cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12254495
title: A family of fuchs endothelial corneal dystrophy and anterior polar cataract with an analysis of whole exome sequencing

description: Our aim was to introduce a family affected by this rare phenotype, and perform the whole exome sequencing (WES) to explore the potential candidate genes causing the disorders. A five-generation family including five patients affected by FECD with APC, and nine patients suffered from only FECD was recruited from the First Affiliated Hospital of Harbin Medical University. All participants received ophthalmic examinations. Eight family members were selected to perform WES with a bioinformatics analysis and genome-wide linkage analysis. The candidate genes were identified by polymerase chain reaction (PCR) and Sanger sequencing. Patients in this family had FECD as the common feature. The proband (a 65-year-old female) was affected by FECD and APC in both eyes, with epithelial bullae in the left eye. Slit-lamp, specular, and confocal microscope and OCT images showed guttae more serious in the central cornea than the peripheral area, confirming the diagnosis of FECD. In this family, most corneal guttae was bilateral with an almost equal degree of progression in the Descemet membrane, APC was found around the age of 10, perhaps even earlier. According to the analysis of bioinformatics analysis, two candidate genes were found and confirmed by PCR and Sanger sequencing, but could not achieve genotype-phenotype co-segregation in the family. We introduced a family of FECD with APC, with no known causative gene found by WES, inferring that there may be a novel gene-locus in the non-coding regions of genome, which needs further study by WGS. The contribution of this study was to exclude the possibility of the rare phenotype pathogenic site in exome and narrow the scope of pathogenic genes.
DOI: 10.6084/m9.figshare.12254495.v1
title: A family of fuchs endothelial corneal dystrophy and anterior polar cataract with an analysis of whole exome sequencing

description: Our aim was to introduce a family affected by this rare phenotype, and perform the whole exome sequencing (WES) to explore the potential candidate genes causing the disorders. A five-generation family including five patients affected by FECD with APC, and nine patients suffered from only FECD was recruited from the First Affiliated Hospital of Harbin Medical University. All participants received ophthalmic examinations. Eight family members were selected to perform WES with a bioinformatics analysis and genome-wide linkage analysis. The candidate genes were identified by polymerase chain reaction (PCR) and Sanger sequencing. Patients in this family had FECD as the common feature. The proband (a 65-year-old female) was affected by FECD and APC in both eyes, with epithelial bullae in the left eye. Slit-lamp, specular, and confocal microscope and OCT images showed guttae more serious in the central cornea than the peripheral area, confirming the diagnosis of FECD. In this family, most corneal guttae was bilateral with an almost equal degree of progression in the Descemet membrane, APC was found around the age of 10, perhaps even earlier. According to the analysis of bioinformatics analysis, two candidate genes were found and confirmed by PCR and Sanger sequencing, but could not achieve genotype-phenotype co-segregation in the family. We introduced a family of FECD with APC, with no known causative gene found by WES, inferring that there may be a novel gene-locus in the non-coding regions of genome, which needs further study by WGS. The contribution of this study was to exclude the possibility of the rare phenotype pathogenic site in exome and narrow the scope of pathogenic genes.
DOI: 10.6084/m9.figshare.25196507.v1
title: MV-ASD-2 (incomplete multiview dataset)

description: Pre-computed and filtered dataset.
DOI: 10.6084/m9.figshare.25196507
title: MV-ASD-2 (incomplete multiview dataset)

description: Pre-computed and filtered dataset.
DOI: 10.6084/m9.figshare.25145615
title: A framework to study and predict functional trait syndromes using phylogenetic and environmental data.

description: Data used in the paper titled "A framework to study and predict functional trait syndromes using phylogenetic and environmental data" published in Methods in Ecology and Evolution in 2024.R scripts used are also included.
DOI: 10.6084/m9.figshare.12254690
title: Identifying and profiling the microRNAs associated with skin colour in the Muchuan black-bone chicken

description: MicroRNAs (miRNAs) are an abundant class of small non-protein-coding RNAs that regulate gene expression in plants and animals. Skin colour is an important economic consideration in chicken production, and chickens with black skin have high market value. Nevertheless, little research has been conducted on miRNA regulation of melanogenesis in chicken skin. In this study, we sampled the dorsal skins of chickens with black (BS) and white (WS) skin to construct six small RNA libraries. High-throughput sequencing technology was then used to identify which miRNAs were expressed differentially between the BS and WS phenotypes. A total of 645 known and 64 novel miRNAs were identified from the six sequencing libraries. Additionally, the expression of 18 miRNAs was significantly different between the two phenotypes, including 9 miRNAs that were up-regulated, and 9 that were down-regulated. We identified 2 miRNAs, i.e. miR-204 and miR-6631-5p, that may be important for melanogenesis in chicken skin. Our data contribute to the understanding of the molecular mechanism, through miRNA regulation, of melanin formation in chicken skin.HighlightsDifferentially expressed miRNAs were identified in black skin (BS) and white skin (WS) of black-bone chickensEighteen DEMs were detected in BS and WS groups.miR-204 and miR-6631-5p were potential candidates influencing skin melanogenesis in chicken.
 Differentially expressed miRNAs were identified in black skin (BS) and white skin (WS) of black-bone chickens Eighteen DEMs were detected in BS and WS groups. miR-204 and miR-6631-5p were potential candidates influencing skin melanogenesis in chicken.
DOI: 10.6084/m9.figshare.25196501
title: MV-ASD-1 (incomplete multiview dataset)

description: Pre-computed and filtered dataset.
DOI: 10.6084/m9.figshare.25196501.v1
title: MV-ASD-1 (incomplete multiview dataset)

description: Pre-computed and filtered dataset.
DOI: 10.6084/m9.figshare.7527896.v1
title: Additional file 2: of Genome-wide association study of Mycobacterium avium subspecies Paratuberculosis infection in Chinese Holstein

description: PED file of SNP data. (PARTIAL 776 kb)
DOI: 10.6084/m9.figshare.7012034
title: TFEB-driven endocytosis coordinates MTORC1 signaling and autophagy

description: The mechanistic target of rapamycin kinase complex 1 (MTORC1) is a central cellular kinase that integrates major signaling pathways, allowing for regulation of anabolic and catabolic processes including macroautophagy/autophagy and lysosomal biogenesis. Essential to these processes is the regulatory activity of TFEB (transcription factor EB). In a regulatory feedback loop modulating transcriptional levels of RRAG/Rag GTPases, TFEB controls MTORC1 tethering to membranes and induction of anabolic processes upon nutrient replenishment. We now show that TFEB promotes expression of endocytic genes and increases rates of cellular endocytosis during homeostatic baseline and starvation conditions. TFEB-mediated endocytosis drives assembly of the MTORC1-containing nutrient sensing complex through the formation of endosomes that carry the associated proteins RRAGD, the amino acid transporter SLC38A9, and activate AKT/protein kinase B (AKT p-T308). TFEB-induced signaling endosomes en route to lysosomes are induced by amino acid starvation and are required to dissociate TSC2, re-tether and activate MTORC1 on endolysosomal membranes. This study characterizes TFEB-mediated endocytosis as a critical process leading to activation of MTORC1 and autophagic function, thus identifying the importance of the dynamic endolysosomal system in cellular clearance. <b>Abbreviations</b>: CAD: central adrenergic tyrosine hydroxylase-expressing-a-differentiated; ChIP-seq: chromosome immunoprecipitation sequencing; DAPI: 4ʹ,6-diamidino-2-phenylindole; DMSO: dimethyl sulfoxide; EDTA: ethylenediaminetetraacetic acid; EEA1: early endosomal antigen 1; EGF: epidermal growth factor; FBS: fetal bovine serum; GFP: green fluorescent protein; GTPase: guanosine triphosphatase; HEK293T: human embryonic kidney 293 cells expressing a temperature-sensitive mutant of the SV40 large T antigen; LAMP: lysosomal-associated membrane protein; LYNUS: lysosomal nutrient-sensing complex; MAP1LC3/LC3: microtubule associated protein 1 light chain 3 alpha/beta; MTOR: mechanistic target of rapamycin kinase; MTORC: mechanistic target of rapamycin kinase complex; OE: overexpression; PH: pleckstrin homology; PtdIns(3,4,5)P<sub>3</sub>: phosphatidylinositol 3,4,5-trisphosphate; RRAGD: Ras related GTPase binding D; RHEB: Ras homolog enriched in brain; SLC38A9: solute carrier family 38 member 9; SQSTM1: sequestosome 1; TFEB: transcription factor EB; TSC2: tuberous sclerosis 2; TMR: tetramethylrhodamine; ULK1: unc-51 like kinase 1; WT: wild type
DOI: 10.6084/m9.figshare.7012034.v1
title: TFEB-driven endocytosis coordinates MTORC1 signaling and autophagy

description: The mechanistic target of rapamycin kinase complex 1 (MTORC1) is a central cellular kinase that integrates major signaling pathways, allowing for regulation of anabolic and catabolic processes including macroautophagy/autophagy and lysosomal biogenesis. Essential to these processes is the regulatory activity of TFEB (transcription factor EB). In a regulatory feedback loop modulating transcriptional levels of RRAG/Rag GTPases, TFEB controls MTORC1 tethering to membranes and induction of anabolic processes upon nutrient replenishment. We now show that TFEB promotes expression of endocytic genes and increases rates of cellular endocytosis during homeostatic baseline and starvation conditions. TFEB-mediated endocytosis drives assembly of the MTORC1-containing nutrient sensing complex through the formation of endosomes that carry the associated proteins RRAGD, the amino acid transporter SLC38A9, and activate AKT/protein kinase B (AKT p-T308). TFEB-induced signaling endosomes en route to lysosomes are induced by amino acid starvation and are required to dissociate TSC2, re-tether and activate MTORC1 on endolysosomal membranes. This study characterizes TFEB-mediated endocytosis as a critical process leading to activation of MTORC1 and autophagic function, thus identifying the importance of the dynamic endolysosomal system in cellular clearance. <b>Abbreviations</b>: CAD: central adrenergic tyrosine hydroxylase-expressing-a-differentiated; ChIP-seq: chromosome immunoprecipitation sequencing; DAPI: 4ʹ,6-diamidino-2-phenylindole; DMSO: dimethyl sulfoxide; EDTA: ethylenediaminetetraacetic acid; EEA1: early endosomal antigen 1; EGF: epidermal growth factor; FBS: fetal bovine serum; GFP: green fluorescent protein; GTPase: guanosine triphosphatase; HEK293T: human embryonic kidney 293 cells expressing a temperature-sensitive mutant of the SV40 large T antigen; LAMP: lysosomal-associated membrane protein; LYNUS: lysosomal nutrient-sensing complex; MAP1LC3/LC3: microtubule associated protein 1 light chain 3 alpha/beta; MTOR: mechanistic target of rapamycin kinase; MTORC: mechanistic target of rapamycin kinase complex; OE: overexpression; PH: pleckstrin homology; PtdIns(3,4,5)P<sub>3</sub>: phosphatidylinositol 3,4,5-trisphosphate; RRAGD: Ras related GTPase binding D; RHEB: Ras homolog enriched in brain; SLC38A9: solute carrier family 38 member 9; SQSTM1: sequestosome 1; TFEB: transcription factor EB; TSC2: tuberous sclerosis 2; TMR: tetramethylrhodamine; ULK1: unc-51 like kinase 1; WT: wild type
DOI: 10.6084/m9.figshare.25196378
title: CRC preprocessing OTU tables (complete multiview dataset)

description: Amplicon sequence data preprocessing was performed using QIIME 2, version 2021.2. Forward sequences were denoised with DADA2, truncated at 240 bp and closed-reference clustered against SILVA database by varying the similarity threshold in { 90%, 94%, 97%, 99% }. Each of the produced OTU tables after clustering was than subjected to feature filtering, that has been performed according to the following criteria:- by <i>frequency</i>, i.e., on the minimum number of individuals for whom a given feature must be present, in { 2, 5, 10, 50 };-by <i>samples</i>, i.e., on the minimum percentage of the individuals for whom a given feature must be present, in \{ 2%, 5%, 10%, 20%, 50% \}.<br>Moreover, unfiltered OTU tables are also included. In total, 40 different OTU tables were obtained, considering 4 different similarity thresholds in the clustering phase, multiplied by 10 different filtering configurations, i.e., 4 (filtering by frequency) + 5 (filtering by samples) + 1 (unfiltered).
DOI: 10.6084/m9.figshare.25196372
title: ASD-16S preprocessing OTU tables (complete multiview dataset)

description: Amplicon sequence data preprocessing was performed using QIIME 2, version 2021.2. Forward sequences were denoised with DADA2, truncated at 240 bp and closed-reference clustered against SILVA database by varying the similarity threshold in { 90%, 94%, 97%, 99% }. Each of the produced OTU tables after clustering was than subjected to feature filtering, that has been performed according to the following criteria:- by <i>frequency</i>, i.e., on the minimum number of individuals for whom a given feature must be present, in { 2, 5, 10, 50 };by <i>samples</i>, i.e., on the minimum percentage of the individuals for whom a given feature must be present, in { 2%, 5%, 10%, 20%, 50% }.<br>Moreover, unfiltered OTU tables are also included. In total, 40 different OTU tables were obtained, considering 4 different similarity thresholds in the clustering phase, multiplied by 10 different filtering configurations, i.e., 4 (filtering by frequency) + 5 (filtering by samples) + 1 (unfiltered).
DOI: 10.6084/m9.figshare.25196372.v1
title: ASD-16S preprocessing OTU tables (complete multiview dataset)

description: Amplicon sequence data preprocessing was performed using QIIME 2, version 2021.2. Forward sequences were denoised with DADA2, truncated at 240 bp and closed-reference clustered against SILVA database by varying the similarity threshold in { 90%, 94%, 97%, 99% }. Each of the produced OTU tables after clustering was than subjected to feature filtering, that has been performed according to the following criteria:- by <i>frequency</i>, i.e., on the minimum number of individuals for whom a given feature must be present, in { 2, 5, 10, 50 };by <i>samples</i>, i.e., on the minimum percentage of the individuals for whom a given feature must be present, in { 2%, 5%, 10%, 20%, 50% }.<br>Moreover, unfiltered OTU tables are also included. In total, 40 different OTU tables were obtained, considering 4 different similarity thresholds in the clustering phase, multiplied by 10 different filtering configurations, i.e., 4 (filtering by frequency) + 5 (filtering by samples) + 1 (unfiltered).
DOI: 10.6084/m9.figshare.7012133
title: Information of differently expressed high quality transcripts

description: Information of differently expressed high quality transcripts
DOI: 10.6084/m9.figshare.20110659
title: Additional file 3 of Metabolomics and integrated network pharmacology analysis reveal SNKAF decoction suppresses cell proliferation and induced cell apoptisis in hepatocellular carcinoma via PI3K/Akt/P53/FoxO signaling axis

description: Additional file 3: Table S3. Metabolic pathways and corresponding metabolites.
DOI: 10.6084/m9.figshare.7527917.v1
title: Additional file 6: of Genome-wide association study of Mycobacterium avium subspecies Paratuberculosis infection in Chinese Holstein

description: Table S1. The features of genes based on GRAMMAR-GC. (XLSX 20 kb)
DOI: 10.34740/kaggle/dsv/7617495
title: Global Genomic Neurofibromatosis Neoplasia
DOI: 10.6084/m9.figshare.7012226
title: Information of differently expressed unigenes

description: Information of differently expressed unigenes
DOI: 10.6084/m9.figshare.7527890.v1
title: Additional file 1: of Genome-wide association study of Mycobacterium avium subspecies Paratuberculosis infection in Chinese Holstein

description: MAP file of SNP data. (MAP 3577 kb)
DOI: 10.6084/m9.figshare.19586561
title: H22954, a long non-coding RNA, inhibits glucose uptake in leukemia cells in a GLUT10-dependent manner

description: To investigate the performance of H22954, a novel long non-coding RNA (lncRNA), in inhibiting glucose uptake in leukemia cells. <sup>18</sup>F-FDG uptake, RNA half-life quantitative real-time polymerase chain reaction (qRT-PCR) and luciferase assays were performed to detect the glucose uptake in the condition of leukemia. Microarrays and qRT-PCR analyses were used to identify the related genes or proteins and elucidate the underlying these processes. H22954, a novel lncRNA, inhibited glucose uptake in leukemia cells. Using bioinformatics and microarray analyses, GLUT10 was identified as a possible target molecule of H22954. H22954 targeted the 3′untranslated region of GLUT10. In the luciferase assay, the luciferase activity of pGL3-GLUT10 was inhibited by H22954. Consistently, H22954 expression levels were inversely correlated with GLUT10 expression in cell lines and acute myeloid leukemia (AML) samples. Conversely, the degradation rate of <i>GLUT10</i> mRNA was increased after H22954 overexpression. Moreover, glucose uptake was recovered when the GLUT10-interaction sites in H22954 were mutated. The lncRNA H22954 regulated GLUT10 expression to inhibit glucose uptake in leukemia cells. Our findings provide potentially valuable data for designing new targeted strategies based on H22954.
DOI: 10.6084/m9.figshare.7012238
title: Annotation of high quality transcripts and unigenes and differential gene expression

description: Annotation of high quality transcripts and
unigenes
DOI: 10.6084/m9.figshare.22216648
title: Spatial–temporal Distribution of Global Production–Living–Ecological Space during the period 2000–2020

description: Global production–living–ecological space is a concept that integrates land cover with the humanities, social economy, and the ecological environment. The dataset of global production–living–ecological space in this paper was generated by combining the global land cover obtained using GlobeLand30 and the population density supplied by NASA's Socioeconomic Data and Applications Center in 2000, 2010, and 2020. This dataset will be an important reference for the assessment of the coordinated development of the Sustainable Development Goals and also the studies between global climate change and human activity.
DOI: 10.6084/m9.figshare.22216648.v1
title: Spatial–temporal Distribution of Global Production–Living–Ecological Space during the period 2000–2020

description: Global production–living–ecological space is a concept that integrates land cover with the humanities, social economy, and the ecological environment. The dataset of global production–living–ecological space in this paper was generated by combining the global land cover obtained using GlobeLand30 and the population density supplied by NASA's Socioeconomic Data and Applications Center in 2000, 2010, and 2020. This dataset will be an important reference for the assessment of the coordinated development of the Sustainable Development Goals and also the studies between global climate change and human activity.
DOI: 10.6084/m9.figshare.11730951
title: Autophagy-mediated compartmental cytoplasmic deletion is essential for tobacco pollen germination and male fertility

description: In plants, macroautophagy/autophagy has mainly been associated with stress-related processes but how it impacts normal physiological and developmental processes remains largely unexplored. Pollen germination is the critical first step toward fertilization in flowering plants. It is metabolically demanding and relies on high levels of cytoplasmic reorganization activities to support a dramatic morphological transformation that underlies the development of a pollen tube as the conduit to deliver sperm for fertilization. The role of autophagy in this process remains unclear. Here we provide evidence that pollen germination is accompanied by elevated autophagic activity and successful pollen tube emergence depends on autophagy-mediated cytoplasmic deletion. Genetic and cytological experiments demonstrate that inhibition of autophagy prevents pollen germination while induces the persistence of a layer of undegraded cytoplasm at the germination aperture. Together, these results unveil a novel compartmentalized autophagy. Furthermore, high-throughput comparative lipidomic analyses show that suppressed autophagy-induced inhibition of pollen germination is accompanied by altered profiles of stored and signaling lipids. Proteomic analyses reveal that autophagy likely exert its role in pollen germination via downstream mitochondria-related pathways. These findings reveal a critical role for autophagy in initiating pollen germination and provide evidences for compartmental cytoplasmic deletion being crucial for male fertility. <b>Abbreviations</b>: 3-MA: 3-methyladenine; ATG: autophagy-related gene; Cer: ceramide; CL: cardiolipin; Con A: concanamycin A; DAG: diradylglycerol; GO: gene ontology; HAG: hour after germination; LC-MS: liquid chromatography-mass spectrometry; MAG: min after germination; MDC: monodansylcadaverine; PE: phosphatidylethanolamine; PI: phosphatidylinositol; PLD: phospholipase D; PtdIns3K: phosphatidylinositol 3-kinase; RT-qPCR: quantitative real-time reverse transcription PCR; TAG: triradylglycerol; TEM: transmission electron microscopy; TMT: tandem mass tagging.
DOI: 10.6084/m9.figshare.11730951.v2
title: Autophagy-mediated compartmental cytoplasmic deletion is essential for tobacco pollen germination and male fertility

description: In plants, macroautophagy/autophagy has mainly been associated with stress-related processes but how it impacts normal physiological and developmental processes remains largely unexplored. Pollen germination is the critical first step toward fertilization in flowering plants. It is metabolically demanding and relies on high levels of cytoplasmic reorganization activities to support a dramatic morphological transformation that underlies the development of a pollen tube as the conduit to deliver sperm for fertilization. The role of autophagy in this process remains unclear. Here we provide evidence that pollen germination is accompanied by elevated autophagic activity and successful pollen tube emergence depends on autophagy-mediated cytoplasmic deletion. Genetic and cytological experiments demonstrate that inhibition of autophagy prevents pollen germination while induces the persistence of a layer of undegraded cytoplasm at the germination aperture. Together, these results unveil a novel compartmentalized autophagy. Furthermore, high-throughput comparative lipidomic analyses show that suppressed autophagy-induced inhibition of pollen germination is accompanied by altered profiles of stored and signaling lipids. Proteomic analyses reveal that autophagy likely exert its role in pollen germination via downstream mitochondria-related pathways. These findings reveal a critical role for autophagy in initiating pollen germination and provide evidences for compartmental cytoplasmic deletion being crucial for male fertility. <b>Abbreviations</b>: 3-MA: 3-methyladenine; ATG: autophagy-related gene; Cer: ceramide; CL: cardiolipin; Con A: concanamycin A; DAG: diradylglycerol; GO: gene ontology; HAG: hour after germination; LC-MS: liquid chromatography-mass spectrometry; MAG: min after germination; MDC: monodansylcadaverine; PE: phosphatidylethanolamine; PI: phosphatidylinositol; PLD: phospholipase D; PtdIns3K: phosphatidylinositol 3-kinase; RT-qPCR: quantitative real-time reverse transcription PCR; TAG: triradylglycerol; TEM: transmission electron microscopy; TMT: tandem mass tagging.