cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.34740/kaggle/dsv/6181662
title: COVID Vaccination in World (updated daily)
DOI: 10.25345/c53n20q7j
title: MassIVE MSV000092500 - Functional divergence of CYP76AKs shapes the chemodiversity of abietane-type diterpenoids in genus Salvia
title: The genus Salvia L. (Lamiaceae) comprises myriad distinct medicinal herbs, with terpenoids as one of their major active chemical groups. Abietane-type diterpenoids (ATDs), such as tanshinones and carnosic acids, are specific to Salvia, with categorical chemical diversity among lineages. To elucidate how ATDs chemical diversity evolved, we undertook large-scale metabolic and phylogenetic analyses of 71 Salvia species, combined with enzyme function, ancestral sequence and chemical trait reconstruction, and comparative genomics experiments. This integrated approach showed that the lineage-wide ATDs variations in Salvia were induced by differences in the oxidation of the terpenoid skeleton at C-20, which was caused by the loss of a function of the cytochrome P450 subfamily CYP76AK. These findings present a unique pattern resulting in chemical diversity in plants that was driven by the loss of enzyme function and associated catalytic pathways.
DOI: 10.6084/m9.figshare.23733399
title: <strong>Variability of functional groups of rhizosphere fungi of </strong> <strong>Norway spruce (</strong><em><strong>Picea abies</strong></em><strong> (L.) H.Karst) in the boreal range: the Wigry National Park, Poland</strong>

description: Rhizosphere microbial communities can influence plant growth and development. Natural regeneration processes take place in the stands of protected areas, which makes it possible to observe the natural changes taking place in the rhizosphere along with the development of the plant. This study aimed to determine the diversity (taxonomic and functional) of the rhizosphere fungal communities of Norway spruce growing in one of four developmental stages. Our research was based on the ITS region using Illumina system sequencing.
DOI: 10.6084/m9.figshare.23733399.v1
title: <strong>Variability of functional groups of rhizosphere fungi of </strong> <strong>Norway spruce (</strong><em><strong>Picea abies</strong></em><strong> (L.) H.Karst) in the boreal range: the Wigry National Park, Poland</strong>

description: Rhizosphere microbial communities can influence plant growth and development. Natural regeneration processes take place in the stands of protected areas, which makes it possible to observe the natural changes taking place in the rhizosphere along with the development of the plant. This study aimed to determine the diversity (taxonomic and functional) of the rhizosphere fungal communities of Norway spruce growing in one of four developmental stages. Our research was based on the ITS region using Illumina system sequencing.
DOI: 10.5281/zenodo.8175772
title: aix_sponsa_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8175771
title: aix_sponsa_zanfona_1.fasta.gz

description: .
DOI: 10.25345/c5zw19332
title: MassIVE MSV000092501 - Functional divergence of CYP76AKs shapes the chemodiversity of abietane-type diterpenoids in genus Salvia.
title: The genus Salvia L. (Lamiaceae) comprises myriad distinct medicinal herbs, with terpenoids as one of their major active chemical groups. Abietane-type diterpenoids (ATDs), such as tanshinones and carnosic acids, are specific to Salvia, with categorical chemical diversity among lineages. To elucidate how ATDs chemical diversity evolved, we undertook large-scale metabolic and phylogenetic analyses of 71 Salvia species, combined with enzyme function, ancestral sequence and chemical trait reconstruction, and comparative genomics experiments. This integrated approach showed that the lineage-wide ATDs variations in Salvia were induced by differences in the oxidation of the terpenoid skeleton at C-20, which was caused by the loss of a function of the cytochrome P450 subfamily CYP76AK. These findings present a unique pattern resulting in chemical diversity in plants that was driven by the loss of enzyme function and associated catalytic pathways.
DOI: 10.5281/zenodo.8175785
title: branta_hutchinsii_decontaminated_gx.fasta.gz

description: .
DOI: 10.5281/zenodo.8175784
title: branta_hutchinsii_decontaminated_gx.fasta.gz

description: .
DOI: 10.5519/qd.4rpoj4o9
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (30 records)
DOI: 10.5519/qd.at8zrjp3
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (5 records)
DOI: 10.6084/m9.figshare.22261912.v10
title: 博士论文补充材料

description: Supplementary Dataset, MAGs (with locus_tag) and meta-transcripts
DOI: 10.25345/c5v40k89m
title: MassIVE MSV000092502 - Functional divergence of CYP76AKs shapes the chemodiversity of abietane-type diterpenoids in genus Salvia-neg-root
title: The genus Salvia L. (Lamiaceae) comprises myriad distinct medicinal herbs, with terpenoids as one of their major active chemical groups. Abietane-type diterpenoids (ATDs), such as tanshinones and carnosic acids, are specific to Salvia, with categorical chemical diversity among lineages. To elucidate how ATDs chemical diversity evolved, we undertook large-scale metabolic and phylogenetic analyses of 71 Salvia species, combined with enzyme function, ancestral sequence and chemical trait reconstruction, and comparative genomics experiments. This integrated approach showed that the lineage-wide ATDs variations in Salvia were induced by differences in the oxidation of the terpenoid skeleton at C-20, which was caused by the loss of a function of the cytochrome P450 subfamily CYP76AK. These findings present a unique pattern resulting in chemical diversity in plants that was driven by the loss of enzyme function and associated catalytic pathways.
DOI: 10.6084/m9.figshare.23733633
title: <strong>Supplemental Table 2</strong>

description: <strong>Supplemental Table 2.</strong> <strong>Metabolome of gut lumen and serum.</strong> <strong>A</strong>) Luminal metabolites of the intraluminal stool and paired<strong> B</strong>) serum metabolites from the same mice group as indicated by mouse ID. Using KEGG BRITE hierarchical classification system (Hattori et al., 2010), the comparison between lumen and serum metabolism in <strong>C</strong>) KEGG functional class, <strong>D</strong>) pathways, <strong>E</strong>) modules. List of all functional modules in <strong>F</strong>) lumen and <strong>G</strong>) serum. Metabolome of intraluminal stool performed using CE/MS (capillary electrophoresis-mass spectrometry) (Kawamura et al., 2018; Matsumoto et al., 2014; Sugahara et al., 2017). Annotations of metabolites based on PubChem (Kim et al., 2021), KEGG (Hattori et al., 2010), or HMDB (Wishart et al., 2018).
DOI: 10.6084/m9.figshare.23733633.v1
title: <strong>Supplemental Table 2</strong>

description: <strong>Supplemental Table 2.</strong> <strong>Metabolome of gut lumen and serum.</strong> <strong>A</strong>) Luminal metabolites of the intraluminal stool and paired<strong> B</strong>) serum metabolites from the same mice group as indicated by mouse ID. Using KEGG BRITE hierarchical classification system (Hattori et al., 2010), the comparison between lumen and serum metabolism in <strong>C</strong>) KEGG functional class, <strong>D</strong>) pathways, <strong>E</strong>) modules. List of all functional modules in <strong>F</strong>) lumen and <strong>G</strong>) serum. Metabolome of intraluminal stool performed using CE/MS (capillary electrophoresis-mass spectrometry) (Kawamura et al., 2018; Matsumoto et al., 2014; Sugahara et al., 2017). Annotations of metabolites based on PubChem (Kim et al., 2021), KEGG (Hattori et al., 2010), or HMDB (Wishart et al., 2018).
DOI: 10.6084/m9.figshare.23733639
title: <strong>Supplemental Table 3</strong>

description: <strong>Supplemental Table 3. Metabolome comparison among different treatment groups. </strong>Fold change (FC) analysis is to compare the absolute values of change between group means in <strong>A</strong>) lumen and <strong>B</strong>) serum. Original metabolite measurement without normalization in FC analysis. Two-sample t-test to calculate significance value. Metabolites with p value &lt;0.05 included in the table. Pathway enrichment analysis to indicate the significantly affected pathways by treatment in <strong>C</strong>) lumen and <strong>D</strong>) serum. Enrichment analysis using predefined libraries of metabolites using metabolite set enrichment analyses (MSEA) (Xia and Wishart, 2010).
DOI: 10.6084/m9.figshare.23733642
title: <strong>Supplemental Table 4</strong>

description: <strong>Supplemental Table 4. Gut microbiome and metabolome after 7 days treatment of tacrolimus</strong>.<strong> A</strong>) Taxonomic assignment of gut microbiota was performed to compare to gut microbiota after 2 days of tacrolimus treatment. Gut metabolome after <strong>B</strong>) 2 days of tacrolimus was compared to gut metabolome after <strong>C</strong>) 7 days of treatment. To indicate the significantly affected pathways after 7 days of tacrolimus treatment, <strong>D</strong>) pathway enrichment analysis was performed using metabolite set enrichment analyses (MSEA) (Xia and Wishart, 2010). Metabolites of the intraluminal stool using CE/MS (capillary electrophoresis-mass spectrometry) (Kawamura et al., 2018; Matsumoto et al., 2014; Sugahara et al., 2017).
DOI: 10.6084/m9.figshare.23733642.v1
title: <strong>Supplemental Table 4</strong>

description: <strong>Supplemental Table 4. Gut microbiome and metabolome after 7 days treatment of tacrolimus</strong>.<strong> A</strong>) Taxonomic assignment of gut microbiota was performed to compare to gut microbiota after 2 days of tacrolimus treatment. Gut metabolome after <strong>B</strong>) 2 days of tacrolimus was compared to gut metabolome after <strong>C</strong>) 7 days of treatment. To indicate the significantly affected pathways after 7 days of tacrolimus treatment, <strong>D</strong>) pathway enrichment analysis was performed using metabolite set enrichment analyses (MSEA) (Xia and Wishart, 2010). Metabolites of the intraluminal stool using CE/MS (capillary electrophoresis-mass spectrometry) (Kawamura et al., 2018; Matsumoto et al., 2014; Sugahara et al., 2017).
DOI: 10.6084/m9.figshare.23733645
title: <strong>Supplemental Table 5</strong>

description: <strong>Supplemental Table 5: Correlation of microbiome metabolic potentials (CMP) with paired metabolite measurement.</strong> The significance of the correlation between <strong>A</strong>) the total community-level CMP or <strong>B</strong>) individual species and actual serum metabolite measurements across all samples was calculated using rank-based estimation. Same correlation analyses were performed between <strong>C</strong>) the total community-level CMP or <strong>D</strong>) individual species and actual fecal metabolite measurements. HMP Unified Metabolic Analysis Network (v0.11.2) (Franzosa et al., 2018) and Uniref90 protein database (Kanehisa et al., 2012) were used to stratify functional profiles according to contributing species. These microbial features were annotated using the KEGG Enzyme Nomenclature (EC number system) (Kanehisa, 2017) to characterize CMP,. MIMOSA2 (Model-based Integration of Metabolite Observations and Species Abundances) was used to relate variation in the microbiome metabolic potentials to paired metabolite measurement (Noecker et al., 2016).
DOI: 10.6084/m9.figshare.23733624
title: Genome-Centric analyses of 165 metagenomes show the prevalence of antimicrobial resistance in activated sludge and wastewater treatments plants

description: Antimicrobial resistance (AMR) has been recognized as a global challenge threatening human and animal health. However, we are far from knowing all the consequences of AMR on human, animal and ecosystem health. The aim of the present study was to use publicly available metagenomes from activated sludge and wastewater treatment plants to decipher ARG compositions and abundance present in metagenome-assembled genomes (MAGs) and Mobile genetic elements (MGEs) such as plasmids and chromosomes.
DOI: 10.6084/m9.figshare.23733624.v2
title: Genome-Centric analyses of 165 metagenomes show the prevalence of antimicrobial resistance in activated sludge and wastewater treatments plants

description: Antimicrobial resistance (AMR) has been recognized as a global challenge threatening human and animal health. However, we are far from knowing all the consequences of AMR on human, animal and ecosystem health. The aim of the present study was to use publicly available metagenomes from activated sludge and wastewater treatment plants to decipher ARG compositions and abundance present in metagenome-assembled genomes (MAGs) and Mobile genetic elements (MGEs) such as plasmids and chromosomes.
DOI: 10.6084/m9.figshare.23733624.v1
title: Antibiotics_resistance_genes_sequences.zip

description: Antimicrobial resistance (AMR) has been recognized as a global challenge threatening human and animal health. However, we are far from knowing all the consequences of AMR on human, animal and ecosystem health. The aim of the present study was to use publicly available metagenomes from activated sludge and wastewater treatment plants to decipher ARG compositions and abundance present in metagenome-assembled genomes (MAGs) and Mobile genetic elements (MGEs) such as plasmids and chromosomes.
DOI: 10.6084/m9.figshare.23733621
title: Source data for the analysis entitled " Smoking, alcohol consumption and risk of Dupuytren's disease: a Mendelian randomization study"

description: This is the data used for the analysis titled " Smoking, alcohol consumption and risk of Dupuytren's disease: a Mendelian randomization study".
DOI: 10.6084/m9.figshare.23733621.v1
title: Source data for the analysis entitled " Smoking, alcohol consumption and risk of Dupuytren's disease: a Mendelian randomization study"

description: This is the data used for the analysis titled " Smoking, alcohol consumption and risk of Dupuytren's disease: a Mendelian randomization study".
DOI: 10.6084/m9.figshare.23733627
title: <strong>Supplemental Table 1</strong>

description: <strong>Supplemental Table 1. Gut microbiome characteristics.</strong> <strong>A</strong>) Statistics of metagenomic sequencing of gut microbiome and time point information. Intraluminal stool obtained from colon. <strong>B</strong>) Statistics of metagenomic sequencing of gut microbiome using intraluminal stool obtained from jejunum. Taxonomic assignment performed and 222 taxonomic groups <strong>C</strong>) at species level and <strong>D</strong>) at genus level characterized using the Comprehensive Mouse Gut Metagenome catalog (CMGM) (Kieser et al., 2021). <strong>E</strong>) Functional characterization performed using HUMAnN2 (Human Microbiome Project Unified Metabolic Analysis Network) (v0.11.2) (Franzosa et al., 2018) to determine prevalence and abundance of metabolic pathways in a microbial community.
DOI: 10.6084/m9.figshare.23733627.v2
title: <strong>Supplemental Table 1</strong>

description: <strong>Supplemental Table 1. Gut microbiome characteristics.</strong> <strong>A</strong>) Statistics of metagenomic sequencing of gut microbiome and time point information. Intraluminal stool obtained from colon. <strong>B</strong>) Statistics of metagenomic sequencing of gut microbiome using intraluminal stool obtained from jejunum. Taxonomic assignment performed and 222 taxonomic groups <strong>C</strong>) at species level and <strong>D</strong>) at genus level characterized using the Comprehensive Mouse Gut Metagenome catalog (CMGM) (Kieser et al., 2021). <strong>E</strong>) Functional characterization performed using HUMAnN2 (Human Microbiome Project Unified Metabolic Analysis Network) (v0.11.2) (Franzosa et al., 2018) to determine prevalence and abundance of metabolic pathways in a microbial community.
DOI: 10.6084/m9.figshare.23733627.v1
title: <strong>Supplemental Figure 1</strong>

description: <strong>Supplemental Figure 1.</strong> Comparison of relative abundance of bacterial groups in gut microbiota of different experiment groups for <strong>A</strong>) Firmicutes, <strong>B</strong>) <em>Lachnospiraceae</em>, <strong>C</strong>) <em>Oscillospiraceae</em>, <strong>D</strong>) Ruminococcaceae that belong to Firmicutes, and <strong>E</strong>) Bacteroidota. Cumulative relative abundance of bacteria groups shown. Phyloseq R package (v1.38.0) (McMurdie and Holmes, 2013) to generate the barplot.
DOI: 10.25345/c5qb9vg5x
title: MassIVE MSV000092503 - Functional divergence of CYP76AKs shapes the chemodiversity of abietane-type diterpenoids in genus Salvia-pos-leaf
title: The genus Salvia L. (Lamiaceae) comprises myriad distinct medicinal herbs, with terpenoids as one of their major active chemical groups. Abietane-type diterpenoids (ATDs), such as tanshinones and carnosic acids, are specific to Salvia, with categorical chemical diversity among lineages. To elucidate how ATDs chemical diversity evolved, we undertook large-scale metabolic and phylogenetic analyses of 71 Salvia species, combined with enzyme function, ancestral sequence and chemical trait reconstruction, and comparative genomics experiments. This integrated approach showed that the lineage-wide ATDs variations in Salvia were induced by differences in the oxidation of the terpenoid skeleton at C-20, which was caused by the loss of a function of the cytochrome P450 subfamily CYP76AK. These findings present a unique pattern resulting in chemical diversity in plants that was driven by the loss of enzyme function and associated catalytic pathways.
DOI: 10.25345/c5kk94p15
title: MassIVE MSV000092504 - Functional divergence of CYP76AKs shapes the chemodiversity of abietane-type diterpenoids in genus Salvia-pos-root
title: The genus Salvia L. (Lamiaceae) comprises myriad distinct medicinal herbs, with terpenoids as one of their major active chemical groups. Abietane-type diterpenoids (ATDs), such as tanshinones and carnosic acids, are specific to Salvia, with categorical chemical diversity among lineages. To elucidate how ATDs chemical diversity evolved, we undertook large-scale metabolic and phylogenetic analyses of 71 Salvia species, combined with enzyme function, ancestral sequence and chemical trait reconstruction, and comparative genomics experiments. This integrated approach showed that the lineage-wide ATDs variations in Salvia were induced by differences in the oxidation of the terpenoid skeleton at C-20, which was caused by the loss of a function of the cytochrome P450 subfamily CYP76AK. These findings present a unique pattern resulting in chemical diversity in plants that was driven by the loss of enzyme function and associated catalytic pathways.
DOI: 10.6084/m9.figshare.23733675
title: Study data from EyePACS and data analysis file.xlsx

description: Data sheets included grading results of several different parameters of fundus photos on patients who responded to the survey. There are several parameters, not all used for data analysis for the manuscript. A second data sheet includes the results of data analysis performed.
DOI: 10.6084/m9.figshare.23733675.v1
title: Study data from EyePACS and data analysis file.xlsx

description: Data sheets included grading results of several different parameters of fundus photos on patients who responded to the survey. There are several parameters, not all used for data analysis for the manuscript. A second data sheet includes the results of data analysis performed.
DOI: 10.6084/m9.figshare.23731494
title: <strong>ROCK1 is a multi-functional factor maintaining the primordial follicle reserve and follicular development in mice</strong>

description: The follicle is the basic structural and functional unit of the ovary in female mammals. The excessive depletion of follicles will lead to diminished ovarian reserve or even premature ovarian failure, resulting in diminished ovarian oogenesis and endocrine function. Excessive follicular depletion is mainly due to loss of primordial follicles. Our analysis of published human ovarian single-cell sequencing results by others revealed a significant increase in ROCK1 expression during primordial follicle development. However, the role of ROCK1 in primordial follicle development and maintenance is not clear. This study revealed a gradual increase in ROCK1 expression during primordial follicle activation. Inhibition of ROCK1 resulted in reduced primordial follicle activation, decreased follicular reserve, and delayed development of growing follicles. This effect may be achieved through the HIPPO pathway. The present study indicates that ROCK1 is a key molecule for primordial follicular reserve and follicular development.
DOI: 10.25345/c5ft8dv7d
title: MassIVE MSV000092505 - Functional divergence of CYP76AKs shapes the chemodiversity of abietane-type diterpenoids in genus Salvia
title: The genus Salvia L. (Lamiaceae) comprises myriad distinct medicinal herbs, with terpenoids as one of their major active chemical groups. Abietane-type diterpenoids (ATDs), such as tanshinones and carnosic acids, are specific to Salvia, with categorical chemical diversity among lineages. To elucidate how ATDs chemical diversity evolved, we undertook large-scale metabolic and phylogenetic analyses of 71 Salvia species, combined with enzyme function, ancestral sequence and chemical trait reconstruction, and comparative genomics experiments. This integrated approach showed that the lineage-wide ATDs variations in Salvia were induced by differences in the oxidation of the terpenoid skeleton at C-20, which was caused by the loss of a function of the cytochrome P450 subfamily CYP76AK. These findings present a unique pattern resulting in chemical diversity in plants that was driven by the loss of enzyme function and associated catalytic pathways.
DOI: 10.25345/c5b27q230
title: MassIVE MSV000092506 - Functional divergence of CYP76AKs shapes the chemodiversity of abietane-type diterpenoids in genus Salvia
title: The genus Salvia L. (Lamiaceae) comprises myriad distinct medicinal herbs, with terpenoids as one of their major active chemical groups. Abietane-type diterpenoids (ATDs), such as tanshinones and carnosic acids, are specific to Salvia, with categorical chemical diversity among lineages. To elucidate how ATDs chemical diversity evolved, we undertook large-scale metabolic and phylogenetic analyses of 71 Salvia species, combined with enzyme function, ancestral sequence and chemical trait reconstruction, and comparative genomics experiments. This integrated approach showed that the lineage-wide ATDs variations in Salvia were induced by differences in the oxidation of the terpenoid skeleton at C-20, which was caused by the loss of a function of the cytochrome P450 subfamily CYP76AK. These findings present a unique pattern resulting in chemical diversity in plants that was driven by the loss of enzyme function and associated catalytic pathways.
DOI: 10.5519/qd.m2z46lad
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (2 records)
DOI: 10.6084/m9.figshare.23733891
title: 16S and ITS metagenomes raw data from plastisphere and sand at Kung Wiman beach

description: 16S and ITS metagenomes raw data from plastisphere and sand at Kung Wiman beach
DOI: 10.6084/m9.figshare.23733891.v1
title: 16S and ITS metagenomes raw data from plastisphere and sand at Kung Wiman beach

description: 16S and ITS metagenomes raw data from plastisphere and sand at Kung Wiman beach
DOI: 10.6084/m9.figshare.23732991
title: Dataset : <strong>Expansion Grade and Morphokinetic Parameters Associated with Aneuploidy Status of Day 5 Embryo</strong>

description: All raw data and information obtained from the sample during the present study
DOI: 10.6084/m9.figshare.23732991.v2
title: Dataset : <strong>Expansion Grade and Morphokinetic Parameters Associated with Aneuploidy Status of Day 5 Embryo</strong>

description: All raw data and information obtained from the sample during the present study
DOI: 10.6084/m9.figshare.23732991.v1
title: Dataset : <strong>Expansion Grade and Morphokinetic Parameters Associated with Aneuploidy Status of Day 5 Embryo</strong>

description: All raw data and information obtained from the sample during the present study