cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1627930
title: Tetraploid cells produced by absence of substrate adhesion during cytokinesis are limited in their proliferation and enter senescence after DNA replication

description: Tetraploidy has been proposed as an intermediate state in neoplastic transformation due to the intrinsic chromosome instability of tetraploid cells. Despite the identification of p53 as a major factor in growth arrest of tetraploid cells, it is still unclear whether the p53-dependent mechanism for proliferation restriction is intrinsic to the tetraploid status or dependent on the origin of tetraploidy. Substrate adherence is fundamental for cytokinesis completion in adherent untransformed cells. Here we show that untransformed fibroblast cells undergoing mitosis in suspension produce binucleated tetraploid cells due to defective cleavage furrow constriction that leads to incomplete cell abscission. Binucleated cells obtained after loss of substrate adhesion maintain an inactive p53 status and are able to progress into G1 and S phase. However, binucleated cells arrest in G2, accumulate p53 and are not able to enter mitosis as no tetraploid metaphases were recorded after one cell cycle time. In contrast, tetraploid metaphases were found following pharmacological inhibition of Chk1 kinase, suggesting the involvement of the ATR/Chk1 pathway in the G2 arrest of binucleated cells. Interestingly, after persistence in the G2 phase of the cell cycle, a large fraction of binucleated cells become senescent. These findings identify a new pathway of proliferation restriction for tetraploid untransformed cells that seems to be specific for loss of adhesion-dependent cytokinesis failure. This involves Chk1 and p53 activation during G2. Inhibition of growth and entrance into senescence after cytokinesis in suspension may represent an important mechanism to control tumor growth. In fact, anchorage independent growth is a hallmark of cancer and it has been demonstrated that binucleated transformed cells can enter a cycle of anchorage independent growth.
DOI: 10.6084/m9.figshare.1627931
title: Notch3 overexpression causes arrest of cell cycle progression by inducing Cdh1 expression in human breast cancer cells

description: Uncontrolled cell proliferation, genomic instability and cancer are closely related to the abnormal activation of the cell cycle. Therefore, blocking the cell cycle of cancer cells has become one of the key goals for treating malignancies. Unfortunately, the factors affecting cell cycle progression remain largely unknown. In this study, we have explored the effects of Notch3 on the cell cycle in breast cancer cell lines by 3 methods: overexpressing the intra-cellular domain of Notch3 (N3ICD), knocking-down Notch3 by RNA interference, and using X-ray radiation exposure. The results revealed that overexpression of Notch3 arrested the cell cycle at the G0/G1 phase, and inhibited the proliferation and colony-formation rate in the breast cancer cell line, MDA-MB-231. Furthermore, overexpressing N3ICD upregulated Cdh1 expression and resulted in p27<sup>Kip</sup> accumulation by accelerating Skp2 degradation. Conversely, silencing of Notch3 in the breast cancer cell line, MCF-7, caused a decrease in expression levels of Cdh1 and p27<sup>Kip </sup>at both the protein and mRNA levels, while the expression of Skp2 only increased at the protein level. Correspondingly, there was an increase in the percentage of cells in the G0/G1 phase and an elevated proliferative ability and colony-formation rate, which may be caused by alterations of the Cdh1/Skp2/p27 axis. These results were also supported by exposing MDA-MB-231 cells or MCF-7 treated with siN3 to X-irradiation at various doses. Overall, our data showed that overexpression of N3ICD upregulated the expression of Cdh1 and caused p27<sup>Kip</sup> accumulation by accelerating Skp2 degradation, which in turn led to cell cycle arrest at the G0/G1 phase, in the context of proliferating breast cancer cell lines. These findings help to illuminate the precision therapy targeted to cell cycle progression, required for cancer treatment.
DOI: 10.6084/m9.figshare.1627930.v1
title: Tetraploid cells produced by absence of substrate adhesion during cytokinesis are limited in their proliferation and enter senescence after DNA replication

description: Tetraploidy has been proposed as an intermediate state in neoplastic transformation due to the intrinsic chromosome instability of tetraploid cells. Despite the identification of p53 as a major factor in growth arrest of tetraploid cells, it is still unclear whether the p53-dependent mechanism for proliferation restriction is intrinsic to the tetraploid status or dependent on the origin of tetraploidy. Substrate adherence is fundamental for cytokinesis completion in adherent untransformed cells. Here we show that untransformed fibroblast cells undergoing mitosis in suspension produce binucleated tetraploid cells due to defective cleavage furrow constriction that leads to incomplete cell abscission. Binucleated cells obtained after loss of substrate adhesion maintain an inactive p53 status and are able to progress into G1 and S phase. However, binucleated cells arrest in G2, accumulate p53 and are not able to enter mitosis as no tetraploid metaphases were recorded after one cell cycle time. In contrast, tetraploid metaphases were found following pharmacological inhibition of Chk1 kinase, suggesting the involvement of the ATR/Chk1 pathway in the G2 arrest of binucleated cells. Interestingly, after persistence in the G2 phase of the cell cycle, a large fraction of binucleated cells become senescent. These findings identify a new pathway of proliferation restriction for tetraploid untransformed cells that seems to be specific for loss of adhesion-dependent cytokinesis failure. This involves Chk1 and p53 activation during G2. Inhibition of growth and entrance into senescence after cytokinesis in suspension may represent an important mechanism to control tumor growth. In fact, anchorage independent growth is a hallmark of cancer and it has been demonstrated that binucleated transformed cells can enter a cycle of anchorage independent growth.
DOI: 10.6084/m9.figshare.14742865
title: Piperine promotes autophagy flux by P2RX4 activation in <i>SNCA</i>/α-synuclein-induced Parkinson disease model

description: Olfactory dysfunction, one of the earliest non-motor symptoms of Parkinson disease (PD), is accompanied by abnormal deposition of SNCA/α-synuclein in the olfactory bulb (OB). The macroautophagy/autophagy-lysosome pathway (ALP) plays an important role in degrading pathological SNCA and modulating this pathway may be a promising treatment strategy. P2RX4 (purinergic receptor P2X, ligand-gated ion channel 4), a member of the purinergic receptor X family, is a key molecule regulating ALP. Piperine (PIP) is a Chinese medicine with anti-inflammatory and anti-oxidant effects. The present study investigated the neuroprotective effects of PIP on SNCA overexpression-induced PD cell and mouse models. We found that PIP oral administration (25, 50 and 100 mg/kg) for 6 weeks attenuated olfactory deficits and delayed motor deficits in Thy 1-<i>SNCA</i> transgenic mice overexpressing human <i>SNCA</i>. This was accompanied by a degradation of pathological SNCA in OB. In addition, PIP improved cell viability and promoted degradation of human SNCA in SK-N-SH cells. These protective effects were exerted via autophagy flux promotion by enhancing autophagosome-lysosome membrane fusion. Furthermore, tandem mass tag proteomics analyses showed that P2RX4 plays an important role in PIP treatment-induced activation of autophagy flux. These findings demonstrate that PIP exerts neuroprotective effects in PD models via promotion of autophagy flux and may be an effective agent for PD treatment. <b>Abbreviations:</b> 6-OHDA, 6-hydroxydopamine; ALP, autophagy-lysosome pathway; BafA<sub>1</sub>, bafilomycin A<sub>1</sub>; CoQ10, coenzyme Q10; DMSO: dimethyl sulfoxide; HPLC, high-performance liquid chromatography; IVE, ivermectin; LDH, lactate dehydrogenase; MAP1LC3/LC3-II, lipid-conjugated microtubule-associated protein 1 light chain 3; MPTP, 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine; mRFP-GFP, tandem monomeric red fluorescent protein-green fluorescent protein; MTT, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide; OB, olfactory bulb; P2RX4, purinergic receptor P2X, ligand-gated ion channel 4; PD, Parkinson disease; PBS: phosphate-buffered saline; PI: propidium iodide; PIP, piperine; PLG, piperlongumine; p-SNCA, SNCA phosphorylated at Ser129; Rap, rapamycin; RT-PCR: quantitative real-time PCR; SNARE, soluble N-ethylmaleimide-sensitive factor-attachment protein receptor; SNCA/α-synuclein, synuclein, alpha; STX17, syntaxin17; TG, transgenic; TH, tyrosine hydroxylase; UPS, ubiquitin-proteasome system; WT, wild-type
DOI: 10.6084/m9.figshare.10029539
title: Metadata record for: A de novo genome assembly of the dwarfing pear rootstock Zhongai 1

description: This dataset contains key characteristics about the data described in the Data Descriptor A de novo genome assembly of the dwarfing pear rootstock Zhongai 1. <br>
 Contents: <br>
 
 1. human readable metadata summary table in CSV format
 
 
 2. machine readable metadata file in JSON format<br><br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.10029539.v1
title: Metadata record for: A de novo genome assembly of the dwarfing pear rootstock Zhongai 1

description: This dataset contains key characteristics about the data described in the Data Descriptor A de novo genome assembly of the dwarfing pear rootstock Zhongai 1. <br>
 Contents: <br>
 
 1. human readable metadata summary table in CSV format
 
 
 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.22607123
title: Additional file 9 of Transcriptome sequencing and gene expression analysis revealed early ovule abortion of Paeonia ludlowii

description: Additional file 9. DEGs involved in ovule abortion of Paeonia ludlowii.
DOI: 10.6084/m9.figshare.22607114.v1
title: Additional file 7 of Transcriptome sequencing and gene expression analysis revealed early ovule abortion of Paeonia ludlowii

description: Additional file 7. DEGs involved in PCD of Paeonia ludlowii.
DOI: 10.6084/m9.figshare.14738327.v1
title: Additional file 3 of TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes

description: Additional file 3: Supplementary material S3. GO functional enrichment analysis of cell component involved in DAPs.
DOI: 10.6084/m9.figshare.14738333
title: Additional file 5 of TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes

description: Additional file 5: Supplementary material S5. KEGG enrichment analysis the main biochemical metabolic and signal transduction pathways of the DAPs.
DOI: 10.6084/m9.figshare.14738321.v1
title: Additional file 1 of TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes

description: Additional file 1: Supplementary material S1. Totally proteins found in two samples.
DOI: 10.6084/m9.figshare.14738330
title: Additional file 4 of TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes

description: Additional file 4: Supplementary material S4. GO functional enrichment analysis of molecular function involved in DAPs.
DOI: 10.6084/m9.figshare.14738321
title: Additional file 1 of TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes

description: Additional file 1: Supplementary material S1. Totally proteins found in two samples.
DOI: 10.6084/m9.figshare.14738336.v1
title: Additional file 6 of TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes

description: Additional file 6: Supplementary material S6. The data of protein-protein interactions.
DOI: 10.6084/m9.figshare.14738324.v1
title: Additional file 2 of TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes

description: Additional file 2: Supplementary material S2. GO functional enrichment analysis of biological processes involved in DAPs.
DOI: 10.6084/m9.figshare.22607120.v1
title: Additional file 8 of Transcriptome sequencing and gene expression analysis revealed early ovule abortion of Paeonia ludlowii

description: Additional file 8. DEGs involved in the development ovule of Arabidopsis in Paeonia ludlowii.
DOI: 10.6084/m9.figshare.14738324
title: Additional file 2 of TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes

description: Additional file 2: Supplementary material S2. GO functional enrichment analysis of biological processes involved in DAPs.
DOI: 10.6084/m9.figshare.14738327
title: Additional file 3 of TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes

description: Additional file 3: Supplementary material S3. GO functional enrichment analysis of cell component involved in DAPs.
DOI: 10.6084/m9.figshare.14738330.v1
title: Additional file 4 of TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes

description: Additional file 4: Supplementary material S4. GO functional enrichment analysis of molecular function involved in DAPs.
DOI: 10.6084/m9.figshare.22607126
title: Additional file 10 of Transcriptome sequencing and gene expression analysis revealed early ovule abortion of Paeonia ludlowii

description: Additional file 10. DEGs involved in aborted ovules of Paeonia ludlowii.
DOI: 10.6084/m9.figshare.14738336
title: Additional file 6 of TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes

description: Additional file 6: Supplementary material S6. The data of protein-protein interactions.
DOI: 10.6084/m9.figshare.22607099
title: Additional file 2 of Transcriptome sequencing and gene expression analysis revealed early ovule abortion of Paeonia ludlowii

description: Additional file 2. Summary of Sequencing Data Quality.
DOI: 10.6084/m9.figshare.22607099.v1
title: Additional file 2 of Transcriptome sequencing and gene expression analysis revealed early ovule abortion of Paeonia ludlowii

description: Additional file 2. Summary of Sequencing Data Quality.
DOI: 10.6084/m9.figshare.22607111.v1
title: Additional file 6 of Transcriptome sequencing and gene expression analysis revealed early ovule abortion of Paeonia ludlowii

description: Additional file 6. DEGs involved in phytohormones signaling of Paeonia ludlowii.
DOI: 10.5255/ukda-sn-856579
title: Many Happy Returns: Corpora of Public-Facing and Consumer-Generated Single-Use Plastics Discourse, 2016-2021

description: Many Happy Returns (MHR) is a multidisciplinary project funded by UK Research and Innovation (UKRI), as part of UKRI’s Enabling Research competition in its Smart Sustainable Plastic Packaging Challenge. MHR aims to encourage reusable plastic packaging systems as a means of reducing single-use plastic waste. The linguistics work package of MHR aims: (i) to understand how people think about plastic (re)use by examining their language; (ii) to assess how well public perceptions appear to align with public-facing information on reuse; and (iii) to inform best-practice recommendations for communication around plastic reuse. The project built a corpus of relevant language, analysed it using corpus software, and interpreted it in relation to a project ecosophy.
DOI: 10.6084/m9.figshare.22607123.v1
title: Additional file 9 of Transcriptome sequencing and gene expression analysis revealed early ovule abortion of Paeonia ludlowii

description: Additional file 9. DEGs involved in ovule abortion of Paeonia ludlowii.
DOI: 10.6084/m9.figshare.22607126.v1
title: Additional file 10 of Transcriptome sequencing and gene expression analysis revealed early ovule abortion of Paeonia ludlowii

description: Additional file 10. DEGs involved in aborted ovules of Paeonia ludlowii.
DOI: 10.6084/m9.figshare.14738333.v1
title: Additional file 5 of TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes

description: Additional file 5: Supplementary material S5. KEGG enrichment analysis the main biochemical metabolic and signal transduction pathways of the DAPs.
DOI: 10.6084/m9.figshare.20510045.v1
title: Comprehensive analysis of prognosis-related alternative splicing events in ovarian cancer

description: Ovarian cancer (OV) is characterized by high incidence and poor prognosis. Increasing evidence indicates that aberrant alternative splicing (AS) events are associated with the pathogenesis of cancer. We examined prognosis-related alternative splicing events and constructed a clinically applicable model to predict patients’ outcomes. Public database including The Cancer Genome Atlas (TCGA), TCGA SpliceSeq, and the Genomics of Drug Sensitivity in Cancer databases were used to detect the AS expression, immune cell infiltration and IC50. The prognosis-related AS model was constructed and validated by using Cox regression, LASSO regression, C-index, calibration plots, and ROC curves. A total of eight AS events (including FLT3LG|50942|AP) were selected to establish the prognosis-related AS model. Compared with high-risk group, low-risk group had a better outcome (<i>P</i> = 1.794e-06), was more sensitive to paclitaxel (<i>P</i> = 0.022), and higher proportions of plasma cells. We explored the upstream regulatory mechanisms of prognosis-related AS and found that two splicing factor and 156 tag single nucleotide polymorphisms may be involved in the regulation of prognosis-related AS. In order to assess patient prognosis more comprehensively, we constructed a clinically applicable model combining risk score and clinicopathological features, and the 1 -, and 3-year AUCs of the clinically applicable model were 0.812, and 0.726, which were 7.5% and 3.3% higher than that of the risk score. We constructed a prognostic signature for OV patients and comprehensively analysed the regulatory characteristics of the prognostic AS events in OV.
DOI: 10.6084/m9.figshare.20510045
title: Comprehensive analysis of prognosis-related alternative splicing events in ovarian cancer

description: Ovarian cancer (OV) is characterized by high incidence and poor prognosis. Increasing evidence indicates that aberrant alternative splicing (AS) events are associated with the pathogenesis of cancer. We examined prognosis-related alternative splicing events and constructed a clinically applicable model to predict patients’ outcomes. Public database including The Cancer Genome Atlas (TCGA), TCGA SpliceSeq, and the Genomics of Drug Sensitivity in Cancer databases were used to detect the AS expression, immune cell infiltration and IC50. The prognosis-related AS model was constructed and validated by using Cox regression, LASSO regression, C-index, calibration plots, and ROC curves. A total of eight AS events (including FLT3LG|50942|AP) were selected to establish the prognosis-related AS model. Compared with high-risk group, low-risk group had a better outcome (<i>P</i> = 1.794e-06), was more sensitive to paclitaxel (<i>P</i> = 0.022), and higher proportions of plasma cells. We explored the upstream regulatory mechanisms of prognosis-related AS and found that two splicing factor and 156 tag single nucleotide polymorphisms may be involved in the regulation of prognosis-related AS. In order to assess patient prognosis more comprehensively, we constructed a clinically applicable model combining risk score and clinicopathological features, and the 1 -, and 3-year AUCs of the clinically applicable model were 0.812, and 0.726, which were 7.5% and 3.3% higher than that of the risk score. We constructed a prognostic signature for OV patients and comprehensively analysed the regulatory characteristics of the prognostic AS events in OV.
DOI: 10.6084/m9.figshare.22602670.v1
title: Additional file 5 of Nontargeted metabolomics reveals the potential mechanism underlying the association between birthweight and metabolic disturbances

description: Additional file 5: Table S4. Metabolites and pathway information.
DOI: 10.25502/cpgq-rg89/d
title: RCI veg seedling trial data.Nairobi, Kenya season 1 2023

description: WP1 of RCI to improve UPU crop productivity; assessment of tray vegetable seedling benefits
DOI: 10.6084/m9.figshare.14742865.v1
title: Piperine promotes autophagy flux by P2RX4 activation in <i>SNCA</i>/α-synuclein-induced Parkinson disease model

description: Olfactory dysfunction, one of the earliest non-motor symptoms of Parkinson disease (PD), is accompanied by abnormal deposition of SNCA/α-synuclein in the olfactory bulb (OB). The macroautophagy/autophagy-lysosome pathway (ALP) plays an important role in degrading pathological SNCA and modulating this pathway may be a promising treatment strategy. P2RX4 (purinergic receptor P2X, ligand-gated ion channel 4), a member of the purinergic receptor X family, is a key molecule regulating ALP. Piperine (PIP) is a Chinese medicine with anti-inflammatory and anti-oxidant effects. The present study investigated the neuroprotective effects of PIP on SNCA overexpression-induced PD cell and mouse models. We found that PIP oral administration (25, 50 and 100 mg/kg) for 6 weeks attenuated olfactory deficits and delayed motor deficits in Thy 1-<i>SNCA</i> transgenic mice overexpressing human <i>SNCA</i>. This was accompanied by a degradation of pathological SNCA in OB. In addition, PIP improved cell viability and promoted degradation of human SNCA in SK-N-SH cells. These protective effects were exerted via autophagy flux promotion by enhancing autophagosome-lysosome membrane fusion. Furthermore, tandem mass tag proteomics analyses showed that P2RX4 plays an important role in PIP treatment-induced activation of autophagy flux. These findings demonstrate that PIP exerts neuroprotective effects in PD models via promotion of autophagy flux and may be an effective agent for PD treatment. <b>Abbreviations:</b> 6-OHDA, 6-hydroxydopamine; ALP, autophagy-lysosome pathway; BafA<sub>1</sub>, bafilomycin A<sub>1</sub>; CoQ10, coenzyme Q10; DMSO: dimethyl sulfoxide; HPLC, high-performance liquid chromatography; IVE, ivermectin; LDH, lactate dehydrogenase; MAP1LC3/LC3-II, lipid-conjugated microtubule-associated protein 1 light chain 3; MPTP, 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine; mRFP-GFP, tandem monomeric red fluorescent protein-green fluorescent protein; MTT, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide; OB, olfactory bulb; P2RX4, purinergic receptor P2X, ligand-gated ion channel 4; PD, Parkinson disease; PBS: phosphate-buffered saline; PI: propidium iodide; PIP, piperine; PLG, piperlongumine; p-SNCA, SNCA phosphorylated at Ser129; Rap, rapamycin; RT-PCR: quantitative real-time PCR; SNARE, soluble N-ethylmaleimide-sensitive factor-attachment protein receptor; SNCA/α-synuclein, synuclein, alpha; STX17, syntaxin17; TG, transgenic; TH, tyrosine hydroxylase; UPS, ubiquitin-proteasome system; WT, wild-type