cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11285012.v1
title: All differentially expressed genes list from Identification of a novel regulatory pathway for PPARα by RNA-seq characterization of the endothelial cell lipid peroxidative injury transcriptome

description: the details of RNA-seq results including names of total 311 genes and fold changes
DOI: 10.6084/m9.figshare.12333278.v1
title: Comprehensive analyses for genetic diversities of 19 autosomal STRs in Chinese Kazak group and its phylogenetic relationships with other continental populations

description: Short tandem repeats (STRs) play an essential role in forensic genetics due to their high degree of polymorphisms, wide distributions and easy detection method. In this study, allelic frequencies and forensic statistical parameters of the 19 autosomal STR loci in a Kazak ethnic group were calculated, and its genetic relationships with reference populations were assessed in order to understand population structure better and enrich population genetic data for forensic practice in Chinese Kazak ethnic group. There were 226 identified alleles with the corresponding allelic frequencies ranging from 0.0008 to 0.5295 in the 628 unrelated healthy Kazak individuals in Xinjiang Uygur Autonomous Region. All autosomal STRs were conformed to the Hardy-Weinberg equilibrium after Bonferroni’s correction. The cumulative power of discrimination and the combined probability of exclusion of all the 19 autosomal STRs were 0.999 999 999 999 999 999 999 997 162 and 0.999 999 994 484, respectively. Furthermore, the <i>D</i><sub>A</sub> distances and Fixation index values of pairwise populations, principal component analysis, multidimensional scaling analysis, phylogenetic tree analysis and structure analysis were conducted to probe the genetic relationships between the Kazak group and other reference populations. The population genetic results showed that these 19 autosomal STR loci were characterised by high genetic diversities in the Kazak group. Furthermore, the studied Kazak group had close genetic relationships with the Uyghur group and the Uzbek group. The present results may facilitate understanding the genetic background of the Chinese Xinjiang Kazak group.
DOI: 10.6084/m9.figshare.8139368
title: RETRACTED ARTICLE: Hsa_circ_0101432 promotes the development of hepatocellular carcinoma (HCC) by adsorbing miR-1258 and miR-622

description: <b>Hsa_circ_0101432 promotes the development of hepatocellular carcinoma (HCC) by adsorbing miR-1258 and miR-622</b> We, the Editors and Publisher of the journal <i>Cell Cycle</i>, have retracted the following article: Haibo Zou, Xiangang Xu, Lanyun Luo, Yu Zhang, Le Luo, Yutong Yao, Guangming Xiang, Xiaolun Huang, and Guan Wang. Hsa_circ_0101432 promotes the development of hepatocellular carcinoma (HCC) by adsorbing miR-1258 and miR-622. Cell Cycle. 2019;18(19):2398-2413. doi: 10.1080/15384101.2019.1618120. Since publication, significant concerns have been raised about the integrity of the data and reported results in the article. When approached for an explanation, the authors did not provide their original data or any necessary supporting information. As verifying the validity of published work is core to the integrity of the scholarly record, we are therefore retracting the article. The corresponding author listed in this publication has been informed. 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.14954460
title: Additional file 3 of Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars

description: Additional file 3.
DOI: 10.5281/zenodo.10663663
title: UHD database focus on smart cities and smart transport

description: A database of 4K video sequences that cover video sequences of smart traffic and monitoring of smart cities.
DOI: 10.5281/zenodo.10663664
title: UHD database focus on smart cities and smart transport

description: A database of 4K video sequences that cover video sequences of smart traffic and monitoring of smart cities.
DOI: 10.6084/m9.figshare.12858327
title: Additional file 3 of β-catenin represses miR455-3p to stimulate m6A modification of HSF1 mRNA and promote its translation in colorectal cancer

description: Additional file 3. The list of genes containing HSE in their promoters.
DOI: 10.6084/m9.figshare.12858327.v1
title: Additional file 3 of β-catenin represses miR455-3p to stimulate m6A modification of HSF1 mRNA and promote its translation in colorectal cancer

description: Additional file 3. The list of genes containing HSE in their promoters.
DOI: 10.6084/m9.figshare.7091168
title: MOESM2 of Mutational Mtc6p attenuates autophagy and improves secretory expression of heterologous proteins in Kluyveromyces marxianus

description: Additional file 2. Detail information of the transcriptional analysis.
DOI: 10.6084/m9.figshare.7091168.v1
title: MOESM2 of Mutational Mtc6p attenuates autophagy and improves secretory expression of heterologous proteins in Kluyveromyces marxianus

description: Additional file 2. Detail information of the transcriptional analysis.
DOI: 10.6084/m9.figshare.12858336
title: Additional file 3 of CircRNA inhibits DNA damage repair by interacting with host gene

description: Additional file 3: Table S2. Probes for circRNA detection.
DOI: 10.6084/m9.figshare.11285012
title: All differentially expressed genes list from Identification of a novel regulatory pathway for PPARα by RNA-seq characterization of the endothelial cell lipid peroxidative injury transcriptome

description: the details of RNA-seq results including names of total 311 genes and fold changes
DOI: 10.17861/4bc12cb2-9403-49aa-a7a4-2f32e645c7f1
title: Data supporting Nature Communications paper, "Continuous Ultraviolet to Blue-Green Astrocomb"

description: MATLAB figures containing datasets and supporting Nature Communications paper, "Continuous Ultraviolet to Blue-Green Astrocomb"
DOI: 10.6084/m9.figshare.8139368.v2
title: Hsa_circ_0101432 promotes the development of hepatocellular carcinoma (HCC) by adsorbing miR-1258 and miR-622

description: The present research was major in investigating the regulation association among hsa_circ_0101432 (has_circ_RPPH1), miR-1258, miR-622 and <i>MAPK1</i> in hepatocellular carcinoma (HCC), and we explored the mechanism underlying pathogenesis of HCC. Microarray analysis was employed to detect hsa_circ_0101432 expression in HCC. Hsa_circ_0101432 was verified as a circRNA by testing divergent primers and RNase R. And qRT-PCR was performed to determine the expression of hsa_circ_0101432, miR-1258, miR-622 and <i>MAPK1</i> mRNA. Furthermore, miRanda predicted that mRNAs targeted miR-1258 and miR-622. CCK-8 assay, colony formation assay, flow cytometry as well as transwell assay were performed to detect cell viability, proliferation, apoptosis and invasive ability, respectively. Xenograft in nude mice was applied to observe tumor growth <i>in vivo</i>. Up-regulated hsa_circ_0101432 and down-regulated miR-1258 and miR-622 were detected in HCC while Hsa_circ_0101432 enhanced expression of <i>MAPK1</i> mRNA by targeting miR-1258 and miR-622. Knocking down hsa_circ_0101432 or overexpressing miR-1258 and miR-622 inhibited proliferation and invasive ability of HCC cell and promoted cell apoptosis. Hsa_circ_0101432 was confirmed to promote tumor growth via inhibiting miR-1258 and miR-622 expression and promoting <i>MAPK1</i> mRNA expression by <i>in vivo</i> experiment. Hsa_circ_0101432 inhibited HCC cell apoptosis, promoted cell proliferation, invasive ability and HCC tumor growth by targeting miR-1258 and miR-622 and upregulating <i>MAPK1</i> mRNA expression.
DOI: 10.25386/genetics.7616171
title: Supplemental Material for Liu et al., 2019

description: File S1 contains all Supplementary Results and Figures.<br><br>File S2 contains all the R scripts for data analyses and generation of the figures in the paper.
DOI: 10.25386/genetics.7616171.v1
title: Supplemental Material for Liu et al., 2019

description: File S1 contains all Supplementary Results and Figures.<br><br>File S2 contains all the R scripts for data analyses and generation of the figures in the paper.
DOI: 10.6084/m9.figshare.14954457
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.16529178
title: Sea island cotton_GWAS _VCFs_project

description: In GWAS research on 336 sea island cotton accessions, high-quality SNPs (depth≥4 (1/3 of the average depth), map quality≥20, the missing ratio of samples within the population≤of of 20% (4,052,759 SNPs) , and minor allele frequency (MAF) &gt;0.05) were retained for GWAS analyses.
DOI: 10.6084/m9.figshare.8139368.v4
title: RETRACTED ARTICLE: Hsa_circ_0101432 promotes the development of hepatocellular carcinoma (HCC) by adsorbing miR-1258 and miR-622

description: <b>Hsa_circ_0101432 promotes the development of hepatocellular carcinoma (HCC) by adsorbing miR-1258 and miR-622</b> We, the Editors and Publisher of the journal <i>Cell Cycle</i>, have retracted the following article: Haibo Zou, Xiangang Xu, Lanyun Luo, Yu Zhang, Le Luo, Yutong Yao, Guangming Xiang, Xiaolun Huang, and Guan Wang. Hsa_circ_0101432 promotes the development of hepatocellular carcinoma (HCC) by adsorbing miR-1258 and miR-622. Cell Cycle. 2019;18(19):2398-2413. doi: 10.1080/15384101.2019.1618120. Since publication, significant concerns have been raised about the integrity of the data and reported results in the article. When approached for an explanation, the authors did not provide their original data or any necessary supporting information. As verifying the validity of published work is core to the integrity of the scholarly record, we are therefore retracting the article. The corresponding author listed in this publication has been informed. 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.14954715.v1
title: Additional file 3 of YTHDF2 facilitates UBXN1 mRNA decay by recognizing METTL3-mediated m6A modification to activate NF-κB and promote the malignant progression of glioma

description: Additional file 3. The raw gel figures used in this manuscript.
DOI: 10.6084/m9.figshare.12858336.v1
title: Additional file 3 of CircRNA inhibits DNA damage repair by interacting with host gene

description: Additional file 3: Table S2. Probes for circRNA detection.
DOI: 10.6084/m9.figshare.12858339
title: Additional file 4 of CircRNA inhibits DNA damage repair by interacting with host gene

description: Additional file 4: Table S3. Probe for transcribed RNA and expression plasmid.
DOI: 10.6084/m9.figshare.14431284.v3
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.7091300
title: Additional file 2: of Secondary findings in 421 whole exome-sequenced Chinese children

description: Sequencing depth and breadth of the overall target region and 59 gene-specific regions. (XLSX 61 kb)
DOI: 10.6084/m9.figshare.12858339.v1
title: Additional file 4 of CircRNA inhibits DNA damage repair by interacting with host gene

description: Additional file 4: Table S3. Probe for transcribed RNA and expression plasmid.
DOI: 10.6084/m9.figshare.12858414.v1
title: Additional file 2 of Circular RNA SIPA1L1 promotes osteogenesis via regulating the miR-617/Smad3 axis in dental pulp stem cells

description: Additional file 2.
DOI: 10.6084/m9.figshare.7091300.v1
title: Additional file 2: of Secondary findings in 421 whole exome-sequenced Chinese children

description: Sequencing depth and breadth of the overall target region and 59 gene-specific regions. (XLSX 61 kb)
DOI: 10.6084/m9.figshare.12858414
title: Additional file 2 of Circular RNA SIPA1L1 promotes osteogenesis via regulating the miR-617/Smad3 axis in dental pulp stem cells

description: Additional file 2.
DOI: 10.6084/m9.figshare.8139368.v1
title: Hsa_circ_0101432 promotes the development of hepatocellular carcinoma (HCC) by adsorbing miR-1258 and miR-622

description: The present research was major in investigating the regulation association among hsa_circ_0101432 (has_circ_RPPH1), miR-1258, miR-622 and <i>MAPK1</i> in hepatocellular carcinoma (HCC), and we explored the mechanism underlying pathogenesis of HCC. Microarray analysis was employed to detect hsa_circ_0101432 expression in HCC. Hsa_circ_0101432 was verified as a circRNA by testing divergent primers and RNase R. And qRT-PCR was performed to determine the expression of hsa_circ_0101432, miR-1258, miR-622 and <i>MAPK1</i> mRNA. Furthermore, miRanda predicted that mRNAs targeted miR-1258 and miR-622. CCK-8 assay, colony formation assay, flow cytometry as well as transwell assay were performed to detect cell viability, proliferation, apoptosis and invasive ability, respectively. Xenograft in nude mice was applied to observe tumor growth <i>in vivo</i>. Up-regulated hsa_circ_0101432 and down-regulated miR-1258 and miR-622 were detected in HCC while Hsa_circ_0101432 enhanced expression of <i>MAPK1</i> mRNA by targeting miR-1258 and miR-622. Knocking down hsa_circ_0101432 or overexpressing miR-1258 and miR-622 inhibited proliferation and invasive ability of HCC cell and promoted cell apoptosis. Hsa_circ_0101432 was confirmed to promote tumor growth via inhibiting miR-1258 and miR-622 expression and promoting <i>MAPK1</i> mRNA expression by <i>in vivo</i> experiment. Hsa_circ_0101432 inhibited HCC cell apoptosis, promoted cell proliferation, invasive ability and HCC tumor growth by targeting miR-1258 and miR-622 and upregulating <i>MAPK1</i> mRNA expression.
DOI: 10.6084/m9.figshare.14431323.v1
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.12858459
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.8139368.v3
title: Hsa_circ_0101432 promotes the development of hepatocellular carcinoma (HCC) by adsorbing miR-1258 and miR-622

description: The present research was major in investigating the regulation association among hsa_circ_0101432 (has_circ_RPPH1), miR-1258, miR-622 and <i>MAPK1</i> in hepatocellular carcinoma (HCC), and we explored the mechanism underlying pathogenesis of HCC. Microarray analysis was employed to detect hsa_circ_0101432 expression in HCC. Hsa_circ_0101432 was verified as a circRNA by testing divergent primers and RNase R. And qRT-PCR was performed to determine the expression of hsa_circ_0101432, miR-1258, miR-622 and <i>MAPK1</i> mRNA. Furthermore, miRanda predicted that mRNAs targeted miR-1258 and miR-622. CCK-8 assay, colony formation assay, flow cytometry as well as transwell assay were performed to detect cell viability, proliferation, apoptosis and invasive ability, respectively. Xenograft in nude mice was applied to observe tumor growth <i>in vivo</i>. Up-regulated hsa_circ_0101432 and down-regulated miR-1258 and miR-622 were detected in HCC while Hsa_circ_0101432 enhanced expression of <i>MAPK1</i> mRNA by targeting miR-1258 and miR-622. Knocking down hsa_circ_0101432 or overexpressing miR-1258 and miR-622 inhibited proliferation and invasive ability of HCC cell and promoted cell apoptosis. Hsa_circ_0101432 was confirmed to promote tumor growth via inhibiting miR-1258 and miR-622 expression and promoting <i>MAPK1</i> mRNA expression by <i>in vivo</i> experiment. Hsa_circ_0101432 inhibited HCC cell apoptosis, promoted cell proliferation, invasive ability and HCC tumor growth by targeting miR-1258 and miR-622 and upregulating <i>MAPK1</i> mRNA expression.
DOI: 10.6084/m9.figshare.12858462.v1
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.12858456.v1
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.14431284.v2
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.14955745.v1
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