cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.15183435.v1
title: Torin 1 alleviates impairment of TFEB-mediated lysosomal biogenesis and autophagy in <i>TGFBI</i> (p.G623_H626del)-linked Thiel-Behnke corneal dystrophy

description: Thiel-Behnke corneal dystrophy (TBCD) is an epithelial-stromal <i>TGFBI</i> dystrophy caused by mutations in the <i>TGFBI</i> (transforming growth factor beta induced) gene, though the underlying mechanisms and pathogenesis of TBCD are still obscure. The study identifies a novel mutation in the <i>TGFBI</i> gene (p.Gly623_His626del) in a TBCD pedigree. Characteristics of the typical vacuole formation, irregular corneal epithelial thickening and thinning, deposition of eosinophilic substances beneath the epithelium, and involvement of the anterior stroma were observed in this pedigree via transmission electron microscopy (TEM) and histological staining. <i>Tgfbi</i>-p.Gly623_Tyr626del mouse models of TBCD were subsequently generated via CRISPR/Cas9 technology, and the above characteristics were further verified via TEM and histological staining. Lysosomal dysfunction and downregulation of differential expression protein CTSD (cathepsin D) were observed using LysoTracker Green DND-26 and proteomic analysis, respectively. Hence, lysosomal dysfunction probably leads to autophagic flux obstruction in TBCD; this was supported by enhanced LC3-II and SQSTM1 levels and decreased CTSD. TFEB (transcription factor EB) was prominently decreased in TBCD corneal fibroblasts and administration of ATP-competitive MTOR inhibitor torin 1 reversed this decline, resulting in the degradation of accumulated mut-TGFBI (mutant TGFBI protein) via the ameliorative lysosomal function and autophagic flux owing to elevated TFEB activity as measured by western blot, confocal microscopy, and flow cytometry. Transfected HEK 293 cells overexpressing human full-length WT-<i>TGFBI</i> and mut-<i>TGFBI</i> were generated to further verify the results obtained in human corneal fibroblasts. Amelioration of lysosome dysfunction may therefore have therapeutic efficacy in the treatment of TBCD.
DOI: 10.6084/m9.figshare.15183435.v3
title: Torin 1 alleviates impairment of TFEB-mediated lysosomal biogenesis and autophagy in <i>TGFBI</i> (p.G623_H626del)-linked Thiel-Behnke corneal dystrophy

description: Thiel-Behnke corneal dystrophy (TBCD) is an epithelial-stromal <i>TGFBI</i> dystrophy caused by mutations in the <i>TGFBI</i> (transforming growth factor beta induced) gene, though the underlying mechanisms and pathogenesis of TBCD are still obscure. The study identifies a novel mutation in the <i>TGFBI</i> gene (p.Gly623_His626del) in a TBCD pedigree. Characteristics of the typical vacuole formation, irregular corneal epithelial thickening and thinning, deposition of eosinophilic substances beneath the epithelium, and involvement of the anterior stroma were observed in this pedigree via transmission electron microscopy (TEM) and histological staining. <i>Tgfbi</i>-p.Gly623_Tyr626del mouse models of TBCD were subsequently generated via CRISPR/Cas9 technology, and the above characteristics were further verified via TEM and histological staining. Lysosomal dysfunction and downregulation of differential expression protein CTSD (cathepsin D) were observed using LysoTracker Green DND-26 and proteomic analysis, respectively. Hence, lysosomal dysfunction probably leads to autophagic flux obstruction in TBCD; this was supported by enhanced LC3-II and SQSTM1 levels and decreased CTSD. TFEB (transcription factor EB) was prominently decreased in TBCD corneal fibroblasts and administration of ATP-competitive MTOR inhibitor torin 1 reversed this decline, resulting in the degradation of accumulated mut-TGFBI (mutant TGFBI protein) via the ameliorative lysosomal function and autophagic flux owing to elevated TFEB activity as measured by western blot, confocal microscopy, and flow cytometry. Transfected HEK 293 cells overexpressing human full-length WT-<i>TGFBI</i> and mut-<i>TGFBI</i> were generated to further verify the results obtained in human corneal fibroblasts. Amelioration of lysosome dysfunction may therefore have therapeutic efficacy in the treatment of TBCD. <b>Abbreviations</b> AS-OCT: anterior segment optical coherence tomography; ATP: adenosine triphosphate; Cas9: CRISPR-associated protein 9; CLEAR: coordinated lysosomal expression and regulation; CRISPR: clustered regularly interspaced short palindromic repeats; CTSB: cathepsin B; CTSD: cathepsin D; CTSF: cathepsin F; CTSL: cathepsin L; DNA: deoxyribonucleic acid; ECM: extracellular matrix; Fas1: fasciclin 1; FC: flow cytometry; GAPDH: glyceraldeyde-3-phosphate dehydrogenase; GCD2: granular corneal dystrophy type 2; HE: hematoxylin and eosin; LAMP2: lysosomal-associated membrane protein; MT: mutation type; MTOR: mechanistic target of rapamycin kinase; MTORC1: MTOR complex 1; mut-TGFBI: mutant TGFBI protein; SD: standard deviation; TBCD: Thiel-Behnke corneal dystrophy; TEM: transmission electron microscopy; TFEB: transcription factor EB; TGFBI: transforming growth factor beta induced; WT: wild type
DOI: 10.6084/m9.figshare.15183435.v2
title: Torin 1 alleviates impairment of TFEB-mediated lysosomal biogenesis and autophagy in <i>TGFBI</i> (p.G623_H626del)-linked Thiel-Behnke corneal dystrophy

description: Thiel-Behnke corneal dystrophy (TBCD) is an epithelial-stromal <i>TGFBI</i> dystrophy caused by mutations in the <i>TGFBI</i> (transforming growth factor beta induced) gene, though the underlying mechanisms and pathogenesis of TBCD are still obscure. The study identifies a novel mutation in the <i>TGFBI</i> gene (p.Gly623_His626del) in a TBCD pedigree. Characteristics of the typical vacuole formation, irregular corneal epithelial thickening and thinning, deposition of eosinophilic substances beneath the epithelium, and involvement of the anterior stroma were observed in this pedigree via transmission electron microscopy (TEM) and histological staining. <i>Tgfbi</i>-p.Gly623_Tyr626del mouse models of TBCD were subsequently generated via CRISPR/Cas9 technology, and the above characteristics were further verified via TEM and histological staining. Lysosomal dysfunction and downregulation of differential expression protein CTSD (cathepsin D) were observed using LysoTracker Green DND-26 and proteomic analysis, respectively. Hence, lysosomal dysfunction probably leads to autophagic flux obstruction in TBCD; this was supported by enhanced LC3-II and SQSTM1 levels and decreased CTSD. TFEB (transcription factor EB) was prominently decreased in TBCD corneal fibroblasts and administration of ATP-competitive MTOR inhibitor torin 1 reversed this decline, resulting in the degradation of accumulated mut-TGFBI (mutant TGFBI protein) via the ameliorative lysosomal function and autophagic flux owing to elevated TFEB activity as measured by western blot, confocal microscopy, and flow cytometry. Transfected HEK 293 cells overexpressing human full-length WT-<i>TGFBI</i> and mut-<i>TGFBI</i> were generated to further verify the results obtained in human corneal fibroblasts. Amelioration of lysosome dysfunction may therefore have therapeutic efficacy in the treatment of TBCD.
DOI: 10.6084/m9.figshare.7843268
title: Additional file 11: of Comprehensive analysis of dynamic gene expression and investigation of the roles of hydrogen peroxide during adventitious rooting in poplar

description: Table S1. Primers used for RT-qPCR assay. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7843286
title: Additional file 4: of Comprehensive analysis of dynamic gene expression and investigation of the roles of hydrogen peroxide during adventitious rooting in poplar

description: Table S3. Phytohormone-related genes in poplar (XLSX 30 kb)
DOI: 10.6084/m9.figshare.7843295
title: Additional file 5: of Comprehensive analysis of dynamic gene expression and investigation of the roles of hydrogen peroxide during adventitious rooting in poplar

description: Table S4. Normalized expression values of differentially expressed phytohormone-related genes (XLSX 28 kb)
DOI: 10.6084/m9.figshare.7843295.v1
title: Additional file 5: of Comprehensive analysis of dynamic gene expression and investigation of the roles of hydrogen peroxide during adventitious rooting in poplar

description: Table S4. Normalized expression values of differentially expressed phytohormone-related genes (XLSX 28 kb)
DOI: 10.6084/m9.figshare.7843415
title: Additional file 14: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

description: Table S7. Functional enrichment analysis of the specific gene families from C. gigantea. The full list of Gene Ontology (GO) enriched functional categories are shown. (XLSX 108 kb)
DOI: 10.5281/zenodo.10732603
title: Vitis Cultivated vs Wild Type Clusters

description: This document presents a VCF file that encompasses both Vitis species and Vitis Vinifera cultivars. The reference utilized for variant calling is Pinot Noir and the relevant information regarding the tools' parameters for variant calling can be found in the VCF header. For access to the Pinot Noir reference, please visit https://www.grapegenomics.com/pages/PN40024/download.php. The presented VCF underwent filtration using a Python script that excluded lines with "./." entries. As a result, the provided VCF is free from any missing positions. For instance, if there was at least one "./." entry at position 14, it would be disregarded.

NGS data: https://www.nature.com/articles/s41467-019-09135-8
DOI: 10.5281/zenodo.10732604
title: Vitis Cultivated vs Wild Type Clusters

description: This document presents a VCF file that encompasses both Vitis species and Vitis Vinifera cultivars. The reference utilized for variant calling is Pinot Noir and the relevant information regarding the tools' parameters for variant calling can be found in the VCF header. For access to the Pinot Noir reference, please visit https://www.grapegenomics.com/pages/PN40024/download.php. The presented VCF underwent filtration using a Python script that excluded lines with "./." entries. As a result, the provided VCF is free from any missing positions. For instance, if there was at least one "./." entry at position 14, it would be disregarded.

NGS data: https://www.nature.com/articles/s41467-019-09135-8
DOI: 10.6084/m9.figshare.7843415.v1
title: Additional file 14: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

description: Table S7. Functional enrichment analysis of the specific gene families from C. gigantea. The full list of Gene Ontology (GO) enriched functional categories are shown. (XLSX 108 kb)
DOI: 10.6084/m9.figshare.7843451
title: Additional file 20: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

description: Table S8. Characteristics of the transcriptome assemblies from related conifer species and re-analysis results from TRAPID. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.7843451.v1
title: Additional file 20: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

description: Table S8. Characteristics of the transcriptome assemblies from related conifer species and re-analysis results from TRAPID. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.15183495
title: Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease (Data Set)

description: Summary statistic data of eGFRcrea GWAS, kidney eQTL and kidney mQTL data<br>Kidney mQTL mapping was performed based on genotype and DNA methylation data of kidney samples from 443 trans-ancestry individuals (79% are of European ancestry). The significance of the top associated variants per CpG was estimated by adaptive permutation in FastQTL using the covariates above and the setting “--permute 1000”. Beta distribution-adjusted empirical p-values from FastQTL were used to calculate q-values using Storey’s q method, and a false discovery rate (FDR) threshold of ≤0.01 was applied to identify CpGs with a significant mQTL. Totally, we identified 139,313 mCpGs and 13,771,378 significant SNP-mCpG pairs<br>eGFRcrea GWAS meta-analysis was performed in 1,508,659 trans-ancestry individuals (80% are of European ancestry) by integrating five GWAS studies. We identified 90,950 variants showing genome wide significant (p &lt; 5E-8) association with eGFRcrea.<br>Kidney eQTL meta-analysis was performed in 686 trans-ancestry individuals (72% are of European ancestry) by integrating four eQTL studies. To define eGenes, we used the Storey approach to calculate q values for all associations for each gene. With significant q value (&lt; 0.01), we identified 10,430 eGenes and 1,222,250 significant SNP-gene pairs.<br><br>
DOI: 10.6084/m9.figshare.16756377.v2
title: Thickness change of the Tibetan lithosphere since Early Cretaceous as revealed by Ce/Yb and Sm/Yb ratios of volcanic rocks

description: The growth of lithospheric thickness beneath the Tibetan Plateau since Early Cretaceous is demonstrated by changes in partial melting depth of the mantle as reflected in the Ce/Yb and Sm/Yb ratios of volcanic rocks. The ratios indicate that the lithospheric thickness of the Tibetan blocks ranged between 50–90 km in most areas and between 100–120 km in several areas during the Cretaceous. It increased from 60–110 km in Eocene to 170–200 km in Early Miocene in the Lhasa block, from 110–120 km in Early Oligocene to 170–180 km in Early Miocene in the Qiangtang block, and from ~130 km in Late Palaeogene to 160–190 km in Early Miocene for the Hohxil and Kunlun blocks. The thickness of the Lhasa block thus increased ~100 km at an average rate of 3.0 mm/a during Early Cenozoic. The indicated increase in Early Miocene for the Lhasa, Qiangtang, and Hohxil and Kunlun blocks to 160–195 km nearly matches the present 160–200 km plateau lithospheric thickness as inferred from seismic tomography. It is reasonable to assume that the crust, as well as the lithospheric mantle for all blocks thickened during the Palaeogene and reached its present thickness in Early Miocene.
DOI: 10.6084/m9.figshare.16756377.v1
title: Thickness change of the Tibetan lithosphere since Early Cretaceous as revealed by Ce/Yb and Sm/Yb ratios of volcanic rocks

description: The growth of lithospheric thickness beneath the Tibetan Plateau since Early Cretaceous is demonstrated by changes in partial melting depth of the mantle as reflected in the Ce/Yb and Sm/Yb ratios of volcanic rocks. The ratios indicate that the lithospheric thickness of the Tibetan blocks ranged between 50–90 km in most areas and between 100–120 km in several areas during the Cretaceous. It increased from 60–110 km in Eocene to 170–200 km in Early Miocene in the Lhasa block, from 110–120 km in Early Oligocene to 170–180 km in Early Miocene in the Qiangtang block, and from ~130 km in Late Palaeogene to 160–190 km in Early Miocene for the Hohxil and Kunlun blocks. The thickness of the Lhasa block thus increased ~100 km at an average rate of 3.0 mm/a during Early Cenozoic. The indicated increase in Early Miocene for the Lhasa, Qiangtang, and Hohxil and Kunlun blocks to 160–195 km nearly matches the present 160–200 km plateau lithospheric thickness as inferred from seismic tomography. It is reasonable to assume that the crust, as well as the lithospheric mantle for all blocks thickened during the Palaeogene and reached its present thickness in Early Miocene.
DOI: 10.6084/m9.figshare.16756377
title: Thickness change of the Tibetan lithosphere since Early Cretaceous as revealed by Ce/Yb and Sm/Yb ratios of volcanic rocks

description: The growth of lithospheric thickness beneath the Tibetan Plateau since Early Cretaceous is demonstrated by changes in partial melting depth of the mantle as reflected in the Ce/Yb and Sm/Yb ratios of volcanic rocks. The ratios indicate that the lithospheric thickness of the Tibetan blocks ranged between 50–90 km in most areas and between 100–120 km in several areas during the Cretaceous. It increased from 60–110 km in Eocene to 170–200 km in Early Miocene in the Lhasa block, from 110–120 km in Early Oligocene to 170–180 km in Early Miocene in the Qiangtang block, and from ~130 km in Late Palaeogene to 160–190 km in Early Miocene for the Hohxil and Kunlun blocks. The thickness of the Lhasa block thus increased ~100 km at an average rate of 3.0 mm/a during Early Cenozoic. The indicated increase in Early Miocene for the Lhasa, Qiangtang, and Hohxil and Kunlun blocks to 160–195 km nearly matches the present 160–200 km plateau lithospheric thickness as inferred from seismic tomography. It is reasonable to assume that the crust, as well as the lithospheric mantle for all blocks thickened during the Palaeogene and reached its present thickness in Early Miocene.
DOI: 10.6084/m9.figshare.7843493.v1
title: Additional file 6: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

description: Table S3. Database matches (full results) for C. gigantea unigenes. (XLSX 1763 kb)
DOI: 10.6084/m9.figshare.7843499
title: Additional file 7: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

description: Table S4. BLASTX hits for all unigenes in the Nr database. (XLSX 4233 kb)
DOI: 10.6084/m9.figshare.7843499.v1
title: Additional file 7: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

description: Table S4. BLASTX hits for all unigenes in the Nr database. (XLSX 4233 kb)
DOI: 10.6084/m9.figshare.7843505
title: Additional file 8: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

description: Table S5. Swiss-Prot annotations for all unigenes. (XLSX 2954 kb)
DOI: 10.6084/m9.figshare.7843505.v1
title: Additional file 8: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

description: Table S5. Swiss-Prot annotations for all unigenes. (XLSX 2954 kb)
DOI: 10.6084/m9.figshare.7843541
title: MOESM1 of Prediction and characterization of promoters and ribosomal binding sites of Zymomonas mobilis in system biology era

description: Additional file 1: Table S1. Nucleotide sequences of promoters with different strengths and their gene name and function. Table S2. Primers used in this study. The lowercases in each primer are the homologous arms designed to assembly with the vector. The primers prefixed with Q are used in qPCR.
DOI: 10.6084/m9.figshare.7843541.v1
title: MOESM1 of Prediction and characterization of promoters and ribosomal binding sites of Zymomonas mobilis in system biology era

description: Additional file 1: Table S1. Nucleotide sequences of promoters with different strengths and their gene name and function. Table S2. Primers used in this study. The lowercases in each primer are the homologous arms designed to assembly with the vector. The primers prefixed with Q are used in qPCR.
DOI: 10.5255/ukda-sn-856990
title: Experiences and Challenges of Plastic Waste Collectors in Kenya; A Qualitative Study Among Informal Waste Collectors in Kisumu City, Kenya, 2023

description: This qualitative data set comprises transcripts from focus group discussions with informal collectors of plastic and general waste in Kisumu, Kenya. The study aims to determine the extent to which informal waste collectors facilitate waste separation and recycling in off-grid neighborhoods in Kisumu. It also aimed to assess the impact of recycled plastic prices and international policy initiatives on businesses in the water sachet recycling chain in Kisumu as well as other barriers to informal waste collector businesses. A similar set of FGDs with waste collectors in Greater Accra, Ghana, is archived separately. Specialist plastic waste collection businesses are almost non-existent in Kisumu, so the study recruited general (mixed) waste collectors at different points in the supply chain via a grassroots waste collectors’ association. A total sample of 32 collectors were identified via this route within Kisumu City. These were segmented into three broad groups: a) Waste Pickers, b) Intermediate Traders and finally, c) Apex Traders. The Waste Pickers were defined as informal enterprises that mostly pick wastes directly from the waste generation sites such as households, streets, or waste dumps. The intermediate Traders were defined as the relatively more formal enterprises collecting waste from the pickers, carrying out some level of processing and selling the processed waste to apex traders. The Apex traders were then defined as the more formal enterprises purchasing the wastes from the intermediate enterprises and then selling the waste to recycling industries, mostly located in Nairobi. Two focus group discussions were held with two groups of waste pickers and two groups of intermediate traders, with a single small group discussion then held with two apex traders. Focus and small group discussions consisted of open-ended questions on business establishment, business history, waste collection operations, and enablers and barriers to waste collection.
DOI: 10.6084/m9.figshare.7843493
title: Additional file 6: of In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived speciesâ adaptability to environmental cues

description: Table S3. Database matches (full results) for C. gigantea unigenes. (XLSX 1763 kb)
DOI: 10.6084/m9.figshare.14135021
title: Fractional crystallization causes the iron isotope contrast between mid-ocean ridge basalts and abyssal peridotites

description: Supplementary Information and Supplementary data 1-4 for the paper entitled "Fractional crystallization causes the iron isotope contrast between mid-ocean ridge basalts and abyssal peridotites". Topography data from Smith and Sandwell (1997) used to reproduce Figure 1b are also provided here. The files with Petrolog_Output prefix are the output of Petrolog3, which can be used to reproduce Figure 3.<br>
DOI: 10.6084/m9.figshare.16756000
title: Additional file 4 of Construction of a ceRNA network in glioma and analysis of its clinical significance

description: Additional file 4: Table S4. Kaplan-Meier analysis data of 21 lncRNAs.
DOI: 10.6084/m9.figshare.16755880.v1
title: Additional file 16 of Genome and transcriptome analysis to understand the role diversification of cytochrome P450 gene under excess nitrogen treatment

description: Additional file 16: Table S12. List of identified P. notoginseng ABA, JA, GA, saponins biosynthesis related genes.