cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19174151.v1
title: Additional file 1 of Differential responses of the rhizosphere microbiome structure and soil metabolites in tea (Camellia sinensis) upon application of cow manure

description: Addditional file 1: Figure S1. Relative abundance (%) of the major bacterial phyla present in the soil microbial community upon different treatments. Major contributing phyla are displayed in different colors. Figure S2. PLS-DA score plots derived from metabolites (a) at spring, (b) early summer and (c) late summer. Each season corresponds to a soil sample and different colors indicate the field treatments. The score of variation explained by each principal component is indicated on the axes. R2X[1] and R2X[2], the degree of explanation in first component axes and the degree of explanation in second principal component axes, respectively. The t[1] and t[2], first and second principal component axes, respectively. Ellipses represent the 95% confidence regions for each sub-class of observations, assuming normal distributions. Figure S3. Map of significant soil metabolite-metabolite correlations (A, Spring; B, Early summer; C, Late summer). Table S1. The metabolic and microbial profiling of the applied cow manure. Table S2. OTUs of samples obtained in at the different seasons. Table S3. The relative abundance of the dominant phyla in soil bacterial communities. Table S4. The Permutational multivariate analysis of variance (PERMANOVA) among different treatments and sampling time on bacterial presence in the rhizosphere soils. Table S5. The abundance of Genus grouped as the phyla of Proteobacteria and Actinobacteria. Table S6. The soil metabolite compounds in the rhizosphere soils with three different treatments in different sampling time. Table S7. Variance Inflation Factor (VIF) value of organic acids and fatty acids in the rhizosphere soils in different sampling time.
DOI: 10.6084/m9.figshare.19174126.v1
title: Additional file 1 of Combination of gut microbiota and plasma amyloid-β as a potential index for identifying preclinical Alzheimer’s disease: a cross-sectional analysis from the SILCODE study

description: Additional file 1 : Supplementary Table S1. The items of the semi-structured interview for lifestyles. Supplementary Table S2. Demographic information and neuropsychological assessments for CI patients. Supplementary Table S3. Gut microbial differences between CN- and CN+ with correction for multiple comparisons. Supplementary Table S4. The interaction effect between APOE and diagnosis in the altered gut microbiota for CN- and CN+ participants. Supplementary Figure S1. The alpha diversity of gut microbiota among the CN-, CN+, and CI groups. Each bar graph represented the mean and standard deviation. The Chao1 and ACE indexes showed significantly decline in CI compared with CN-. There were no significant differences in Simpson and Shannon indexes among the three groups. *, p &lt; 0.05. CN-, amyloid-β negative cognitively normal participants; CN+, amyloid-β positive cognitively normal participants; CI, cognitive impairment participants. Supplementary Figure S2. The PCoA and NMDS based on the distribution of ASVs. (A) PCoA showed that the difference of gut taxonomic composition between CN- and CI was marginal in statistical significance (F = 1.383, p &lt; 0.052); (B) NMDS showed that the gut taxonomic composition was significantly different between CN- and CI (R = 0.097, p &lt; 0.009); (C) PCoA showed that the gut taxonomic composition between CN+ and CI was not significantly different (F = 0.850, p &lt; 0.712); (D) NMDS showed that the structure of gut microbiota in the CN+ group was not significantly different from that in the CI group (F = -0.020, p &lt; 0.698). CN-, amyloid-β negative cognitively normal participants; CN+, amyloid-β positive cognitively normal participants; CI, cognitive impairment participants; ASV, amplicon sequence variants; PCoA, principal coordinates analysis; PERMANOVA, permutational multivariate analysis of variance; NMDS, non-metric multidimensional scaling; ANOSIM, analysis of similarities. Supplementary Figure S3. The relative abundance of altered gut microbiota at different taxonomic levels among the CN-, CN+ and CI groups. Bar graphs indicated the relative abundance of phylum-level (A), class-level (B), order-level (C), family-level (D), and genus-level (E) taxa. The phylum Firmicutes and its corresponding class Clostridia, order Clostridiales, family Desulfovibrionaceae, family Ruminococcaceae, genus Lachnospiracea_incertae_sedis and genus Faecalibacterium taxa showed a progressive decline from CN- to CN+ and CI. CN-, amyloid-β negative cognitively normal participants; CN+, amyloid-β positive cognitively normal participants; CI, cognitive impairment participants.
DOI: 10.6084/m9.figshare.8164100.v1
title: Additional file 10: of lncRNA profile of Apis mellifera and its possible role in behavioural transition from nurses to foragers

description: The top 20 enriched KEGG pathways of differentially expressed mRNAs from the three comparison groups. (XLS 31 kb)
DOI: 10.6084/m9.figshare.8164154
title: Additional file 8: of lncRNA profile of Apis mellifera and its possible role in behavioural transition from nurses to foragers

description: The top 20 enriched KEGG pathways in the TC_F vs. TC_N, SCC_YF vs. SCC_YN and SCC_OF vs. SCC_ ON comparisons (trans). (XLS 30 kb)
DOI: 10.6084/m9.figshare.8164106
title: Additional file 1: of lncRNA profile of Apis mellifera and its possible role in behavioural transition from nurses to foragers

description: Detailed information on six honey bee samples for RNA-seq. (XLS 25 kb)
DOI: 10.6084/m9.figshare.8164148
title: Additional file 7: of lncRNA profile of Apis mellifera and its possible role in behavioural transition from nurses to foragers

description: The significantly enriched GO terms (corrected p-value &lt;â 0.05) detected in the TC_F vs. TC_N, SCC_YF vs. SCC_YN and SCC_OF vs. SCC_ON comparisons (trans). (XLS 68 kb)
DOI: 10.6084/m9.figshare.8164148.v1
title: Additional file 7: of lncRNA profile of Apis mellifera and its possible role in behavioural transition from nurses to foragers

description: The significantly enriched GO terms (corrected p-value &lt;â 0.05) detected in the TC_F vs. TC_N, SCC_YF vs. SCC_YN and SCC_OF vs. SCC_ON comparisons (trans). (XLS 68 kb)
DOI: 10.6084/m9.figshare.8164160.v1
title: Additional file 9: of lncRNA profile of Apis mellifera and its possible role in behavioural transition from nurses to foragers

description: The significantly enriched GO terms (corrected p-value &lt;â 0.05) of differentially expressed mRNAs from the three comparison groups. (XLS 74 kb)
DOI: 10.6084/m9.figshare.19174151
title: Additional file 1 of Differential responses of the rhizosphere microbiome structure and soil metabolites in tea (Camellia sinensis) upon application of cow manure

description: Addditional file 1: Figure S1. Relative abundance (%) of the major bacterial phyla present in the soil microbial community upon different treatments. Major contributing phyla are displayed in different colors. Figure S2. PLS-DA score plots derived from metabolites (a) at spring, (b) early summer and (c) late summer. Each season corresponds to a soil sample and different colors indicate the field treatments. The score of variation explained by each principal component is indicated on the axes. R2X[1] and R2X[2], the degree of explanation in first component axes and the degree of explanation in second principal component axes, respectively. The t[1] and t[2], first and second principal component axes, respectively. Ellipses represent the 95% confidence regions for each sub-class of observations, assuming normal distributions. Figure S3. Map of significant soil metabolite-metabolite correlations (A, Spring; B, Early summer; C, Late summer). Table S1. The metabolic and microbial profiling of the applied cow manure. Table S2. OTUs of samples obtained in at the different seasons. Table S3. The relative abundance of the dominant phyla in soil bacterial communities. Table S4. The Permutational multivariate analysis of variance (PERMANOVA) among different treatments and sampling time on bacterial presence in the rhizosphere soils. Table S5. The abundance of Genus grouped as the phyla of Proteobacteria and Actinobacteria. Table S6. The soil metabolite compounds in the rhizosphere soils with three different treatments in different sampling time. Table S7. Variance Inflation Factor (VIF) value of organic acids and fatty acids in the rhizosphere soils in different sampling time.
DOI: 10.6084/m9.figshare.8164115
title: Additional file 2: of lncRNA profile of Apis mellifera and its possible role in behavioural transition from nurses to foragers

description: The distribution of reads mapped to reference annotation. (XLS 25 kb)
DOI: 10.6084/m9.figshare.8164130
title: Additional file 4: of lncRNA profile of Apis mellifera and its possible role in behavioural transition from nurses to foragers

description: Common differentially expressed lncRNAs and mRNAs among the three comparisons. (XLS 134 kb)
DOI: 10.6084/m9.figshare.8164205
title: MOESM3 of Effect of intestinal tapeworms on the gut microbiota of the common carp, Cyprinus carpio

description: Additional file 3: Table S1. Maturity of the two tapeworms Khawia japonensis and Atractolytocestus tenuicollis in the intestine of common carp (Cyprinus carpio) from China.
DOI: 10.6084/m9.figshare.20222853.v1
title: Lattice_SIM_test_Data.zip

description: Dataset 1
DOI: 10.6084/m9.figshare.8164130.v1
title: Additional file 4: of lncRNA profile of Apis mellifera and its possible role in behavioural transition from nurses to foragers

description: Common differentially expressed lncRNAs and mRNAs among the three comparisons. (XLS 134 kb)
DOI: 10.6084/m9.figshare.7639889.v1
title: Estimation of conditional prevalence from group testing data with missing covariates

description: We consider estimating the conditional prevalence of a disease from data pooled according to the group testing mechanism. Consistent estimators have been proposed in the literature, but they rely on the data being available for all individuals. In infectious disease studies where group testing is frequently applied, the covariate is often missing for some individuals. There, unless the missing mechanism occurs completely at random, applying the existing techniques to the complete cases without adjusting for missingness does not generally provide consistent estimators, and finding appropriate modifications is challenging. We develop a consistent spline estimator, derive its theoretical properties, and show how to adapt local polynomial and likelihood estimators to the missing data problem. We illustrate the numerical performance of our methods on simulated and real examples.
DOI: 10.6084/m9.figshare.7639889.v3
title: Estimation of Conditional Prevalence From Group Testing Data With Missing Covariates

description: We consider estimating the conditional prevalence of a disease from data pooled according to the group testing mechanism. Consistent estimators have been proposed in the literature, but they rely on the data being available for all individuals. In infectious disease studies where group testing is frequently applied, the covariate is often missing for some individuals. There, unless the missing mechanism occurs completely at random, applying the existing techniques to the complete cases without adjusting for missingness does not generally provide consistent estimators, and finding appropriate modifications is challenging. We develop a consistent spline estimator, derive its theoretical properties, and show how to adapt local polynomial and likelihood estimators to the missing data problem. We illustrate the numerical performance of our methods on simulated and real examples. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.8164160
title: Additional file 9: of lncRNA profile of Apis mellifera and its possible role in behavioural transition from nurses to foragers

description: The significantly enriched GO terms (corrected p-value &lt;â 0.05) of differentially expressed mRNAs from the three comparison groups. (XLS 74 kb)
DOI: 10.6084/m9.figshare.20222817.v1
title: Autophagy Loss Impedes Cancer-Associated Fibroblast Activation via Downregulating Proline Biosynthesis

description: Cancer-associated fibroblasts (CAFs) are considered one of the most critical stromal cells that interact with pancreatic ductal adenocarcinoma (PDAC) and promote tumor growth, metastasis, and treatment resistance. Previous studies illustrated macroautophagy/autophagy contributes to CAF activation during tumor progression. Here in our study, we found that autophagy deficiency in CAFs impedes CAF activation by inhibiting proline biosynthesis and collagen production. Furthermore, we uncovered that autophagy promotes proline biosynthesis through mitophagy-mediated regulation of NADK2 (NAD kinase 2, mitochondrial), an enzyme responsible for production of mitochondrial NADP(H). Using an orthotopic mouse model of PDAC, we found that inhibiting mitophagy by targeting PRKN (parkin RBR E3 ubiquitin protein ligase) in the stroma reduced tumor weight. Thus, inhibition of CAFs mitophagy might be an attractive strategy for stroma-focused anti-cancer intervention.
DOI: 10.6084/m9.figshare.20222853
title: Lattice_SIM_test_Data.zip

description: Dataset 1
DOI: 10.6084/m9.figshare.8164211
title: MOESM4 of Effect of intestinal tapeworms on the gut microbiota of the common carp, Cyprinus carpio

description: Additional file 4: Table S2. Complete OTU table of gut microbiota at the genus level in the intestine of common carp (Cyprinus carpio).
DOI: 10.6084/m9.figshare.8164223.v1
title: Additional file 3: of Iso-Seq analysis of the Taxus cuspidata transcriptome reveals the complexity of Taxol biosynthesis

description: Table S3. RNA-Seq data of identified genes and candidates for Taxol biosynthesis in T. cuspidata. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.8164214
title: Additional file 1: of Iso-Seq analysis of the Taxus cuspidata transcriptome reveals the complexity of Taxol biosynthesis

description: Table S1. Proteins derived from GenBank used for the phylogenetic analysis. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8164214.v1
title: Additional file 1: of Iso-Seq analysis of the Taxus cuspidata transcriptome reveals the complexity of Taxol biosynthesis

description: Table S1. Proteins derived from GenBank used for the phylogenetic analysis. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8164217.v1
title: Additional file 2: of Iso-Seq analysis of the Taxus cuspidata transcriptome reveals the complexity of Taxol biosynthesis

description: Table S2. Primers used in this study. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.8164223
title: Additional file 3: of Iso-Seq analysis of the Taxus cuspidata transcriptome reveals the complexity of Taxol biosynthesis

description: Table S3. RNA-Seq data of identified genes and candidates for Taxol biosynthesis in T. cuspidata. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.19698490.v1
title: Anatexis of late Neoarchean-Early Paleoproterozoic and late Paleoproterozoic garnet-bearing leucogranite from the Khondalite Belt in the North China Craton

description: Two episodes of late Neoarchean-early Paleoproterozoic and late Paleoproterozoic garnet-bearing leucogranite, named the Baotou and Jining–Liangcheng garnet-bearing leucogranite are recognized from the Khondalite Belt in the North China Craton. Geochemical studies show that garnet-bearing leucogranite has high Al<sub>2</sub>O<sub>3</sub> content and FeO<sup>T</sup>/MgO ratio, with a large variation in the CaO content and K<sub>2</sub>O/Na<sub>2</sub>O ratio. Additionally, the garnet-bearing leucogranite is enriched in light rare earth elements and large ion lithophile elements and depleted in Nb, Ta, P, and Ti. However, there are some variations in Eu anomalies, as indicated by the Eu-enriched and Eu-depleted patterns. The sensitive high-resolution ion microprobe (SHRIMP) zircon U-Pb dating of the Baotou garnet-bearing leucogranite and Jining–Liangcheng garnet-bearing leucogranite show that their anatectic ages were 2.35–2.43 Ga and 1.90–1.92 Ga, respectively, with zircon εHf (t) values of −0.01–3.93 and −4.36–1.99, and two-stage model ages <sub>(TDM2)</sub> of 2.76–3.02 Ga and 2.57–2.83 Ga, respectively. U-Th-Pb SHRIMP analyses on zircon reveal ages of ca. 2.35–2.47 Ga for the Baotou metapelite gneiss and ca. 1.90–1.91 Ga for the Jining–Liangcheng metapelite gneiss, which represent the ages of tectonic metamorphic events related to the anatexis. Our results, combined with geological and petrographical observations, geochemistry, and geochronology, suggest that (1) Garnet-bearing leucogranites formed as a result of anatexis of metapelite gneisses; (2) They are mixtures of leucosomes, residual minerals and mantle-derived materials; (3) Two episodes of garnet-bearing leucogranites have been identified; (4) Both two episodes of garnet-bearing leucogranites corresponded to late Neoarchean-early Paleoproterozoic and late Palaeoproterozoic tectonothermal events, respectively.
DOI: 10.6084/m9.figshare.19698490
title: Anatexis of late Neoarchean-Early Paleoproterozoic and late Paleoproterozoic garnet-bearing leucogranite from the Khondalite Belt in the North China Craton

description: Two episodes of late Neoarchean-early Paleoproterozoic and late Paleoproterozoic garnet-bearing leucogranite, named the Baotou and Jining–Liangcheng garnet-bearing leucogranite are recognized from the Khondalite Belt in the North China Craton. Geochemical studies show that garnet-bearing leucogranite has high Al<sub>2</sub>O<sub>3</sub> content and FeO<sup>T</sup>/MgO ratio, with a large variation in the CaO content and K<sub>2</sub>O/Na<sub>2</sub>O ratio. Additionally, the garnet-bearing leucogranite is enriched in light rare earth elements and large ion lithophile elements and depleted in Nb, Ta, P, and Ti. However, there are some variations in Eu anomalies, as indicated by the Eu-enriched and Eu-depleted patterns. The sensitive high-resolution ion microprobe (SHRIMP) zircon U-Pb dating of the Baotou garnet-bearing leucogranite and Jining–Liangcheng garnet-bearing leucogranite show that their anatectic ages were 2.35–2.43 Ga and 1.90–1.92 Ga, respectively, with zircon εHf (t) values of −0.01–3.93 and −4.36–1.99, and two-stage model ages <sub>(TDM2)</sub> of 2.76–3.02 Ga and 2.57–2.83 Ga, respectively. U-Th-Pb SHRIMP analyses on zircon reveal ages of ca. 2.35–2.47 Ga for the Baotou metapelite gneiss and ca. 1.90–1.91 Ga for the Jining–Liangcheng metapelite gneiss, which represent the ages of tectonic metamorphic events related to the anatexis. Our results, combined with geological and petrographical observations, geochemistry, and geochronology, suggest that (1) Garnet-bearing leucogranites formed as a result of anatexis of metapelite gneisses; (2) They are mixtures of leucosomes, residual minerals and mantle-derived materials; (3) Two episodes of garnet-bearing leucogranites have been identified; (4) Both two episodes of garnet-bearing leucogranites corresponded to late Neoarchean-early Paleoproterozoic and late Palaeoproterozoic tectonothermal events, respectively.
DOI: 10.6084/m9.figshare.20222846
title: <i>Epg5</i> deficiency leads to primary ovarian insufficiency due to WT1 accumulation in mouse granulosa cells

description: Primary ovarian insufficiency (POI), also known as premature ovarian failure, is an ovarian defect in humans characterized by the premature depletion of ovarian follicles before the age of 40. However, the mechanisms underlying POI remain largely unknown. Here, we show that knockout of <i>Epg5</i> (ectopic P-granules autophagy protein 5 homolog (<i>C. elegans</i>)) results in subfertility in female mice, which exhibit a POI-like phenotype. Single-cell RNA sequencing analysis revealed that the knockout of <i>Epg5</i> affected the differentiation of granulosa cells (GCs). Further investigation demonstrated that knockout of <i>Epg5</i> blocks macroautophagic/autophagic flux, resulting in the accumulation of WT1 (WT1 transcription factor), an essential transcription factor for GCs, suggesting WT1 needs to be selectively degraded by the autophagy pathway. We found that the insufficient degradation of WT1 in the antral follicular stage contributes to reduced expression of steroidogenesis-related genes, thereby disrupting GC differentiation. Collectively, our studies show that EPG5 promotes WT1 degradation in GCs, indicating that the dysregulation of <i>Epg5</i> in GCs can trigger POI pathogenesis. <b>Abbreviations:</b> 3-MA, 3-methyladenine; CHX, cycloheximide; CQ, chloroquine; EPG5, ectopic P-granules autophagy protein 5 homolog (<i>C. elegans</i>); GC, granulosa cell; MAP1LC3/LC3, microtubule-associated protein 1 light chain 3; MII, metaphase II; POI, primary ovarian insufficiency; PB1, polar body 1; SQSTM1/p62, sequestosome 1; WT1, WT1 transcription factor
DOI: 10.6084/m9.figshare.20222846.v1
title: <i>Epg5</i> deficiency leads to primary ovarian insufficiency due to WT1 accumulation in mouse granulosa cells

description: Primary ovarian insufficiency (POI), also known as premature ovarian failure, is an ovarian defect in humans characterized by the premature depletion of ovarian follicles before the age of 40. However, the mechanisms underlying POI remain largely unknown. Here, we show that knockout of <i>Epg5</i> (ectopic P-granules autophagy protein 5 homolog (<i>C. elegans</i>)) results in subfertility in female mice, which exhibit a POI-like phenotype. Single-cell RNA sequencing analysis revealed that the knockout of <i>Epg5</i> affected the differentiation of granulosa cells (GCs). Further investigation demonstrated that knockout of <i>Epg5</i> blocks macroautophagic/autophagic flux, resulting in the accumulation of WT1 (WT1 transcription factor), an essential transcription factor for GCs, suggesting WT1 needs to be selectively degraded by the autophagy pathway. We found that the insufficient degradation of WT1 in the antral follicular stage contributes to reduced expression of steroidogenesis-related genes, thereby disrupting GC differentiation. Collectively, our studies show that EPG5 promotes WT1 degradation in GCs, indicating that the dysregulation of <i>Epg5</i> in GCs can trigger POI pathogenesis. <b>Abbreviations:</b> 3-MA, 3-methyladenine; CHX, cycloheximide; CQ, chloroquine; EPG5, ectopic P-granules autophagy protein 5 homolog (<i>C. elegans</i>); GC, granulosa cell; MAP1LC3/LC3, microtubule-associated protein 1 light chain 3; MII, metaphase II; POI, primary ovarian insufficiency; PB1, polar body 1; SQSTM1/p62, sequestosome 1; WT1, WT1 transcription factor
DOI: 10.6084/m9.figshare.20222936.v1
title: Evaluation model of downhole vortex tools drainage and gas recovery effects according to TOPSIS method

description: A new index for the evaluation of the effect of vortex tools is proposedAn evaluation model (SCORE model) was developed to more intuitively predict the effectiveness of using vortex toolsThe effect of the vortex tools in the actual wells is consistent with the SCORE model prediction points.The SCORE model can predict the effects of vortex tools and provides reference values for determining whether vortex tools are suitable for actual gas field production. A new index for the evaluation of the effect of vortex tools is proposed An evaluation model (SCORE model) was developed to more intuitively predict the effectiveness of using vortex tools The effect of the vortex tools in the actual wells is consistent with the SCORE model prediction points. The SCORE model can predict the effects of vortex tools and provides reference values for determining whether vortex tools are suitable for actual gas field production.