cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22609715
title: Additional file 4 of The collateral activity of RfxCas13d can induce lethality in a RfxCas13d knock-in mouse model

description: Additional file 4: Table S3. Transcriptome profiles of N2a cells transfected of RfxCas13d/dRfxCas13d with or without crRNA, and DEGs identified through comparisons (Linked to Additional file 1: Fig. S12).
DOI: 10.6084/m9.figshare.20508446.v1
title: Additional file 11 of The LINC00623/NAT10 signaling axis promotes pancreatic cancer progression by remodeling ac4C modification of mRNA

description: Additional file 11: Table S11. Twelve predicted downstream target genes of NAT10 have been proved to contribute to PDAC progression.
DOI: 10.6084/m9.figshare.20508443
title: Additional file 10 of The LINC00623/NAT10 signaling axis promotes pancreatic cancer progression by remodeling ac4C modification of mRNA

description: Additional file 10: Table S10. The predicted downstream target genes of NAT10 in BxPC-3 cells.
DOI: 10.6084/m9.figshare.12124005.v1
title: Long non-coding RNA PCAT1 drives clear cell renal cell carcinoma by upregulating YAP via sponging miR-656 and miR-539

description: Clear cell renal cell carcinoma (ccRCC) is the most common RCC subtype with high metastasis, poor prognosis and conventional chemotherapy resistance. Prostate cancer associated transcript 1 (PCAT1) is an important lncRNA that was reported to be involved in cell proliferation, migration and invasion of several types of cancer cells. However, its role in ccRCC is still undetermined. This study found that PCAT1 levels were elevated in ccRCC tumors as well as several ccRCC cells, and knockdown of PCAT1 with siRNA (si-PCAT1) alleviated cell proliferation, migration and invasion of Caki-2 and ACHN cells. With bioinformatics analysis, dual-luciferase reported assay, RNA pull-down assay and Spearman’s correlation analysis, we demonstrated that PCAT1 acted as a sponge for miR-656 and miR-539. Moreover, we found dual competitive interaction of miR-656/539 with PCAT1 and yes-associated protein (YAP), resulting in the identification of PCAT1-miR-656/539-YAP axis in Caki-2 and ACHN cells. With CCK-8 assay and transwell assay, miR-656/539 inhibitor or YAP overexpression could alleviate the effects of si-PCAT1 on the proliferation, migration and invasion of Caki-2 and ACHN cells. Our data indicated that PCAT1 promotes proliferation, migration and invasion of ccRCC cells by upregulating YAP via sponging miR-656 and miR-539. Taken together, this study provided a novel therapeutic target for ccRCC treatment.
DOI: 10.6084/m9.figshare.12124005.v2
title: Long non-coding RNA PCAT1 drives clear cell renal cell carcinoma by upregulating YAP via sponging miR-656 and miR-539

description: Clear cell renal cell carcinoma (ccRCC) is the most common RCC subtype with high metastasis, poor prognosis and conventional chemotherapy resistance. Prostate cancer associated transcript 1 (PCAT1) is an important lncRNA that was reported to be involved in cell proliferation, migration and invasion of several types of cancer cells. However, its role in ccRCC is still undetermined. This study found that PCAT1 levels were elevated in ccRCC tumors as well as several ccRCC cells, and knockdown of PCAT1 with siRNA (si-PCAT1) alleviated cell proliferation, migration and invasion of Caki-2 and ACHN cells. With bioinformatics analysis, dual-luciferase reported assay, RNA pull-down assay and Spearman’s correlation analysis, we demonstrated that PCAT1 acted as a sponge for miR-656 and miR-539. Moreover, we found dual competitive interaction of miR-656/539 with PCAT1 and yes-associated protein (YAP), resulting in the identification of PCAT1-miR-656/539-YAP axis in Caki-2 and ACHN cells. With CCK-8 assay and transwell assay, miR-656/539 inhibitor or YAP overexpression could alleviate the effects of si-PCAT1 on the proliferation, migration and invasion of Caki-2 and ACHN cells. Our data indicated that PCAT1 promotes proliferation, migration and invasion of ccRCC cells by upregulating YAP via sponging miR-656 and miR-539. Taken together, this study provided a novel therapeutic target for ccRCC treatment.
DOI: 10.6084/m9.figshare.22085485
title: The complete chloroplast genome sequence of <i>Salvia chienii</i> E.Peter, 1936 (Lamiaceae)

description: <i>Salvia chienii</i> E.Peter is a medicinal herb mainly distributed in Huangshan Mountain of Anhui province, China. In this study, the first complete chloroplast genome of <i>S. chienii</i> was sequenced and assembled. The genome length was 151,530 bp and encoded 143 genes (91 protein-coding genes, eight rRNA genes, and 37 tRNA genes). The phylogenomic analysis showed that <i>S. chienii</i> was closely related to <i>S. miltiorrhiza</i>. Further evolutionary studies of the genus <i>Salvia</i> could benefit from the complete chloroplast genome of <i>S. chienii</i> present in this study.
DOI: 10.6084/m9.figshare.22085485.v1
title: The complete chloroplast genome sequence of <i>Salvia chienii</i> E.Peter, 1936 (Lamiaceae)

description: <i>Salvia chienii</i> E.Peter is a medicinal herb mainly distributed in Huangshan Mountain of Anhui province, China. In this study, the first complete chloroplast genome of <i>S. chienii</i> was sequenced and assembled. The genome length was 151,530 bp and encoded 143 genes (91 protein-coding genes, eight rRNA genes, and 37 tRNA genes). The phylogenomic analysis showed that <i>S. chienii</i> was closely related to <i>S. miltiorrhiza</i>. Further evolutionary studies of the genus <i>Salvia</i> could benefit from the complete chloroplast genome of <i>S. chienii</i> present in this study.
DOI: 10.5281/zenodo.10630634
title: Dataset related to article: A novel KCNC1 gain-of-function variant causing developmental and epileptic encephalopathy: "Precision medicine" approach with fluoxetine.

description: Genetic Analysis
DOI: 10.5281/zenodo.10630635
title: Dataset related to article: A novel KCNC1 gain-of-function variant causing developmental and epileptic encephalopathy: "Precision medicine" approach with fluoxetine.

description: Genetic Analysis
DOI: 10.6084/m9.figshare.13172553
title: Additional file 2 of LAMP: disease classification derived from layered assessment on modules and pathways in the human gene network

description: The size of modules in each part of LCC. UP $$\cup$$ ∪ LSCC is the union of UP_LSCC and LSCC. DOWN $$\cup$$ ∪ LSCC is the union of DOWN_LSCC and LSCC. The number in brackets is the number of driver nodes obtained by implementing the maximum matching algorithm.
DOI: 10.6084/m9.figshare.13172550.v1
title: Additional file 1 of LAMP: disease classification derived from layered assessment on modules and pathways in the human gene network

description: The 1726 diseases screened in KEGG DISEASE. For each disease, detailed information is listed, including H number in KEGG DISEASE, disease class in KEGG, gene symbol and gene ID.
DOI: 10.6084/m9.figshare.13172556.v1
title: Additional file 3 of LAMP: disease classification derived from layered assessment on modules and pathways in the human gene network

description: The 151 diseases in CATG-0. For each of the 151 CATG-0 diseases, detailed information is listed. All the disease genes are in DOWN_LSCC.
DOI: 10.6084/m9.figshare.13172568
title: Additional file 7 of LAMP: disease classification derived from layered assessment on modules and pathways in the human gene network

description: The percentage of KEGG categories in each LAMP category, and the percentage of LAMP categories in each KEGG category.
DOI: 10.6084/m9.figshare.13172568.v1
title: Additional file 7 of LAMP: disease classification derived from layered assessment on modules and pathways in the human gene network

description: The percentage of KEGG categories in each LAMP category, and the percentage of LAMP categories in each KEGG category.
DOI: 10.6084/m9.figshare.12124089.v1
title: Somatic ASXL1 p.R693X mutation identified by next generation sequencing in isolated myeloid sarcoma involving the mediastinum

description: Isolated myeloid sarcoma (MS) is characterized by extramedullary immature myeloid cell infiltration without bone marrow involvement. The diagnosis of isolated MS is sometimes difficult in cases without expression of typical immunohistochemical markers, such as CD64, MPO or lysozyme. We report a case of isolated MS involving the mediastinum, with negative staining of MPO and lysozyme, which was misdiagnosed for 20 months. A comprehensive analysis in our institution showed MS with a characteristic staining pattern positive for CD34, CD117 and CD33, but negative for MPO, lysozyme, CD3 and CD79a. Next-generation sequencing (NGS) targeting 112 acute myeloid leukemia (AML)- and myelodysplastic syndromes (MDS)-associated genes confirmed the existence of an ASXL1 p.R693X mutation with a frequency of 13.17% of total cells. The patient acquired sustainable remission under the alternative treatment of intermediate-dose cytarabine and decitabine. The ASXL1 p.R693X mutation, a truncated mutation, has been widely reported to be associated with poor prognosis in myeloid malignance. We report the role of this mutation and recommend the utilization of NGS to discover more profound pathobiological information with limited samples, facilitate the diagnosis, and further clarify the uncertainties of prognosis and treatment in more isolated MS patients.
DOI: 10.6084/m9.figshare.25170008
title: Correlation of secreted protein coding gene expression and gene modules between tissues

description: We implemented the proposed computational approach to apply low dimension representations of gene expression and transfer learning to predict long-range tissue crosstalk signals. Tissue crosstalk signals include many proteins circulating in the blood. Discovering the signaling function carried by these signals is difficult, because the source and destination of these signals cannot be easily disaggregated. Cross-tissue co-expression can be used to find some unexpected connection between gene expression from one tissue with that of another tissue and hence generate hypothesis about cross tissue crosstalk. However, this method suffers from low discovery power because of to the very large number of pairwise correlations that need to be made across all genes between two tissues, leading to severe multiple testing burden. The approach we proposed uses a regularized matrix factorization method (PLIER). Which reduces transcriptome data into a lower dimension representation that corresponds to one or few annotated pathways, which has the effect of reducing multiple testing burden in the cross-tissue gene correlation matrix. Moreover, we can generate hypothesis about the downstream signaling function of pairs of source endocrine genes and target tissue latent variables.GTEx v8 contains ~17,000 transcriptome profiles from 54 tissue and cell types. However, two tissues in GTEx may share only limited number of common donors as not every donor had every tissue sequenced. To overcome this small data size, we implemented a transfer learning paradigm, where the PLIER matrices are first trained using a larger transcriptomics data set (the entire GTEx v8 RNA-seq collection of over 17,000 transcriptomes), then projected onto the smaller subset of samples (i.e., matching RNA-seq data from any two pairs if tissues from the same donors), which typically contains tens to hundreds of donors. We then constructed correlation matrices between known secreted proteins in the source tissue with the latent variables in the target tissue. Using a Bonferroni-adjusted P value to correct for the number of correlations (source endocrine proteins x target latent variables) and further adjusted for the number of tissue pairs (54 x 54; i.e. second Bonferroni threshold of adjusted P &lt; 3.4e–6), we found 122,852 significant cross-tissue signals from 1680 tissue pairs (average 73 signals per pair).
DOI: 10.6084/m9.figshare.25170008.v1
title: Correlation of secreted protein coding gene expression and gene modules between tissues

description: We implemented the proposed computational approach to apply low dimension representations of gene expression and transfer learning to predict long-range tissue crosstalk signals. Tissue crosstalk signals include many proteins circulating in the blood. Discovering the signaling function carried by these signals is difficult, because the source and destination of these signals cannot be easily disaggregated. Cross-tissue co-expression can be used to find some unexpected connection between gene expression from one tissue with that of another tissue and hence generate hypothesis about cross tissue crosstalk. However, this method suffers from low discovery power because of to the very large number of pairwise correlations that need to be made across all genes between two tissues, leading to severe multiple testing burden. The approach we proposed uses a regularized matrix factorization method (PLIER). Which reduces transcriptome data into a lower dimension representation that corresponds to one or few annotated pathways, which has the effect of reducing multiple testing burden in the cross-tissue gene correlation matrix. Moreover, we can generate hypothesis about the downstream signaling function of pairs of source endocrine genes and target tissue latent variables.GTEx v8 contains ~17,000 transcriptome profiles from 54 tissue and cell types. However, two tissues in GTEx may share only limited number of common donors as not every donor had every tissue sequenced. To overcome this small data size, we implemented a transfer learning paradigm, where the PLIER matrices are first trained using a larger transcriptomics data set (the entire GTEx v8 RNA-seq collection of over 17,000 transcriptomes), then projected onto the smaller subset of samples (i.e., matching RNA-seq data from any two pairs if tissues from the same donors), which typically contains tens to hundreds of donors. We then constructed correlation matrices between known secreted proteins in the source tissue with the latent variables in the target tissue. Using a Bonferroni-adjusted P value to correct for the number of correlations (source endocrine proteins x target latent variables) and further adjusted for the number of tissue pairs (54 x 54; i.e. second Bonferroni threshold of adjusted P &lt; 3.4e–6), we found 122,852 significant cross-tissue signals from 1680 tissue pairs (average 73 signals per pair).
DOI: 10.5281/zenodo.7003380
title: 2020 UL 9540A Installation-Level Test Experimental Data

description: This repository contains the data and supporting files from walk-in containerized lithium-ion battery energy storage system experiments in which a unit rack was forced to thermal runaway and the resulting thermal energy and chemicals released were quantified with a wide array of sensors. The tests were conducted in accordance with the 2019 version of the UL 9540A Standard Test Method. A full report of the experimental series is available here: UL 9540A Installation Level Tests with Outdoor Lithium-ion Energy Storage System Mockups.
DOI: 10.6084/m9.figshare.7405514
title: Additional file 1: of In vivo haploid induction leads to increased frequency of twin-embryo and abnormal fertilization in maize

description: Frequency of twin-embryo kernels among 20 different inbred lines. The number of tested kernels, twin embryos and frequency of twin embryos among 20 different inbred lines after maternal haploid induction. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.7405526
title: Additional file 3: of In vivo haploid induction leads to increased frequency of twin-embryo and abnormal fertilization in maize

description: Information for 20 females. The detail information of these 20 females, including their names and heterotic groups respectively. (XLSX 8Â kb)
DOI: 10.6084/m9.figshare.22609756.v1
title: Additional file 1 of Neutrophil extracellular traps induce the bone erosion of gout

description: Additional file 1.
DOI: 10.6084/m9.figshare.22609756
title: Additional file 1 of Neutrophil extracellular traps induce the bone erosion of gout

description: Additional file 1.
DOI: 10.6084/m9.figshare.12124029.v1
title: KIAA1429 promotes osteosarcoma progression by promoting stem cell properties and is regulated by miR-143-3p

description: <b>Background</b>: Osteosarcoma (OS) is the most common primary bone malignancy, it has a dismal prognosis and mainly affects the children and adolescents. Previous reports have demonstrated that aberrantly expressed KIAA1429 plays crucial roles in the carcinogenesis of several cancers, but its expression status and functional role in the progression of OS have not previously been investigated. <b>Methods</b>: Immunohistochemistry (IHC) and western blotting were conducted to determine KIAA1429 expression status in OS. The relationship between KIAA1429 expression and OS prognosis was analyzed based on public database and tissue microarray (TMA). Cell proliferation ability was evaluated by CCK8, EdU and colony formation assays, and Transwell and wound healing potential were also assessed <i>in vitro</i>. Xenograft nude mouse model was performed to elucidate the tumor growth <i>in vivo</i>. The main specific miRNA targeting KIAA1429 in OS cells was identified. <b>Results</b>: KIAA1429 expression is markedly overexpressed in OS, and elevated KIAA1429 expression is significantly associated with an unfavorable prognosis. Functional investigations demonstrate that KIAA1429 silencing could attenuate proliferation, migration and invasion abilities of OS <i>in vitro</i>, as well as tumor growth <i>in vivo</i>. Mechanistically, microRNA-143-3p (miR-143-3p) was identified as the crucial specific mediator of KIAA1429 expression in OS cells. Furthermore, restoring KIAA1429 expression could partially reverse miR-143-3p mediated tumor-inhibition effects. Additionally, we found that knockdown of KIAA1429 or ectopic overexpression of miR-143-3p could repress stemness cell properties and the inhibition could be partly abolished by overexpression of KIAA1429. <b>Conclusions</b>: In summary, this study establishes miR-143-3p/KIAA1429 axis as promising therapeutic target for OS patients.
DOI: 10.6084/m9.figshare.7405514.v1
title: Additional file 1: of In vivo haploid induction leads to increased frequency of twin-embryo and abnormal fertilization in maize

description: Frequency of twin-embryo kernels among 20 different inbred lines. The number of tested kernels, twin embryos and frequency of twin embryos among 20 different inbred lines after maternal haploid induction. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.7405538
title: Additional file 4: of In vivo haploid induction leads to increased frequency of twin-embryo and abnormal fertilization in maize

description: SSR markers used for genotyping twin plants. The SSR markersâ names and their genetic positions. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.23658357
title: Additional file 1 of YWHAH, a member of 14-3-3 family proteins, and PSME2, the proteasome activator subunit 2, are key host factors of Japanese encephalitis virus infection

description: Additional file 1.
DOI: 10.6084/m9.figshare.23658357.v1
title: Additional file 1 of YWHAH, a member of 14-3-3 family proteins, and PSME2, the proteasome activator subunit 2, are key host factors of Japanese encephalitis virus infection

description: Additional file 1.
DOI: 10.6084/m9.figshare.7405526.v1
title: Additional file 3: of In vivo haploid induction leads to increased frequency of twin-embryo and abnormal fertilization in maize

description: Information for 20 females. The detail information of these 20 females, including their names and heterotic groups respectively. (XLSX 8Â kb)
DOI: 10.6084/m9.figshare.7405538.v1
title: Additional file 4: of In vivo haploid induction leads to increased frequency of twin-embryo and abnormal fertilization in maize

description: SSR markers used for genotyping twin plants. The SSR markersâ names and their genetic positions. (XLSX 9Â kb)
DOI: 10.5281/zenodo.10630661
title: Base de datos- IJRDM

description: Base de datos utilizada para la elaboración del trabajo:

Gil-Saura, I., Ruiz-Molina, M.-E., Marín-García, A. and Michel, G. (2023), "Sustainability-oriented commerce innovation: How does it influence consumer satisfaction?", International Journal of Retail & Distribution Management, Vol. 51 No. 11, pp. 1477-1496. https://doi.org/10.1108/IJRDM-07-2022-0267
DOI: 10.5281/zenodo.10630662
title: Base de datos- IJRDM

description: Base de datos utilizada para la elaboración del trabajo:

Gil-Saura, I., Ruiz-Molina, M.-E., Marín-García, A. and Michel, G. (2023), "Sustainability-oriented commerce innovation: How does it influence consumer satisfaction?", International Journal of Retail & Distribution Management, Vol. 51 No. 11, pp. 1477-1496. https://doi.org/10.1108/IJRDM-07-2022-0267
DOI: 10.6084/m9.figshare.20508482
title: Additional file 2 of The LINC00623/NAT10 signaling axis promotes pancreatic cancer progression by remodeling ac4C modification of mRNA

description: Additional file 2: Table S2. Sequences of primers used in RT-qPCR assays.
DOI: 10.6084/m9.figshare.22085663
title: Forensic parameters of 41 Y-STR loci in Shandong Han individuals and comparison with 42 other populations

description: Forensic parameters of 41 Y-STR loci in Shandong Han individuals and comparison with 42 other populations
DOI: 10.6084/m9.figshare.7405595.v1
title: Additional file 3: of Purification and partial characterization of LdtP, a cell envelope modifying enzyme in Liberibacter asiaticus

description: Table S1. Peak areas of HPLC-separated muropeptides isolated from E. coli strains. Peak areas were calculated as a percentage of the total integrated area and are numbered as labeled in Fig. 6. *Peaks that were reintroduced in the complemented strain. (XLS 33 kb)
DOI: 10.6084/m9.figshare.22085663.v1
title: Forensic parameters of 41 Y-STR loci in Shandong Han individuals and comparison with 42 other populations

description: Forensic parameters of 41 Y-STR loci in Shandong Han individuals and comparison with 42 other populations
DOI: 10.6084/m9.figshare.20508476.v1
title: Additional file 1 of The LINC00623/NAT10 signaling axis promotes pancreatic cancer progression by remodeling ac4C modification of mRNA

description: Additional file 1: Table S1. Characteristics of patients enrolled in this study.
DOI: 10.5519/qd.xjhcfa0g
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (461 records)
DOI: 10.6084/m9.figshare.22605650.v1
title: Additional file 4 of A reappraisal of the phylogeny and historical biogeography of Sparganium (Typhaceae) using complete chloroplast genomes

description: Additional file 4: Table S1. Sequence similarity among the chloroplast genomes of Sparganium species.
DOI: 10.6084/m9.figshare.13172583.v1
title: Additional file 1 of Quantitative proteomics revealed modulation of macrophages by MetQ gene of Streptococcus suis serotype 2

description: Additional file 1: Table S1. All proteins identified by LC–MS.
DOI: 10.6084/m9.figshare.22609963.v1
title: Additional file 1 of A novel glycosylation-related gene signature predicts survival in patients with lung adenocarcinoma

description: Additional file 1. Original data and codes related to this article.
DOI: 10.6084/m9.figshare.22609963
title: Additional file 1 of A novel glycosylation-related gene signature predicts survival in patients with lung adenocarcinoma

description: Additional file 1. Original data and codes related to this article.
DOI: 10.6084/m9.figshare.22609972.v1
title: Additional file 4 of A novel glycosylation-related gene signature predicts survival in patients with lung adenocarcinoma

description: Additional file 4. Table S1. The differentially expressed analysis with 519 LUAD samples and 58 control samples from the TCGA database.
DOI: 10.6084/m9.figshare.13172934
title: Additional file 1 of Physiological and transcriptome changes induced by exogenous putrescine in anthurium under chilling stress

description: Additional file 1: Table S1. The primers of the target genes and the internal reference gene used for qRT-PCR. Table S2. Gene information of DEGs in anthurium seedlings treated with Put.