cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22650101
title: Expression of miR-210-3p in the aqueous humor of patients with age-related cataracts and its effect on human lens epithelial cell injury induced by hydrogen peroxide

description: ABSTRACT Purpose: The regulatory effect of microRNA on diseases has been confirmed. This study aimed to evaluate the expression of microRNA-210-3p in age-related cataracts and assess the effect of abnormal miR-210-3p expressions on H2O2-induced SAR01/04 cells. Methods: Reverse-transcription quantitative polymerase chain reaction method was performed to assess the levels of miR-210-3p in aqueous humor samples. Receiver operating characteristic analysis was employed to assess the discrimination ability of miR-210-3p between patients with age-related cataracts and healthy people, and Pearson correlation analysis was used to identify the correlation between miR-210-3p and oxidative stress indices such as superoxide dismutase, glutathione peroxidase, malonaldehyde. Cell counting kit-8 assay and Transwell assay were used to estimate the biological function of H2O2-induced age-related cataract cell model. The levels of oxidative stress indices such as superoxide dismutase, glutathione peroxidase, and malonaldehyde were measured to evaluate the degree of oxidative stress damage in the age-related cataract cell model. The relationship between miR-210-3p and its target gene was verified by luciferase reporter gene analysis. Results: The miR-210-3p expression was elevated in the aqueous humor of patients with age-related cataracts. A high miR-210-3p expression showed a high diagnostic value for age-related cataracts and was significantly associated with the level of oxidative stress markers in patients with age-related cataracts. The inhibition of miR-210-3p can reverse oxidative stress stimulation and adverse effects on H2O2-induced cell function. Conclusions: The results suggested that miR-210-3p could promote cell viability, cell migration, and oxidative stress by targeting autophagy-related gene 7 in in vitro age-related cataract cell model.
DOI: 10.6084/m9.figshare.16880473
title: Additional file 1 of Exploring biological basis of Syndrome differentiation in coronary heart disease patients with two distinct Syndromes by integrated multi-omics and network pharmacology strategy

description: Additional file 1. Materials and methods for proteomics and metabolomics experiments. Table S1. List of differential metabolites. Table S2. Herbs in the 6 TCM formulae under study. Table S3. Active compounds in each formula. Table S4. Putative targets in each formula. Table S5. Diseases the most highly associated with CHD and corresponding drug ATC codes.
DOI: 10.6084/m9.figshare.22650101.v1
title: Expression of miR-210-3p in the aqueous humor of patients with age-related cataracts and its effect on human lens epithelial cell injury induced by hydrogen peroxide

description: ABSTRACT Purpose: The regulatory effect of microRNA on diseases has been confirmed. This study aimed to evaluate the expression of microRNA-210-3p in age-related cataracts and assess the effect of abnormal miR-210-3p expressions on H2O2-induced SAR01/04 cells. Methods: Reverse-transcription quantitative polymerase chain reaction method was performed to assess the levels of miR-210-3p in aqueous humor samples. Receiver operating characteristic analysis was employed to assess the discrimination ability of miR-210-3p between patients with age-related cataracts and healthy people, and Pearson correlation analysis was used to identify the correlation between miR-210-3p and oxidative stress indices such as superoxide dismutase, glutathione peroxidase, malonaldehyde. Cell counting kit-8 assay and Transwell assay were used to estimate the biological function of H2O2-induced age-related cataract cell model. The levels of oxidative stress indices such as superoxide dismutase, glutathione peroxidase, and malonaldehyde were measured to evaluate the degree of oxidative stress damage in the age-related cataract cell model. The relationship between miR-210-3p and its target gene was verified by luciferase reporter gene analysis. Results: The miR-210-3p expression was elevated in the aqueous humor of patients with age-related cataracts. A high miR-210-3p expression showed a high diagnostic value for age-related cataracts and was significantly associated with the level of oxidative stress markers in patients with age-related cataracts. The inhibition of miR-210-3p can reverse oxidative stress stimulation and adverse effects on H2O2-induced cell function. Conclusions: The results suggested that miR-210-3p could promote cell viability, cell migration, and oxidative stress by targeting autophagy-related gene 7 in in vitro age-related cataract cell model.
DOI: 10.25549/usctheses-c89-355624
title: etd-DankwaLind-8852
DOI: 10.6084/m9.figshare.16880473.v1
title: Additional file 1 of Exploring biological basis of Syndrome differentiation in coronary heart disease patients with two distinct Syndromes by integrated multi-omics and network pharmacology strategy

description: Additional file 1. Materials and methods for proteomics and metabolomics experiments. Table S1. List of differential metabolites. Table S2. Herbs in the 6 TCM formulae under study. Table S3. Active compounds in each formula. Table S4. Putative targets in each formula. Table S5. Diseases the most highly associated with CHD and corresponding drug ATC codes.
DOI: 10.25549/usctheses-c89-355625
title: etd-DankwaLind-8852-a
DOI: 10.6084/m9.figshare.16880363.v1
title: Additional file 4 of Smoothness metrics for reaching performance after stroke. Part 1: which one to choose?

description: Additional file 4. This compressed folder includes all MATLAB™ scripts used in the simulation analyses, and the resulting metric values.
DOI: 10.6084/m9.figshare.22649291
title: Additional file 3 of Haplotype-resolved genomes of two buckwheat crops provide insights into their contrasted rutin concentrations and reproductive systems

description: Additional file 3: Table S1. Sequencing reads used for assembly of F. esculentum genome. Table S2. Sequencing reads used for assembly of F. tataricum genome. Tables S3. BUSCO analysis of genome assembly completeness of F. esculentum and F. tataricum. Table S4. Classification of repetitive elements in F. esculentum and F. tataricum genomes. Table S5. Summary of RNA sequencing data. Table S6. Gene model characteristics of F. esculentum genome. Tables S7. BUSCO evaluation of predicted gene models for two Fagopyrum genomes. Table S8. Gene model characteristics of F. tataricum genome. Table S9. Functional annotation of predicted gene for F. esculentum genome. Table S10. Functional annotation of predicted gene for F. tataricum genome. Table S11. Gene data sets used for comparative genomic analysis. Table S12. Syntenic gene pairs within F. esculentum genome. Table S13. Syntenic gene pairs within F. tataricum genome. Table S14. Summary of gene family clustering. Table S15. GO enrichment analysis of lineage-specific genes in the Fagopyrum. Table S16. Summary of gene families expansion/contraction in species. Table S17. GO enrichment analysis of the expanded gene families in F. tataricum. Table S18. GO enrichment analysis of the expanded gene families in F. esculentum. Table S19. Summary of FeUGT2 promoter cis-acting elements prediction. Table S20. Summary of FtUGT2 promoter cis-acting elements prediction. Table S21. The list of S-RNase in different species. Table S22. The genetic differences within the haploid genome.
DOI: 10.6084/m9.figshare.22649266.v1
title: Additional file 2 of SynBioTools: a one-stop facility for searching and selecting synthetic biology tools

description: Additional file 2. The code zip file on extracting tabular information from papers by paring the full-text XML file.
DOI: 10.6084/m9.figshare.22649252
title: Additional file 1 of Population genomic analysis provides evidence of the past success and future potential of South China tiger captive conservation

description: Additional file 1: Table S1. Sample characteristics and genome sequencing information before and after filtering. Table S2. Sequencing data statistics. Table S3. 17-mer statistic information. Table S4. Genome assembly information. Table S5. Sizes of individual chromosomes. Table S6. Assessment of completeness of the South China tiger genome assembly. Table S7. Summary of repeat contents. Table S8. Statistics of gene structure prediction. Table S9. Result of gene functional annotation. Table S10. Summary of non-coding RNA in genome. Table S11. Sampling information included in the analyses. Table S12. Re-sequencing data statistics in this study. Table S13. Genome mapping and coverage information for all accessions analyzed in this study. Table S14. Number and distribution of SNPs in each genome. Table S15. Distribution of whole-genome SNPs in different subspecies/species. Table S16. Average genome-wide nucleotide diversity in six tiger subspecies. Table S17. Pairwise FST values between six tiger subspecies. Table S18. ABBA-BABA estimates. Only results with |Z score| &gt; 3 were remained. Table S19. f4-ratio calculated between individual South China tigers and other tiger subspecies. Only results with FDR &lt; 0.05 were retained. Table S20. Pairwise relatedness estimates based on allelic identity-by-descent (IBD). Table S21. Inbreeding coefficients and ROH information. Table S22. Deleterious mutations segregating across and within six tiger subspecies. Table S23. Individual homozygote and heterozygote SNP counts per impact category in each tiger subspecies.
DOI: 10.6084/m9.figshare.22649260.v1
title: Additional file 1 of SynBioTools: a one-stop facility for searching and selecting synthetic biology tools

description: Additional file 1. The code zip file on extracting tabular information from papers in PDF format based on OCR.
DOI: 10.5281/zenodo.10636332
title: Dataset for the publication: Electrochemical depolymerisation of polylactic acid

description: The dataset covers the research data of the publication in Green Chemistry from RSC with the title "Electrochemical depolymerisation of polylactic acid". The provided data comprehend the main experimental data with raw data for GPC and HPLC as well as a python script for data analysis and plotting.
description: Funding & Acknowledgement: We thank Werner Siemens Foundation for funding in the frame of the WSS research prize. This work was also supported by the Cluster of Excellence Fuel Science Center (EXC 2186, ID: 390919832) funded by the Excellence Initiative by the German federal and state governments to promote science and research at German universities, the German Research Foundation within DFG PA 1689/17-1 as well as by German Research Foundations in the frame of NFDI4CAT (ID 441926934). Sonja Mürtz thanks Cusanuswerk e.V. for funding. The scientific activities of the Bioeconomy Science Center were financially supported by the Ministry of Culture and Science within the framework of the NRW Strategieprojekt BioSC (No. 313/323‐400‐002 13). The authors thank the analytical staff members Noah Avraham and Jens Heller for performing HPLC analysis.
DOI: 10.5281/zenodo.10636333
title: Dataset for the publication: Electrochemical depolymerisation of polylactic acid

description: The dataset covers the research data of the publication in Green Chemistry from RSC with the title "Electrochemical depolymerisation of polylactic acid". The provided data comprehend the main experimental data with raw data for GPC and HPLC as well as a python script for data analysis and plotting.
description: Funding & Acknowledgement: We thank Werner Siemens Foundation for funding in the frame of the WSS research prize. This work was also supported by the Cluster of Excellence Fuel Science Center (EXC 2186, ID: 390919832) funded by the Excellence Initiative by the German federal and state governments to promote science and research at German universities, the German Research Foundation within DFG PA 1689/17-1 as well as by German Research Foundations in the frame of NFDI4CAT (ID 441926934). Sonja Mürtz thanks Cusanuswerk e.V. for funding. The scientific activities of the Bioeconomy Science Center were financially supported by the Ministry of Culture and Science within the framework of the NRW Strategieprojekt BioSC (No. 313/323‐400‐002 13). The authors thank the analytical staff members Noah Avraham and Jens Heller for performing HPLC analysis.
DOI: 10.6084/m9.figshare.13212142
title: Additional file 2 of Elevated blood urea nitrogen is associated with recurrence of post-operative chronic subdural hematoma

description: Additional file 2. The complete data used and analysed during the current study.
DOI: 10.6084/m9.figshare.22649266
title: Additional file 2 of SynBioTools: a one-stop facility for searching and selecting synthetic biology tools

description: Additional file 2. The code zip file on extracting tabular information from papers by paring the full-text XML file.
DOI: 10.6084/m9.figshare.22649260
title: Additional file 1 of SynBioTools: a one-stop facility for searching and selecting synthetic biology tools

description: Additional file 1. The code zip file on extracting tabular information from papers in PDF format based on OCR.
DOI: 10.6084/m9.figshare.24751223
title: Additional file 1 of StableDNAm: towards a stable and efficient model for predicting DNA methylation based on adaptive feature correction learning

description: Additional file 1.
DOI: 10.6084/m9.figshare.24751223.v1
title: Additional file 1 of StableDNAm: towards a stable and efficient model for predicting DNA methylation based on adaptive feature correction learning

description: Additional file 1.
DOI: 10.6084/m9.figshare.22649434.v1
title: Additional file 2 of Type 1 diabetes and diet-induced obesity predispose C57BL/6J mice to PM2.5-induced lung injury: a comparative study

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.13212220
title: Additional file 1 of RGG1, Involved in the Cytokinin Regulatory Pathway, Controls Grain Size in Rice

description: Additional file 1 : Fig. S1. Sequence alignment of the Gγ proteins in rice, Arabidopsis and maize. The red line indicates the predicted nuclear localization signal sequence. The red box indicates the CaaX isoprenylation motif at the C-terminal end. The green line indicates the GGL domain. Fig. S2. Subcellular localization of RGG1ΔNLS-GFP. Scale bar, 20 μm. Fig. S3. Internode lengths of NIP and the RGG1 OE lines. Scale bar, 5 cm. Fig. S4. Comparison of plant and grain phenotypes between WYJ30 and the OE lines. Fig. S5. Targeted mutagenesis of RGG1 in the WYJ30 background and protein sequence alignment of WYJ30 and the mutants. Fig. S6. Gene Ontology (GO) DEG enrichment of the biological process, molecular function and cellular component categories. Fig. S7. Relative expression levels of genes concerning cytokinin biosynthesis. Fig. S8. NaCl treatment of NIP and the transgenic lines. Table S1. Comparison of major agronomic traits between NIP and the transgenic lines. Table S2. Comparison of major agronomic traits between WYJ30 and the transgenic lines. Table S3. Primers used in this study.
DOI: 10.6084/m9.figshare.24751295
title: Additional file 1 of Y chromosome microdeletions in Chinese men with infertility: prevalence, phenotypes, and intracytoplasmic sperm injection outcomes

description: Additional file 1 Description of data: table with detailed results of semen analysis and Y-chromosome microdeletion analysis of the 4,714 men with infertility.
DOI: 10.6084/m9.figshare.24751295.v1
title: Additional file 1 of Y chromosome microdeletions in Chinese men with infertility: prevalence, phenotypes, and intracytoplasmic sperm injection outcomes

description: Additional file 1 Description of data: table with detailed results of semen analysis and Y-chromosome microdeletion analysis of the 4,714 men with infertility.
DOI: 10.6084/m9.figshare.24751299
title: Additional file 1 of Exploring the mechanism of artificial selection signature in Chinese indigenous pigs by leveraging multiple bioinformatics database tools

description: Additional file 1. Figures S1-S11 and Tables S1-S9.
DOI: 10.6084/m9.figshare.24751299.v1
title: Additional file 1 of Exploring the mechanism of artificial selection signature in Chinese indigenous pigs by leveraging multiple bioinformatics database tools

description: Additional file 1. Figures S1-S11 and Tables S1-S9.
DOI: 10.6084/m9.figshare.21077316.v1
title: Additional file 6 of Leveraging genomic diversity for discovery in an electronic health record linked biobank: the UCLA ATLAS Community Health Initiative

description: Additional file 6: Table S10. Summary of GWAS analyses in ATLAS.
DOI: 10.6084/m9.figshare.21077322.v1
title: Additional file 8 of Leveraging genomic diversity for discovery in an electronic health record linked biobank: the UCLA ATLAS Community Health Initiative

description: Additional file 8: Table S12. Effective sample sizes and effect sizes of correlated phenotypes for chronic nonalcoholic liver disease. Table S13. Role of phecode occurrences for defining cases. Table S14. Summary of methods. Table S15. Comparison of GIA clusters when restricting to unrelated individuals. Table S16. Comparison of genetic ancestry proportions within SIREs when using unrelated individuals.
DOI: 10.6084/m9.figshare.22649434
title: Additional file 2 of Type 1 diabetes and diet-induced obesity predispose C57BL/6J mice to PM2.5-induced lung injury: a comparative study

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.24032430.v1
title: Glucocorticoids increase adiposity by stimulating Krüppel-like factor 9 expression in macrophages

description: Glucocorticoids increase adiposity by stimulating Krüppel-like factor 9 expression in macrophages
DOI: 10.6084/m9.figshare.23702871
title: Dynamics and Crosstalk between Gut Microbiota, Metabolome, and Fecal Calprotectin in Very Preterm Infants: Insights into Feeding Intolerance

description: Untargeted metabolome data of 1908 metabolites with HMDB annotations in feces 118 very preterm infants with and without feeding intolerance
DOI: 10.6084/m9.figshare.9547136
title: In-depth characterization of the placental imprintome reveals novel differentially methylated regions across birth weight categories

description: Imprinted genes play a pivotal role in placental processes underlying fetal development, and much interest centers on discerning whether these loci, via changes in DNA methylation and/or gene expression, inform disruptions in appropriate fetal growth. In this study, we comprehensively profiled DNA methylation across the placental imprintome and assessed the relationship with gene expression levels and aberrant fetal growth. Placental DNA methylation across 153 imprinted loci, including imprint control regions (ICR) and surrounding non-ICR regions, was surveyed using the Nimblegen TruSeq bisulfite sequencing platform among participants enrolled in the Rhode Island Child Health Study (RICHS, n = 163). Methylation and gene expression associations were assessed using eQTM analysis. Differential methylation analysis contrasting small (SGA) and large for gestational age (LGA) infants against appropriate for gestational age (AGA) infants was assessed using the DMRcate R package. We identified 34 SGA-related differentially methylated regions (DMRs) and 9 LGA-related DMRs (FDR&lt;0.05), and these BW-DMRs predominated in promoter and intronic regions. We observed overall hypomethylation among SGA-DMRs overlapping maternally expressed (paternally imprinted) genes while no parent-of-origin effect was observed among LGA DMRs. Three BW-DMRs, mapping to <i>GABRG3, IGF1R</i> and <i>MEST</i>, were common to SGA and LGA placenta. We did not observe significant correlations between BW-DMR-associated CpG methylation and gene expression levels. We report the first in-depth characterization of the placental imprintome in a population-wide setting. Our findings reveal growth-related differences in methylation without concomitant expression differences in regions that extend beyond typically interrogated imprinted loci, highlighting potentially novel placental biomarkers of growth and development.
DOI: 10.6084/m9.figshare.9547136.v1
title: In-depth characterization of the placental imprintome reveals novel differentially methylated regions across birth weight categories

description: Imprinted genes play a pivotal role in placental processes underlying fetal development, and much interest centers on discerning whether these loci, via changes in DNA methylation and/or gene expression, inform disruptions in appropriate fetal growth. In this study, we comprehensively profiled DNA methylation across the placental imprintome and assessed the relationship with gene expression levels and aberrant fetal growth. Placental DNA methylation across 153 imprinted loci, including imprint control regions (ICR) and surrounding non-ICR regions, was surveyed using the Nimblegen TruSeq bisulfite sequencing platform among participants enrolled in the Rhode Island Child Health Study (RICHS, n = 163). Methylation and gene expression associations were assessed using eQTM analysis. Differential methylation analysis contrasting small (SGA) and large for gestational age (LGA) infants against appropriate for gestational age (AGA) infants was assessed using the DMRcate R package. We identified 34 SGA-related differentially methylated regions (DMRs) and 9 LGA-related DMRs (FDR&lt;0.05), and these BW-DMRs predominated in promoter and intronic regions. We observed overall hypomethylation among SGA-DMRs overlapping maternally expressed (paternally imprinted) genes while no parent-of-origin effect was observed among LGA DMRs. Three BW-DMRs, mapping to <i>GABRG3, IGF1R</i> and <i>MEST</i>, were common to SGA and LGA placenta. We did not observe significant correlations between BW-DMR-associated CpG methylation and gene expression levels. We report the first in-depth characterization of the placental imprintome in a population-wide setting. Our findings reveal growth-related differences in methylation without concomitant expression differences in regions that extend beyond typically interrogated imprinted loci, highlighting potentially novel placental biomarkers of growth and development.
DOI: 10.6084/m9.figshare.21601533.v1
title: Additional file 4 of HNRNPA2B1-mediated m6A modification of TLR4 mRNA promotes progression of multiple myeloma

description: Additional file 4. The 23 genes differentially expressed in both the transcriptome and methylation sequencing for MM cells transfected with sh-HNRNPA2B1-8226 and the control sh-NC-8226.
DOI: 10.34740/kaggle/dsv/7594120
title: Egypt Gold Prices | Daily Updated
DOI: 10.6084/m9.figshare.21077415
title: Additional file 1 of Quantitative assessment of eye movements using a binocular paradigm: comparison among amblyopic, recovered amblyopic and normal children

description: Additional file 1: eTable 1. Results of repeated measures.
DOI: 10.6084/m9.figshare.21077415.v1
title: Additional file 1 of Quantitative assessment of eye movements using a binocular paradigm: comparison among amblyopic, recovered amblyopic and normal children

description: Additional file 1: eTable 1. Results of repeated measures.
DOI: 10.6084/m9.figshare.21601533
title: Additional file 4 of HNRNPA2B1-mediated m6A modification of TLR4 mRNA promotes progression of multiple myeloma

description: Additional file 4. The 23 genes differentially expressed in both the transcriptome and methylation sequencing for MM cells transfected with sh-HNRNPA2B1-8226 and the control sh-NC-8226.
DOI: 10.6084/m9.figshare.20552311.v1
title: Additional file 11 of Comparative transcriptome in large-scale human and cattle populations

description: Additional file 11: Table S10. Summary of novel variants detected by PolyFun + SuSiE in human height.