cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16752215.v2
title: Long non-coding RNA CASC9 promotes tumor progression in oral squamous cell carcinoma by regulating microRNA-545-3p/laminin subunit gamma 2

description: Long non-coding RNA (lncRNA) CASC9 is reported to be a tumor promoter in oral cancer, but its mechanism in oral squamous cell carcinoma (OSCC) has not been fully explored. Our study aimed to identify the interaction between lncRNA CASC9, microRNA-545-3p (miR-545-3p), and laminin subunit gamma 2 (LAMC2) in OSCC cells. Our study confirmed that lncRNA CASC9 and LAMC2 were upregulated in OSCC, whereas miR-545-3p expression was reduced. After performing a series of cell functional experiments, it was found that knockdown of lncRNA CASC9 or LAMC2 resulted in the inhibition of proliferation, colony formation, and migration of OSCC cells, but their negative effects could be partly impaired by the miR-545-3p inhibitor. In addition, we proved for the first time that lncRNA CASC9 can sponge miR-545-3p to upregulate LAMC2. In conclusion, our study revealed that lncRNA CASC9 promotes the malignancy of OSCC cells by sponging miR-545-3p to enhance LAMC2 expression, implying that lncRNA CASC9/miR-545-3p/LAMC2 may be an intervention approach in OSCC therapy.
DOI: 10.6084/m9.figshare.16752215.v1
title: Long non-coding RNA CASC9 promotes tumor progression in oral squamous cell carcinoma by regulating microRNA-545-3p/laminin subunit gamma 2

description: Long non-coding RNA (lncRNA) CASC9 is reported to be a tumor promoter in oral cancer, but its mechanism in oral squamous cell carcinoma (OSCC) has not been fully explored. Our study aimed to identify the interaction between lncRNA CASC9, microRNA-545-3p (miR-545-3p), and laminin subunit gamma 2 (LAMC2) in OSCC cells. Our study confirmed that lncRNA CASC9 and LAMC2 were upregulated in OSCC, whereas miR-545-3p expression was reduced. After performing a series of cell functional experiments, it was found that knockdown of lncRNA CASC9 or LAMC2 resulted in the inhibition of proliferation, colony formation, and migration of OSCC cells, but their negative effects could be partly impaired by the miR-545-3p inhibitor. In addition, we proved for the first time that lncRNA CASC9 can sponge miR-545-3p to upregulate LAMC2. In conclusion, our study revealed that lncRNA CASC9 promotes the malignancy of OSCC cells by sponging miR-545-3p to enhance LAMC2 expression, implying that lncRNA CASC9/miR-545-3p/LAMC2 may be an intervention approach in OSCC therapy.
DOI: 10.6084/m9.figshare.16847483
title: Interferon alpha-inducible protein 27 (IFI27) is a prognostic marker for pancreatic cancer based on comprehensive bioinformatics analysis

description: Accurate biomarkers to predict the genesis and progression of pancreatic adenocarcinoma (PAAD) are needed in the fight against this deadly disease. Here, we combined multiple datasets (GEO, TCGA and GTEx) to conduct a comprehensive analysis of pancreatic cancer. Through an in-depth analysis, we discovered that the expression of the gene encoding interferon alpha-inducible protein 27 (IFI27) was significantly higher in pancreatic cancer tissues than that in normal tissues, and that higher expression of IFI27 was negatively correlated with the overall survival rate of pancreatic cancer patients. The functional annotation of IFI27 demonstrated relationships to cellular immunity and metabolism, especially glycolysis. Analysis of infiltrating immune cells displayed that higher expression of IFI27 expression correlates with decreased CD8 + T cells and increased M2 macrophages in the tumor immune microenvironment (TIME), then biochemical analyses of a mouse model and immunohistochemical (IHC) staining verified that glycolytic enzymes and M2 macrophages increased significantly in pancreatic cancer tissues. We speculate that IFI27 may affect the tumor microenvironment (TME) of PAAD by regulating cellular immunity and metabolism, thereby promoting the progression of pancreatic carcinoma and worsening the prognosis. These findings of our present study are solid evidence that IFI27 is a potential prognostic biomarker of pancreatic cancer and that it affects the tumor immune microenvironment.
DOI: 10.6084/m9.figshare.16847483.v1
title: Interferon alpha-inducible protein 27 (IFI27) is a prognostic marker for pancreatic cancer based on comprehensive bioinformatics analysis

description: Accurate biomarkers to predict the genesis and progression of pancreatic adenocarcinoma (PAAD) are needed in the fight against this deadly disease. Here, we combined multiple datasets (GEO, TCGA and GTEx) to conduct a comprehensive analysis of pancreatic cancer. Through an in-depth analysis, we discovered that the expression of the gene encoding interferon alpha-inducible protein 27 (IFI27) was significantly higher in pancreatic cancer tissues than that in normal tissues, and that higher expression of IFI27 was negatively correlated with the overall survival rate of pancreatic cancer patients. The functional annotation of IFI27 demonstrated relationships to cellular immunity and metabolism, especially glycolysis. Analysis of infiltrating immune cells displayed that higher expression of IFI27 expression correlates with decreased CD8 + T cells and increased M2 macrophages in the tumor immune microenvironment (TIME), then biochemical analyses of a mouse model and immunohistochemical (IHC) staining verified that glycolytic enzymes and M2 macrophages increased significantly in pancreatic cancer tissues. We speculate that IFI27 may affect the tumor microenvironment (TME) of PAAD by regulating cellular immunity and metabolism, thereby promoting the progression of pancreatic carcinoma and worsening the prognosis. These findings of our present study are solid evidence that IFI27 is a potential prognostic biomarker of pancreatic cancer and that it affects the tumor immune microenvironment.
DOI: 10.6084/m9.figshare.14555042.v1
title: Identification of biomarkers related to Tumor-Infiltrating Lymphocytes (TILs) infiltration with gene co-expression network in colorectal cancer

description: Colorectal cancer (CRC) is one of the most common tumors, ranking second in the global cause of death from cancer. The prognosis of advanced patients is still very poor. In this study, hub modules with the highest association with tumor-infiltrating immune cells were identified by weighted gene co-expression network analysis based on CRC expression data from the Gene Expression Omnibus database. Next, three hub genes (ADAM8, IL-1A, VAV3) related to infiltrating immune cells were identified by co-expression network and prognostic analysis. After analysis and verification of the TIMER database, ADAM8 was selected as a prognostic biomarker. Finally, the result of functional test showed that ADAM8 gene expression down-regulation partially reversed the immune tolerance of CRC cells to TILs. By bioinformatics analysis methods and the experimental techniques, we identified ADAM8 as a prognostic biomarker and clinical therapeutic target related to tumor-infiltrating immune cells in CRC.
DOI: 10.6084/m9.figshare.13491015
title: A critical review on advances in the practices and perspectives for the treatment of dye industry wastewater

description: Rapid industrialization has provided comforts to mankind but has also impacted the environment harmfully. There has been severe increase in the pollution due to several industries, in particular due to dye industry, which generate huge quantities of wastewater containing hazardous chemicals. Although tremendous developments have taken place for the treatment and management of such wastewater through chemical or biological processes, there is an emerging shift in the approach, with focus shifting on resource recovery from such wastewater and also their management in sustainable manner. This review article aims to present and discuss the most advanced and state-of-art technical and scientific developments about the treatment of dye industry wastewater, which include advanced oxidation process, membrane filtration technique, microbial technologies, bio-electrochemical degradation, photocatalytic degradation, etc. Among these technologies, microbial degradation seems highly promising for resource recovery and sustainability and has been discussed in detail as a promising approach. This paper also covers the challenges and future perspectives in this field.
DOI: 10.6084/m9.figshare.13491015.v1
title: A critical review on advances in the practices and perspectives for the treatment of dye industry wastewater

description: Rapid industrialization has provided comforts to mankind but has also impacted the environment harmfully. There has been severe increase in the pollution due to several industries, in particular due to dye industry, which generate huge quantities of wastewater containing hazardous chemicals. Although tremendous developments have taken place for the treatment and management of such wastewater through chemical or biological processes, there is an emerging shift in the approach, with focus shifting on resource recovery from such wastewater and also their management in sustainable manner. This review article aims to present and discuss the most advanced and state-of-art technical and scientific developments about the treatment of dye industry wastewater, which include advanced oxidation process, membrane filtration technique, microbial technologies, bio-electrochemical degradation, photocatalytic degradation, etc. Among these technologies, microbial degradation seems highly promising for resource recovery and sustainability and has been discussed in detail as a promising approach. This paper also covers the challenges and future perspectives in this field.
DOI: 10.6084/m9.figshare.13385165.v1
title: Characteristics of immune cell infiltration and associated diagnostic biomarkers in ulcerative colitis: results from bioinformatics analysis

description: Ulcerative colitis (UC) is a type of refractory and recurrent inflammatory disorder that occurs in colon and rectum. Immune cell infiltration plays a critical role in UC progression; therefore, this study aims to explore potential biomarkers for UC and to analyze characteristics of immune cell infiltration based on the bioinformatic analysis. In this study, 248 differentially expressed genes (DEGs) were screened, and the top 20 immune-related hub genes and pathways were assessed. Moreover, four candidate diagnostic biomarkers (DPP10, S100P, AMPD1, and ASS1) were identified and validated. Immune cell infiltration analysis identified 13 differentially infiltrated immune cells (IICs) in UC samples compared to normal samples, and the result showed that two IICs only expressed in UC samples. In addition, the present research found that DPP10 was negatively correlated with neutrophils, S100P exhibited a positive correlation with resting CD4 memory T cells, AMPD1 was positively correlated with M2 macrophages, and ASS1 was inversely associated with neutrophils and positively related to CD8 T cells. Taken together, these findings indicated that DPP10, S100P, AMPD1, and ASS1 may act as diagnostic biomarkers for UC, and that differential IICs may help to illustrate the progression of UC.
DOI: 10.6084/m9.figshare.13385165
title: Characteristics of immune cell infiltration and associated diagnostic biomarkers in ulcerative colitis: results from bioinformatics analysis

description: Ulcerative colitis (UC) is a type of refractory and recurrent inflammatory disorder that occurs in colon and rectum. Immune cell infiltration plays a critical role in UC progression; therefore, this study aims to explore potential biomarkers for UC and to analyze characteristics of immune cell infiltration based on the bioinformatic analysis. In this study, 248 differentially expressed genes (DEGs) were screened, and the top 20 immune-related hub genes and pathways were assessed. Moreover, four candidate diagnostic biomarkers (DPP10, S100P, AMPD1, and ASS1) were identified and validated. Immune cell infiltration analysis identified 13 differentially infiltrated immune cells (IICs) in UC samples compared to normal samples, and the result showed that two IICs only expressed in UC samples. In addition, the present research found that DPP10 was negatively correlated with neutrophils, S100P exhibited a positive correlation with resting CD4 memory T cells, AMPD1 was positively correlated with M2 macrophages, and ASS1 was inversely associated with neutrophils and positively related to CD8 T cells. Taken together, these findings indicated that DPP10, S100P, AMPD1, and ASS1 may act as diagnostic biomarkers for UC, and that differential IICs may help to illustrate the progression of UC.
DOI: 10.6084/m9.figshare.16613800
title: Long non-coding RNA ARAP1-AS1 contributes to cell proliferation and migration in clear cell renal cell carcinoma via the miR-361-3p/placental growth factor axis

description: Clear cell renal cell carcinoma (ccRCC) is an aggressive malignancy with a poor prognosis. Therefore, investigating the molecular mechanism of ccRCC is important for ccRCC treatment. Here, we aimed to explore the effect of the long non-coding RNA ARAP1-AS1/miR-361-3p/PGF axis on ccRCC. The expression of lncRNA ARAP1-AS1, miR-361-3p, and placental growth factor (PGF) in ccRCC cells was verified by real-time quantitative PCR (RT-qPCR). The influence of the ARAP1-AS1/miR-361-3p/PGF axis on ccRCC cells was identified using the Cell Counting Kit-8 (CCK-8) assay, colony formation assay, flow cytometry, and wound healing assay. The interaction between ARAP1-AS1, miR-361-3p, and PGF was confirmed by bioinformatics analysis and luciferase assay. The results showed that the levels of ARAP1-AS1 and PGF increased in ccRCC cells, while miR-361-3p expression decreased. Cell functional experiments showed that cell proliferation and migration were inhibited by silencing ARAP1-AS1 or PGF, while miR-361-3p inhibitor or PGF overexpression could relieve the inhibitory effect of silencing ARAP1-AS1 on ccRCC cells. Moreover, ARAP1-AS1 sponges miR-361-3p to increase PGF expression. In conclusion, our study revealed that ARAP1-AS1 enhanced the malignancy of ccRCC cells by regulating the miR-361-3p/PGF axis.
DOI: 10.6084/m9.figshare.16613800.v2
title: Long non-coding RNA ARAP1-AS1 contributes to cell proliferation and migration in clear cell renal cell carcinoma via the miR-361-3p/placental growth factor axis

description: Clear cell renal cell carcinoma (ccRCC) is an aggressive malignancy with a poor prognosis. Therefore, investigating the molecular mechanism of ccRCC is important for ccRCC treatment. Here, we aimed to explore the effect of the long non-coding RNA ARAP1-AS1/miR-361-3p/PGF axis on ccRCC. The expression of lncRNA ARAP1-AS1, miR-361-3p, and placental growth factor (PGF) in ccRCC cells was verified by real-time quantitative PCR (RT-qPCR). The influence of the ARAP1-AS1/miR-361-3p/PGF axis on ccRCC cells was identified using the Cell Counting Kit-8 (CCK-8) assay, colony formation assay, flow cytometry, and wound healing assay. The interaction between ARAP1-AS1, miR-361-3p, and PGF was confirmed by bioinformatics analysis and luciferase assay. The results showed that the levels of ARAP1-AS1 and PGF increased in ccRCC cells, while miR-361-3p expression decreased. Cell functional experiments showed that cell proliferation and migration were inhibited by silencing ARAP1-AS1 or PGF, while miR-361-3p inhibitor or PGF overexpression could relieve the inhibitory effect of silencing ARAP1-AS1 on ccRCC cells. Moreover, ARAP1-AS1 sponges miR-361-3p to increase PGF expression. In conclusion, our study revealed that ARAP1-AS1 enhanced the malignancy of ccRCC cells by regulating the miR-361-3p/PGF axis.
DOI: 10.5281/zenodo.7670715
title: Sea-level rise impacts - FASTTRACK runs

description: Fasttrack results from SLR simulations in PROTECT.
DOI: 10.6084/m9.figshare.16613800.v1
title: Long non-coding RNA ARAP1-AS1 contributes to cell proliferation and migration in clear cell renal cell carcinoma via the miR-361-3p/placental growth factor axis

description: Clear cell renal cell carcinoma (ccRCC) is an aggressive malignancy with a poor prognosis. Therefore, investigating the molecular mechanism of ccRCC is important for ccRCC treatment. Here, we aimed to explore the effect of the long non-coding RNA ARAP1-AS1/miR-361-3p/PGF axis on ccRCC. The expression of lncRNA ARAP1-AS1, miR-361-3p, and placental growth factor (PGF) in ccRCC cells was verified by real-time quantitative PCR (RT-qPCR). The influence of the ARAP1-AS1/miR-361-3p/PGF axis on ccRCC cells was identified using the Cell Counting Kit-8 (CCK-8) assay, colony formation assay, flow cytometry, and wound healing assay. The interaction between ARAP1-AS1, miR-361-3p, and PGF was confirmed by bioinformatics analysis and luciferase assay. The results showed that the levels of ARAP1-AS1 and PGF increased in ccRCC cells, while miR-361-3p expression decreased. Cell functional experiments showed that cell proliferation and migration were inhibited by silencing ARAP1-AS1 or PGF, while miR-361-3p inhibitor or PGF overexpression could relieve the inhibitory effect of silencing ARAP1-AS1 on ccRCC cells. Moreover, ARAP1-AS1 sponges miR-361-3p to increase PGF expression. In conclusion, our study revealed that ARAP1-AS1 enhanced the malignancy of ccRCC cells by regulating the miR-361-3p/PGF axis.
DOI: 10.5281/zenodo.7670714
title: Sea-level rise impacts - FASTTRACK runs

description: Fasttrack results from SLR simulations in PROTECT.
DOI: 10.6084/m9.figshare.14610517
title: A novel circular RNA (hsa_circ_0059930)-mediated miRNA–mRNA axis in the lipopolysaccharide-induced acute lung injury model of MRC-5 cells

description: Circular RNA (circRNA) is a class of newly discovered endogenous non-coding RNA with closed circular structure. Some circRNAs have been reported to be closely associated with acute lung injury (ALI). While the expression profile of circRNAs in lipopolysaccharide (LPS)-induced ALI and the underlying roles are still not completely clear. The LPS-induced ALI model of MRC-5 cells was first established, and the expression profiles of circRNAs and mRNAs in LPS-induced MRC-5 cells were confirmed through RNA sequencing analysis. Gene Ontologyanalysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis were also applied to predict the latent functions and pathways of the differential mRNAs. After hsa_circ_0059930 knockdown, the proliferation and apoptosis of MRC-5 cells were identified by CCK-8, flow cytometer, and western blot assays. And we predicted the network analysis of hsa_circ_0059930. We testified that LPS could markedly prevent proliferation and induce apoptosis of MRC-5 cells. We discovered a total of 820 differential circRNAs (560 upregulated and 260 downregulated circRNAs) and 484 differential mRNAs (240 upregulated and 244 downregulated mRNAs) in LPS-induced MRC-5 cells. Besides, hsa_circ_0059930 was identified to be significantly upregulated in LPS-induced MRC-5 cells, and knockdown of hsa_circ-0059930 could notably accelerate proliferation and suppress apoptosis of LPS-mediated MRC-5 cells. Moreover, through the network analysis of hsa_circ_0059930, we preliminarily screened the potential regulatory axis hsa_circ_0059930/hsa-miR-382-5p/Topoisomerase 1 (TOP1) in LPS-induced ALI. Our data contribute to understand the importance of circRNAs and mRNAs in LPS-induced ALI. We also provided many hsa_circ_0059930-mediated microRNA (miRNA)–mRNA axis, especially hsa_circ_0059930/hsa-miR-382-5p/TOP1 in LPS-induced ALI.
DOI: 10.6084/m9.figshare.14610517.v1
title: A novel circular RNA (hsa_circ_0059930)-mediated miRNA–mRNA axis in the lipopolysaccharide-induced acute lung injury model of MRC-5 cells

description: Circular RNA (circRNA) is a class of newly discovered endogenous non-coding RNA with closed circular structure. Some circRNAs have been reported to be closely associated with acute lung injury (ALI). While the expression profile of circRNAs in lipopolysaccharide (LPS)-induced ALI and the underlying roles are still not completely clear. The LPS-induced ALI model of MRC-5 cells was first established, and the expression profiles of circRNAs and mRNAs in LPS-induced MRC-5 cells were confirmed through RNA sequencing analysis. Gene Ontologyanalysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis were also applied to predict the latent functions and pathways of the differential mRNAs. After hsa_circ_0059930 knockdown, the proliferation and apoptosis of MRC-5 cells were identified by CCK-8, flow cytometer, and western blot assays. And we predicted the network analysis of hsa_circ_0059930. We testified that LPS could markedly prevent proliferation and induce apoptosis of MRC-5 cells. We discovered a total of 820 differential circRNAs (560 upregulated and 260 downregulated circRNAs) and 484 differential mRNAs (240 upregulated and 244 downregulated mRNAs) in LPS-induced MRC-5 cells. Besides, hsa_circ_0059930 was identified to be significantly upregulated in LPS-induced MRC-5 cells, and knockdown of hsa_circ-0059930 could notably accelerate proliferation and suppress apoptosis of LPS-mediated MRC-5 cells. Moreover, through the network analysis of hsa_circ_0059930, we preliminarily screened the potential regulatory axis hsa_circ_0059930/hsa-miR-382-5p/Topoisomerase 1 (TOP1) in LPS-induced ALI. Our data contribute to understand the importance of circRNAs and mRNAs in LPS-induced ALI. We also provided many hsa_circ_0059930-mediated microRNA (miRNA)–mRNA axis, especially hsa_circ_0059930/hsa-miR-382-5p/TOP1 in LPS-induced ALI.
DOI: 10.6084/m9.figshare.13385168
title: Production of L-carnitine-enriched edible filamentous fungal biomass through submerged cultivation

description: The edible filamentous fungi are hot candidate for future supply of functional food and feed with e.g. protein, essential amino acids, and compounds with immunostimulant activity. L-carnitine that plays a crucial role in energy metabolism represents a functional compound normally produced by Zygomycetes filamentous fungus <i>Rhizopus oligosporus</i> in solid-state fermentation. The present study provides the first insights on production of L-carnitine-enriched edible fungal biomass through submerged cultivation of several Ascomycetes and Zygomycetes including <i>Aspergillus oryzae</i>, <i>Neurospora intermedia</i>, <i>Rhizopus oryzae</i>, and <i>Rhizopus oligosporus</i>. <i>A. oryzae</i> with 3 mg L-carnitine yield per gram of fungal biomass, indicates great potential on production of this bioactive compound which is remarkably higher than the other tested fungi in this work and also previous studies. In addition to fungal strain, other factors such as cultivation time and presence of yeast extract were found to play a role. Further studies on submerged growth optimization of <i>A</i>. <i>oryzae</i> in both high-quality recipes and in medium based on low-value substrates are proposed in order to clarify its potential for production of L-carnitine-enriched fungal biomass.