cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12851510
title: Proteomic analysis of meiosis and characterization of novel short open reading frames in the fission yeast <i>Schizosaccharomyces pombe</i>

description: Meiosis is the process by which haploid gametes are produced from diploid precursor cells. We used stable isotope labeling by amino acids in cell culture (SILAC) to characterize the meiotic proteome in the fission yeast <i>Schizosaccharomyces pombe</i>. We compared relative levels of proteins extracted from cells harvested around meiosis I with those of meiosis II, and proteins from premeiotic S phase with the interval between meiotic divisions, when S phase is absent. Our proteome datasets revealed peptides corresponding to short open reading frames (sORFs) that have been previously identified by ribosome profiling as new translated regions. We verified expression of selected sORFs by Western blotting and analyzed the phenotype of deletion mutants. Our data provide a resource for studying meiosis that may help understand differences between meiosis I and meiosis II and how S phase is suppressed between the two meiotic divisions.
DOI: 10.6084/m9.figshare.12851510.v1
title: Proteomic analysis of meiosis and characterization of novel short open reading frames in the fission yeast <i>Schizosaccharomyces pombe</i>

description: Meiosis is the process by which haploid gametes are produced from diploid precursor cells. We used stable isotope labeling by amino acids in cell culture (SILAC) to characterize the meiotic proteome in the fission yeast <i>Schizosaccharomyces pombe</i>. We compared relative levels of proteins extracted from cells harvested around meiosis I with those of meiosis II, and proteins from premeiotic S phase with the interval between meiotic divisions, when S phase is absent. Our proteome datasets revealed peptides corresponding to short open reading frames (sORFs) that have been previously identified by ribosome profiling as new translated regions. We verified expression of selected sORFs by Western blotting and analyzed the phenotype of deletion mutants. Our data provide a resource for studying meiosis that may help understand differences between meiosis I and meiosis II and how S phase is suppressed between the two meiotic divisions.
DOI: 10.6084/m9.figshare.12851507
title: Five transcriptional factors reprogram fibroblast into myogenic lineage cells via paraxial mesoderm stage

description: It is hard to supply satellite cells as a cell source for therapy of muscle degenerative disease since the sampling of muscle tissue is very invasive to a patient with muscular disease. Direct conversion allows us to get specific cell types by transduction of defined transcriptional factors. To induce myogenic direct conversion, we transduced five transcriptional factors including Pax3, Sox2, Klf4, c-Myc, and Esrrb into mouse embryonic fibroblasts. We found that the transduction of the five transcriptional factors induced myogenic direct conversion of fibroblast. We revealed that the transduced cells with the five transcriptional factors were converted to myogenic lineage cells through a paraxial mesoderm-like stage. The expression level of myogenic-related genes of the transduced cells gradually increased as the passage increased. The induced myogenic lineage cells differentiated into muscle fibers <i>in virto</i> and <i>in vivo</i>. The current study revealed that the five transcription factors generated myogenic lineage cells from fibroblast via a paraxial mesoderm stage. The induced myogenic lineage cells may have a potential being applied as cell source for degenerative muscle disease.
DOI: 10.6084/m9.figshare.12851507.v1
title: Five transcriptional factors reprogram fibroblast into myogenic lineage cells via paraxial mesoderm stage

description: It is hard to supply satellite cells as a cell source for therapy of muscle degenerative disease since the sampling of muscle tissue is very invasive to a patient with muscular disease. Direct conversion allows us to get specific cell types by transduction of defined transcriptional factors. To induce myogenic direct conversion, we transduced five transcriptional factors including Pax3, Sox2, Klf4, c-Myc, and Esrrb into mouse embryonic fibroblasts. We found that the transduction of the five transcriptional factors induced myogenic direct conversion of fibroblast. We revealed that the transduced cells with the five transcriptional factors were converted to myogenic lineage cells through a paraxial mesoderm-like stage. The expression level of myogenic-related genes of the transduced cells gradually increased as the passage increased. The induced myogenic lineage cells differentiated into muscle fibers <i>in virto</i> and <i>in vivo</i>. The current study revealed that the five transcription factors generated myogenic lineage cells from fibroblast via a paraxial mesoderm stage. The induced myogenic lineage cells may have a potential being applied as cell source for degenerative muscle disease.
DOI: 10.6084/m9.figshare.16823079.v2
title: M<sup>6</sup>A-mediated up-regulation of LncRNA LIFR-AS1 enhances the progression of pancreatic cancer via miRNA-150-5p/ VEGFA/Akt signaling

description: N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) modification, the most abundant internal methylation of eukaryotic RNA transcripts, is critically implicated in RNA processing. There is extensive evidence indicating that long non-coding RNAs (lncRNAs) serve as key regulators of oncogenesis and tumor progression in humans. Through prior study has assessed that LIFR-AS1 plays a key role in various kinds of malignant tumors. However, the exact role of m<sup>6</sup>A induced LIFR-AS1 in pancreatic cancer (PC) and its potential molecular mechanisms remain largely unknown. In this study, we determined that PC cell lines and tumors exhibit increased LIFR-AS1 expression that correlates with larger tumor size, lymph node metastasis, and more advanced TNM stage. Functionally, loss-of-function studies indicated that LIFR-AS1 knockdown decreased the proliferation, migration, and invasion of PC cells in vitro. Mechanistically, we found that METTL3 induced m<sup>6</sup>A hyper-methylation on the 3′ UTR of LIFR-AS1 to enhance its mRNA stability and LIFR-AS1 could directly interact with miR-150-5p, thereby indirectly up-regulating VEGFA expressions within cells. Through rescue experiments, we were able to confirm that the unfavorable impact of LIFR-AS1 knockdown on VEGFA /PI3K/Akt Signaling could be reversed via the inhibition of miR-150-5p expression. Together, these findings indicate that a noval m6A-LIFR-AS1 axis promotes PC progression at least in part via regulation of the miR-150-5p/VEGFA axis, indicating that this regulatory axis may be a viable clinical target for the treatment of PC.
DOI: 10.6084/m9.figshare.16912044
title: Aloin decelerates the progression of hepatocellular carcinoma through circ_0011385/miR-149-5p/WT1 axis

description: CircRNA/miRNA/mRNA axis has been reported to play crucial regulatory roles in multiple cancers, including hepatocellular carcinoma (HCC). In addition, recent investigations revealed that aloin exerted anti-tumor functions in HCC. However, the underlying mechanism of aloin on anti-tumor functions in HCC remained elusive. Therefore, this study aimed to investigate whether circRNA/miRNA/mRNA axis medicated the anti-tumor effect of aloin in HCC. Cell viability, invasion, apoptosis and autophagy were accessed by cell counting kit-8 (CCK-8), transwell invasion assay, flow cytometry, Western blot and immunofluorescence analysis, respectively. Expression levels of circ_0011385, miR-149-5p and WT1 mRNA were determined using qRT-PCR assay. Binding sites between miR-149-5p and circ_0011385 or WT1 were predicted in starBase database. The binding relationship among circ_0011385, miR-149-5p and WT1 were verified by dual-luciferase reporter assay and RNA immunoprecipitation. Besides, the rescue experiments were performed by co-transfection with cric_0011385 overexpression plasmid, si-cric_0011385, miR-149-5p mimic and inhibitor, WT1 pDNA and si-WT1 in HCC cells. Furthermore, tumor growth was also investigated in the xenograft mouse model. Aloin inhibited HCC proliferation and invasion as well as promoted apoptosis and autophagy both <i>in vitro</i> and <i>in vivo</i>. Besides, aloin suppressed circ_0011385 expression. Overexpressed circ_0011385 partially reversed the anti-tumor effect of aloin on HCC. In addition, it was revealed that the circ_0011385, miR-149-5p and WT1 genes were abnormally expressed in HCC. Furthermore, the binding interactions between circ_0011385, miR-149-5p and WT1 were predicted and confirmed. Moreover, the effect of circ_0011385 on the anti-tumor role of aloin in HCC was rescued by miR-149-5p mimics. MiR-149-5p regulated HCC progression via modulating WT1. Aloin suppressed cell proliferation, invasion and tumor growth and promoted apoptosis and autophagy in HCC through regulating circ_0011385/miR-149-5p/WT1 axis. Aloin may be a potential candidate drug for HCC treatment.<b>Abbrevations:</b> HCC: Hepatocellular carcinoma; ceRNA: competing endogenous RNA; miRNA: microRNA; MREs: miRNA response elements; WT1: Wilms’ tumor 1; MMP-2: Matrix metalloproteinase; EMT: epithelial-mesenchymal transition; GADPH: glyceraldehyde 3-phosphate dehydrogenase; WT: wild type; MUT: mutant type; DMEM: dulbecco’s modified eagle medium.
DOI: 10.6084/m9.figshare.16912044.v1
title: Aloin decelerates the progression of hepatocellular carcinoma through circ_0011385/miR-149-5p/WT1 axis

description: CircRNA/miRNA/mRNA axis has been reported to play crucial regulatory roles in multiple cancers, including hepatocellular carcinoma (HCC). In addition, recent investigations revealed that aloin exerted anti-tumor functions in HCC. However, the underlying mechanism of aloin on anti-tumor functions in HCC remained elusive. Therefore, this study aimed to investigate whether circRNA/miRNA/mRNA axis medicated the anti-tumor effect of aloin in HCC. Cell viability, invasion, apoptosis and autophagy were accessed by cell counting kit-8 (CCK-8), transwell invasion assay, flow cytometry, Western blot and immunofluorescence analysis, respectively. Expression levels of circ_0011385, miR-149-5p and WT1 mRNA were determined using qRT-PCR assay. Binding sites between miR-149-5p and circ_0011385 or WT1 were predicted in starBase database. The binding relationship among circ_0011385, miR-149-5p and WT1 were verified by dual-luciferase reporter assay and RNA immunoprecipitation. Besides, the rescue experiments were performed by co-transfection with cric_0011385 overexpression plasmid, si-cric_0011385, miR-149-5p mimic and inhibitor, WT1 pDNA and si-WT1 in HCC cells. Furthermore, tumor growth was also investigated in the xenograft mouse model. Aloin inhibited HCC proliferation and invasion as well as promoted apoptosis and autophagy both <i>in vitro</i> and <i>in vivo</i>. Besides, aloin suppressed circ_0011385 expression. Overexpressed circ_0011385 partially reversed the anti-tumor effect of aloin on HCC. In addition, it was revealed that the circ_0011385, miR-149-5p and WT1 genes were abnormally expressed in HCC. Furthermore, the binding interactions between circ_0011385, miR-149-5p and WT1 were predicted and confirmed. Moreover, the effect of circ_0011385 on the anti-tumor role of aloin in HCC was rescued by miR-149-5p mimics. MiR-149-5p regulated HCC progression via modulating WT1. Aloin suppressed cell proliferation, invasion and tumor growth and promoted apoptosis and autophagy in HCC through regulating circ_0011385/miR-149-5p/WT1 axis. Aloin may be a potential candidate drug for HCC treatment.<b>Abbrevations:</b> HCC: Hepatocellular carcinoma; ceRNA: competing endogenous RNA; miRNA: microRNA; MREs: miRNA response elements; WT1: Wilms’ tumor 1; MMP-2: Matrix metalloproteinase; EMT: epithelial-mesenchymal transition; GADPH: glyceraldehyde 3-phosphate dehydrogenase; WT: wild type; MUT: mutant type; DMEM: dulbecco’s modified eagle medium.
DOI: 10.6084/m9.figshare.16917366
title: Exosomal lncAY927529 enhances prostate cancer cell proliferation and invasion through regulating bone microenvironment

description: Exosomes mediate the interaction between cancer cells and their microenvironment, and play a key role in tumor development. Although exosomes can package lncRNAs to mediate extracellular communication, the role of exosomal lncRNA AY927529 in prostate cancer (PCa) remains unclear. Exosomes were extracted from normal human prostatic epithelial cell lines (BPH-1 and RWPE-1) and PCa cell lines (VCaP and LNCaP, DU145, PC3) by ultrahigh speed centrifugation. Results of Western blot indicated that Alix, HSC70 and TSGl01 protein levels were upregulated in exosomes derived from PCa cells. LncAY927529 level was upregulated in PCa cells and exosomes derived from PCa patient serum and human PCa cells. CCK-8, Transwell and Flow cytometry assays demonstrated that bone marrow stromal cell line (ST2) conditioned medium (ST2-CM), treated with exosomes derived from PCa cells with high lncAY927529 level, promoted proliferation and invasion of PC3 and DU145 cells, and inhibited cell apoptosis. RT-qPCR assay indicated that lncAY927529 level was downregulated in PC3 and DU145 cells, exosomes derived from PCa cells (PCa-Exo) and ST2-CM treated with PCa-Exo with low expression of lncAY927529, and overexpression of lncAY927529 had the opposite results. In addition, Western blot assay showed that the autophagy related protein LC3II level was increased in ST2 cells treated with exosomes derived from DU145 cells with high expression of lncAY927529, and LC3I protein level was decreased. CXCL14 acted as a RNA-binding protein of lncAY927529, and exosome-mediated lncAY927529 positively regulated CXCL14 levels in ST2 cells. In general, exosome-mediated lncAY927529 could promote PCa cell proliferation and invasion by regulating bone microenvironment, suggesting that exosomal lncAY927529 may be a potential molecular diagnostic marker of PCa.
DOI: 10.6084/m9.figshare.16823079
title: M<sup>6</sup>A-mediated up-regulation of LncRNA LIFR-AS1 enhances the progression of pancreatic cancer via miRNA-150-5p/ VEGFA/Akt signaling

description: N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) modification, the most abundant internal methylation of eukaryotic RNA transcripts, is critically implicated in RNA processing. There is extensive evidence indicating that long non-coding RNAs (lncRNAs) serve as key regulators of oncogenesis and tumor progression in humans. Through prior study has assessed that LIFR-AS1 plays a key role in various kinds of malignant tumors. However, the exact role of m<sup>6</sup>A induced LIFR-AS1 in pancreatic cancer (PC) and its potential molecular mechanisms remain largely unknown. In this study, we determined that PC cell lines and tumors exhibit increased LIFR-AS1 expression that correlates with larger tumor size, lymph node metastasis, and more advanced TNM stage. Functionally, loss-of-function studies indicated that LIFR-AS1 knockdown decreased the proliferation, migration, and invasion of PC cells in vitro. Mechanistically, we found that METTL3 induced m<sup>6</sup>A hyper-methylation on the 3′ UTR of LIFR-AS1 to enhance its mRNA stability and LIFR-AS1 could directly interact with miR-150-5p, thereby indirectly up-regulating VEGFA expressions within cells. Through rescue experiments, we were able to confirm that the unfavorable impact of LIFR-AS1 knockdown on VEGFA /PI3K/Akt Signaling could be reversed via the inhibition of miR-150-5p expression. Together, these findings indicate that a noval m6A-LIFR-AS1 axis promotes PC progression at least in part via regulation of the miR-150-5p/VEGFA axis, indicating that this regulatory axis may be a viable clinical target for the treatment of PC.
DOI: 10.6084/m9.figshare.16917366.v1
title: Exosomal lncAY927529 enhances prostate cancer cell proliferation and invasion through regulating bone microenvironment

description: Exosomes mediate the interaction between cancer cells and their microenvironment, and play a key role in tumor development. Although exosomes can package lncRNAs to mediate extracellular communication, the role of exosomal lncRNA AY927529 in prostate cancer (PCa) remains unclear. Exosomes were extracted from normal human prostatic epithelial cell lines (BPH-1 and RWPE-1) and PCa cell lines (VCaP and LNCaP, DU145, PC3) by ultrahigh speed centrifugation. Results of Western blot indicated that Alix, HSC70 and TSGl01 protein levels were upregulated in exosomes derived from PCa cells. LncAY927529 level was upregulated in PCa cells and exosomes derived from PCa patient serum and human PCa cells. CCK-8, Transwell and Flow cytometry assays demonstrated that bone marrow stromal cell line (ST2) conditioned medium (ST2-CM), treated with exosomes derived from PCa cells with high lncAY927529 level, promoted proliferation and invasion of PC3 and DU145 cells, and inhibited cell apoptosis. RT-qPCR assay indicated that lncAY927529 level was downregulated in PC3 and DU145 cells, exosomes derived from PCa cells (PCa-Exo) and ST2-CM treated with PCa-Exo with low expression of lncAY927529, and overexpression of lncAY927529 had the opposite results. In addition, Western blot assay showed that the autophagy related protein LC3II level was increased in ST2 cells treated with exosomes derived from DU145 cells with high expression of lncAY927529, and LC3I protein level was decreased. CXCL14 acted as a RNA-binding protein of lncAY927529, and exosome-mediated lncAY927529 positively regulated CXCL14 levels in ST2 cells. In general, exosome-mediated lncAY927529 could promote PCa cell proliferation and invasion by regulating bone microenvironment, suggesting that exosomal lncAY927529 may be a potential molecular diagnostic marker of PCa.
DOI: 10.15468/dl.u5gm5a
title: Occurrence Download

description: A dataset containing 312781 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aegypius monachus (Linnaeus, 1766)"
 ]
}

 The dataset includes 312781 records from 333 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012006-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12606052
title: Tailoring the Selectivity of 1,3-Butadiene versus 1-Butene Adsorption on Pt(111) by Ultrathin Ionic Liquid Films [DOI: 10.1021/acscatal.3c02126]

description: Data is included [DOI: 10.1021/acscatal.3c02126]
DOI: 10.5281/zenodo.12606053
title: Tailoring the Selectivity of 1,3-Butadiene versus 1-Butene Adsorption on Pt(111) by Ultrathin Ionic Liquid Films [DOI: 10.1021/acscatal.3c02126]

description: Data is included [DOI: 10.1021/acscatal.3c02126]
DOI: 10.15468/dl.3beydy
title: Occurrence Download

description: A dataset containing 372 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is one of (Africa, Asia, Oceania, South America)",
 "OccurrenceStatus is Present",
 "PublishingOrg is 396d5f30-dea9-11db-8ab4-b8a03c50a862",
 "TaxonKey is Rorippa Scop."
 ]
}

 The dataset includes 372 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012011-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11260317
title: Data for Inverse Folding/Structural Evolution paper
DOI: 10.5281/zenodo.11260318
title: Data for Inverse Folding/Structural Evolution paper
DOI: 10.15468/dl.huvevf
title: Occurrence Download

description: A dataset containing 2056 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is MarineGEO Global Seagrass Habitat Monitoring Data"
 ]
}

 The dataset includes 2056 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012013-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ptjfjn
title: Occurrence Download

description: A dataset containing 372 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is one of (Africa, Asia, Oceania, South America)",
 "OccurrenceStatus is Present",
 "PublishingOrg is 396d5f30-dea9-11db-8ab4-b8a03c50a862",
 "TaxonKey is Rorippa Scop."
 ]
}

 The dataset includes 372 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012015-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ryk77c
title: Occurrence Download

description: A dataset containing 145842 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-76.56558 3.54000,-54.26530 3.54000,-54.26530 12.46913,-76.56558 12.46913,-76.56558 3.54000))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Anura",
 "Year 1578-2024"
 ]
}

 The dataset includes 145842 records from 471 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012012-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6cbf9n
title: Occurrence Download

description: A dataset listing the 4 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Argentina",
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Chlorostilbon lucidus (Shaw, 1812)"
 ]
}

 The dataset's 4 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012014-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12608138
title: AIrating annotated datasets

description: AIrating datasets are built to support the manual evaluation of the results of two services (Google vs Impaakt) that return documents related to a given query (e.g. Weatherford,Core Business Impact (Access to Energy)).For each query and each service, the documents are annotated YES/NO on two dimensions: the document's accessibility, and its relevance to the query.The annotators were trained on this task, and the assessment was doubled in case of doubt.
DOI: 10.5281/zenodo.12608139
title: AIrating annotated datasets

description: AIrating datasets are built to support the manual evaluation of the results of two services (Google vs Impaakt) that return documents related to a given query (e.g. Weatherford,Core Business Impact (Access to Energy)).For each query and each service, the documents are annotated YES/NO on two dimensions: the document's accessibility, and its relevance to the query.The annotators were trained on this task, and the assessment was doubled in case of doubt.
DOI: 10.15468/dl.jdahjx
title: Occurrence Download

description: A dataset containing 1131 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Jubaea chilensis (Molina) Baill."
 ]
}

 The dataset includes 1131 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012018-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.up64jq
title: Occurrence Download

description: A dataset containing 2507898 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "TaxonKey is Procellariiformes"
 ]
}

 The dataset includes 2507898 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012016-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.