cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13049980.v1
title: Arabian Primrose leaf extract mediated synthesis of silver nanoparticles: their industrial and biomedical applications

description: The present study encompasses green synthesis of silver nanoparticles (AgNPs) using aqueous leaf extract of Arabian Primrose within 6 min of reaction at 60 °C, pH 7 and their characterisation using physico-chemical analytical techniques. UV-Visible spectroscopy elucidated the surface plasmon resonance around 420 nm. FESEM and TEM images revealed that AgNPs were spherical with average diameter 10–60 nm. XRD pattern confirmed their crystalline nature. The leaf extract rich in phenolics and flavonoids was subjected to GC-MS analysis that identified bioactive compounds helping in reduction and stabilisation of AgNPs. The synthesised AgNPs possessed high anti-oxidant potential against DPPH and H<sub>2</sub>O<sub>2</sub> radicals. Incidentally, the AgNPs acted as excellent nanocatalyst towards borohydride reduction and degradation of structurally different organic dyes. The AgNPs also exhibited selective colorimetric sensing of hazardous mercuric, ferric ions and ammonia. Such AgNPs were cytotoxic against HeLa cells (IC<sub>50</sub> 7.18 µg/mL) and compatible towards normal L<sub>20</sub>B cells. These AgNPs showed effective anti-microbial activity against different human pathogens tested (bacterial and fungal). This is probably the first report of AgNPs synthesis using Arabian Primrose leaf extract showing strong anti-oxidant, catalytic, biosensing, anti-cancer and anti-microbial activities and find remarkable applications in medical, industrial and ecological sectors.
DOI: 10.6084/m9.figshare.11841435
title: Antiviral activity of curcumin-nanoemulsion associated with photodynamic therapy in vulvar cell lines transducing different variants of HPV-16

description: Vulvar intraepithelial neoplasia (VIN) is associated with human papillomavirus (HPV) infection. Curcumin is a natural bioactive compound with antineoplastic properties. The use of nanoparticles containing curcumin could allow a better performance of this compound in therapies. So, VIN biopsies were collected and HPV DNA detection was performed by PCR, positive samples were genotyped by Restriction Fragment Length Polymorphism (RFLP) and HPV-16 variants were determined by sequencing. HPV-16 positive vulva carcinoma cells (A431) were transduced with E-P and E-350G HPV-16 E6 variants. The viability of the transduced cells treated with nanoemulsions was determined by MTT assay. Besides, apoptosis was evaluated by enzymatic activity of Caspase-3/7. The cell viability assay showed that both the empty nanoemulsion (NE-V) and the nanoemulsion of curcumin (NE-CUR) had little effect on cell viability as compared to control cells. Additionally, we observed that cells irradiated in the presence of NE-CUR presented 90% of cell death. The apoptosis assay further revealed a significant increase in the activity of caspases 3 and 7 in A431 cells expressing both HPV-16 E6 variants after treatment with NE-CUR. Finally, we submitted the HPV transduced A431 cells to organotypic cultures and observed that the combination of treatments affected tissue architecture with evident signals of tissue damage. We concluded that nanoemulsions attain good biocompatibility, since no cytotoxicity was observed and NE-CUR associated with photoactivation showed promising results, leading to death only in cells subjected to irradiation. This drug delivery system associated with photodynamic therapy may become promising in the treatment of vulva lesions.
DOI: 10.6084/m9.figshare.11841435.v2
title: Antiviral activity of curcumin-nanoemulsion associated with photodynamic therapy in vulvar cell lines transducing different variants of HPV-16

description: Vulvar intraepithelial neoplasia (VIN) is associated with human papillomavirus (HPV) infection. Curcumin is a natural bioactive compound with antineoplastic properties. The use of nanoparticles containing curcumin could allow a better performance of this compound in therapies. So, VIN biopsies were collected and HPV DNA detection was performed by PCR, positive samples were genotyped by Restriction Fragment Length Polymorphism (RFLP) and HPV-16 variants were determined by sequencing. HPV-16 positive vulva carcinoma cells (A431) were transduced with E-P and E-350G HPV-16 E6 variants. The viability of the transduced cells treated with nanoemulsions was determined by MTT assay. Besides, apoptosis was evaluated by enzymatic activity of Caspase-3/7. The cell viability assay showed that both the empty nanoemulsion (NE-V) and the nanoemulsion of curcumin (NE-CUR) had little effect on cell viability as compared to control cells. Additionally, we observed that cells irradiated in the presence of NE-CUR presented 90% of cell death. The apoptosis assay further revealed a significant increase in the activity of caspases 3 and 7 in A431 cells expressing both HPV-16 E6 variants after treatment with NE-CUR. Finally, we submitted the HPV transduced A431 cells to organotypic cultures and observed that the combination of treatments affected tissue architecture with evident signals of tissue damage. We concluded that nanoemulsions attain good biocompatibility, since no cytotoxicity was observed and NE-CUR associated with photoactivation showed promising results, leading to death only in cells subjected to irradiation. This drug delivery system associated with photodynamic therapy may become promising in the treatment of vulva lesions.
DOI: 10.6084/m9.figshare.11841435.v1
title: Antiviral activity of curcumin-nanoemulsion associated with photodynamic therapy in vulvar cell lines transducing different variants of HPV-16

description: Vulvar intraepithelial neoplasia (VIN) is associated with human papillomavirus (HPV) infection. Curcumin is a natural bioactive compound with antineoplastic properties. The use of nanoparticles containing curcumin could allow a better performance of this compound in therapies. So, VIN biopsies were collected and HPV DNA detection was performed by PCR, positive samples were genotyped by Restriction Fragment Length Polymorphism (RFLP) and HPV-16 variants were determined by sequencing. HPV-16 positive vulva carcinoma cells (A431) were transduced with E-P and E-350G HPV-16 E6 variants. The viability of the transduced cells treated with nanoemulsions was determined by MTT assay. Besides, apoptosis was evaluated by enzymatic activity of Caspase-3/7. The cell viability assay showed that both the empty nanoemulsion (NE-V) and the nanoemulsion of curcumin (NE-CUR) had little effect on cell viability as compared to control cells. Additionally, we observed that cells irradiated in the presence of NE-CUR presented 90% of cell death. The apoptosis assay further revealed a significant increase in the activity of caspases 3 and 7 in A431 cells expressing both HPV-16 E6 variants after treatment with NE-CUR. Finally, we submitted the HPV transduced A431 cells to organotypic cultures and observed that the combination of treatments affected tissue architecture with evident signals of tissue damage. We concluded that nanoemulsions attain good biocompatibility, since no cytotoxicity was observed and NE-CUR associated with photoactivation showed promising results, leading to death only in cells subjected to irradiation. This drug delivery system associated with photodynamic therapy may become promising in the treatment of vulva lesions.
DOI: 10.6084/m9.figshare.12429401
title: Construction of immune-related risk signature for uveal melanoma

description: Uveal melanoma (UM) is the most frequent primary ocular tumour among adults. Here, we aimed to establish the immune cell-based signature to predict the overall survival (OS) of UM patients. The mRNA profile and matched clinical records of 80 UM patients were downloaded from The Cancer Genome Atlas (TCGA) database. CIBERSORT was used to verify the immune cell types of individuals. The univariate analysis found the CD8+ T cell, monocyte, CD4+ memory T cell (resting) and mast cell (resting) were significantly associated with the OS of UM patients. Subsequently, the LASSO Cox regression test was applied to establish the signature, by which the patients were separated into high- and low-risk subgroups. The Kaplan–Meier analyses found for these patients in the high-risk group had a poor survival rate than those in the low-risk group. The predictive value and stability were confirmed by the receiver operative characteristics curves. Pathway analyses found that the differentially expressed genes between the high- and low-risk subgroups were mainly centralised on immune response-related pathways. Further, the comparison of our signature with clinicopathological records confirmed its superiority and independence. In summary, we established an immune cell-based prognosis-predicting signature for UM patients, which will benefit the individual’s treatment.
DOI: 10.6084/m9.figshare.12429401.v1
title: Construction of immune-related risk signature for uveal melanoma

description: Uveal melanoma (UM) is the most frequent primary ocular tumour among adults. Here, we aimed to establish the immune cell-based signature to predict the overall survival (OS) of UM patients. The mRNA profile and matched clinical records of 80 UM patients were downloaded from The Cancer Genome Atlas (TCGA) database. CIBERSORT was used to verify the immune cell types of individuals. The univariate analysis found the CD8+ T cell, monocyte, CD4+ memory T cell (resting) and mast cell (resting) were significantly associated with the OS of UM patients. Subsequently, the LASSO Cox regression test was applied to establish the signature, by which the patients were separated into high- and low-risk subgroups. The Kaplan–Meier analyses found for these patients in the high-risk group had a poor survival rate than those in the low-risk group. The predictive value and stability were confirmed by the receiver operative characteristics curves. Pathway analyses found that the differentially expressed genes between the high- and low-risk subgroups were mainly centralised on immune response-related pathways. Further, the comparison of our signature with clinicopathological records confirmed its superiority and independence. In summary, we established an immune cell-based prognosis-predicting signature for UM patients, which will benefit the individual’s treatment.
DOI: 10.6084/m9.figshare.12601045
title: MicroRNA-155 acts as a diagnostic and prognostic biomarker for oesophageal squamous cell carcinoma

description: MicroRNA-155 is over-expressed in many human cancers, but researches on its association with malignant oesophageal squamous cell carcinoma (ESCC) are limited. The aim of the present study was to evaluate the potential value of <i>miR-155</i> as a biomarker for ESCC diagnosis and prognosis. In this study, we found that <i>miR-155</i> was significantly increased in ESCC tissues compared with the paired adjacent tissues and healthy normal controls (<i>p</i> &lt; .001), according to qRT-PCR, which suggested that <i>miR-155</i> might act as an oncogene in ESCC. In addition, clinical features such as the depth of tumour invasion, tumour size, and TNM stage were all proved to impact the expression of <i>miR-155</i> (<i>p</i> &lt; .01). Then, ROC curve analysis, reaching an AUC of 0.870, and a sensitivity and specificity of 83.5% and 77.5%, respectively, revealed that <i>miR-155</i> was a predictive factor for ESCC. As well, high expression of <i>miR-155</i> was associated with poor overall survival of the patients (log-rank test, <i>p</i> = .004), according to Kaplan-Meier analysis. <i>MiR-155</i> might be an independent predictor for overall survival in ESCC patients, manifested by Cox regression analysis (HR = 16.94, 95%CI = 3.33–86.12, <i>p =</i> .001). Taken together, <i>miR-155</i> could be an independent diagnostic and prognostic biomarker for ESCC.
DOI: 10.6084/m9.figshare.12601045.v1
title: MicroRNA-155 acts as a diagnostic and prognostic biomarker for oesophageal squamous cell carcinoma

description: MicroRNA-155 is over-expressed in many human cancers, but researches on its association with malignant oesophageal squamous cell carcinoma (ESCC) are limited. The aim of the present study was to evaluate the potential value of <i>miR-155</i> as a biomarker for ESCC diagnosis and prognosis. In this study, we found that <i>miR-155</i> was significantly increased in ESCC tissues compared with the paired adjacent tissues and healthy normal controls (<i>p</i> &lt; .001), according to qRT-PCR, which suggested that <i>miR-155</i> might act as an oncogene in ESCC. In addition, clinical features such as the depth of tumour invasion, tumour size, and TNM stage were all proved to impact the expression of <i>miR-155</i> (<i>p</i> &lt; .01). Then, ROC curve analysis, reaching an AUC of 0.870, and a sensitivity and specificity of 83.5% and 77.5%, respectively, revealed that <i>miR-155</i> was a predictive factor for ESCC. As well, high expression of <i>miR-155</i> was associated with poor overall survival of the patients (log-rank test, <i>p</i> = .004), according to Kaplan-Meier analysis. <i>MiR-155</i> might be an independent predictor for overall survival in ESCC patients, manifested by Cox regression analysis (HR = 16.94, 95%CI = 3.33–86.12, <i>p =</i> .001). Taken together, <i>miR-155</i> could be an independent diagnostic and prognostic biomarker for ESCC.
DOI: 10.6084/m9.figshare.11402256
title: Quantitative assessment of lncRNA H19 polymorphisms and cancer risk: a meta-analysis based on 48,166 subjects

description: Recently, numerous studies have been performed to detect the association between H19 polymorphisms and cancer susceptibility. However, their results were inconsistent and controversial. So, we carried out a meta-analysis aiming to define the association exactly. Eligible studies were collected using PubMed and Embase databases up to March 31, 2019. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to assess the strength of association. Sensitivity analysis and publication bias were established to evaluate the robustness of our results. Totally, 60 studies involving 20763 cases and 27403 patients were analysed in our meta-analysis. Our results indicated that H19 rs217727 C &gt; T polymorphism was significantly associated with increased cancer risk. In subgroup analysis, similarly increased risk could be found in gastrointestinal group for rs2839698 and protective effect was observed in rs2107425 polymorphism for cancer development in Caucasian population. Trial sequential analysis strengthened findings of our meta-analysis that cumulative evidence was adequate. In summary, our meta-analysis supported that H19 polymorphisms may be associated with cancer susceptibility.
DOI: 10.6084/m9.figshare.11402256.v1
title: Quantitative assessment of lncRNA H19 polymorphisms and cancer risk: a meta-analysis based on 48,166 subjects

description: Recently, numerous studies have been performed to detect the association between H19 polymorphisms and cancer susceptibility. However, their results were inconsistent and controversial. So, we carried out a meta-analysis aiming to define the association exactly. Eligible studies were collected using PubMed and Embase databases up to March 31, 2019. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to assess the strength of association. Sensitivity analysis and publication bias were established to evaluate the robustness of our results. Totally, 60 studies involving 20763 cases and 27403 patients were analysed in our meta-analysis. Our results indicated that H19 rs217727 C &gt; T polymorphism was significantly associated with increased cancer risk. In subgroup analysis, similarly increased risk could be found in gastrointestinal group for rs2839698 and protective effect was observed in rs2107425 polymorphism for cancer development in Caucasian population. Trial sequential analysis strengthened findings of our meta-analysis that cumulative evidence was adequate. In summary, our meta-analysis supported that H19 polymorphisms may be associated with cancer susceptibility.
DOI: 10.6084/m9.figshare.11871192
title: RETRACTED ARTICLE: Long non-coding RNA 91H regulates IGF2 expression by interacting with IGF2BP2 and promotes tumorigenesis in colorectal cancer

description: We, the Editors and Publisher of the journal <i>Artificial Cells, Nanomedicine, and Biotechnology</i>, have retracted the following article: Tianyi Gao, Xiangxiang Liu, Bangshun He, Yuqin Pan & Shukui Wang (2020) Long non-coding RNA 91H regulates IGF2 expression by interacting with IGF2BP2 and promotes tumorigenesis in colorectal cancer, <i>Artificial Cells, Nanomedicine, and Biotechnology</i>, 48:1, 664-671, DOI: 10.1080/21691401.2020.1727491 Since publication, the authors noticed duplication in Figure 1A and 4A. As this error directly impacts the reported results and conclusions the authors alerted the issue to the Editor and Publisher to request correction. The authors acknowledged that they had made mistakes and the Editor and Publisher found there to be fundamental flaws present within the requested corrections, as well as the rest of the paper. The authors have agreed to the retraction of this article. We have been informed in our decision-making by our policy on publishing ethics and integrity and the COPE guidelines on retractions. The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as ‘Retracted’.
DOI: 10.6084/m9.figshare.11871192.v2
title: RETRACTED ARTICLE: Long non-coding RNA 91H regulates IGF2 expression by interacting with IGF2BP2 and promotes tumorigenesis in colorectal cancer

description: We, the Editors and Publisher of the journal <i>Artificial Cells, Nanomedicine, and Biotechnology</i>, have retracted the following article: Tianyi Gao, Xiangxiang Liu, Bangshun He, Yuqin Pan & Shukui Wang (2020) Long non-coding RNA 91H regulates IGF2 expression by interacting with IGF2BP2 and promotes tumorigenesis in colorectal cancer, <i>Artificial Cells, Nanomedicine, and Biotechnology</i>, 48:1, 664-671, DOI: 10.1080/21691401.2020.1727491 Since publication, the authors noticed duplication in Figure 1A and 4A. As this error directly impacts the reported results and conclusions the authors alerted the issue to the Editor and Publisher to request correction. The authors acknowledged that they had made mistakes and the Editor and Publisher found there to be fundamental flaws present within the requested corrections, as well as the rest of the paper. The authors have agreed to the retraction of this article. We have been informed in our decision-making by our policy on publishing ethics and integrity and the COPE guidelines on retractions. The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as ‘Retracted’.
DOI: 10.6084/m9.figshare.11871192.v1
title: Long non-coding RNA 91H regulates IGF2 expression by interacting with IGF2BP2 and promotes tumorigenesis in colorectal cancer

description: 91H, a long non-coding antisense transcripts located on the position of the H19/IGF2 locus had been suggested to play a critical role in tumour development. However, little study had proved the mechanism in colorectal cancer (CRC). Hence, we performed this study to deeply explore the mechanism of lncRNA 91H in tumour progression. The expression of lncRNA 91H was first detected in CRC tissues and cells which was higher <i>in vitro</i> and <i>in vivo</i> than normal cells or tissues and CRC patients with high lncRNA 91H expression usually had a high risk in tumour metastasis (<i>p</i> &lt; .05). Then, monodansylcadaverine (MDC) staining, scratch wound, migration and invasion assays were conducted which showed to that reduced lncRNA 91H would greatly affect tumour migration, invasion and autophagy. Finally, by RNA pull down and RNA-binding protein immunoprecipitation (RIP) assay, a significant interaction was found between lncRNA 91H and IGF2BP2 which was proved to play an important role in CRC IGF2 expression. All these results suggested lncRNA 91H promotes IGF2 expression by interacting with IGF2BP2 which would provide a new strategy in finding potential CRC diagnostic biomarkers and therapeutic targets.
DOI: 10.6084/m9.figshare.12849914
title: Osteoclastic activity was associated with the development of steroid-induced osteonecrosis of femoral head

description: This study is focussed on evaluating and comparing two mediators of osteoclast, osteoprotegerin (OPG) and nuclear factor-κB ligand (RANKL), in plasma and tissue levels in patients with steroid-induced osteonecrosis of femoral head (SIONFH). Subjects were included in this cross-sectional case-control study in 2016. Bone histomorphology, immunohistochemistry, Western blotting, OPG and RANKL plasma levels, <i>post-hoc</i> statistical power and receiver-operating characteristic (ROC) curves were evaluated. Eighty-six patients diagnosed with SIONFH and 51 healthy subjects were included. OPG expression levels in bone samples increased with ARCO stage, and RANKL expression levels decreased with ARCO stages. Plasma OPG and RANKL levels were significantly higher in the SIONFH group compared with the healthy control group. The plasma OPG level and ratio of OPG and RANKL were positively associated with ARCO stages and significantly higher in stages III and IV. Plasma RANKL levels were negatively associated with ARCO stage and were significantly higher in ARCO stages II and III. Plasma OPG and RANKL may represent potential biomarkers during SIONFH at different stages. Higher plasma OPG levels indicated late-stage SIONFH, and higher plasma RANKL levels indicated early stage. Our findings may provide a clue for the development of diagnostic tools and therapies for SIONFH.
DOI: 10.6084/m9.figshare.12849914.v1
title: Osteoclastic activity was associated with the development of steroid-induced osteonecrosis of femoral head

description: This study is focussed on evaluating and comparing two mediators of osteoclast, osteoprotegerin (OPG) and nuclear factor-κB ligand (RANKL), in plasma and tissue levels in patients with steroid-induced osteonecrosis of femoral head (SIONFH). Subjects were included in this cross-sectional case-control study in 2016. Bone histomorphology, immunohistochemistry, Western blotting, OPG and RANKL plasma levels, <i>post-hoc</i> statistical power and receiver-operating characteristic (ROC) curves were evaluated. Eighty-six patients diagnosed with SIONFH and 51 healthy subjects were included. OPG expression levels in bone samples increased with ARCO stage, and RANKL expression levels decreased with ARCO stages. Plasma OPG and RANKL levels were significantly higher in the SIONFH group compared with the healthy control group. The plasma OPG level and ratio of OPG and RANKL were positively associated with ARCO stages and significantly higher in stages III and IV. Plasma RANKL levels were negatively associated with ARCO stage and were significantly higher in ARCO stages II and III. Plasma OPG and RANKL may represent potential biomarkers during SIONFH at different stages. Higher plasma OPG levels indicated late-stage SIONFH, and higher plasma RANKL levels indicated early stage. Our findings may provide a clue for the development of diagnostic tools and therapies for SIONFH.
DOI: 10.5281/zenodo.11105307
title: Data for: "Rhizospheric miRNAs affect the plant microbiota"

description: Data used for statistical analyses. R code available here: https://github.com/le-labo-yergeau/Middleton_miRNA
DOI: 10.5281/zenodo.11105308
title: Data for: "Rhizospheric miRNAs affect the plant microbiota"

description: Data used for statistical analyses. R code available here: https://github.com/le-labo-yergeau/Middleton_miRNA
DOI: 10.5281/zenodo.11199973
title: Data for: "Rhizospheric miRNAs affect the plant microbiota"

description: Data used for statistical analyses. R code available here: https://github.com/le-labo-yergeau/Middleton_miRNA
DOI: 10.5281/zenodo.12802476
title: Data for: "Rhizospheric miRNAs affect the plant microbiota"

description: Data used for statistical analyses. R code available here: https://github.com/le-labo-yergeau/Middleton_miRNA