cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22623581
title: Additional file 1 of Soil conditions and the plant microbiome boost the accumulation of monoterpenes in the fruit of Citrus reticulata ‘Chachi’

description: Additional file 1: Table S1. Summary of sampled orchards in Guangdong and Guangxi provinces of China. Table S2. Contents of essential oils in peel samples from different orchards. Table S3. Highly expressed genes from the terpenoid backbone pathway in root, leaf, and peel samples from the core region. Table S4. Correlation between monoterpenes and highly expressed KOs from roots, leaves and peels. Table S5. Soil physical and chemical properties of rhizosphere soil samples. Table S6. Phylum composition of all metagenome samples (BS represents bulk soil, and RS represents rhizosphere soil). Table S7. Genus composition of all metagenome samples (BS represents bulk soil, and RS represents rhizosphere soil). Table S8. Detailed information on 3350 metagenome-assembly genomes (MAGs). Table S9. MAG genera differentially enriched between the core and non-core regions. Table S10. Isolation of soil- and root-derived bacteria. Table S11. Genome information of bacterial strains. Table S11. Highly expressed genes detected in C. reticulata ‘Chachi’ leaves after inoculation with Strep-4 and its SynComs. Table S12. Genome information of the bacterial strain. Table S13. Differentially enriched endophyte microbial OTUs in the core and non-core regions. Table S14. Correlation between monoterpenes and endophyte microbial OTUs enriched in the core region. Table S15. The similarities of the MAG 16S rRNA gene and endophyte OTU sequences.
DOI: 10.6084/m9.figshare.14234926.v1
title: Additional file 1 of Investigating the relationships between unfavourable habitual sleep and metabolomic traits: evidence from multi-cohort multivariable regression and Mendelian randomization analyses

description: Additional file 1: Table S1. Characteristics of the study populations in the multivariable-adjusted regression analyses. Table S2. Genetic instruments for insomnia. Table S3. Genetic instruments for total sleep duration. Table S4. Genetic instruments for short sleep duration. Table S5. Genetic instruments for long sleep duration. Table S6. Genetic instruments for chronotype. Table S7. Multivariable-adjusted results for insomnia symptoms. Table S8. Mendelian Randomization results for insomnia symptoms. Table S9. Multivariable-adjusted results for total sleep duration. Table S10. Mendelian Randomization results for total sleep duration. Table S11. Multivariable-adjusted results for short sleep duration. Table S12. Mendelian Randomization results for short sleep duration. Table S13. Multivariable-adjusted results for long sleep duration. Table S14. Mendelian Randomization results for long sleep duration. Table S15. Multivariable-adjusted results for chronotype. Table S16. Mendelian Randomization results for chronotype.
DOI: 10.6084/m9.figshare.12668180
title: Additional file 6 of Intracellular expression of arginine deiminase activates the mitochondrial apoptosis pathway by inhibiting cytosolic ferritin and inducing chromatin autophagy

description: Additional file 6: Figure S6A. is associated with Fig. 6b.
DOI: 10.25345/c5zw19370
title: MassIVE MSV000094042 - EMCN controls myogenic differentiation
title: Here, we report that the abundance of the sialoglycoprotein Endomucin (Emcn) in muscle stem cells increases with age and that reducing these aberrantly high levels of Emcn enhances early regeneration of skeletal muscle. This enhanced regeneration in the aged is also recapitulated in myogenic differentiation of primary myoblast which display enhanced early differentiation after knockdown of Emcn. However, the enhanced differentiation coincided with alterations in the cytoskeletal architecture of myotubes after knockdown of Emcn. We identified Basigin and Integrin-beta-1 as interaction partners of Emcn in myogenic cells, known interactors with the cytoskeleton. When Emcn levels are experimentally reduced we observed an increase in the proximity of Basigin and Integrin-beta-1 in myogenic cells. We suggest that Emcn is controlling the interaction of Basigin and Integrin-beta-1 in myogenic cells thereby limiting the progression of myogenic differentiation to allow proper formation of the cytoskeleton. During aging myogenic differentiation is impaired, potentially through aberrantly high Emcn levels hindering myogenic differentiation. However, Emcn amounts need to be balanced since reduction of Emcn levels enhances myogenic differentiation but at the cost of altered cytoskeletal architecture.
DOI: 10.25345/c5v40k94n
title: MassIVE MSV000094043 - Regulation of Glycogen Synthase kinase 3beta by phosphorylation and O-beta-linked N-acetylglucosaminylation: implications on tau protein phosphorylation
title: Glycogen synthase kinase 3 (GSK3) plays a pivotal role in signaling pathways related to insulin metabolism and in the pathogenesis of Alzheimer s disease (AD) and other neurodegenerative disorders. More particularly, the GSK3beta isoform is involved in AD-associated tau pathology as one of the major kinases involved in the hyperphosphorylation of the microtubule-associated tau protein, one of the neuropathological hallmarks of AD. As a constitutively active serine/threonine proline-directed kinase, GSK3 is inactivated by Akt/PKB-mediated phosphorylation of Ser9 at the N-terminal disordered domain. Furthermore, GSK3 activity requires for most of its substrates a priming (pre-phosphorylation) by another kinase that allows binding of the substrate in a phosphate-specific pocket near to the active site. It has been shown that GSK3 is also post-translationally modified by O-linked beta-N-acetylglucosaminylation (O-GlcNAcylation) with still unknown functional implications. We have found that binding of the phosphorylated, active form of Akt inhibits GSK3beta kinase activity on both primed and unprimed tau substrates, and Akt-mediated Ser9 phosphorylation restores the GSK3beta kinase activity on primed tau only. Therefore, Ser9 phosphorylation only inactivates GSK3 kinase activity on an unprimed substrate. Additionally, we have shown that GSK3beta is O-GlcNAcylated at multiple sites in both its disordered N- and C-terminal domains including Ser9, but O-GlcNAcylation does not alter kinase activity nor the Akt-mediated regulation of GSK3.
DOI: 10.6084/m9.figshare.25188629.v1
title: Supplementary Material for: High-Resolution Characterization of Enamel Remineralization using Time-of-Flight Secondary Ion Mass Spectrometry and Electron Microscopy

description: The aim of this in vitro study was to assess the suitability of high-resolution time-of-flight secondary-ion mass spectrometry (ToF-SIMS) for visualizing cross-sectional changes in human enamel microstructure and chemical composition during treatment and remineralization cycling of artificially generated caries lesions underneath an artificial plaque. Treatments consisted of exposure to twice daily toothpaste/water slurries prepared from 0, 1100, and 5000 µg/g fluoride (F) NaF/Silica toothpastes. In addition, treatments with slurries prepared from 1100 µg/g F SnF2/Silica toothpastes were done using 44Ca in the remineralization solution to allow for differentiation of newly formed mineral and exploration of incorporated metal dopants using ToF-SIMS. Complementary microhardness, scanning electron microscopy, and high-resolution transmission electron microscopy (HR-TEM) investigations were performed on enamel cross-sections. HR-TEM was used for the first time to determine the change in crystallinity during remineralization revealing distinct microstructural zones within one lesion. Chemical mapping using ToF-SIMS demonstrated that the distribution of F, while observed primarily in the new mineral phase, was widespread throughout the lesion with 44Ca substantially limited to the remineralizing mineral. Both penetrated the inter-rod spaces of the sound enamel illustrating how acid damage propagates into the native mineral as the caries lesion deepens. HR-TEM examination revealed different regions within the lesion characterized by distinct micro- and ultra-structures. Importantly, HR-TEM revealed a return of crystallinity following remineralization. Fluoride dose response observations verified the ability of these high-resolution techniques to differentiate remineralization efficacy. The collective results provided new insights such as the visualization of fluoride or calcium penetration pathways, as well as new tools to study the caries process.
DOI: 10.6084/m9.figshare.13192014
title: Additional file 9 of Loss function of SL (sekiguchi lesion) in the rice cultivar Minghui 86 leads to enhanced resistance to (hemi)biotrophic pathogens

description: Additional file 9: Table S3. Quantification of serotonin, tryptamine, L-trytophan and L-glutamine by UHPLC-MS.
DOI: 10.6084/m9.figshare.12667962
title: Additional file 2 of Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek’s disease using next generation sequencing

description: Additional file 2: Table S2. Summary statistics of raw and screened CNVs.
DOI: 10.6084/m9.figshare.13192008.v1
title: Additional file 7 of Loss function of SL (sekiguchi lesion) in the rice cultivar Minghui 86 leads to enhanced resistance to (hemi)biotrophic pathogens

description: Additional file 7: Table S1. Significant differentially expressed genes in sl-MH-1-mock/MH86-mock.
DOI: 10.6084/m9.figshare.13191984
title: Additional file 10 of Loss function of SL (sekiguchi lesion) in the rice cultivar Minghui 86 leads to enhanced resistance to (hemi)biotrophic pathogens

description: Additional file 10: Table S4. Sequences of the qRT-PCR primers in this study.
DOI: 10.6084/m9.figshare.22623544
title: Additional file 3 of Large-scale analysis of putative Euphorbiaceae R2R3-MYB transcription factors identifies a MYB involved in seed oil biosynthesis

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.22623547.v1
title: Additional file 4 of Large-scale analysis of putative Euphorbiaceae R2R3-MYB transcription factors identifies a MYB involved in seed oil biosynthesis

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.12667959.v1
title: Additional file 1 of Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek’s disease using next generation sequencing

description: Additional file 1: Table S1. Summary statistics for sequencing.
DOI: 10.6084/m9.figshare.12667965
title: Additional file 3 of Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek’s disease using next generation sequencing

description: Additional file 3: Table S3. The detailed lists of clusters with enrichment scores &gt; 1.0 from DAVID.
DOI: 10.6084/m9.figshare.12667983.v1
title: Additional file 9 of Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek’s disease using next generation sequencing

description: Additional file 9: Table S8. All the primer sequences used in qPCR for CNVRs validation.
DOI: 10.6084/m9.figshare.12667971.v1
title: Additional file 5 of Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek’s disease using next generation sequencing

description: Additional file 5: Table S4. The detailed lists of all the GO terms and pathways from DAVID.
DOI: 10.6084/m9.figshare.12667959
title: Additional file 1 of Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek’s disease using next generation sequencing

description: Additional file 1: Table S1. Summary statistics for sequencing.
DOI: 10.6084/m9.figshare.12149430
title: Spatial Accessibility

description: Data include origin and bus routes and stops.Code included: .1. extracting travel time using Google Maps API, 2. calculating spatial access index based on the multi-modal E2SFCA method, and 3. merging results tables from step 2.
DOI: 10.6084/m9.figshare.23683797
title: Geochemical elements and magnetic parameters of a 49-m basaltic red soil core on Hainan Island, China

description: The attached files (ordered from 1 to 6) are the geochemical and magnetic parameters for a 49-m red soil core derived from multi-layer basalt in northern Hainan Island, China. File 1 to 4 are excel format. File 5 and 6 were compressed files. File 1 contains data of geochemical elements (Fe, Al, Ti and Th) of the 49 m-red soil. File 2 contains basic magnetic parameters, such as χ, ARM and IRM. File 3 are hysteresis data for day-plot. File 4 are data for selected hysteresis loops. File 5 are data for first order reversal curves (FORC) diagram (.frc format); it can be viewed as txt or processed with FORC software, such as FORCinell. File 6 are data for IRM acquisiton and unmixing curves.
DOI: 10.6084/m9.figshare.12667974
title: Additional file 6 of Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek’s disease using next generation sequencing

description: Additional file 6: Table S5. Lists of line-specific and shared CNVRs in all the chicken lines.
DOI: 10.6084/m9.figshare.22623581.v1
title: Additional file 1 of Soil conditions and the plant microbiome boost the accumulation of monoterpenes in the fruit of Citrus reticulata ‘Chachi’

description: Additional file 1: Table S1. Summary of sampled orchards in Guangdong and Guangxi provinces of China. Table S2. Contents of essential oils in peel samples from different orchards. Table S3. Highly expressed genes from the terpenoid backbone pathway in root, leaf, and peel samples from the core region. Table S4. Correlation between monoterpenes and highly expressed KOs from roots, leaves and peels. Table S5. Soil physical and chemical properties of rhizosphere soil samples. Table S6. Phylum composition of all metagenome samples (BS represents bulk soil, and RS represents rhizosphere soil). Table S7. Genus composition of all metagenome samples (BS represents bulk soil, and RS represents rhizosphere soil). Table S8. Detailed information on 3350 metagenome-assembly genomes (MAGs). Table S9. MAG genera differentially enriched between the core and non-core regions. Table S10. Isolation of soil- and root-derived bacteria. Table S11. Genome information of bacterial strains. Table S11. Highly expressed genes detected in C. reticulata ‘Chachi’ leaves after inoculation with Strep-4 and its SynComs. Table S12. Genome information of the bacterial strain. Table S13. Differentially enriched endophyte microbial OTUs in the core and non-core regions. Table S14. Correlation between monoterpenes and endophyte microbial OTUs enriched in the core region. Table S15. The similarities of the MAG 16S rRNA gene and endophyte OTU sequences.
DOI: 10.6084/m9.figshare.12668084
title: Additional file 3 of YYFZBJS ameliorates colorectal cancer progression in ApcMin/+ mice by remodeling gut microbiota and inhibiting regulatory T-cell generation

description: Additional file 2: Table S3.
DOI: 10.6084/m9.figshare.12667980
title: Additional file 8 of Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek’s disease using next generation sequencing

description: Additional file 8: Table S7. The detailed information of CNVRs identified in this study and previous studies.
DOI: 10.6084/m9.figshare.12667980.v1
title: Additional file 8 of Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek’s disease using next generation sequencing

description: Additional file 8: Table S7. The detailed information of CNVRs identified in this study and previous studies.
DOI: 10.6084/m9.figshare.13192435.v1
title: Additional file 11 of Human umbilical cord mesenchymal stem cells restore the ovarian metabolome and rescue premature ovarian insufficiency in mice

description: Additional file 11: Supplementary table 4. Pseudotargeted metabolic differences of nonlipid metabolites in ovarian tissue samples of 3 groups (control, POI and POI+hUCMSCs). (XLS 292 kb)
DOI: 10.6084/m9.figshare.14235123
title: Additional file 1 of MassARRAY multigene screening combined with LDL-C and sdLDL-C detection for more favorable outcomes in type 2 diabetes mellitus therapy

description: Additional file 1. Cohort baseline and LDL monitoring results. I) The baseline information of our cohort. II) The LDL baseline of patients before drug treatment. III) The LDL level of patients after drug treatment
DOI: 10.6084/m9.figshare.13192432
title: Additional file 10 of Human umbilical cord mesenchymal stem cells restore the ovarian metabolome and rescue premature ovarian insufficiency in mice

description: Additional file 10: Supplementary table 3. Differential lipid metabolomic changes in ovarian tissue samples of 3 groups (control, POI and POI+hUCMSCs). (XLS 314 kb)
DOI: 10.6084/m9.figshare.13192432.v1
title: Additional file 10 of Human umbilical cord mesenchymal stem cells restore the ovarian metabolome and rescue premature ovarian insufficiency in mice

description: Additional file 10: Supplementary table 3. Differential lipid metabolomic changes in ovarian tissue samples of 3 groups (control, POI and POI+hUCMSCs). (XLS 314 kb)
DOI: 10.6084/m9.figshare.14759348
title: Additional file 1 of The use of coping strategies “shift-persist” mediates associations between physical activity and mental health problems in adolescents: a cross-sectional study

description: Additional file 1: Table S1. Bivariate correlations between variables.
DOI: 10.6084/m9.figshare.14235126
title: Additional file 2 of MassARRAY multigene screening combined with LDL-C and sdLDL-C detection for more favorable outcomes in type 2 diabetes mellitus therapy

description: Additional file 2. Gene polymorphisms result of our cohort. Gene polymorphism data of patients at baseline timing
DOI: 10.6084/m9.figshare.13192459
title: Additional file 8 of Human umbilical cord mesenchymal stem cells restore the ovarian metabolome and rescue premature ovarian insufficiency in mice

description: Additional file 8: Supplementary table 1. Differential metabolomic changes induced by chemotherapy in ovarian tissue samples. (XLS 108 kb)
DOI: 10.6084/m9.figshare.22623745
title: Additional file 1 of Genome-wide analysis of the GLP gene family and overexpression of GLP1-5–1 to promote lignin accumulation during early somatic embryo development in Dimocarpus longan

description: Addiional file 1: Table 1. qRT- PCR primer sequence. Table 2. Gene cloning and subcellular localization primer sequences. Table 3. Expression of DlGLP in different tissues of ‘SJM’ Longan. Table 4. Expression of DlGLP genes in early somatic embryogenesis of longan. Expression of DlGLP genes in EC under 2,4-D treatment. Table 5. Expression of DlGLP genes in EC under temperature and SL treatment.
DOI: 10.6084/m9.figshare.24208291
title: Severe pneumonia and pathogenic damage in human airway epithelium caused by Coxsackievirus B4

description: Coxsackievirus B4 (CVB4) has one of the highest proportions of fatal outcomes of other enterovirus serotypes. However, the pathogenesis of severe respiratory disease caused by CVB4 infection remains unclear. In this study, 3 of 42 (7.2%, GZ-R6, GZ-R7 and GZ-R8) patients with severe pneumonia tested positive for CVB4 infection in southern China. Three full-length genomes of pneumonia-derived CVB4 were sequenced and annotated for the first time, showing their high nucleotide similarity and clustering within genotype V. To analyze the pathogenic damage caused by CVB4 in the lungs, a well-differentiated human airway epithelium (HAE) was established and infected with the pneumonia-derived CVB4 isolate GZ-R6. The outcome was compared with that of a severe hand-foot-mouth disease (HFMD)-derived CVB4 strain GZ-HFM01. Compared with HFMD-derived CVB4, pneumonia-derived CVB4 caused more intense and rapid disruption of HAE polarity, leading to tight-junction barrier disruption, loss of cilia, and airway epithelial cell hypertrophy. More pneumonia-derived CVB4 were released from the basolateral side of the HAE than HFMD-derived CVB4. Of the 18 cytokines tested, only IL-6 and IL-1b secretion significantly increased on bilateral sides of HAE during the early stage of pneumonia-derived CVB4 infection, while multiple cytokine secretions significantly increased in HFMD-derived CVB4-infected HAE. HFMD-derived CVB4 exhibited stronger neurovirulence in the human neuroblastoma cells SH-SY5Y than pneumonia-derived CVB4, which is consistent with the clinical manifestations of patients infected with these two viruses. This study has increased the depth of our knowledge of severe pneumonia infection caused by CVB4 and will benefit its prevention and treatment.
DOI: 10.6084/m9.figshare.24208291.v1
title: Severe pneumonia and pathogenic damage in human airway epithelium caused by Coxsackievirus B4

description: Coxsackievirus B4 (CVB4) has one of the highest proportions of fatal outcomes of other enterovirus serotypes. However, the pathogenesis of severe respiratory disease caused by CVB4 infection remains unclear. In this study, 3 of 42 (7.2%, GZ-R6, GZ-R7 and GZ-R8) patients with severe pneumonia tested positive for CVB4 infection in southern China. Three full-length genomes of pneumonia-derived CVB4 were sequenced and annotated for the first time, showing their high nucleotide similarity and clustering within genotype V. To analyze the pathogenic damage caused by CVB4 in the lungs, a well-differentiated human airway epithelium (HAE) was established and infected with the pneumonia-derived CVB4 isolate GZ-R6. The outcome was compared with that of a severe hand-foot-mouth disease (HFMD)-derived CVB4 strain GZ-HFM01. Compared with HFMD-derived CVB4, pneumonia-derived CVB4 caused more intense and rapid disruption of HAE polarity, leading to tight-junction barrier disruption, loss of cilia, and airway epithelial cell hypertrophy. More pneumonia-derived CVB4 were released from the basolateral side of the HAE than HFMD-derived CVB4. Of the 18 cytokines tested, only IL-6 and IL-1b secretion significantly increased on bilateral sides of HAE during the early stage of pneumonia-derived CVB4 infection, while multiple cytokine secretions significantly increased in HFMD-derived CVB4-infected HAE. HFMD-derived CVB4 exhibited stronger neurovirulence in the human neuroblastoma cells SH-SY5Y than pneumonia-derived CVB4, which is consistent with the clinical manifestations of patients infected with these two viruses. This study has increased the depth of our knowledge of severe pneumonia infection caused by CVB4 and will benefit its prevention and treatment.
DOI: 10.6084/m9.figshare.13710827.v1
title: Additional file 2 of Comprehensive landscape and future perspectives of circular RNAs in colorectal cancer

description: Additional file 2. Biological functions and molecular mechanisms of circRNAs in colorectal cancer [224–261].
DOI: 10.15156/bio/sh2055295.08fu
title: SH2055295.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.