cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7249033
title: ValRun: GMP-grade Manufacturing and Quality Control of a Non-Virally engineered Advanced Therapy Medicinal Product for Personalized Treatment of Age-Related Macular Degeneration

description: <strong>VaLRun: </strong> <strong>Raw data of "GMP-grade Manufacturing and Quality Control of a Non-Virally engineered Advanced Therapy Medicinal Product for Personalized Treatment of Age-Related Macular Degeneration"</strong> (Excel-, pdf-, GraphPad-files, mp4 videos and a READ-ME text file) The introduction of new therapeutics requires validation of Good Manufacturing Practice (GMP)-grade manufacturing including suitable quality controls. This is challenging for Advanced Therapy Medicinal Products (ATMP) with personalized batches. We have developed a person-alized, cell-based gene therapy to treat age-related macular degeneration and established a vali-dation strategy of the GMP-grade manufacture for the ATMP; manufacturing and quality control were challenging due to a low cell number, batch-to-batch variability and short production duration. Instead of patient iris pigment epithelial cells, human donor tissue was used to produce the transfected cell product (“tIPE”). We implemented an extended validation of 104 tIPE productions. Procedure, operators and devices have been validated and qualified by determining cell number, viability, extracellular DNA, sterility, duration, temperature and volume. Transfected autologous cells were transplanted to rabbits verifying feasibility of the treatment. A container has been engineered to insure a safe transport from the production to the surgery site. Criteria for successful validation and qualification were based on tIPE’s Critical Quality Attributes and Process Parameters, its manufacture and release criteria. The validated process and qualified operators are essential to bring the ATMP into clinic and offer a general strategy for the transfer to other manufacture centers and personalized ATMPs.
description: M.K. and G.T: Conceptualization M.K., N.H., S.J., P.A., M. R., R.C., C.Z., D.S., Z.I., C.M., Z.I. and G.T: methodology M.K., N.H. and T.B: validation M.K., N.H., T.B., S.J., P.A., M. R., R.C., C.Z., D.S., Z.I., C.M., and Z.I..: data analysis G.T.: supervision, project administration, funding acquisition,
DOI: 10.6084/m9.figshare.22584349.v2
title: Dataset for the article in RPD (doi: 10.1093/rpd/ncad138)

description: This is a dataset which we used to prepare Fiugres 2 to 4 in the paper "Investigation of the provenance of Okinose sand using ESR signals of quartz in granite and granodiorite around Osaka Bay" by Kobayashi, Kojima, and Tani in RPD. It is an 'Excel' file with 4 sheets. The followings are brief description for them. The detailed information is in the paper. <br> <strong>#1 Figure 2a</strong> ESR spectrum in Fig2-a. <br> <strong>#2 Figure 2b</strong> ESR spectrum in Fig2-b. <br> <strong>#3 Figure 3</strong> Variation of the signal intensity of the heat-treated E1’ centre in the quartz samples. <br> <strong>#4 Figure 4</strong> Variation of the signal intensity ratio of the Ti-Li centre to the Al centre in the quartz samples.
DOI: 10.6084/m9.figshare.22584349
title: Dataset for the article in RPD (doi: 10.1093/rpd/ncad138)

description: This is a dataset which we used to prepare Fiugres 2 to 4 in the paper "Investigation of the provenance of Okinose sand using ESR signals of quartz in granite and granodiorite around Osaka Bay" by Kobayashi, Kojima, and Tani in RPD. It is an 'Excel' file with 4 sheets. The followings are brief description for them. The detailed information is in the paper. <br> <strong>#1 Figure 2a</strong> ESR spectrum in Fig2-a. <br> <strong>#2 Figure 2b</strong> ESR spectrum in Fig2-b. <br> <strong>#3 Figure 3</strong> Variation of the signal intensity of the heat-treated E1’ centre in the quartz samples. <br> <strong>#4 Figure 4</strong> Variation of the signal intensity ratio of the Ti-Li centre to the Al centre in the quartz samples.
DOI: 10.5281/zenodo.7249032
title: ValRun: GMP-grade Manufacturing and Quality Control of a Non-Virally engineered Advanced Therapy Medicinal Product for Personalized Treatment of Age-Related Macular Degeneration

description: <strong>VaLRun: </strong> <strong>Raw data of "GMP-grade Manufacturing and Quality Control of a Non-Virally engineered Advanced Therapy Medicinal Product for Personalized Treatment of Age-Related Macular Degeneration"</strong> (Excel-, pdf-, GraphPad-files, mp4 videos and a READ-ME text file) The introduction of new therapeutics requires validation of Good Manufacturing Practice (GMP)-grade manufacturing including suitable quality controls. This is challenging for Advanced Therapy Medicinal Products (ATMP) with personalized batches. We have developed a person-alized, cell-based gene therapy to treat age-related macular degeneration and established a vali-dation strategy of the GMP-grade manufacture for the ATMP; manufacturing and quality control were challenging due to a low cell number, batch-to-batch variability and short production duration. Instead of patient iris pigment epithelial cells, human donor tissue was used to produce the transfected cell product (“tIPE”). We implemented an extended validation of 104 tIPE productions. Procedure, operators and devices have been validated and qualified by determining cell number, viability, extracellular DNA, sterility, duration, temperature and volume. Transfected autologous cells were transplanted to rabbits verifying feasibility of the treatment. A container has been engineered to insure a safe transport from the production to the surgery site. Criteria for successful validation and qualification were based on tIPE’s Critical Quality Attributes and Process Parameters, its manufacture and release criteria. The validated process and qualified operators are essential to bring the ATMP into clinic and offer a general strategy for the transfer to other manufacture centers and personalized ATMPs.
description: M.K. and G.T: Conceptualization M.K., N.H., S.J., P.A., M. R., R.C., C.Z., D.S., Z.I., C.M., Z.I. and G.T: methodology M.K., N.H. and T.B: validation M.K., N.H., T.B., S.J., P.A., M. R., R.C., C.Z., D.S., Z.I., C.M., and Z.I..: data analysis G.T.: supervision, project administration, funding acquisition,
DOI: 10.15156/bio/sh1018138.09fu
title: SH1018138.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1018139.09fu
title: SH1018139.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1018140.09fu
title: SH1018140.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1018141.09fu
title: SH1018141.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1018142.09fu
title: SH1018142.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1018143.09fu
title: SH1018143.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1018144.09fu
title: SH1018144.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1018145.09fu
title: SH1018145.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.6084/m9.figshare.20517354
title: Tear Film miRNAs and Their Association With Human Dry Eye Disease

description: miRNAs can regulate inflammatory pathways. The purpose of this work was to determine if inflammatory-related tear film miRNAs are associated with extracellular vesicles (EVs) in human non-Sjögren’s Syndrome dry eye disease (DED) participants. Five DED and 5 non-DED human participants were recruited. Tears samples were collected by washing the ocular surface of both eyes with phosphate buffered saline, pooling samples from the right and left eyes, and purifying EVs from the samples with a polyethylene glycol (PEG) 8000 precipitation procedure. Samples were directly analyzed via ELISA or transmission electron microscopy (TEM), or RNA was isolated first from the EVs and evaluated with RNA-Seq. EVs were identified in the tear film of both groups using TEM and ELISA. Following EV purification and RNA isolation, RNA-Seq determined that there were 126 EV miRNAs differentially expressed between the two groups when comparing their RNA cargoes. Ingenuity Pathways Analysis found 9 upregulated miRNAs that were associated with inflammation (miR-127-5p, miR-1273h-3p, miR-1288-5p, miR-130b-5p, miR-139-3p, miR-1910-5p, miR-203b-5p, miR-22-5p, and miR-4632-3p; all <i>p</i> &lt; 0.049; fold regulation range = 1.43–1.67). This study determined that EVs are present in the tear film and that tear EVs contain miRNAs that may be associated with DED inflammatory pathways.
DOI: 10.6084/m9.figshare.21197138
title: Paired Box Gene 6 Regulates Heme Oxygenase-1 Expression and Mitigates Hydrogen Peroxide-Induced Oxidative Stress in Lens Epithelial Cells

description: This study aimed to investigate the regulation of heme oxygenase-1 (HO-1) by paired box gene 6 (Pax6) and their roles in hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>)-induced oxidative stress and apoptosis in lens epithelial cells (LECs) (SRA01/04, HLE-B3). Lens anterior capsule membranes of mice of different ages were obtained to compare differences in the expression of Pax6 and HO-1 using Western blotting. Pax6-overexpressing plasmid and small interfering RNA were designed to overexpress and silence Pax6, respectively. Cobalt protoporphyrin (CoPP) was used to promote the expression of HO-1. Oxidative damage in LECs was induced by treatment with H<sub>2</sub>O<sub>2</sub> (400 µM) for 24 h. Cell viability was measured using the Cell Counting Kit-8 assay. Intracellular reactive oxygen species (ROS) were detected using flow cytometry and immunofluorescence. Superoxide dismutase (SOD) level was measured using SOD Assay Kit and apoptotic cells were quantified using annexin V-fluorescein isothiocyanate/propidium iodide staining. Pax6 and HO-1 expression levels showed an age-dependent decrease in LECs of mouse. Overexpressing Pax6 upregulated HO-1 expression level. Silencing Pax6 downregulated the HO-1 expression level, resulting in increased generation of ROS, reduced SOD activity, decreased cell viability, and increased apoptotic cells of LECs under H<sub>2</sub>O<sub>2</sub>-induced oxidative stress. Overexpressing Pax6 and CoPP both mitigates H<sub>2</sub>O<sub>2</sub>-induced oxidative stress by increasing the expression of HO-1 of LECs. Pax6 and HO-1 expression levels showed an age-dependent decrease in LECs in mouse anterior capsules. Pax6 could regulate the expression of HO-1 in LECs. The decrease of Pax6 weakened the antioxidant ability of LECs under H<sub>2</sub>O<sub>2</sub>-induced oxidative stress by downregulating HO-1, which may be a potential mechanism for the formation of age-related cataract.
DOI: 10.6084/m9.figshare.20517354.v1
title: Tear Film miRNAs and Their Association With Human Dry Eye Disease

description: miRNAs can regulate inflammatory pathways. The purpose of this work was to determine if inflammatory-related tear film miRNAs are associated with extracellular vesicles (EVs) in human non-Sjögren’s Syndrome dry eye disease (DED) participants. Five DED and 5 non-DED human participants were recruited. Tears samples were collected by washing the ocular surface of both eyes with phosphate buffered saline, pooling samples from the right and left eyes, and purifying EVs from the samples with a polyethylene glycol (PEG) 8000 precipitation procedure. Samples were directly analyzed via ELISA or transmission electron microscopy (TEM), or RNA was isolated first from the EVs and evaluated with RNA-Seq. EVs were identified in the tear film of both groups using TEM and ELISA. Following EV purification and RNA isolation, RNA-Seq determined that there were 126 EV miRNAs differentially expressed between the two groups when comparing their RNA cargoes. Ingenuity Pathways Analysis found 9 upregulated miRNAs that were associated with inflammation (miR-127-5p, miR-1273h-3p, miR-1288-5p, miR-130b-5p, miR-139-3p, miR-1910-5p, miR-203b-5p, miR-22-5p, and miR-4632-3p; all <i>p</i> &lt; 0.049; fold regulation range = 1.43–1.67). This study determined that EVs are present in the tear film and that tear EVs contain miRNAs that may be associated with DED inflammatory pathways.
DOI: 10.6084/m9.figshare.21197138.v1
title: Paired Box Gene 6 Regulates Heme Oxygenase-1 Expression and Mitigates Hydrogen Peroxide-Induced Oxidative Stress in Lens Epithelial Cells

description: This study aimed to investigate the regulation of heme oxygenase-1 (HO-1) by paired box gene 6 (Pax6) and their roles in hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>)-induced oxidative stress and apoptosis in lens epithelial cells (LECs) (SRA01/04, HLE-B3). Lens anterior capsule membranes of mice of different ages were obtained to compare differences in the expression of Pax6 and HO-1 using Western blotting. Pax6-overexpressing plasmid and small interfering RNA were designed to overexpress and silence Pax6, respectively. Cobalt protoporphyrin (CoPP) was used to promote the expression of HO-1. Oxidative damage in LECs was induced by treatment with H<sub>2</sub>O<sub>2</sub> (400 µM) for 24 h. Cell viability was measured using the Cell Counting Kit-8 assay. Intracellular reactive oxygen species (ROS) were detected using flow cytometry and immunofluorescence. Superoxide dismutase (SOD) level was measured using SOD Assay Kit and apoptotic cells were quantified using annexin V-fluorescein isothiocyanate/propidium iodide staining. Pax6 and HO-1 expression levels showed an age-dependent decrease in LECs of mouse. Overexpressing Pax6 upregulated HO-1 expression level. Silencing Pax6 downregulated the HO-1 expression level, resulting in increased generation of ROS, reduced SOD activity, decreased cell viability, and increased apoptotic cells of LECs under H<sub>2</sub>O<sub>2</sub>-induced oxidative stress. Overexpressing Pax6 and CoPP both mitigates H<sub>2</sub>O<sub>2</sub>-induced oxidative stress by increasing the expression of HO-1 of LECs. Pax6 and HO-1 expression levels showed an age-dependent decrease in LECs in mouse anterior capsules. Pax6 could regulate the expression of HO-1 in LECs. The decrease of Pax6 weakened the antioxidant ability of LECs under H<sub>2</sub>O<sub>2</sub>-induced oxidative stress by downregulating HO-1, which may be a potential mechanism for the formation of age-related cataract.
DOI: 10.15156/bio/sh1018146.09fu
title: SH1018146.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.