cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17708072
title: Exploration of the typical features of tubulovillous adenoma using in-depth quantitative proteomics analysis

description: This present study aimed to explore the typical protein features of tubulovillous adenoma (TVA) using proteomic and bioinformatic analyses. Tandem mass tag (TMT)-based quantitative proteomic analyses were conducted on normal mucosa, tubular adenoma, TVA and adenocarcinoma tissues. We identified 5,665 proteins categorized into seven clusters based on Pearson’s correlation analysis. The bioinfomatic analysis showed mitochondrial and metabolism-related events were typical characteristics of TVA and mitochondrial-, ribosome- and matrisome-related biological processes may contribute to carcinogenesis. PLOD3 was identified as a key protein associated with the malignant potential of TVA and promoted the viability of adenoma organoids. The Cancer Genome Atlas (TCGA) analysis revealed PLOD3 as a risk factor for disease-free and overall survival. Furthermore, the PLOD3 expression correlated negatively with the abundance of B cells, CD8 + T cells, CD4 + T cells, neutrophils, macrophages and myeloid dendritic cells. In conclusion, enhanced metabolic and mitochondrial reprogramming are typical features of TVA, and PLOD3 might be related to the “immune desert” phenotype and contribute to TVA tumorigenesis and colorectal cancer development.
DOI: 10.6084/m9.figshare.17708081.v1
title: Upregulation of microRNA miR-652-3p is a prognostic risk factor for hepatocellular carcinoma and regulates cell proliferation, migration, and invasion

description: As powerful regulatory factors, microRNAs (miRNAs) are involved in tumor progression. The current research aimed to excavate the prognostic significance and potential regulatory mechanisms of miR-652-3p in hepatocellular carcinoma (HCC). Expression of miR-652-3p in HCC tissues and cells was exposed by Quantitative real-time polymerase chain reaction (RT-qPCR) assay, and we found that miR-652-3p was elevated in HCC tissues and cells than in the control group (<i>P</i> &lt; 0.05). Then, the relationship between miR-652-3p levels and clinical characteristics was obtained from the Chi-square test. Kaplan-Meier survival analysis and Cox regression model to explore the outcome of miR-652-3p on the prognosis of HCC. The results investigated that overexpression of miR-652-3p was related to clinical tumor-node-metastasis (TNM) stage (<i>P</i> = 0.020) and differentiation (<i>P</i> = 0.031). HCC patients with elevated miR-652-3p levels were correlated with poor overall survival (log-rank, <i>P</i> = 0.007), and maybe a possible prognostic marker for HCC. Finally, CCK-8, colony formation, wound healing and Transwell assay was detected after transfection of HCC cells with miR-652-3p mimic or inhibitor. And the results confirmed that elevation miR-652-3p promoted the proliferation, migration, and invasion of tumor cells (<i>P</i> &lt; 0.05). All data indicated that elevated miR-652-3p is a prognostic marker and would be able to participate in tumor progression of HCC by regulating cell proliferation, migration, and invasion.
DOI: 10.6084/m9.figshare.17708090
title: A seven-gene signature and the C–C motif chemokine receptor family genes are the sarcoma-related immune genes

description: Cells of the tumor microenvironment exert a vital influence on sarcoma prognosis. This study aimed to analyze and identify differentially expressed genes (DEGs) related to immunity and their significance as immune biomarkers for the accurate prediction of overall survival of patients with sarcoma. The Cancer Genome Atlas was adopted for obtaining sarcoma gene microarray and corresponding clinical information. ESTIMATE algorithm was used to calculate tumor immune microenvironment indices. Immune-associated DEGs were identified using the limma packages and were further analyzed using the ClusterProfiler package and STRING website. Based on the results of these analyses, we constructed a prognostic model. Furthermore, we assessed the prognosis prediction model through functional evaluation and analysis of GSE17674. The functional analysis revealed that the upregulated immune DEGs were related to immune-related aspects. Chemokine ligands/receptors and immune-related genes were found to be vital for sarcoma formation and progression. We established a prognostic signature of seven genes, which indicated that high-risk cases exhibit poor prognostic outcome. The prognostic signature constructed in this study can accurately predict the overall prognosis in patients with sarcoma. Moreover, the novel immune gene expression analysis may provide clinical guidance for predicting prognosis in patients with sarcoma.
DOI: 10.6084/m9.figshare.14037907
title: Additional file 6 of Molecular characterization, expression and functional analysis of acyl-CoA-binding protein gene family in maize (Zea mays)

description: Additional file 6: Table S4. The correlation among ZmACBP genes expression levels and oil content in maize kernel.
DOI: 10.6084/m9.figshare.17708090.v1
title: A seven-gene signature and the C–C motif chemokine receptor family genes are the sarcoma-related immune genes

description: Cells of the tumor microenvironment exert a vital influence on sarcoma prognosis. This study aimed to analyze and identify differentially expressed genes (DEGs) related to immunity and their significance as immune biomarkers for the accurate prediction of overall survival of patients with sarcoma. The Cancer Genome Atlas was adopted for obtaining sarcoma gene microarray and corresponding clinical information. ESTIMATE algorithm was used to calculate tumor immune microenvironment indices. Immune-associated DEGs were identified using the limma packages and were further analyzed using the ClusterProfiler package and STRING website. Based on the results of these analyses, we constructed a prognostic model. Furthermore, we assessed the prognosis prediction model through functional evaluation and analysis of GSE17674. The functional analysis revealed that the upregulated immune DEGs were related to immune-related aspects. Chemokine ligands/receptors and immune-related genes were found to be vital for sarcoma formation and progression. We established a prognostic signature of seven genes, which indicated that high-risk cases exhibit poor prognostic outcome. The prognostic signature constructed in this study can accurately predict the overall prognosis in patients with sarcoma. Moreover, the novel immune gene expression analysis may provide clinical guidance for predicting prognosis in patients with sarcoma.
DOI: 10.6084/m9.figshare.17708096
title: Screening of key biomarkers and immune infiltration in Pulmonary Arterial Hypertension via integrated bioinformatics analysis

description: This study aimed to screen key biomarkers and investigate immune infiltration in pulmonary arterial hypertension (PAH) based on integrated bioinformatics analysis. The Gene Expression Omnibus (GEO) database was used to download three mRNA expression profiles comprising 91 PAH lung specimens and 49 normal lung specimens. Three mRNA expression datasets were combined, and differentially expressed genes (DEGs) were obtained. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses and the protein-protein interaction (PPI) network of DEGs were performed using the STRING and DAVID databases, respectively. The diagnostic value of hub gene expression in PAH was also analyzed. Finally, the infiltration of immune cells in PAH was analyzed using the CIBERSORT algorithm. Total 182 DEGs (117 upregulated and 65 downregulated) were identified, and 15 hub genes were screened. These 15 hub genes were significantly associated with immune system functions such as myeloid leukocyte migration, neutrophil migration, cell chemotaxis, Toll-like receptor signaling pathway, and NF-κB signaling pathway. A 7-gene-based model was constructed and had a better diagnostic value in identifying PAH tissues compared with normal controls. The immune infiltration profiles of the PAH and normal control samples were significantly different. High proportions of resting NK cells, activated mast cells, monocytes, and neutrophils were found in PAH samples, while high proportions of resting T cells CD4 memory and Macrophages M1 cell were found in normal control samples. Functional enrichment of DEGs and immune infiltration analysis between PAH and normal control samples might help to understand the pathogenesis of PAH.
DOI: 10.6084/m9.figshare.17708093
title: Identification and validation of seven RNA binding protein genes as a prognostic signature in oral cavity squamous cell carcinoma

description: RNA binding proteins (RBPs) play a pivotal role in various biological processes, and aberrant expression of RBPs is closely associated with tumorigenesis and progression. However, the role of RBPs in oral cavity squamous cell carcinoma (OCSCC) is yet unveiled. In this study, RNA sequences and clinical information of OCSCC samples were acquired from The Cancer Genome Atlas (TCGA) database. A total of 650 RBPs, with significantly different expression between healthy and OCSCC samples, were identified using the limma package. A prognostic model was constructed by Lasso-Cox analysis, resulting in the determination of 7 prognosis-related RBPs: ERMP1, RNASE3, ARL4D, CSRP2, ULK1, ZC3H12D, and RPS28. Based on the prognostic model, the risk scores of the OCSCC samples were calculated. The capability of the prognostic model was further evaluated using the receiver operating characteristic curve (ROC). The areas under ROC were 0.764, 0.771, and 0.809 at 1, 3 and 5-year respectively in the TCGA dataset. Internal and external validation showed satisfactory predictive capability for prognosis in OCSCC. In addition, a nomogram was created to graphically present the model. To further validate the analytical data, qRT-PCR was performed on normal and OCSCC cell lines. The mRNA expression of the 7 prognostic genes was in accordance with the analytical results. Functional analysis and gene connection networks were used to describe the biological functions and underlying interactions among the 7 prognostic genes Overall, 7 prognosis-related RBPs were identified, which could be used to predict clinical prognosis and to identify potential therapeutic targets for OCSCC.
DOI: 10.6084/m9.figshare.14037904
title: Additional file 5 of Molecular characterization, expression and functional analysis of acyl-CoA-binding protein gene family in maize (Zea mays)

description: Additional file 5: Table S3. The ZmACBP genes list associated with agronomic traits in maize.
DOI: 10.6084/m9.figshare.17708096.v1
title: Screening of key biomarkers and immune infiltration in Pulmonary Arterial Hypertension via integrated bioinformatics analysis

description: This study aimed to screen key biomarkers and investigate immune infiltration in pulmonary arterial hypertension (PAH) based on integrated bioinformatics analysis. The Gene Expression Omnibus (GEO) database was used to download three mRNA expression profiles comprising 91 PAH lung specimens and 49 normal lung specimens. Three mRNA expression datasets were combined, and differentially expressed genes (DEGs) were obtained. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses and the protein-protein interaction (PPI) network of DEGs were performed using the STRING and DAVID databases, respectively. The diagnostic value of hub gene expression in PAH was also analyzed. Finally, the infiltration of immune cells in PAH was analyzed using the CIBERSORT algorithm. Total 182 DEGs (117 upregulated and 65 downregulated) were identified, and 15 hub genes were screened. These 15 hub genes were significantly associated with immune system functions such as myeloid leukocyte migration, neutrophil migration, cell chemotaxis, Toll-like receptor signaling pathway, and NF-κB signaling pathway. A 7-gene-based model was constructed and had a better diagnostic value in identifying PAH tissues compared with normal controls. The immune infiltration profiles of the PAH and normal control samples were significantly different. High proportions of resting NK cells, activated mast cells, monocytes, and neutrophils were found in PAH samples, while high proportions of resting T cells CD4 memory and Macrophages M1 cell were found in normal control samples. Functional enrichment of DEGs and immune infiltration analysis between PAH and normal control samples might help to understand the pathogenesis of PAH.
DOI: 10.6084/m9.figshare.17708093.v1
title: Identification and validation of seven RNA binding protein genes as a prognostic signature in oral cavity squamous cell carcinoma

description: RNA binding proteins (RBPs) play a pivotal role in various biological processes, and aberrant expression of RBPs is closely associated with tumorigenesis and progression. However, the role of RBPs in oral cavity squamous cell carcinoma (OCSCC) is yet unveiled. In this study, RNA sequences and clinical information of OCSCC samples were acquired from The Cancer Genome Atlas (TCGA) database. A total of 650 RBPs, with significantly different expression between healthy and OCSCC samples, were identified using the limma package. A prognostic model was constructed by Lasso-Cox analysis, resulting in the determination of 7 prognosis-related RBPs: ERMP1, RNASE3, ARL4D, CSRP2, ULK1, ZC3H12D, and RPS28. Based on the prognostic model, the risk scores of the OCSCC samples were calculated. The capability of the prognostic model was further evaluated using the receiver operating characteristic curve (ROC). The areas under ROC were 0.764, 0.771, and 0.809 at 1, 3 and 5-year respectively in the TCGA dataset. Internal and external validation showed satisfactory predictive capability for prognosis in OCSCC. In addition, a nomogram was created to graphically present the model. To further validate the analytical data, qRT-PCR was performed on normal and OCSCC cell lines. The mRNA expression of the 7 prognostic genes was in accordance with the analytical results. Functional analysis and gene connection networks were used to describe the biological functions and underlying interactions among the 7 prognostic genes Overall, 7 prognosis-related RBPs were identified, which could be used to predict clinical prognosis and to identify potential therapeutic targets for OCSCC.
DOI: 10.6084/m9.figshare.14037907.v1
title: Additional file 6 of Molecular characterization, expression and functional analysis of acyl-CoA-binding protein gene family in maize (Zea mays)

description: Additional file 6: Table S4. The correlation among ZmACBP genes expression levels and oil content in maize kernel.
DOI: 10.6084/m9.figshare.11940963.v1
title: Incidence and risk of proteinuria associated with newly approved vascular endothelial growth factor receptor tyrosine kinase inhibitors in cancer patients: an up-to-date meta-analysis of randomized controlled trials

description: <b>Objective</b>: We performed a meta-analysis to quantify the overall incidence and risk of proteinuria associated with five newly approved VEGFR-TKIs (regorafenib, vandetanib, cabozantinib, lenvatinib, axitinib) in cancer patients. <b>Methods</b>: Pubmed, Embase, ASCO abstracts, and ESMO abstracts were searched to identify relevant studies. Overall incidence rates, relative risk (RR), and 95% confidence intervals (CI) were estimated using random or fixed effects models according to the heterogeneity of included studies. <b>Results</b>: A total of 9,446 patients from 20 RCTs were included for the meta-analysis. The use of newly approved VEGFR-TKIs was associated with an increased risk of all-grade (RR 2.35, 95% CI 1.69–3.27, P &lt; 0.001) and high-grade (RR 3.70, 95% CI 2.09–6.54, P &lt; 0.001) proteinuria. On subgroup analysis, lenvatinib, axitinib, and vandetanib significantly increased the risk of all-grade proteinuria, and lenvatinib was associated with an increased risk of high-grade proteinuria. In addition, the risk of developing high-grade proteinuria events was significant for patients with hepatocellular carcinoma (HCC) and renal cell carcinoma (RCC), but not for patients with colorectal cancer (CRC) and thyroid cancer (TC). <b>Conclusion</b>: Treatment with newly approved VEGFR-TKIs significantly increases the risk of developing proteinuria events in cancer patients, especially for patients treated with lenvatinib.
DOI: 10.6084/m9.figshare.11940963
title: Incidence and risk of proteinuria associated with newly approved vascular endothelial growth factor receptor tyrosine kinase inhibitors in cancer patients: an up-to-date meta-analysis of randomized controlled trials

description: <b>Objective</b>: We performed a meta-analysis to quantify the overall incidence and risk of proteinuria associated with five newly approved VEGFR-TKIs (regorafenib, vandetanib, cabozantinib, lenvatinib, axitinib) in cancer patients. <b>Methods</b>: Pubmed, Embase, ASCO abstracts, and ESMO abstracts were searched to identify relevant studies. Overall incidence rates, relative risk (RR), and 95% confidence intervals (CI) were estimated using random or fixed effects models according to the heterogeneity of included studies. <b>Results</b>: A total of 9,446 patients from 20 RCTs were included for the meta-analysis. The use of newly approved VEGFR-TKIs was associated with an increased risk of all-grade (RR 2.35, 95% CI 1.69–3.27, P &lt; 0.001) and high-grade (RR 3.70, 95% CI 2.09–6.54, P &lt; 0.001) proteinuria. On subgroup analysis, lenvatinib, axitinib, and vandetanib significantly increased the risk of all-grade proteinuria, and lenvatinib was associated with an increased risk of high-grade proteinuria. In addition, the risk of developing high-grade proteinuria events was significant for patients with hepatocellular carcinoma (HCC) and renal cell carcinoma (RCC), but not for patients with colorectal cancer (CRC) and thyroid cancer (TC). <b>Conclusion</b>: Treatment with newly approved VEGFR-TKIs significantly increases the risk of developing proteinuria events in cancer patients, especially for patients treated with lenvatinib.
DOI: 10.6084/m9.figshare.7222340
title: Additional file 1: of WRKY transcription factors in legumes

description: Table S1. The name, chromosomal location, number, and type of WRKY in 12 legumes. aNull indicates that the protein lacks WRKY features. bThe bold font indicates an amino acid mutation. (XLSX 107 kb)
DOI: 10.5281/zenodo.10269257
title: Reproduction package for the paper "Disk Evolution Study Through Imaging of Nearby Young Stars (DESTINYS): Scattered light detection of a possible disk wind in RY Tau"
DOI: 10.5281/zenodo.10269258
title: Reproduction package for the paper "Disk Evolution Study Through Imaging of Nearby Young Stars (DESTINYS): Scattered light detection of a possible disk wind in RY Tau"
DOI: 10.6084/m9.figshare.7222463.v1
title: Additional file 3: of A combined small RNA and transcriptome sequencing analysis reveal regulatory roles of miRNAs during anther development of Upland cotton carrying cytoplasmic male sterile Gossypium harknessii (D2) cytoplasm

description: Table S3. Information of novel miRNA in A, B, and R lines. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.20329441.v1
title: Additional file 2 of Identification and validation of necroptosis-related prognostic gene signature and tumor immune microenvironment infiltration characterization in esophageal carcinoma

description: Additional file 2: Table S2. 52 NRGs among the DEGs between EC and normal samples.
DOI: 10.6084/m9.figshare.20329438
title: Additional file 1 of Identification and validation of necroptosis-related prognostic gene signature and tumor immune microenvironment infiltration characterization in esophageal carcinoma

description: Additional file 1: Table S1. 159 NRGs from KEGG in EC.
DOI: 10.6084/m9.figshare.20329441
title: Additional file 2 of Identification and validation of necroptosis-related prognostic gene signature and tumor immune microenvironment infiltration characterization in esophageal carcinoma

description: Additional file 2: Table S2. 52 NRGs among the DEGs between EC and normal samples.
DOI: 10.6084/m9.figshare.23982549
title: Untitled Item

description: Ambulatory training
DOI: 10.6084/m9.figshare.23982549.v1
title: Untitled Item

description: Ambulatory training
DOI: 10.6084/m9.figshare.17708191
title: Selectivity of Exportin 5 binding to human precursor microRNAs

description: Exportin 5 (Exp5, XPO5) is a nuclear export factor that functions in the microRNA (miRNA) biogenesis pathway to transport precursor miRNAs (pre-miRNAs) from the nucleus to the cytoplasm. Most of our current understanding of the Exp5 and pre-miRNA interaction is based on the investigation of how Exp5 binds to human pre-miR-30a (pre-miR-30 for short). As there are hundreds of human miRNA genes, how representative pre-miR-30 is, whether or how Exp5 interacts with distinct cargoes differentially, or whether Exp5 regulates miRNA expression, is unknown. Here we examined and compared the interactions between Exp5 and 157 human pre-miRNAs. We found that Exp5 binds distinct pre-miRNAs with modest variations in efficiencies, with the 3ʹ overhang and the apical loop in pre-miRNAs being the two major discriminating factors. Exp5 binding efficiencies do not significantly correlate with endogenous miRNA expression, suggesting that Exp5 activity does not contribute to differential miRNA expression <i>in vivo</i>. Nonetheless, in human cells with reduced Exp5 levels, preferential Exp5 binding correlated with miRNA expression changes. Thus, our study provides a global picture of how Exp5 interacts with human pre-miRNAs and its role in regulating miRNA expression. <b>Abbreviations:</b> Exp5: Exportin 5; miRNA: microRNA; pri-miRNA: primary microRNA; pre-miRNA: precursor microRNA; nt: nucleotide
DOI: 10.6084/m9.figshare.7222487
title: Additional file 5: of A combined small RNA and transcriptome sequencing analysis reveal regulatory roles of miRNAs during anther development of Upland cotton carrying cytoplasmic male sterile Gossypium harknessii (D2) cytoplasm

description: Table S5. Annotation of predicted target genes for known and novel miRNAs. (XLSX 661Â kb)
DOI: 10.7910/dvn/tcy0uh
title: Brustvergrößerung

description: Brustvergrößerungen sind chirurgische Eingriffe, die darauf abzielen, die Größe, Form oder das Volumen der Brüste zu erhöhen, häufig durch den Einsatz von Implantaten oder Fetttransfer-Methoden. Diese Eingriffe können nicht nur das ästhetische Erscheinungsbild verbessern, sondern auch das Selbstbewusstsein steigern, erfordern jedoch eine sorgfältige Überlegung der potenziellen Risiken und Nebenwirkungen.