cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh1914260.08fu
title: SH1914260.08FU

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/sh1914261.08fu
title: SH1914261.08FU

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/sh1914262.08fu
title: SH1914262.08FU

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/sh1914263.08fu
title: SH1914263.08FU

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/sh1914264.08fu
title: SH1914264.08FU

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.20626382.v1
title: Additional file 2 of The Musa troglodytarum L. genome provides insights into the mechanism of non-climacteric behaviour and enrichment of carotenoids

description: Additional file 2: Data 1. List of M. troglodytarum specific genes. Genes were annotated by eggNOG-mapper. Data 2. List of genes of rapidly evolving families in M. troglodytarum. Genes were annotated by eggNOG-mapper. Data 3. Metabolites of karat pulp identified by widely targeted metabolomics analysis. Data 4. Clustered metabolites of karat pulp identified by widely targeted metabolomics analysis. Data 5. Carotenoid contents of pulp at different developmental stages. Data 6. Expression levels of genes involved in fruit ripening in karat. Data 7. Expression levels of genes involved in fruit ripening in BXJ. Data 8. Expression levels of genes involved in fruit ripening in FJ. Data 9. Sugar contents in the pulp of ripening karat fruit. Data 10. Expression levels of nodes of the ripening-related coexpression network.
DOI: 10.6084/m9.figshare.14339195.v1
title: Novel insights into clear cell renal cell carcinoma prognosis by comprehensive characterization of aberrant alternative splicing signature: a study based on large-scale sequencing data

description: Clear cell renal cell carcinoma (ccRCC) is the most common type with poor prognosis in kidney tumor. Growing evidence has indicated that aberrant alternative splicing (AS) events are efficacious signatures for tumor prognosis prediction and therapeutic targets. However, the detailed roles of AS events in ccRCC are largely unknown. In our study, level 3 RNA-seq data was acquired from The Cancer Genome Atlas dataset and corresponding AS profiles were detected with the assistance of SpliceSeq software. A total of 2100 aberrant survival-associated AS events were identified via differential expression and univariate cox regression analysis. The final prognostic panel formed by 17 specific events was developed by stepwise least absolute shrinkage and selection operator (LASSO) penalty, with the area under curve (AUC) values of receiver operator characteristic (ROC) curves keeping above 0.7 spanning 1 year to 5 years. And the results from functional enrichment analyses are unanimous that autophagy could be a potential mechanism of splicing regulation in ccRCC. Furthermore, splicing regulatory network was constructed via Spearman correlation between splicing factors and AS events. Finally, unsupervised clustering analysis revealed three clusters with distinct survival patterns, and associated with specific clinicopathological phenotypes. In overall, we developed a robust and individualized predictive model based on large-scale sequencing data. The identified AS events and splicing network may be valuable in deciphering the crucial posttranscriptional mechanisms on tumorigenesis of ccRCC.
DOI: 10.6084/m9.figshare.19581963.v1
title: Additional file 13 of Identification of circRNA-associated ceRNA networks using longissimus thoracis of pigs of different breeds and growth stages

description: Additional file 13. 12864_2022_8515_MOESM13_ESM.xlsx.
DOI: 10.6084/m9.figshare.19581981.v1
title: Additional file 6 of Identification of circRNA-associated ceRNA networks using longissimus thoracis of pigs of different breeds and growth stages

description: Additional file 6. 12864_2022_8515_MOESM6_ESM.xlsx.
DOI: 10.6084/m9.figshare.14339213
title: Identification of a foetal epigenetic compartment in adult human kidney

description: The mammalian kidney has extensive repair capacity; however, identifying adult renal stem cells has proven elusive. We applied an epigenetic marker of foetal cell origin (FCO) in diverse human tissues as a probe for developmental cell persistence, finding a 5.4-fold greater FCO proportion in kidney. Normal kidney FCO proportions averaged 49% with extensive interindividual variation. FCO proportions were significantly negatively correlated with immune-related gene expression and positively correlated with genes expressed in the renal medulla, including those involved in renal organogenesis (e.g., <i>FGF2, PAX8, and HOXB7)</i>. FCO associated genes also mapped to medullary nephron segments in mouse and rat, suggesting evolutionary conservation of this cellular compartment. Renal cancer patients whose tumours contained non-zero FCO scores survived longer. The kidney appears unique in possessing substantial foetal epigenetic features. Further study of FCO-related gene methylation may elucidate regenerative regulatory programmes in tissues without apparent discrete stem cell compartments.
DOI: 10.6084/m9.figshare.14863504.v1
title: Additional file 3 of Association between STAT4 gene polymorphism and type 2 diabetes risk in Chinese Han population

description: Additional file 3: Table Genotyping results of all participants.
DOI: 10.6084/m9.figshare.14339213.v1
title: Identification of a foetal epigenetic compartment in adult human kidney

description: The mammalian kidney has extensive repair capacity; however, identifying adult renal stem cells has proven elusive. We applied an epigenetic marker of foetal cell origin (FCO) in diverse human tissues as a probe for developmental cell persistence, finding a 5.4-fold greater FCO proportion in kidney. Normal kidney FCO proportions averaged 49% with extensive interindividual variation. FCO proportions were significantly negatively correlated with immune-related gene expression and positively correlated with genes expressed in the renal medulla, including those involved in renal organogenesis (e.g., <i>FGF2, PAX8, and HOXB7)</i>. FCO associated genes also mapped to medullary nephron segments in mouse and rat, suggesting evolutionary conservation of this cellular compartment. Renal cancer patients whose tumours contained non-zero FCO scores survived longer. The kidney appears unique in possessing substantial foetal epigenetic features. Further study of FCO-related gene methylation may elucidate regenerative regulatory programmes in tissues without apparent discrete stem cell compartments.
DOI: 10.6084/m9.figshare.20363118.v1
title: Mtr_annotaion_gff_V2.tar.gz

description: The Gene and TE annotation of the genome of <em>Musa troglodytarum</em> L.(version 2).
DOI: 10.6084/m9.figshare.14863504
title: Additional file 3 of Association between STAT4 gene polymorphism and type 2 diabetes risk in Chinese Han population

description: Additional file 3: Table Genotyping results of all participants.
DOI: 10.6084/m9.figshare.19767559.v1
title: Mtr_supplementary_seqs.fasta

description: The cDNA sequences of <em>MtrSSUIIs and MtrGALK. </em>The promoter sequences of <em>MtrACO1</em> and <em>MtrACS1</em>.
DOI: 10.6084/m9.figshare.20626382
title: Additional file 2 of The Musa troglodytarum L. genome provides insights into the mechanism of non-climacteric behaviour and enrichment of carotenoids

description: Additional file 2: Data 1. List of M. troglodytarum specific genes. Genes were annotated by eggNOG-mapper. Data 2. List of genes of rapidly evolving families in M. troglodytarum. Genes were annotated by eggNOG-mapper. Data 3. Metabolites of karat pulp identified by widely targeted metabolomics analysis. Data 4. Clustered metabolites of karat pulp identified by widely targeted metabolomics analysis. Data 5. Carotenoid contents of pulp at different developmental stages. Data 6. Expression levels of genes involved in fruit ripening in karat. Data 7. Expression levels of genes involved in fruit ripening in BXJ. Data 8. Expression levels of genes involved in fruit ripening in FJ. Data 9. Sugar contents in the pulp of ripening karat fruit. Data 10. Expression levels of nodes of the ripening-related coexpression network.
DOI: 10.6084/m9.figshare.20626427.v1
title: Additional file 2 of Proteomics-based evaluation of the mechanism underlying vascular injury via DNA interstrand crosslinks, glutathione perturbation, mitogen-activated protein kinase, and Wnt and ErbB signaling pathways induced by crotonaldehyde

description: Additional file 2: Table S2. Identification of total protein by TMT- based proteomics analysis.
DOI: 10.6084/m9.figshare.19590683
title: Characterization of the fatty acid binding protein 3 (FABP3) promoter and its transcriptional regulation by cAMP response element binding protein 1 (CREB1) in goat mammary epithelial cells

description: Fatty acid binding protein 3 (FABP3) is involved in signal transduction pathways, and in the uptake and utilization of long-chain fatty acids. However, the transcriptional regulation of <i>FABP3</i> in goat is unclear. In this study, the <i>FABP3</i> 5′ flanking region was amplified from goat (<i>Capra hircus</i>) genomic DNA. Luciferase reporter vectors containing promoter fragments of five different lengths were constructed and transfected into dairy goat mammary epithelial cells. The region of the promoter located between −1801 and −166 bp upstream of the transcription start site (TSS) exhibited the highest luciferase activity, and contained two cAMP response elements (CREs) located at −1632 bp and −189 bp. Interference with <i>CREB1</i> significantly downregulated <i>FABP3</i> promoter activity. In addition, <i>FABP3</i> promoter activity was significantly reduced after mutation of the CRE1 (−1632 bp) and CRE2 (−189 bp) sites. Further analysis indicated that the CRE2 site was essential for the transcriptional activity induced by <i>CREB1</i>. These results demonstrated that CREB1 is involved in the transcriptional regulation of <i>FABP3</i> expression in the goat mammary gland via a direct mechanism, thus revealing a novel signaling pathway involved in fatty acid metabolism in goat.
DOI: 10.6084/m9.figshare.19590683.v1
title: Characterization of the fatty acid binding protein 3 (FABP3) promoter and its transcriptional regulation by cAMP response element binding protein 1 (CREB1) in goat mammary epithelial cells

description: Fatty acid binding protein 3 (FABP3) is involved in signal transduction pathways, and in the uptake and utilization of long-chain fatty acids. However, the transcriptional regulation of <i>FABP3</i> in goat is unclear. In this study, the <i>FABP3</i> 5′ flanking region was amplified from goat (<i>Capra hircus</i>) genomic DNA. Luciferase reporter vectors containing promoter fragments of five different lengths were constructed and transfected into dairy goat mammary epithelial cells. The region of the promoter located between −1801 and −166 bp upstream of the transcription start site (TSS) exhibited the highest luciferase activity, and contained two cAMP response elements (CREs) located at −1632 bp and −189 bp. Interference with <i>CREB1</i> significantly downregulated <i>FABP3</i> promoter activity. In addition, <i>FABP3</i> promoter activity was significantly reduced after mutation of the CRE1 (−1632 bp) and CRE2 (−189 bp) sites. Further analysis indicated that the CRE2 site was essential for the transcriptional activity induced by <i>CREB1</i>. These results demonstrated that CREB1 is involved in the transcriptional regulation of <i>FABP3</i> expression in the goat mammary gland via a direct mechanism, thus revealing a novel signaling pathway involved in fatty acid metabolism in goat.
DOI: 10.6084/m9.figshare.9105032
title: Empirical Likelihood Ratio Tests of Conditional Moment Restrictions With Unknown Functions

description: This article introduces empirical likelihood ratio tests for conditional moment models in which the unknown parameter contains infinite-dimensional components. We allow unknown functions to be included in the conditional moment restrictions. We discusses (1) the limiting distribution of the sieve conditional empirical likelihood ratio (SCELR) test statistic for functionals of parameters under the null hypothesis and local alternatives; and (2) the limiting distribution of the SCELR test statistic for conditional moment restrictions (a consistent specification test) under the null hypothesis and local alternatives. A Monte Carlo study examines finite sample performance. We then apply these tests in an empirical application to construct confidence intervals for Engel curves and test restrictions on the curves.
DOI: 10.6084/m9.figshare.18542244
title: Identification of prognostic biomarkers in papillary renal cell carcinoma and PTTG1 may serve as a biomarker for predicting immunotherapy response

description: This study aims to identify potential prognostic and therapeutic biomarkers in papillary renal cell carcinoma (pRCC). Two microarray datasets were downloaded from the Gene Expression Omnibus (GEO) database and differentially expressed genes (DEGs) were identified. The protein-protein interaction (PPI) networks and functional annotations of DEGs were established. Survival analysis was utilized to evaluate the prognostic significance of the DEGs and the association between the expression level of candidate biomarkers and various tumour-infiltrating immune cells was explored. The role of <i>PTTG1</i> in tumour microenvironments (TME) was further explored using Single-cell RNA-seq and its prognostic and therapeutic significance was validated in Fudan University Shanghai Cancer Centre (FUSCC) cohort. Eight genes, including <i>BUB1B</i>, <i>CCNB1</i>, <i>CCNB2</i>, <i>MAD2L1</i>, <i>TTK</i>, <i>CDC20</i>, <i>PTTG1,</i> and <i>MCM</i> were found to be negatively associated with patients’ prognosis. The expression level of <i>PTTG1</i> was found to be significantly associated with lymphocytes, immunomodulators, and chemokine in the TCGA cohort. Single-cell RNA-seq information indicated that <i>PTTG1</i> was strongly associated with the proliferation of T cells. In the FUSCC cohort, the expression level of PTTG1 was also statistically significant for both progression-free survival (PFS) and overall survival (OS) prediction (HR = 2.683, <i>p</i> &lt; .001; HR = 2.673, <i>p</i> = .001). And higher expression level of PTTG1 was significantly associated with immune checkpoint blockade (ICB) response in the FUSCC cohort (<i>χ</i><sup>2</sup>=3.99, <i>p</i><b> </b>&lt;<b> </b>.05). Eight genes were identified as a prognostic biomarker and the expression level of PTTG1 was also found to serve as a potential predictor for ICB response in pRCC patients.Key messages:Eight genes, including <i>BUB1B</i>, <i>CCNB1</i>, <i>CCNB2</i>, <i>MAD2L1</i>, <i>TTK</i>, <i>CDC20</i>, <i>PTTG1,</i> and <i>MCM</i> were found to be negatively associated with pRCC patients’ prognosis.Expression level of PTTG1 was significantly associated with tumour microenvironment including lymphocytes, immunomodulators, and chemokines.Higher expression level of PTTG1 was significantly associated with immune checkpoint blockade (ICB) response in FUSCC cohort Eight genes, including <i>BUB1B</i>, <i>CCNB1</i>, <i>CCNB2</i>, <i>MAD2L1</i>, <i>TTK</i>, <i>CDC20</i>, <i>PTTG1,</i> and <i>MCM</i> were found to be negatively associated with pRCC patients’ prognosis. Expression level of PTTG1 was significantly associated with tumour microenvironment including lymphocytes, immunomodulators, and chemokines. Higher expression level of PTTG1 was significantly associated with immune checkpoint blockade (ICB) response in FUSCC cohort
DOI: 10.6084/m9.figshare.7532234.v1
title: Additional file 4: of MLH1 enhances the sensitivity of human endometrial carcinoma cells to cisplatin by activating the MLH1/c-Abl apoptosis signaling pathway

description: Table S1. The information about the sequences. (XLS 21 kb)
DOI: 10.6084/m9.figshare.25211579
title: Appendix B: The Bowland Shale Formation in the Blacon Basin: syngenetic processes, stacking patterns and heat productivity

description: Appendix C: original TOC.
DOI: 10.6084/m9.figshare.25211579.v1
title: Appendix B: The Bowland Shale Formation in the Blacon Basin: syngenetic processes, stacking patterns and heat productivity

description: Appendix C: original TOC.
DOI: 10.6084/m9.figshare.25211582
title: Appendix A: The Bowland Shale Formation in the Blacon Basin: syngenetic processes, stacking patterns and heat productivity

description: Appendix A: discrete sample geochemical datasets (RockEval pyrolysis, XRF elemental analysis, stable C and S isotopes).
DOI: 10.6084/m9.figshare.25211582.v1
title: Appendix A: The Bowland Shale Formation in the Blacon Basin: syngenetic processes, stacking patterns and heat productivity

description: Appendix A: discrete sample geochemical datasets (RockEval pyrolysis, XRF elemental analysis, stable C and S isotopes).
DOI: 10.6084/m9.figshare.21151133.v1
title: Additional file 2 of Super-enhancer-associated INSM2 regulates lipid metabolism by modulating mTOR signaling pathway in neuroblastoma

description: Additional file 2: Differentially expressed genes in INSM2-knockdown SK-N-BE(2) cells with abs(log2(foldchange))&gt;0.5 and adjusted p value&lt;0.05.
DOI: 10.6084/m9.figshare.16960663.v1
title: Additional file 3 of TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations

description: Additional file 3: Supplementary Table 2. Sequences of the chromatin tracing template oligo pools.
DOI: 10.6084/m9.figshare.16960666
title: Additional file 4 of TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations

description: Additional file 4: Supplementary Table 3. Sequences of the XIST RNA FISH template oligo pool.
DOI: 10.6084/m9.figshare.16960666.v1
title: Additional file 4 of TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations

description: Additional file 4: Supplementary Table 3. Sequences of the XIST RNA FISH template oligo pool.
DOI: 10.6084/m9.figshare.16960672.v1
title: Additional file 6 of TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations

description: Additional file 6: Supplementary Table 5. Sequences of limited-cycle PCR primers, dye-labeled reverse transcription primers and dye-labeled secondary probes.
DOI: 10.5281/zenodo.10653676
title: REACH_3rdCall_Shortlist_Anonymised

description: File with all participants of the 3rd round of the incubator, from the initially submitted applicants to the final winners.
DOI: 10.5281/zenodo.10653677
title: REACH_3rdCall_Shortlist_Anonymised

description: File with all participants of the 3rd round of the incubator, from the initially submitted applicants to the final winners.