cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20198656
title: Identification of the Integrated Prognostic Signature Associated with Immuno-relevant Genes and Long Non-coding RNAs in Acute Myeloid Leukemia

description: Like other cancers, considerable effort has been made in acute myeloid leukemia (AML) to identify prognostic genes and long noncoding RNAs (lncRNAs) with their potential clinical applications. However, to date, no integrated prognostic model has been developed that combines both gene expression and lncRNAs as a singular approach in AML. Comprehensive bioinformatic approaches (Weighted gene co-expression network analysis, Univariate Cox regression analyses, Pearson correlation, LASSO-Cox regression, Wilcoxon test) were used to construct the signature and to define high- and low-risk groups in AML datasets. ESTIMATE and CIBERSORT algorithms were applied to investigate the potential impact of infiltrating immune cells based on the obtained signature in tumor microenvironment. In addition, gene ontology (GO) and KEGG enrichment were applied to explore the potential function of the signature. Herein, we focused on immune-related genes (IRGs) and immune-related long noncoding RNAs (IRlncRNAs) and constructed an integrated prognostic immunorelevant signature in AML. The obtained signature exhibit five IRGs (DAXX, PSMB8, CSRP1, RAC2 and PTPN6) and one IRlncRNA (AC080037.2) and is strictly associated with age and FAB (French–American–British classification). Importantly, the high-risk AML group (defined by the signature) correlated positively with three types of scores (immune score, stroma score, and ESTIMATE score). We also identified a few immune cells (resting mast cells and monocytes) potentially involved in the correlation between signature and survival of AML patients. The prognostic ability of the obtained signature was tested in the training cohort and then validated in both test and total cohorts. The pathway enrichment analysis confirmed the possible immune- related role of the signature. We constructed an integrated prognostic signature comprising five immune-related protein-coding genes (IRPCG) (DAXX, PSMB8, CSRP1, RAC2, and PTPN6) and one immune-related lncRNA (AC080037.2) that may serve as potential biomarkers for predicting survival and further stratifying AML patients.
DOI: 10.6084/m9.figshare.7091270
title: Additional file 3: of Effective surveillance systems for vector-borne diseases in urban settings and translation of the data into action: a scoping review

description: Data extraction grid. (XLSX 139 kb)
DOI: 10.6084/m9.figshare.7091270.v1
title: Additional file 3: of Effective surveillance systems for vector-borne diseases in urban settings and translation of the data into action: a scoping review

description: Data extraction grid. (XLSX 139 kb)
DOI: 10.6084/m9.figshare.12858456
title: Additional file 1 of Features of alternative splicing in stomach adenocarcinoma and their clinical implication: a research based on massive sequencing data

description: Additional file 1. The initial clinical data downloaded from the TCGA website is in the file Additional file 1.
DOI: 10.6084/m9.figshare.14431323
title: NRF1-regulated CircNSUN2 promotes lymphoma progression through activating Wnt signaling pathway via stabilizing HMGA1

description: Lymphoma is the malignant tumor in the lymphatic system. Circular RNAs (circRNAs) are non-coding RNAs with closed structure, which have been reported to perform critical functions in various tumor progressions. However, the role of circNSUN2 in lymphoma has not been well explored. Quantitative reverse transcription real-time polymerase chain reaction (RT-qPCR) assay was performed to test the expression of circNSUN2 in malignant lymphoma tissues and normal lymph tissues, as well as in human peripheral blood lymphocyte cell line and malignant lymphoma cell lines. Cell counting kit-8 (CCK-8) assay and Transwell assays were used to evaluate the function of circNSUN2 on lymphoma cell proliferation, migration and invasion. DNA pull-down assay, chromatin immunoprecipitation (ChIP) and luciferase reporter assay were employed to test the interaction between circNSUN2 and NRF1. TOP/FOP flash reporter assay was performed to detect influence of circNSUN2 on Wnt pathway. Luciferase reporter assay and RNA pull-down assay were performed to explore interaction between HMGA1 and circNSUN2 through Wnt pathway. CircNSUN2 expression was abnormally high in malignant lymphoma tissues and cell lines. CircNSUN2 inhibition could reduce proliferation and invasion of lymphoma. Bioinformatic analysis, DNA pull-down, ChIP and luciferase reporter experiments confirmed that circNSUN2 could be modulated by transcription factor NRF1. Through RT-qPCR, western blot and luciferase reporter assays, circNSUN2 was proved to influence Wnt pathway by modulating HMGA1. CircNSUN2 regulated by transcription factor NRF1 could promote lymphoma progression through activating Wnt pathway via stabilizing HMGA1.
DOI: 10.6084/m9.figshare.20198656.v2
title: Identification of the Integrated Prognostic Signature Associated with Immuno-relevant Genes and Long Non-coding RNAs in Acute Myeloid Leukemia

description: Like other cancers, considerable effort has been made in acute myeloid leukemia (AML) to identify prognostic genes and long noncoding RNAs (lncRNAs) with their potential clinical applications. However, to date, no integrated prognostic model has been developed that combines both gene expression and lncRNAs as a singular approach in AML. Comprehensive bioinformatic approaches (Weighted gene co-expression network analysis, Univariate Cox regression analyses, Pearson correlation, LASSO-Cox regression, Wilcoxon test) were used to construct the signature and to define high- and low-risk groups in AML datasets. ESTIMATE and CIBERSORT algorithms were applied to investigate the potential impact of infiltrating immune cells based on the obtained signature in tumor microenvironment. In addition, gene ontology (GO) and KEGG enrichment were applied to explore the potential function of the signature. Herein, we focused on immune-related genes (IRGs) and immune-related long noncoding RNAs (IRlncRNAs) and constructed an integrated prognostic immunorelevant signature in AML. The obtained signature exhibit five IRGs (DAXX, PSMB8, CSRP1, RAC2 and PTPN6) and one IRlncRNA (AC080037.2) and is strictly associated with age and FAB (French–American–British classification). Importantly, the high-risk AML group (defined by the signature) correlated positively with three types of scores (immune score, stroma score, and ESTIMATE score). We also identified a few immune cells (resting mast cells and monocytes) potentially involved in the correlation between signature and survival of AML patients. The prognostic ability of the obtained signature was tested in the training cohort and then validated in both test and total cohorts. The pathway enrichment analysis confirmed the possible immune- related role of the signature. We constructed an integrated prognostic signature comprising five immune-related protein-coding genes (IRPCG) (DAXX, PSMB8, CSRP1, RAC2, and PTPN6) and one immune-related lncRNA (AC080037.2) that may serve as potential biomarkers for predicting survival and further stratifying AML patients.
DOI: 10.6084/m9.figshare.12858459.v1
title: Additional file 2 of Features of alternative splicing in stomach adenocarcinoma and their clinical implication: a research based on massive sequencing data

description: Additional file 2. The file Additional file 2 contains all surviving-related AS events.
DOI: 10.6084/m9.figshare.12858462
title: Additional file 3 of Features of alternative splicing in stomach adenocarcinoma and their clinical implication: a research based on massive sequencing data

description: Additional file 3. All R code and annotations in the file Additional file 3 have also been submitted.
DOI: 10.6084/m9.figshare.14431284.v1
title: <i>Panzhousaurus Rotundirostris</i> Jiang et al., 2019 (Diapsida: Sauropterygia) and the Recovery of the Monophyly of Pachypleurosauridae

description: <i>Panzhousaurus rotundirostris</i> Jiang, Lin, Rieppel, Motani and Sun, 2019, is restudied on the basis of a second specimen from the Upper Member of the Guanling Formation near Panzhou City, Guizhou Province, China. The second specimen offers hitherto unknown or unconfirmed information regarding the dermal palate, the ventral aspect of the cervical vertebrae, and the hind limbs, thus permitting a refinement of the diagnosis. Newly added or modified diagnostic characters include paired frontals with no posterolateral process, elongated and slender phalanges in the manus and pes, and a phalangeal formula of 3-4-5-4-3 for the manus, and 2-3-4-5-3 for the pes. A new phylogenetic analysis of Eosauropterygia demonstrates that Pachypleurosauridae is the sister taxon of Eusauropterygia, and the monophyly of these groups as traditionally upheld is confirmed. <i>Panzhousaurus</i> is most closely related to <i>Dianopachysaurus</i> and <i>Keichousaurus</i> within Pachypleurosauridae. In this study, the monophyletic Pistosauroidea excludes <i>Corosaurus</i> and <i>Cymatosaurus</i>. The latter two genera are found to form a monophyletic clade that represents the basal-most members of Eusauropterygia, which is in accordance with their stratigraphic distribution.
DOI: 10.6084/m9.figshare.20198656.v1
title: Identification of the integrated prognostic signature associated with immuno-relevant genes and long non-coding RNAs in acute myeloid leukemia

description: Like other cancers, considerable effort has been made in acute myeloid leukemia (AML) to identify prognostic genes and long non-coding RNAs (lncRNAs) with their potential clinical applications. However, to date, no integrated prognostic model has been developed that combines both gene expression and lncRNAs as a singular approach in AML. Comprehensive bioinformatic approaches (Weighted gene co-expression network analysis, Univariate Cox regression analyses, Pearson correlation, LASSO-Cox regression, Wilcoxon test) were used to construct the signature and to define high- and low-risk groups in AML datasets. ESTIMATE and CIBERSORT algorithms were applied to investigate the potential impact of infiltrating immune cells based on the obtained signature in tumor microenvironment. In addition, gene ontology (GO) and KEGG enrichment were applied to explore the potential function of the signature. Herein, we focused on immune-related genes (IRGs) and immune-related long non-coding RNAs (IRlncRNAs) and constructed an integrated prognostic immunorelevant signature in AML. The obtained signature exhibit five IRGs (DAXX, PSMB8, CSRP1, RAC2 and PTPN6) and one IRlncRNA (AC080037.2), and is strictly associated with age and FAB (French-American-British classification). Importantly, the high-risk AML group (defined by the signature) correlated positively with three types of scores (immune score, stroma score, and ESTIMATE score). We also identified a few immune cells (resting mast cells and monocytes) potentially involved in the correlation between signature and survival of AML patients. The prognostic ability of the obtained signature was tested in the training cohort and then validated in both test and total cohorts. The pathway enrichment analysis confirmed the possible immune- related role of the signature. We constructed an integrated prognostic signature comprising five immune-related protein-coding genes (IRPCG) (DAXX, PSMB8, CSRP1, RAC2, and PTPN6) and one immune-related lncRNA (AC080037.2) that may serve as potential biomarkers for predicting survival and further stratifying AML patients.
DOI: 10.6084/m9.figshare.14954457.v1
title: Additional file 2 of Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars

description: Additional file 2.
DOI: 10.6084/m9.figshare.12858792.v1
title: Additional file 9 of Metabolome and transcriptome analyses reveal chlorophyll and anthocyanin metabolism pathway associated with cucumber fruit skin color

description: Additional file 9: Table S5. List of primer of qRT-PCR.
DOI: 10.6084/m9.figshare.14955745
title: An enhanced methodology for predicting protein-protein interactions between human and hepatitis C virus via ensemble learning algorithms

description: Hepatitis C virus (HCV) is responsible for a variety of human life-threatening diseases, which include liver cirrhosis, chronic hepatitis, fibrosis and hepatocellular carcinoma (HCC) . Computational study of protein-protein interactions between human and HCV could boost the findings of antiviral drugs in HCV therapy and might optimize the treatment procedures for HCV infections. In this analysis, we constructed a prediction model for protein-protein interactions between HCV and human by incorporating the features generated by pseudo amino acid compositions, which were then carried out at two levels: categories and features. In brief, extra-tree was initially used for feature selection while SVM was then used to build the classification model. After that, the most suitable models for each category and each feature were selected by comparing with the three ensemble learning algorithms, that is, Random Forest, Adaboost, and Xgboost. According to our results, profile-based features were more suitable for building predictive models among the four categories. AUC value of the model constructed by Xgboost algorithm on independent data set could reach 92.66%. Moreover, Distance-based Residue, Physicochemical Distance Transformation and Profile-based Physicochemical Distance Transformation performed much better among the 17 features. AUC value of the Adaboost classifier constructed by Profile-based Physicochemical Distance Transformation on the independent dataset achieved 93.74%. Taken together, we proposed a better model with improved prediction capacity for protein-protein interactions between human and HCV in this study, which could provide practical reference for further experimental investigation into HCV-related diseases in future. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12858786.v1
title: Additional file 7 of Metabolome and transcriptome analyses reveal chlorophyll and anthocyanin metabolism pathway associated with cucumber fruit skin color

description: Additional file 7: Table S3. Differentially expressed genes between Lv and Bai fruit skin.
DOI: 10.5258/soton/d2955
title: Dataset supporting the University of Southampton Doctoral Thesis "Ultra-high speed imaging of cell-microbubble interactions for bone repair"- MatchID DIC Data

description: Dataset supporting the University of Southampton Doctoral Thesis "Ultra-high speed imaging of cell-microbubble interactions for bone repair"- MatchID DIC Data.

Excel data files for deformation data within cell microbubble interactions as measured by DIC using MatchID software for a range of different 5 million FPS ultra-high speed videos over 127 frames. Individual videos are cross-referenced with the 'UHS Image' data set using date and time stamps. Excel files each represent
individual interactions, recording the time point(1-127), the cartesian position within the image, the horizontal deformation and the vertical deformation. 
Matlab results analysis.

Related publication:
Pattinson, O., Keller, S. B., Evans, N. D., Pierron, F., & Carugo, D. (2023). An acoustic device for ultra high-speed quantification of cell strain during cell-microbubble interaction. ACS Biomaterials Science & Engineering, 9(10), 5912–5923. https://doi.org/10.1021/acsbiomaterials.3c00757

Related projects/Funders:
EP/R513325/1, NE/W503150/1
DOI: 10.6084/m9.figshare.14954474
title: Additional file 11 of Transcriptome and metabolome analyses of cold and darkness-induced pellicle cysts of Scrippsiella trochoidea

description: Additional file 11: Supplementary Table S10 Full lists of differentially accumulated metabolites with annotations during encystment.
DOI: 10.6084/m9.figshare.14954504
title: Additional file 8 of Transcriptome and metabolome analyses of cold and darkness-induced pellicle cysts of Scrippsiella trochoidea

description: Additional file 8: Supplementary Table S8 Differentially expressed genes related to cell stress response.
DOI: 10.6084/m9.figshare.14954474.v1
title: Additional file 11 of Transcriptome and metabolome analyses of cold and darkness-induced pellicle cysts of Scrippsiella trochoidea

description: Additional file 11: Supplementary Table S10 Full lists of differentially accumulated metabolites with annotations during encystment.
DOI: 10.6084/m9.figshare.12859591
title: Pleiotropin enhances the osteo/dentinogenic differentiation potential of dental pulp stem cells

description: <b>Purpose:</b> Pleiotrophin (PTN) is a heparin-binding growth-associated molecule and expressed in ameloblasts and odontoblasts throughout tooth maturation. Our previous study has shown that PTN expressed more than 20-fold higher in dental tissue than dental stem cells. However, the role of PTN on proliferation and osteo/dentinogenesis of dental pulp stem cells (DPSCs) is unclear. The purpose of the present study was to investigate the role of PTN on the DPSCs’ function. <b>Methods:</b> DPSCs were isolated from human third molars. Short hairpin RNAs (shRNAs) was used to knock down the PTN expression in DPSCs. Real-time RT-PCR, alizarin red staining, quantitative calcium analysis, in vivo transplantation and cell counting kit-8 (CCK8) assay were used to study the function of DPSCs. Possible mechanism was studied by RNA sequencing. <b>Results:</b> After PTN depletion, ALP activity and mineralization ability of DPSCs decreased. Expression of DMP-1 and BSP weakened. Proliferation of DPSCs at 48 h and 72 h was inhibited. Furthermore, 50 pg/mL PTN recombinant protein rescued the impaired osteo/dentinogenic differentiation potential and proliferation ability caused by PTN depletion. In addition, RNA sequencing showed 221 genes were downregulated and 233 genes upregulated in PTN depleted DPSCs. Several genes including BMP2 and IGFBP5 might be associated with PTN function on the DPSCs. P53 and the AMPK signaling pathways were involved. LncRNA analysis displayed 47 significantly upregulated lncRNA and 31 downregulated lncRNA comparing PTN depleted DPSCs with the control. <b>Conclusion:</b> Our research demonstrated that PTN has a positive role in maintaining DPSCs proliferation and osteo/dentinogenic differentiation potential.
DOI: 10.6084/m9.figshare.12859594
title: Magnolin exhibits anti-inflammatory effects on chondrocytes via the NF-κB pathway for attenuating anterior cruciate ligament transection-induced osteoarthritis

description: <b>Purpose:</b> This study aimed to investigate whether magnolin (MGL) possesses the capability of suppressing inflammatory responses that can in turn alleviate osteoarthritis (OA). <b>Methods:</b> We investigated the effects of MGL on the viability of rat chondrocytes at concentrations of 5 to 100 µM, and selected 10 µM for further study. We elucidated the molecular mechanisms and signaling pathways mediating these effects via RNA sequencing, qRT-PCR, immunofluorescent staining, and Western blotting techniques. Following this, we established an anterior cruciate ligament (ACL) transection-induced OA rat model, and injected MGL into the knee articular cavities to verify the <i>in vivo</i> anti-inflammatory effects of MGL. <b>Results:</b> We found that MGL could recover the TNF-α-induced upregulation of IL-1β, COX2, ADAMTS-5, and MMP-1/3/13 at the gene/protein level, as well as the downregulation of cartilaginous ECM synthesis. Gene expression profiles of different groups identified 49 common differentially expressed genes (DEGs), which were mainly enriched in the structural constituents of the ribosome, the extracellular space, and inflammatory response. The NF-κB pathway was highly enriched, and the expression levels of DEGs associated with it (<i>Nfkbia, Ptgs2, Rela, Tnfrsf1a, Tradd, Traf2</i>) under TNF-α stimulation were reversed by MGL. Further studies proved that MGL simultaneously suppressed the cell nucleus translocation of p65 and the phosphorylation of IκBα. Moreover, <i>in vivo</i>, MGL suppressed cartilage matrix degradation, inhibited MMP-13 expression, and promoted cartilage matrix construction by upregulating SOX9 synthesis. <b>Conclusion:</b> MGL demonstrated significant anti-inflammatory bioactivity on chondrocytes by suppressing the activation of NF-κB pathway, which in turn exhibited a significant alleviation of OA.
DOI: 10.6084/m9.figshare.14956769
title: Supplemental Digital Content 2 from Excessive adventitial stress drives inflammation-mediated fibrosis in hypertensive aortic remodelling in mice

description: Biomechanical Data
DOI: 10.6084/m9.figshare.14956775
title: Supplemental Digital Content 3 from Excessive adventitial stress drives inflammation-mediated fibrosis in hypertensive aortic remodelling in mice

description: Genotyping Data
DOI: 10.6084/m9.figshare.14956778
title: Supplemental Digital Content 5 from Excessive adventitial stress drives inflammation-mediated fibrosis in hypertensive aortic remodelling in mice

description: MATLAB and R Source Codes
DOI: 10.6084/m9.figshare.12858509.v1
title: Additional file 2 of GBAT: a gene-based association test for robust detection of trans-gene regulation

description: Additional file 2: Supplementary Table S1. 166 trans signal in DGN detected by GBAT at 10% FDR.
DOI: 10.6084/m9.figshare.12858509
title: Additional file 2 of GBAT: a gene-based association test for robust detection of trans-gene regulation

description: Additional file 2: Supplementary Table S1. 166 trans signal in DGN detected by GBAT at 10% FDR.