cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24174441.v1
title: Supplementary Material for: Green tea polyphenols alleviate kidney injury induced by di(2-ethylhexyl) phthalate in mice

description: Background: Di(2-ethylhexyl) phthalate (DEHP) is a common plasticizer. Studies have revealed that DEHP exposure can cause kidney damage. Green tea is among the most popular beverages in China. Green tea polyphenols (GTPs) have been proven to have therapeutic effects on organ damage induced by heavy metal exposure. However, few studies have reported on GTP relieving DEHP-induced kidney damage. Methods: C57BL/6J male mice aged 6–8 weeks were treated with distilled water (control group), 1500 mg/kg/d DEHP + corn oil (model group), 1500 mg/kg/d DEHP + corn oil + 70 mg/kg GTP (treatment group), corn oil (oil group), and 70 mg/kg GTP (GTP group) by gavage for 8 weeks, respectively. The renal function of mice and renal tissue histopathology of each group were evaluated. The renal tissues of mice in the model, treatment, and control groups were analyzed using high-throughput sequencing. We calculated the differentially expressed miRNAs and mRNAs using the limma R package, the CIBERSORT algorithm was used to predict immune infiltration, the starBase database was used to screen the miRNA–mRNA regulatory axis, and immunohistochemical analyses were performed to verify protein expression. Results: GTP alleviated the deterioration of renal function, renal inflammation and fibrosis, and mitochondrial and endoplasmic reticulum lesions induced by DEHP in mice. Differential immune infiltrations of plasma, dendritic, T, and B cells were noted between the model and treatment groups. We found that three differentially expressed miRNAs (mmu-miR-383-5p, mmu-miR-152-3p, and mmu-miR-144-3p), three differentially expressed mRNAs (Ddit4, Dusp1, and Snx18), and three differentially expressed proteins (Ddit4, Dusp1, and Snx18) played crucial roles in the miRNA–mRNA–protein regulatory axes when GTPs mitigate DEHP-induced kidney damage in mice. Conclusion: GTP can alleviate DEHP-induced kidney damage and regulate immune cell infiltration. We screened four important miRNA–mRNA–protein regulatory axes of GTP mitigating DEHP-induced kidney damage in mice.
DOI: 10.6084/m9.figshare.24115812.v2
title: <b>30 by 30 for plant diversity: how can we protect more of nature?</b>

description: <b>specimen_localities_for_mapping_FD.csv</b>Point localities of specimens held in natural history collections for a random sample of 575 angiosperm species that all occur in the continent of Africa. Some of the localities were georeferenced as part of this research. Localities were spatially disaggregated using the R package <i>ecospat</i> prior to use in Species Distribution Models that were then used to spatially project biodiversity metrics.Fields:1. SourceHow the specimen locality data was obtained: <b>GBIF</b> = from the Global Biodiversity Information Facility, <b>TROPICOS</b><b> </b>= from Tropicos.org. Missouri Botanical Garden, <b>Taxonomic_literature</b> = specimens cited in published taxonomic literature, <b>Kew_herbarium</b><b> </b>= specimens seen by authors in the herbarium of the Royal Botanic Gardens, Kew, London. <b>RAINBIO =</b> RAINBIO species checklist of tropical African vascular plants, <b>LMA_herbarium</b> = specimens seen by authors in the herbarium of the Agricultural Research Institute of Mozambique, Maputo, Mozambique, <b>Kitwe_herbarium</b> = specimens seen by authors in the herbarium of the Division of Forest Research Forestry Department, Kitwe, Zambia, <b>Edinburgh_herbarium</b> = specimens seen by authors in the herbarium of the Royal Botanic Garden Edinburgh, <b>Windhoek_herbarium</b> = specimens seen by authors in the herbarium of the National Herbarium of Namibia, <b>UPS_herbarium</b><b> </b>= specimens seen by authors in the herbarium of the Museum of Evolution, Uppsala, Sweden.2. Identitiy_numberIdentity number applied by GBIF to the specimen record3. scientificNameBinomial species name4. CountryCountry in which the specimen was made5. localityTextual description of the locality in which the specimen was made6. habitatTextual description of the habitat in which the specimen was made7. dayDay of the month on which the specimen was made8. monthMonth of the year on which the specimen was made9. yearYear in which the specimen was made10. recordedByPerson or people who made the specimen11. rec.NumberNumber given by collector to collection12. Error.Diam.Spatial error of georefencing (km)13. Min_Elev.M.Minimum altitude (m)14. Max_Elev.M.Maximum altitude (m)15. decimalLatitudeCoordinates of latitude16. decimalLongitudeCoordinates of longitude17. Label..notesAdditional information recorded about the location of specimen collection18. GeoreferencedWhether each specimen record was (1) or was not (0) georeferenced (i.e. coordinates inferred from a textual description of locality) during this research<br><b>taxonomic_references_from_which_trait_values_obtained.docx</b>Taxonomic publications from which trait values were extracted.
DOI: 10.5281/zenodo.8366860
title: Wykaz 33. Wykaz stanowisk Leptoglossus occidentalis wykorzystanych podczas modelowania niszy ekologicznej

description: Zielińska, Anna. Ocena warunków siedliskowych dla inwazyjnych gatunków pluskwiaków różnoskrzydłych (Hemiptera: Heteroptera) na terenie Europy, ze szczególnym uwzględnieniem Polski (praca doktorska). Wykaz 33. Wykaz stanowisk Leptoglossus occidentalis wykorzystanych podczas modelowania niszy ekologicznej (dane na dzień: 26.02.2023).
DOI: 10.5281/zenodo.8366859
title: Wykaz 33. Wykaz stanowisk Leptoglossus occidentalis wykorzystanych podczas modelowania niszy ekologicznej

description: Zielińska, Anna. Ocena warunków siedliskowych dla inwazyjnych gatunków pluskwiaków różnoskrzydłych (Hemiptera: Heteroptera) na terenie Europy, ze szczególnym uwzględnieniem Polski (praca doktorska). Wykaz 33. Wykaz stanowisk Leptoglossus occidentalis wykorzystanych podczas modelowania niszy ekologicznej (dane na dzień: 26.02.2023).
DOI: 10.6084/m9.figshare.22699810
title: SNP_clean_sorted.vcf.gz

description: We obtained approximately 5.57 Tb of whole-genome sequencing data for the 220 <i>Vaccinium</i> accessionsThese reads covered around 93.22% of the reference genome with an average depth of 35-fold.
DOI: 10.6084/m9.figshare.22699810.v2
title: SNP_clean_sorted.vcf.gz

description: We obtained approximately 5.57 Tb of whole-genome sequencing data for the 220 <i>Vaccinium</i> accessionsThese reads covered around 93.22% of the reference genome with an average depth of 35-fold.
DOI: 10.6084/m9.figshare.22699810.v1
title: SNP_clean_sorted.vcf.gz

description: We obtained approximately 5.41 Tb of whole-genome sequencing data for the 219 <em>Vaccinium</em> accessionsThese reads covered around 93.27% of the reference genome with an average depth of 34.98-fold. After filtering based on the quality score and allele frequency, we retained a total of 3,407,572 high-quality SNPs for further analysis
DOI: 10.6084/m9.figshare.22616945.v1
title: Additional file 15 of Untargeted metabolomics reveals alternations in metabolism of bovine mammary epithelial cells upon IFN-γ treatment

description: Additional file 15: Table S5. List of differentially expressed metabolites (DEMs) upon 12 h IFN-γ treatment compared to 6 h IFN-γ treatment in both negative and positive ion modes.
DOI: 10.6084/m9.figshare.8142638
title: MOESM2 of Low diversity of Angiostrongylus cantonensis complete mitochondrial DNA sequences from Australia, Hawaii, French Polynesia and the Canary Islands revealed using whole genome next-generation sequencing

description: Additional file 2: Alignment S2. Alignment of complete mtDNA sequences of all available A. cantonensis and A. malaysiensis in CLC format including annotations.
DOI: 10.6084/m9.figshare.8142638.v1
title: MOESM2 of Low diversity of Angiostrongylus cantonensis complete mitochondrial DNA sequences from Australia, Hawaii, French Polynesia and the Canary Islands revealed using whole genome next-generation sequencing

description: Additional file 2: Alignment S2. Alignment of complete mtDNA sequences of all available A. cantonensis and A. malaysiensis in CLC format including annotations.
DOI: 10.6084/m9.figshare.16850419
title: #GlobalCollembola: site-level database and analyses

description: Site-level database of the #GlobalCollembola initiative and programming code for path analysis and geospatial modelling in the synthesis publication: "Globally invariant metabolism but density-diversity mismatch in springtails". Four files are attached:
1) GCdatabase_sites.csv - site-level database structured for path analysis
2) Rcode_PathAnalysis - markdown pdf with the R code for path analysis
3) 20210527_collembola_sampled.csv - site-level database structured for geospatial modelling
4) 20210630_collembola_pipeline.py - the Python code for geospatial modelling
4) #GCdatabase Events - sampling even database used for additional analysis (accounting for the sampling year and months)
DOI: 10.6084/m9.figshare.24190494
title: Honokiol Attenuates Choroidal Neovascularization by Inhibiting the Hypoxia-Inducible Factor-α/Vascular Endothelial Growth Factor Axis via Nuclear Transcription Factor-Kappa B Activation

description: Honokiol is a lignan isolated from <i>Magnolia officinalis</i> and exhibits anti-angiogenic properties. This study was conducted to investigate the role of honokiol in choroidal neovascularization. C57BL/6 mice were treated with honokiol at 10–20 mg/kg by daily intraperitoneal injection from day 1 to 6 after laser photocoagulation. ARPE-19 cells were cultured under hypoxic conditions with or without the presence of honokiol. After laser photocoagulation and honokiol treatment, hematoxylin and eosin staining, immunofluorescence and fundus fluorescein angiography were used to analyze the effect of honokiol on choroidal neovascularization formation. Quantitative real-time PCR, western blot, enzyme-linked immunosorbent assay, immunofluorescence, luciferase assay, and chromatin immunoprecipitation were performed to explore the mechanism of honokiol in the pathological process of choroidal neovascularization. Finally, the role of honokiol on the human choroidal vascular endothelial cells was detected by using 5-ethynyl-20-deoxyuridine assay, Transwell and Tube formation assays. The results of hematoxylin and eosin staining and immunofluorescence suggested that honokiol reduced the thickness, length, and area of choroidal neovascularization lesions in laser-induced choroidal neovascularization mouse model. Fundus fluorescein angiography showed that choroidal neovascularization leakage was reduced in honokiol group and the concentration of 20 mg/kg showed better effects. Mechanism studies have shown that honokiol exerted inhibitory effects on choroidal neovascularization by inactivating hypoxia-inducible factor-1α/vascular endothelial growth factor axis through the nuclear transcription factor-kappa B signaling pathway. The same results were obtained in ARPE-19 cells under hypoxic conditions. Furthermore, the conditional medium of retinal pigmented epithelial cells promoted the proliferation, migration, and tube formation of human choroidal vascular endothelial cells, while honokiol reversed these. We demonstrated that honokiol attenuated choroidal neovascularization formation by inactivating the hypoxia-inducible factor-1α/vascular endothelial growth factor axis through nuclear transcription factor-kappa B signaling pathway.
DOI: 10.6084/m9.figshare.24190494.v1
title: Honokiol Attenuates Choroidal Neovascularization by Inhibiting the Hypoxia-Inducible Factor-α/Vascular Endothelial Growth Factor Axis via Nuclear Transcription Factor-Kappa B Activation

description: Honokiol is a lignan isolated from <i>Magnolia officinalis</i> and exhibits anti-angiogenic properties. This study was conducted to investigate the role of honokiol in choroidal neovascularization. C57BL/6 mice were treated with honokiol at 10–20 mg/kg by daily intraperitoneal injection from day 1 to 6 after laser photocoagulation. ARPE-19 cells were cultured under hypoxic conditions with or without the presence of honokiol. After laser photocoagulation and honokiol treatment, hematoxylin and eosin staining, immunofluorescence and fundus fluorescein angiography were used to analyze the effect of honokiol on choroidal neovascularization formation. Quantitative real-time PCR, western blot, enzyme-linked immunosorbent assay, immunofluorescence, luciferase assay, and chromatin immunoprecipitation were performed to explore the mechanism of honokiol in the pathological process of choroidal neovascularization. Finally, the role of honokiol on the human choroidal vascular endothelial cells was detected by using 5-ethynyl-20-deoxyuridine assay, Transwell and Tube formation assays. The results of hematoxylin and eosin staining and immunofluorescence suggested that honokiol reduced the thickness, length, and area of choroidal neovascularization lesions in laser-induced choroidal neovascularization mouse model. Fundus fluorescein angiography showed that choroidal neovascularization leakage was reduced in honokiol group and the concentration of 20 mg/kg showed better effects. Mechanism studies have shown that honokiol exerted inhibitory effects on choroidal neovascularization by inactivating hypoxia-inducible factor-1α/vascular endothelial growth factor axis through the nuclear transcription factor-kappa B signaling pathway. The same results were obtained in ARPE-19 cells under hypoxic conditions. Furthermore, the conditional medium of retinal pigmented epithelial cells promoted the proliferation, migration, and tube formation of human choroidal vascular endothelial cells, while honokiol reversed these. We demonstrated that honokiol attenuated choroidal neovascularization formation by inactivating the hypoxia-inducible factor-1α/vascular endothelial growth factor axis through nuclear transcription factor-kappa B signaling pathway.
DOI: 10.6084/m9.figshare.22616800
title: Additional file 1 of Establishment of dynamic nomogram and risk score models for T2DM: a retrospective cohort study in Beijing

description: Additional file 1.
DOI: 10.6084/m9.figshare.12656222
title: Global Monitoring of Geomagnetic Storm-Induced Ionosphere Anomalies Using 3D Ionospheric Modeling with Multi-GNSS and COSMIC Measurements

description: 3-D ionospheric electron
density (IED) products by CIT and IRI models during the September 7-8, 2017 storm.
DOI: 10.6084/m9.figshare.10034798
title: MOESM2 of Non-contact, synchronous dynamic measurement of respiratory rate and heart rate based on dual sensitive regions

description: Additional file 2. Reference RR recorded by commercial medical sensors during recording video 7.
DOI: 10.6084/m9.figshare.10034798.v1
title: MOESM2 of Non-contact, synchronous dynamic measurement of respiratory rate and heart rate based on dual sensitive regions

description: Additional file 2. Reference RR recorded by commercial medical sensors during recording video 7.
DOI: 10.6084/m9.figshare.10034801
title: MOESM3 of Non-contact, synchronous dynamic measurement of respiratory rate and heart rate based on dual sensitive regions

description: Additional file 3. Reference HR recorded by commercial medical sensors during recording video 7.
DOI: 10.6084/m9.figshare.10034801.v1
title: MOESM3 of Non-contact, synchronous dynamic measurement of respiratory rate and heart rate based on dual sensitive regions

description: Additional file 3. Reference HR recorded by commercial medical sensors during recording video 7.
DOI: 10.6084/m9.figshare.10034807
title: MOESM5 of Non-contact, synchronous dynamic measurement of respiratory rate and heart rate based on dual sensitive regions

description: Additional file 5. Reference RR recorded by commercial medical sensors during recording video 2.
DOI: 10.6084/m9.figshare.22616933
title: Additional file 11 of Untargeted metabolomics reveals alternations in metabolism of bovine mammary epithelial cells upon IFN-γ treatment

description: Additional file 11: Table S1. Summary of the number of differentially expressed metabolites (DEMs) in each comparison group in both negative and positive ion modes
DOI: 10.6084/m9.figshare.10034807.v1
title: MOESM5 of Non-contact, synchronous dynamic measurement of respiratory rate and heart rate based on dual sensitive regions

description: Additional file 5. Reference RR recorded by commercial medical sensors during recording video 2.
DOI: 10.6084/m9.figshare.10034810
title: MOESM6 of Non-contact, synchronous dynamic measurement of respiratory rate and heart rate based on dual sensitive regions

description: Additional file 6. Reference HR recorded by commercial medical sensors during recording video 2.
DOI: 10.6084/m9.figshare.10034810.v1
title: MOESM6 of Non-contact, synchronous dynamic measurement of respiratory rate and heart rate based on dual sensitive regions

description: Additional file 6. Reference HR recorded by commercial medical sensors during recording video 2.
DOI: 10.6084/m9.figshare.22616899
title: Additional file 9 of The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution

description: Additional file 9: Table S6. Synopsis of the morphological information from the 22 species.
DOI: 10.6084/m9.figshare.22616936.v1
title: Additional file 12 of Untargeted metabolomics reveals alternations in metabolism of bovine mammary epithelial cells upon IFN-γ treatment

description: Additional file 12: Table S2. List of differentially expressed metabolites (DEMs) upon 6 h IFN-γ treatment compared to control in both negative and positive ion modes.
DOI: 10.6084/m9.figshare.22616939
title: Additional file 13 of Untargeted metabolomics reveals alternations in metabolism of bovine mammary epithelial cells upon IFN-γ treatment

description: Additional file 13: Table S3. List of differentially expressed metabolites (DEMs) upon 12 h IFN-γ treatment compared to control in both negative and positive ion modes.
DOI: 10.6084/m9.figshare.22616945
title: Additional file 15 of Untargeted metabolomics reveals alternations in metabolism of bovine mammary epithelial cells upon IFN-γ treatment

description: Additional file 15: Table S5. List of differentially expressed metabolites (DEMs) upon 12 h IFN-γ treatment compared to 6 h IFN-γ treatment in both negative and positive ion modes.
DOI: 10.6084/m9.figshare.22616948.v1
title: Additional file 16 of Untargeted metabolomics reveals alternations in metabolism of bovine mammary epithelial cells upon IFN-γ treatment

description: Additional file 16: Table S6. List of differentially expressed metabolites (DEMs) upon 24 h IFN-γ treatment compared to 6 h IFN-γ treatment in both negative and positive ion modes. Additional file 17: Table S7.  List of differentially expressed metabolites (DEMs) upon 24 h IFN-γ treatment compared to 12 h IFN-γ treatment  in both negative and positive ion modes.
DOI: 10.6084/m9.figshare.22616887.v1
title: Additional file 5 of The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution

description: Additional file 5: Table S2. Simple sequence repeats (SSRs) distribution in the twenty-two plastomes.
DOI: 10.6084/m9.figshare.22616948
title: Additional file 16 of Untargeted metabolomics reveals alternations in metabolism of bovine mammary epithelial cells upon IFN-γ treatment

description: Additional file 16: Table S6. List of differentially expressed metabolites (DEMs) upon 24 h IFN-γ treatment compared to 6 h IFN-γ treatment in both negative and positive ion modes. Additional file 17: Table S7.  List of differentially expressed metabolites (DEMs) upon 24 h IFN-γ treatment compared to 12 h IFN-γ treatment  in both negative and positive ion modes.
DOI: 10.6084/m9.figshare.22616902
title: Additional file 10 of The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution

description: Additional file 10: Table S7. The result of  positive selection analysis based on the branch-site model.
DOI: 10.6084/m9.figshare.12655558.v1
title: Additional file 2 of Survey of rumen microbiota of domestic grazing yak during different growth stages revealed novel maturation patterns of four key microbial groups and their dynamic interactions

description: Additional file 2 Table S1. The statistical analysis of alpha diversity from 7 days to 1 year based on repeated methods ANOVA (mixed-effects model). Table S2. The results of the pairwise PERMANOVA test. Table S3. The results of DESeq2 analysis. Table S4. The results of age discriminatory feature importance score. Table S5. The topological features of intra-interactions of core taxa in each rumen microbial kingdom. Table S6. The topological features of inter-interactions of core taxa among rumen microbial kingdoms. Table S7. The keystone species in the network within each age group.
DOI: 10.6084/m9.figshare.12655558
title: Additional file 2 of Survey of rumen microbiota of domestic grazing yak during different growth stages revealed novel maturation patterns of four key microbial groups and their dynamic interactions

description: Additional file 2 Table S1. The statistical analysis of alpha diversity from 7 days to 1 year based on repeated methods ANOVA (mixed-effects model). Table S2. The results of the pairwise PERMANOVA test. Table S3. The results of DESeq2 analysis. Table S4. The results of age discriminatory feature importance score. Table S5. The topological features of intra-interactions of core taxa in each rumen microbial kingdom. Table S6. The topological features of inter-interactions of core taxa among rumen microbial kingdoms. Table S7. The keystone species in the network within each age group.
DOI: 10.6084/m9.figshare.12655597
title: Additional file 14 of H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts

description: Additional file 14. Supplementary Table 8. The chromatin acetylation changes and the mRNA expression changes of key regulators and targets in the Hippo pathway.
DOI: 10.6084/m9.figshare.24190659
title: Exploration of anti-tumour inhibitors from colchicine derivatives based on 3D-QSAR, molecular docking and molecular dynamics simulations

description: Microtubulin is an important research target for anti-tumour drugs, which can be used to inhibit microtubulin polymerisation and improve the efficacy of tumour therapy. In this paper, 61 microtubule protein inhibitors with anticancer activity are selected as the data set for building a stable and effective QSAR (Topomer CoMFA) model, resulting in a Topomer CoMFA model with validation coefficients of q2 = 0.737 and r2<sub> </sub>= 0.922. Fifteen new inhibitors with theoretically high activity are designed by screening the zinc database for new fragments with good activity through the contribution descriptors obtained by Topomer CoMFA. After simulating the binding affinity and interaction of the inhibitors with the proteins by molecular docking, all these compounds formed strong interactions such as hydrogen bonds with multiple amino acids in the receptor proteins. Furthermore, molecular dynamics results show that the predicted highly active compounds exhibited stable and favourable binding patterns to the active pocket. In addition, these new compounds exhibit good ADMET properties. The present work establishes a reliable QSAR model for computational simulation screening of microtubulin drug development and provides a basis for further access to novel microtubulin inhibitors.