenza A(H1N1)pdm09 virus has remained in a seasonal circulation since being recognized in 2009. Although it followed a mild course in most patients, in others it caused a series of severe clinical illnesses. Epidemiologic studies have implicated that host factors have a major influence on the disease severity of influenza A(H1N1)pdm09 infection. However, an understanding of relevant genetic variations and the underlying mechanisms is still limited. In this present study, we used a host-based whole genome sequencing (WGS) method to comprehensively explore the genetic risk loci associated with severity of influenza A(H1N1)pdm09 infection. From the common single-nucleotide variants (SNVs) analysis, we identified the abnormal nominally significant (<i>P</i> &lt; 1 × 10<sup>−4</sup>) common SNVs enriched in <i>PTBP3</i> gene. The results of rare functional SNVs analysis supported that there were several novel candidate genes might confer risk of severe influenza A(H1N1)pdm09 diseases, such as <i>FTSJ3</i>, <i>CPVL</i>, <i>BST2</i>, <i>NOD2</i> and <i>MAVS</i>. Moreover, our results of gene set based analysis indicated that the HIF-1 transcription factor and IFN-γ pathway might play an important role in the underlying mechanism of severe influenza A(H1N1)pdm09. These findings will increase our knowledge about biological mechanism underlying the severe influenza A(H1N1)pdm09 and facilitate to design novel personalized treatments.
DOI: 10.6084/m9.figshare.13516318.v2
title: A host-based whole genome sequencing study reveals novel risk loci associated with severity of influenza A(H1N1)pdm09 infection

description: Influenza A(H1N1)pdm09 virus has remained in a seasonal circulation since being recognized in 2009. Although it followed a mild course in most patients, in others it caused a series of severe clinical illnesses. Epidemiologic studies have implicated that host factors have a major influence on the disease severity of influenza A(H1N1)pdm09 infection. However, an understanding of relevant genetic variations and the underlying mechanisms is still limited. In this present study, we used a host-based whole genome sequencing (WGS) method to comprehensively explore the genetic risk loci associated with severity of influenza A(H1N1)pdm09 infection. From the common single-nucleotide variants (SNVs) analysis, we identified the abnormal nominally significant (<i>P</i> &lt; 1 × 10<sup>−4</sup>) common SNVs enriched in <i>PTBP3</i> gene. The results of rare functional SNVs analysis supported that there were several novel candidate genes might confer risk of severe influenza A(H1N1)pdm09 diseases, such as <i>FTSJ3</i>, <i>CPVL</i>, <i>BST2</i>, <i>NOD2</i> and <i>MAVS</i>. Moreover, our results of gene set based analysis indicated that the HIF-1 transcription factor and IFN-γ pathway might play an important role in the underlying mechanism of severe influenza A(H1N1)pdm09. These findings will increase our knowledge about biological mechanism underlying the severe influenza A(H1N1)pdm09 and facilitate to design novel personalized treatments.
DOI: 10.6084/m9.figshare.21904927
title: Origin of high-Cr podiform chromitites from Kabaena Island, Southeast Sulawesi, Indonesia: constraints from mineralogy and geochemistry

description: The East Sulawesi Ophiolite, one of the three largest ophiolites in the world, contains important podiform chromitites. However, the origin of these chromite deposits is not well constrained. Here, we present the detailed mineralogy and in situ chemistry of chromite and solid inclusions within chromite for podiform chromitites from the Kabaena Island, Southeast Sulawesi. Chromite grains have low TiO<sub>2</sub> (0.17–0.27 wt%) and Al<sub>2</sub>O<sub>3</sub> (13.4–15.1 wt%) contents and high Cr# [Cr/(Cr+Al), molar] of 0.70–0.74 and Mg# [Mg/(Mg+Fe<sup>2+</sup>), molar] of 0.69–0.75, which resemble those of other high-Cr podiform chromitites worldwide. The MORB-normalized patterns for some selected major-trace elements of chromite show slightly positive slopes from Al<sub>2</sub>O<sub>3</sub> to Mn. Chromite-hosted silicate inclusions include olivine, clinopyroxene, orthopyroxene and amphibole and are characterized by higher Mg/Fe ratios than those of host peridotites. The geothermobarometry of chromite-hosted clinopyroxene-orthopyroxene pairs indicates that the estimated T-P conditions of the parental magma of the Kabaena chromitites are 950–1010°C and 7.0–8.4 Kbar. The extreme-Mg-rich olivine inclusions (Fo &gt;96) with extremely high Ni (5300–8200 ppm) and Cr (1500–6700 ppm) contents are interpreted to have crystallized from high-Mg and Cr boninitic melts, and the Fo contents were then elevated by subsolidus re-equilibration (Fe–Mg and Fe–Ni exchange) with chromite. Sulfide inclusions contain base metal minerals containing millerite with rare pentlandite and chalcopyrite, and platinum-group minerals that include the laurite-erlichmanite series, Ir–Ni monosulfide, irarsite and cuproiridsite. This sulfide assemblage reveals that their parental magmas experienced the evolution of high T and low <i>f</i>(S<sub>2</sub>) to low T and high <i>f</i>(S<sub>2</sub>) from the early to late stage. Finally, combined with the palaeogeographic reconstruction in Sulawesi, we propose that the high-Cr chromitites in this region were formed by the reaction of depleted mantle and boninitic magma beneath a juvenile island arc, implying the initiation of a new subduction in the Miocene.
DOI: 10.6084/m9.figshare.21904927.v1
title: Origin of high-Cr podiform chromitites from Kabaena Island, Southeast Sulawesi, Indonesia: constraints from mineralogy and geochemistry

description: The East Sulawesi Ophiolite, one of the three largest ophiolites in the world, contains important podiform chromitites. However, the origin of these chromite deposits is not well constrained. Here, we present the detailed mineralogy and in situ chemistry of chromite and solid inclusions within chromite for podiform chromitites from the Kabaena Island, Southeast Sulawesi. Chromite grains have low TiO<sub>2</sub> (0.17–0.27 wt%) and Al<sub>2</sub>O<sub>3</sub> (13.4–15.1 wt%) contents and high Cr# [Cr/(Cr+Al), molar] of 0.70–0.74 and Mg# [Mg/(Mg+Fe<sup>2+</sup>), molar] of 0.69–0.75, which resemble those of other high-Cr podiform chromitites worldwide. The MORB-normalized patterns for some selected major-trace elements of chromite show slightly positive slopes from Al<sub>2</sub>O<sub>3</sub> to Mn. Chromite-hosted silicate inclusions include olivine, clinopyroxene, orthopyroxene and amphibole and are characterized by higher Mg/Fe ratios than those of host peridotites. The geothermobarometry of chromite-hosted clinopyroxene-orthopyroxene pairs indicates that the estimated T-P conditions of the parental magma of the Kabaena chromitites are 950–1010°C and 7.0–8.4 Kbar. The extreme-Mg-rich olivine inclusions (Fo &gt;96) with extremely high Ni (5300–8200 ppm) and Cr (1500–6700 ppm) contents are interpreted to have crystallized from high-Mg and Cr boninitic melts, and the Fo contents were then elevated by subsolidus re-equilibration (Fe–Mg and Fe–Ni exchange) with chromite. Sulfide inclusions contain base metal minerals containing millerite with rare pentlandite and chalcopyrite, and platinum-group minerals that include the laurite-erlichmanite series, Ir–Ni monosulfide, irarsite and cuproiridsite. This sulfide assemblage reveals that their parental magmas experienced the evolution of high T and low <i>f</i>(S<sub>2</sub>) to low T and high <i>f</i>(S<sub>2</sub>) from the early to late stage. Finally, combined with the palaeogeographic reconstruction in Sulawesi, we propose that the high-Cr chromitites in this region were formed by the reaction of depleted mantle and boninitic magma beneath a juvenile island arc, implying the initiation of a new subduction in the Miocene.
DOI: 10.6084/m9.figshare.13516377
title: Comprehensive identification, fragmentation pattern, and metabolic pathways of gefitinib metabolites via UHPLC-Q-TOF-MS/MS: <i>in vivo</i> study of rat plasma, urine, bile, and faeces

description: Gefitinib, the first approved inhibitor for oral epidermal growth factor receptor (EGFR), has been proved to be effective in non-small cell lung cancer with EGFR mutation. However, there are many metabolites of gefitinib that have not been identified in vivo.This study aims to identify the metabolites of gefitinib and its metabolic pathways in rats using ultra-high-performance liquid chromatography coupled with a quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS/MS) detector. Protein precipitation, solid-phase and ultrasonic extraction were used for the pre-treatment of plasma, urine, bile and faeces samples.In this study, a total of 28 compounds were identified in rat plasma, 29 in bile, 20 in urine and 16 in faeces. 20 new compounds were firstly reported as metabolites of gefitinib. Reduction, hydroxylation, dealkylation and dehalogenation were the major metabolic pathways in phase I. For phase II, the main pathways were sulphate and glucuronide conjugation. The fragment ions of gefitinib and its metabolites were usually generated via the fracture of C<sub>1</sub>–O bond of propoxy on the C<sub>6</sub> position of aniline quinazoline ring.The results may be valuable and important for understanding the metabolic process of gefitinib in clinical application and drug safety. Gefitinib, the first approved inhibitor for oral epidermal growth factor receptor (EGFR), has been proved to be effective in non-small cell lung cancer with EGFR mutation. However, there are many metabolites of gefitinib that have not been identified in vivo. This study aims to identify the metabolites of gefitinib and its metabolic pathways in rats using ultra-high-performance liquid chromatography coupled with a quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS/MS) detector. Protein precipitation, solid-phase and ultrasonic extraction were used for the pre-treatment of plasma, urine, bile and faeces samples. In this study, a total of 28 compounds were identified in rat plasma, 29 in bile, 20 in urine and 16 in faeces. 20 new compounds were firstly reported as metabolites of gefitinib. Reduction, hydroxylation, dealkylation and dehalogenation were the major metabolic pathways in phase I. For phase II, the main pathways were sulphate and glucuronide conjugation. The fragment ions of gefitinib and its metabolites were usually generated via the fracture of C<sub>1</sub>–O bond of propoxy on the C<sub>6</sub> position of aniline quinazoline ring. The results may be valuable and important for understanding the metabolic process of gefitinib in clinical application and drug safety.
DOI: 10.6084/m9.figshare.13516377.v1
title: Comprehensive identification, fragmentation pattern, and metabolic pathways of gefitinib metabolites via UHPLC-Q-TOF-MS/MS: <i>in vivo</i> study of rat plasma, urine, bile, and faeces

description: Gefitinib, the first approved inhibitor for oral epidermal growth factor receptor (EGFR), has been proved to be effective in non-small cell lung cancer with EGFR mutation. However, there are many metabolites of gefitinib that have not been identified in vivo.This study aims to identify the metabolites of gefitinib and its metabolic pathways in rats using ultra-high-performance liquid chromatography coupled with a quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS/MS) detector. Protein precipitation, solid-phase and ultrasonic extraction were used for the pre-treatment of plasma, urine, bile and faeces samples.In this study, a total of 28 compounds were identified in rat plasma, 29 in bile, 20 in urine and 16 in faeces. 20 new compounds were firstly reported as metabolites of gefitinib. Reduction, hydroxylation, dealkylation and dehalogenation were the major metabolic pathways in phase I. For phase II, the main pathways were sulphate and glucuronide conjugation. The fragment ions of gefitinib and its metabolites were usually generated via the fracture of C<sub>1</sub>–O bond of propoxy on the C<sub>6</sub> position of aniline quinazoline ring.The results may be valuable and important for understanding the metabolic process of gefitinib in clinical application and drug safety. Gefitinib, the first approved inhibitor for oral epidermal growth factor receptor (EGFR), has been proved to be effective in non-small cell lung cancer with EGFR mutation. However, there are many metabolites of gefitinib that have not been identified in vivo. This study aims to identify the metabolites of gefitinib and its metabolic pathways in rats using ultra-high-performance liquid chromatography coupled with a quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS/MS) detector. Protein precipitation, solid-phase and ultrasonic extraction were used for the pre-treatment of plasma, urine, bile and faeces samples. In this study, a total of 28 compounds were identified in rat plasma, 29 in bile, 20 in urine and 16 in faeces. 20 new compounds were firstly reported as metabolites of gefitinib. Reduction, hydroxylation, dealkylation and dehalogenation were the major metabolic pathways in phase I. For phase II, the main pathways were sulphate and glucuronide conjugation. The fragment ions of gefitinib and its metabolites were usually generated via the fracture of C<sub>1</sub>–O bond of propoxy on the C<sub>6</sub> position of aniline quinazoline ring. The results may be valuable and important for understanding the metabolic process of gefitinib in clinical application and drug safety.
DOI: 10.6084/m9.figshare.16137825
title: figshare file 5

description: The 51 sectors in the Chinese economy.
DOI: 10.6084/m9.figshare.16137825.v1
title: figshare file 5

description: The 51 sectors in the Chinese economy.
DOI: 10.6084/m9.figshare.20332149
title: Global profiling and annotation of templated isomiRs dynamics across <i>Caenorhabditis elegans</i> development

description: microRNAs (miRNAs) are small non-coding RNAs that regulate gene expression through translational repression and mRNA destabilization. During canonical miRNA biogenesis, several miRNA isoforms, or isomiRs, are produced from a single precursor miRNA. Templated isomiRs are generated through Drosha or Dicer cleavage at alternate positions on either the primary or the precursor miRNAs, generating truncated or extended 5’ and/or 3’ miRNA ends. As changes to the mature miRNA sequence can alter miRNA gene target repertoire, we investigated the extent of templated isomiR prevalence, providing a profiling map for templated isomiRs across stages of <i>C. elegans</i> development. While most miRNA loci did not produce abundant templated isomiRs, a substantial number of miRNA loci produced isomiRs were just as, or more, abundant than their annotated canonical mature miRNAs. 3’ end miRNA alterations were more frequent than the seed-altering 5’ end extensions or truncations. However, we identified several miRNA loci that produced a considerable amount of isomiRs with 5’ end alterations, predicted to target new, distinct sets of genes. Overall, the presented annotation of templated isomiR dynamics across <i>C. elegans</i> developmental stages provides a basis for further studies into miRNA biogenesis and the intriguing potential of functional miRNA diversification through isomiR production.
DOI: 10.6084/m9.figshare.20332149.v1
title: Global profiling and annotation of templated isomiRs dynamics across <i>Caenorhabditis elegans</i> development

description: microRNAs (miRNAs) are small non-coding RNAs that regulate gene expression through translational repression and mRNA destabilization. During canonical miRNA biogenesis, several miRNA isoforms, or isomiRs, are produced from a single precursor miRNA. Templated isomiRs are generated through Drosha or Dicer cleavage at alternate positions on either the primary or the precursor miRNAs, generating truncated or extended 5’ and/or 3’ miRNA ends. As changes to the mature miRNA sequence can alter miRNA gene target repertoire, we investigated the extent of templated isomiR prevalence, providing a profiling map for templated isomiRs across stages of <i>C. elegans</i> development. While most miRNA loci did not produce abundant templated isomiRs, a substantial number of miRNA loci produced isomiRs were just as, or more, abundant than their annotated canonical mature miRNAs. 3’ end miRNA alterations were more frequent than the seed-altering 5’ end extensions or truncations. However, we identified several miRNA loci that produced a considerable amount of isomiRs with 5’ end alterations, predicted to target new, distinct sets of genes. Overall, the presented annotation of templated isomiR dynamics across <i>C. elegans</i> developmental stages provides a basis for further studies into miRNA biogenesis and the intriguing potential of functional miRNA diversification through isomiR production.
DOI: 10.6084/m9.figshare.8797820
title: Data for chromosome size in Figure 2

description: Data for chromosome size in Figure 2.
DOI: 10.6084/m9.figshare.8797823.v1
title: Data for Total Gpysy-type TE density in Figure 2

description: Data for Total Gpysy-type TE density in Figure 2.
DOI: 10.6084/m9.figshare.8797820.v1
title: Data for chromosome size in Figure 2

description: Data for chromosome size in Figure 2.
DOI: 10.6084/m9.figshare.8797823
title: Data for Total Gpysy-type TE density in Figure 2

description: Data for Total Gpysy-type TE density in Figure 2.
DOI: 10.6084/m9.figshare.8797826
title: Code for Circos software to generate Figure 2

description: Code for Circos software to generate Figure 2.
DOI: 10.6084/m9.figshare.8797826.v1
title: Code for Circos software to generate Figure 2

description: Code for Circos software to generate Figure 2.
DOI: 10.6084/m9.figshare.8797829.v1
title: Data for Total TE density in Figure 2

description: Data for Total TE density in Figure 2.
DOI: 10.6084/m9.figshare.8797829
title: Data for Total TE density in Figure 2

description: Data for Total TE density in Figure 2.
DOI: 10.6084/m9.figshare.8797841
title: Data for Total TIR-type TE density in Figure 2.

description: Data for Total TIR-type TE density in Figure 2.
DOI: 10.6084/m9.figshare.8797832.v1
title: Data for collinearity in figure 2

description: Data for collinearity in figure 2.
DOI: 10.6084/m9.figshare.8797835
title: Data for Total Copia-type TE density in Figure 2

description: Data for Total Copia-type TE density in Figure 2.
DOI: 10.6084/m9.figshare.8797841.v1
title: Data for Total TIR-type TE density in Figure 2.

description: Data for Total TIR-type TE density in Figure 2.
DOI: 10.6084/m9.figshare.8797832
title: Data for collinearity in figure 2

description: Data for collinearity in figure 2.
DOI: 10.6084/m9.figshare.8797835.v1
title: Data for Total Copia-type TE density in Figure 2

description: Data for Total Copia-type TE density in Figure 2.
DOI: 10.6084/m9.figshare.8797838
title: Data for gene density in Figure 2

description: Data for gene density in Figure 2.
DOI: 10.6084/m9.figshare.8797838.v1
title: Data for gene density in Figure 2

description: Data for gene density in Figure 2.
DOI: 10.6084/m9.figshare.19807682
title: Additional file 2 of Transcriptomics and metagenomics of common cutworm (Spodoptera litura) and fall armyworm (Spodoptera frugiperda) demonstrate differences in detoxification and development

description: Additional file 2. Supplementary Tables
DOI: 10.6084/m9.figshare.19807682.v1
title: Additional file 2 of Transcriptomics and metagenomics of common cutworm (Spodoptera litura) and fall armyworm (Spodoptera frugiperda) demonstrate differences in detoxification and development

description: Additional file 2. Supplementary Tables
DOI: 10.6084/m9.figshare.19807910
title: Additional file 1 of Physiological and comparative transcriptome analyses reveal the mechanisms underlying waterlogging tolerance in a rapeseed anthocyanin-more mutant

description: Additional file 1: Figure S1. The phenotypes of seedlings after 8 day of recovery growth following waterlogging for 0, 12, 24 and 36 h. Bars = 1 cm. Figure S2. Sequencing randomness analysis of the waterlogging-treatment and control groups in both the WT and am mutant. Figure S3. Schematic diagram of the expression level saturation distribution curve. Figure S4. Schematic diagram of the correlations between samples. Figure S5. The MA and volcano plots of gene expression in (a) amCK-vs-amWL and (b) Z11CK-vs-Z11WL. “Z11CK-vs-Z11WL” indicates waterlogging-treated WT compared with the untreated WT, and “amCK-vs-amWL” indicates waterlogging-treated am mutant compared with the untreated am mutant. Figure S6. Co-expression clustering showing the expression profile of DEGs in WT (a) and am mutant (b). The X-axis represents with or without waterlogging treatment. The Y-axis represents the value of the relative expression level [log10 (FPKM + 1)].
DOI: 10.6084/m9.figshare.19807913
title: Additional file 2 of Physiological and comparative transcriptome analyses reveal the mechanisms underlying waterlogging tolerance in a rapeseed anthocyanin-more mutant

description: Additional file 2: Table S1. List of DEGs detected in the WT ZS11after the waterlogging treatment. Table S2. List of DEGs detected in the am mutant after the waterlogging treatment. Table S3. Differential expression of subclusters 1–5 in the am mutant. Table S4. Differential expression of subclusters 1–6 in the WT. Table S5. All the up- and downregulated DEGs with GO annotations in the am mutant. Table S6. All the up- and downregulated DEGs with GO annotations in the WT. Table S7. KEGG pathway enrichment of the DEGs in the WT. Table S8. KEGG pathway enrichment of the DEGs in the am mutant. Table S9. The DEG enrichment in the phenylalanine biosynthetic and metabolic pathways. Table S10. A list of differentially expressed TFs in the WT. Table S11. A list of differentially expressed TFs in the am mutant. Table S12. The DEG enrichment in plant hormone signal transduction pathways. Table S13. New transcript predictions as assessed by RNA-seq. Table S14. Primers used for qPCR validation of the selected DEGs.
DOI: 10.6084/m9.figshare.19807913.v1
title: Additional file 2 of Physiological and comparative transcriptome analyses reveal the mechanisms underlying waterlogging tolerance in a rapeseed anthocyanin-more mutant

description: Additional file 2: Table S1. List of DEGs detected in the WT ZS11after the waterlogging treatment. Table S2. List of DEGs detected in the am mutant after the waterlogging treatment. Table S3. Differential expression of subclusters 1–5 in the am mutant. Table S4. Differential expression of subclusters 1–6 in the WT. Table S5. All the up- and downregulated DEGs with GO annotations in the am mutant. Table S6. All the up- and downregulated DEGs with GO annotations in the WT. Table S7. KEGG pathway enrichment of the DEGs in the WT. Table S8. KEGG pathway enrichment of the DEGs in the am mutant. Table S9. The DEG enrichment in the phenylalanine biosynthetic and metabolic pathways. Table S10. A list of differentially expressed TFs in the WT. Table S11. A list of differentially expressed TFs in the am mutant. Table S12. The DEG enrichment in plant hormone signal transduction pathways. Table S13. New transcript predictions as assessed by RNA-seq. Table S14. Primers used for qPCR validation of the selected DEGs.