cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.6zkd7x
title: Occurrence Download

description: A dataset containing 5166 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Noccaea fendleri (A.Gray) Holub"
 ]
}

 The dataset includes 5166 records from 158 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063908-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.grt3am
title: Occurrence Download

description: A dataset containing 1583 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Striga hermonthica (Delile) Benth."
 ]
}

 The dataset includes 1583 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0290935-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3zfeuy
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Noccaea densiflora (Boiss. & Kotschy) F.K.Mey."
 ]
}

 The dataset includes 42 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063902-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.87v2j5
title: Occurrence Download

description: A dataset containing 127304 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Year 1990-2017",
 "HasCoordinate is true",
 "TaxonKey is Amaranthaceae",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 127304 records from 388 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010194-170826194755519/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.19807967
title: Additional file 9 of Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica)

description: Additional file 9: Table S9. Primer sequences for qRT-PCR.
DOI: 10.5281/zenodo.10695955
title: redt
DOI: 10.5281/zenodo.10695956
title: redt
DOI: 10.6084/m9.figshare.8798126
title: Exploring toxicity of perfluorinated compounds through complex network and pathway modeling

description: Perfluorinated compounds (PFCs) have serious impacts on human health, which could interfere with the body's signal pathways and affect the normal hormone balance of humans. PFCs were reported to bind to many proteins causing a series of biological effects. It was quite possible that the in vivo action of PFCs was not a single target or a single pathway, suggesting the toxic effect was due to the disturbance of protein or gene network, not limited to the modification of a single target protein or gene. Thus, a PFCs-targets interaction network was constructed and the significant differences in the characteristics of complex networks between the branched PFCs and linear PFCs were observed. A molecular dynamics simulation proved that binding ability of the branched PFCs to the target protein was much weaker than that of the linear PFCs, explaining why the branched PFCs presented significantly difference from the linear PFCs in terms of complex network characteristics. In addition, four target genes were identified as the central node genes of the network. The four target genes were proved to present certain influences on some diseases, which suggested a high correlation between PFCs to these diseases, including obesity, hepatocellular carcinoma and diabetes. The present work was helpful to develop new approaches to identify the key toxic targets of compounds and to explore the toxicity effects on pathways.
AbbreviationsARandrogen receptorBPAbisphenol AESR1estrogen receptor 1ESR2estrogen receptor 2GLTPglycolipid transfer proteinHbFthe fetal hemoglobinHBG1hemoglobin subunit γ-1hERαhuman ERαHSD17B1hydroxysteroid 17-β dehydrogenase 1KEGGKenya encyclopedia of genes and genomesMDmolecular dynamics simulationPFCsperfluorinated compoundsPFOAperfluorooctanoic acidPFOSperfluorooctane sulfonatePOPspersistent organic pollutantsRMSDroot-mean-square deviationSHBGsex hormone binding globulinSPC/Eextended simple point charge modelTRthyroid hormone receptor androgen receptor bisphenol A estrogen receptor 1 estrogen receptor 2 glycolipid transfer protein the fetal hemoglobin hemoglobin subunit γ-1 human ERα hydroxysteroid 17-β dehydrogenase 1 Kenya encyclopedia of genes and genomes molecular dynamics simulation perfluorinated compounds perfluorooctanoic acid perfluorooctane sulfonate persistent organic pollutants root-mean-square deviation sex hormone binding globulin extended simple point charge model thyroid hormone receptor Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.19807955
title: Additional file 6 of Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica)

description: Additional file 6: Table S6. Ka/Ks values of each subfamily genepair and all fragment repeat sequence gene pairs.
DOI: 10.6084/m9.figshare.19807955.v1
title: Additional file 6 of Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica)

description: Additional file 6: Table S6. Ka/Ks values of each subfamily genepair and all fragment repeat sequence gene pairs.
DOI: 10.6084/m9.figshare.19807958
title: Additional file 7 of Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica)

description: Additional file 7: Table S7. One-to-one orthologous generelationships between Setaria italica and other plants.
DOI: 10.6084/m9.figshare.19807937.v1
title: Additional file 1 of Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica)

description: Additional file 1: Table S1. List of the 18 Setaria italicaSPL genes identified in this study.
DOI: 10.6084/m9.figshare.19807940.v1
title: Additional file 2 of Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica)

description: Additional file 2: Table S2. Analysis and distribution of theconserved motifs in SPL proteins of Setaria italica and other species.
DOI: 10.6084/m9.figshare.19807958.v1
title: Additional file 7 of Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica)

description: Additional file 7: Table S7. One-to-one orthologous generelationships between Setaria italica and other plants.
DOI: 10.6084/m9.figshare.19807967.v1
title: Additional file 9 of Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica)

description: Additional file 9: Table S9. Primer sequences for qRT-PCR.
DOI: 10.6084/m9.figshare.8798138.v1
title: Modulation of p53 N-terminal transactivation domain 2 conformation ensemble and kinetics by phosphorylation

description: Phosphorylation of protein is critical for various cell processes, which preferentially happens in intrinsically disordered proteins (IDPs). How phosphorylation modulates structural ensemble of disordered peptide remains largely unexplored. Here, using replica exchange molecular dynamics (REMD) and Markov state model (MSM), the conformational distribution and kinetics of p53 N-terminal transactivation domain (TAD) 2 as well as its dual-site phosphorylated form (pSer46, pThr55) were simulated. It reveals that the dual phosphorylation does not change overall size and secondary structure element fraction, while a change in the distribution of hydrogen bonds induces slightly more pre-existing bound helical conformations. MSM analysis indicates that the dual phosphorylation accelerates conformation exchange between disordered and order-like states in target-binding region. It suggests that p53 TAD2 after phosphorylation would be more apt to bind to both the human p62 pleckstrin homology (PH) domain and the yeast tfb1 PH domain through different binding mechanism, where experimentally it exhibits an extended and α-helix conformation, respectively, with increased binding strength in both complexes. Our study implies except binding interface, both conformation ensemble and kinetics should be considered for the effects of phosphorylation on IDPs.
AbbreviationsIDPsintrinsically disordered proteinsREMDreplica exchange molecular dynamicsMSMMarkov state modelTADtransactivation domainPHpleckstrin homologyPRRproline-rich regionDBDDNA-binding domainTETTetramerization domainREGregulatory domainMDmolecular dynamicsPMEparticle-mesh EwaldTICAtime-lagged independent component analysisCKChapman–KolmogorovGMRQgeneralized matrix Rayleigh quotientSARWself-avoiding random walkKIDkinase-inducible domainMFPTmean first passage timeDSSPdefinition of secondary structure of proteinsRMSDroot mean square deviation<i>R<sub>g</sub></i>radius of gyration<i>R<sub>ee</sub></i>end to end distance intrinsically disordered proteins replica exchange molecular dynamics Markov state model transactivation domain pleckstrin homology proline-rich region DNA-binding domain Tetramerization domain regulatory domain molecular dynamics particle-mesh Ewald time-lagged independent component analysis Chapman–Kolmogorov generalized matrix Rayleigh quotient self-avoiding random walk kinase-inducible domain mean first passage time definition of secondary structure of proteins root mean square deviation radius of gyration end to end distance Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.8798138
title: Modulation of p53 N-terminal transactivation domain 2 conformation ensemble and kinetics by phosphorylation

description: Phosphorylation of protein is critical for various cell processes, which preferentially happens in intrinsically disordered proteins (IDPs). How phosphorylation modulates structural ensemble of disordered peptide remains largely unexplored. Here, using replica exchange molecular dynamics (REMD) and Markov state model (MSM), the conformational distribution and kinetics of p53 N-terminal transactivation domain (TAD) 2 as well as its dual-site phosphorylated form (pSer46, pThr55) were simulated. It reveals that the dual phosphorylation does not change overall size and secondary structure element fraction, while a change in the distribution of hydrogen bonds induces slightly more pre-existing bound helical conformations. MSM analysis indicates that the dual phosphorylation accelerates conformation exchange between disordered and order-like states in target-binding region. It suggests that p53 TAD2 after phosphorylation would be more apt to bind to both the human p62 pleckstrin homology (PH) domain and the yeast tfb1 PH domain through different binding mechanism, where experimentally it exhibits an extended and α-helix conformation, respectively, with increased binding strength in both complexes. Our study implies except binding interface, both conformation ensemble and kinetics should be considered for the effects of phosphorylation on IDPs.
AbbreviationsIDPsintrinsically disordered proteinsREMDreplica exchange molecular dynamicsMSMMarkov state modelTADtransactivation domainPHpleckstrin homologyPRRproline-rich regionDBDDNA-binding domainTETTetramerization domainREGregulatory domainMDmolecular dynamicsPMEparticle-mesh EwaldTICAtime-lagged independent component analysisCKChapman–KolmogorovGMRQgeneralized matrix Rayleigh quotientSARWself-avoiding random walkKIDkinase-inducible domainMFPTmean first passage timeDSSPdefinition of secondary structure of proteinsRMSDroot mean square deviation<i>R<sub>g</sub></i>radius of gyration<i>R<sub>ee</sub></i>end to end distance intrinsically disordered proteins replica exchange molecular dynamics Markov state model transactivation domain pleckstrin homology proline-rich region DNA-binding domain Tetramerization domain regulatory domain molecular dynamics particle-mesh Ewald time-lagged independent component analysis Chapman–Kolmogorov generalized matrix Rayleigh quotient self-avoiding random walk kinase-inducible domain mean first passage time definition of secondary structure of proteins root mean square deviation radius of gyration end to end distance Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.8273915.v1
title: Additional file 1 of Changes in the gut microbiome and fermentation products concurrent with enhanced longevity in acarbose-treated mice

description: Summary statistics, associations with design parameters and metabolites, and inferred taxonomic identity of common bacterial OTUs. Table includes all OTUs with mean relative abundance greater than 0.01% and found in greater than 5% of samples. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.19807940
title: Additional file 2 of Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica)

description: Additional file 2: Table S2. Analysis and distribution of theconserved motifs in SPL proteins of Setaria italica and other species.
DOI: 10.6084/m9.figshare.19807937
title: Additional file 1 of Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica)

description: Additional file 1: Table S1. List of the 18 Setaria italicaSPL genes identified in this study.
DOI: 10.58032/agh/wzt3sd
title: Scimago Journal Country Rank service data on 4 years citations per document collected in November 2023, for the period 2000-2020, including titles for which full data is available for these 21 years

description: Citations per document counts the number of citations received by documents from a journal and divides them by the total number of documents published in that journal.
DOI: 10.6084/m9.figshare.23506536
title: Mammal responses to global changes in human activity vary by trophic group and landscape [Data files]

description:  Data files to reproduce the analysis and figures in  <strong>Mammal responses to global changes in human activity vary by trophic group and landscape. </strong>Where:
<br>
<em>"rai_with_covariates.csv"</em> - contains the animal activity effect sizes for all of the project-species included in the analyses, and their corresponding covariates
<em>"noct_with_covariates.csv"</em> - contrains the animal nocturnality effect sizes for all of the project-species included in the analyses, and their corresponding covariates
"<em>example1_summary.csv</em>" - contains the human use data for Figure1B of the main text
"<em>example2_summary.csv</em>" - contains the human use data for Figure1C of the main text
"<em>trait_appendix.csv</em>" - contains the trait data for all of the species included in the analyses
<em>"project_covariates.csv"</em> - contains the project-level covariates for each of the studies included in the analysis
<em>"camera_stations_covariates.csv"</em> - contains the camera station-level covariates for all of the camera traps included in the analysis
DOI: 10.6084/m9.figshare.25273165
title: Shipping Guide

description: Guide for shipping samples to Novogene
DOI: 10.6084/m9.figshare.25273165.v2
title: Shipping Guide

description: Guide for shipping samples to Novogene
DOI: 10.6084/m9.figshare.25273165.v1
title: Shipping Guide

description: Guide for shipping samples to Novogene
DOI: 10.6084/m9.figshare.19807943.v1
title: Additional file 3 of Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica)

description: Additional file 3: Table S3. SiSPL gene promoter regioncis-acting element details.
DOI: 10.6084/m9.figshare.19807952
title: Additional file 5 of Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica)

description: Additional file 5: Table S5. Segmental duplications of Setariaitalica SPL genes.
DOI: 10.6084/m9.figshare.8273975
title: Additional file 2: of A preclinical studyâ systemic evaluation of safety on mesenchymal stem cells derived from human gingiva tissue

description: Table S1. Rating criteria of abnormal behavior. (XLS 26 kb)
DOI: 10.6084/m9.figshare.8273975.v1
title: Additional file 2: of A preclinical studyâ systemic evaluation of safety on mesenchymal stem cells derived from human gingiva tissue

description: Table S1. Rating criteria of abnormal behavior. (XLS 26 kb)
DOI: 10.6084/m9.figshare.19808143.v1
title: Additional file 14 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 14: Table S13. Differentially expressed metabolites.
DOI: 10.6084/m9.figshare.19808146.v1
title: Additional file 15 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 15: Table S14. Information of correlation analysis by multiple omics.
DOI: 10.6084/m9.figshare.8273981
title: Additional file 3: of A preclinical study—systemic evaluation of safety on mesenchymal stem cells derived from human gingiva tissue

description: Table S2. Electrocardiogram of rhesus by intravenous injection of GMSCs in short-term toxicity test (n = 4, x ¯ $$ \overline{x} $$  ± S). (XLS 29 kb)
DOI: 10.6084/m9.figshare.19808173
title: Additional file 9 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 9: Table S8. KEGG enrich for CT53vsBT45.
DOI: 10.6084/m9.figshare.8273987.v1
title: Additional file 4: of A preclinical study—systemic evaluation of safety on mesenchymal stem cells derived from human gingiva tissue

description: Table S3. Electrocardiogram of rhesus by intravenous injection of GMSCs in long-term toxicity test (n = 4, x ¯ $$ \overline{x} $$  ± S). (XLS 29 kb)
DOI: 10.6084/m9.figshare.8273990.v1
title: Additional file 5: of A preclinical study—systemic evaluation of safety on mesenchymal stem cells derived from human gingiva tissue

description: Table S4. Bone marrow count of rhesus by intravenous injection of GMSCs in long-term toxicity test (n = 4, x ¯ $$ \overline{x} $$  ± S). (XLS 31 kb)
DOI: 10.6084/m9.figshare.8273981.v1
title: Additional file 3: of A preclinical study—systemic evaluation of safety on mesenchymal stem cells derived from human gingiva tissue

description: Table S2. Electrocardiogram of rhesus by intravenous injection of GMSCs in short-term toxicity test (n = 4, x ¯ $$ \overline{x} $$  ± S). (XLS 29 kb)
DOI: 10.6084/m9.figshare.19808152.v1
title: Additional file 2 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 2: Table S1. The data set summary of transcriptome sequence.
DOI: 10.6084/m9.figshare.19808161.v1
title: Additional file 5 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 5: Table S4. GO enrich for CT53vsAT37.
DOI: 10.6084/m9.figshare.19808167.v1
title: Additional file 7 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 7: Table S6. KEGG enrich for BT45vsAT37.
DOI: 10.6084/m9.figshare.19808131.v1
title: Additional file 10 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 10: Table S9. List of DEPs.
DOI: 10.6084/m9.figshare.19808134
title: Additional file 11 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 11: Table S10. GO annotation enrichment analysis in BP45_vs_AP37.
DOI: 10.6084/m9.figshare.19808170
title: Additional file 8 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 8: Table S7. KEGG enrich for CT53vsAT37.
DOI: 10.6084/m9.figshare.19808173.v1
title: Additional file 9 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 9: Table S8. KEGG enrich for CT53vsBT45.
DOI: 10.6084/m9.figshare.19808161
title: Additional file 5 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 5: Table S4. GO enrich for CT53vsAT37.
DOI: 10.6084/m9.figshare.19808164
title: Additional file 6 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 6: Table S5. GO enrich for CT53vsBT45
DOI: 10.6084/m9.figshare.19808164.v1
title: Additional file 6 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 6: Table S5. GO enrich for CT53vsBT45
DOI: 10.6084/m9.figshare.19808170.v1
title: Additional file 8 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 8: Table S7. KEGG enrich for CT53vsAT37.
DOI: 10.6084/m9.figshare.19808140.v1
title: Additional file 13 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 13: Table S12. GO Annotation Enrichment Analysis in CP53_vs_BP45.