cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21069405
title: Additional file 2 of Integrative network analysis of circular RNAs reveals regulatory mechanisms for hepatic specification of human iPSC-derived endoderm

description: Additional file 2. Appendix 2. Table S1: Upregulated and downregulated differentially expressed circRNAs during the hepatic specification.
DOI: 10.6084/m9.figshare.6389534
title: MOESM2 of Distinct mutations with different inheritance mode caused similar retinal dystrophies in one family: a demonstration of the importance of genetic annotations in complicated pedigrees

description: Additional file 2: Table S2. Post-filtration variants in family B.
DOI: 10.6084/m9.figshare.21069398.v2
title: Additional file 5 of Analysis of complete chloroplast genome sequences and insight into the phylogenetic relationships of Ferula L.

description: Additional file 5: Table S5. Nucleotide variability (Pi) of Ferula species.
DOI: 10.6084/m9.figshare.15826522.v1
title: <i>In-vitro</i> antioxidant and <i>in-vivo</i> anti-aging with stress resistance on <i>Caenorhabditis elegans</i> of herbaceous peony stamen tea

description: Herbaceous peony (<i>Paeonia lactiflora</i> Pall.) is a traditional Chinese medicinal herb with roots; however, the flowers, specifically the stamens have not been exploited. In this study, the main active components of <i>P. lactiflora</i> stamens (PLS) were identified, and <i>in vitro</i> antioxidant, <i>in vivo</i> anti-aging and stress resistance properties were examined using the nematode <i>Caenorhabditis elegans</i>. Our results showed that PLS contains 350 active components including flavonoids, phenolic acids, terpenoids, alkaloids, and others. PLS extracts at concentrations of 0.2–1.2 mg·mL<sup>−1</sup> had strong antioxidant activity <i>in vitro</i> and showed a linear increase of concentration. The value of absorbance, scavenging activity of ·OH, DPPH and ABTS was 0.84, 31.55%, 84.67%, and 99.49% at 1.2 mg·mL<sup>−1</sup>, respectively. Moreover, PLS extracted at the same concentrations had no toxic effects on <i>C. elegans</i>, and the treatment with 1.2 mg·mL<sup>−1</sup> PLS extract significantly extended <i>C. elegans</i> lifespan that was not at the expense of reducing its reproduction and <i>Escherichia coli</i> OP50 growth. Furthermore, the same treatment extract enhanced their locomotion behavior and decreased their intestinal autofluorescence during the aging process. Additionally, the stress resistance of <i>C. elegans</i> under both heat and oxidative stress conditions were significantly induced by 1.2 mg·mL<sup>−1</sup> PLS extract treatment. Collectively, these results demonstrated that PLS extract exerted both <i>in vitro</i> antioxidant and <i>in vivo</i> anti-aging together with stress resistance properties, which could provide the theoretical basis for its production and popularization in China.
DOI: 10.6084/m9.figshare.21069402
title: Additional file 1 of Integrative network analysis of circular RNAs reveals regulatory mechanisms for hepatic specification of human iPSC-derived endoderm

description: Additional file 1. Appendix. 1: Changed genes lists of GSE66282 and GSE128060.
DOI: 10.6084/m9.figshare.6389534.v1
title: MOESM2 of Distinct mutations with different inheritance mode caused similar retinal dystrophies in one family: a demonstration of the importance of genetic annotations in complicated pedigrees

description: Additional file 2: Table S2. Post-filtration variants in family B.
DOI: 10.6084/m9.figshare.6389537
title: Additional file 2 of TSVdb: a web-tool for TCGA splicing variants analysis

description: MongoDB database scheme. (TXT 2 kb)
DOI: 10.6084/m9.figshare.6389537.v1
title: Additional file 2 of TSVdb: a web-tool for TCGA splicing variants analysis

description: MongoDB database scheme. (TXT 2 kb)
DOI: 10.6084/m9.figshare.21069456.v1
title: Additional file 3 of TSLP promoting B cell proliferation and polarizing follicular helper T cell as a therapeutic target in IgG4-related disease

description: Additional file 3: Table S2. List of differential expression genes of TSLP activated B cells and B cells from IgG4-RD.
DOI: 10.6084/m9.figshare.21069386.v2
title: Additional file 1 of Analysis of complete chloroplast genome sequences and insight into the phylogenetic relationships of Ferula L.

description: Additional file 1: Table S1. All the materials used in this article.
DOI: 10.6084/m9.figshare.21069456
title: Additional file 3 of TSLP promoting B cell proliferation and polarizing follicular helper T cell as a therapeutic target in IgG4-related disease

description: Additional file 3: Table S2. List of differential expression genes of TSLP activated B cells and B cells from IgG4-RD.
DOI: 10.6084/m9.figshare.21069401
title: Additional file 6 of Analysis of complete chloroplast genome sequences and insight into the phylogenetic relationships of Ferula L.

description: Additional file 6: Table S6. Non-synonymous to synonymous nucleotide substitution rates (Ka/Ks) of Ferula species.
DOI: 10.6084/m9.figshare.21069401.v1
title: Additional file 6 of Analysis of complete chloroplast genome sequences and insight into the phylogenetic relationships of Ferula L

description: Additional file 6: Table S6. Non-synonymous to synonymous nucleotide substitution rates (Ka/Ks) of Ferula species.
DOI: 10.34740/kaggle/dsv/7590824
title: Balochi Language to English Translation Dataset
DOI: 10.25549/usctheses-ouc11225870
title: 00001.tif
DOI: 10.6084/m9.figshare.21069380.v1
title: Additional file 1 of Newly reported chloroplast genome of Sinosenecio albonervius Y. Liu & Q. E. Yang and comparative analyses with other Sinosenecio species

description: Additional file 1.
DOI: 10.6084/m9.figshare.6913796
title: RETRACTED ARTICLE: The lncRNA RHPN1-AS1 downregulation promotes gefitinib resistance by targeting miR-299-3p/TNFSF12 pathway in NSCLC

description: We, the Editors and Publisher of the journal <i>Cell Cycle</i>, have retracted the following article: Xuehao Li, Xin Zhang, Chunlu Yang, Sui Cui, Qiming Shen and Shun Xu. The lncRNA RHPN1-AS1 downregulation promotes gefitinib resistance by targeting miR-299-3p/TNFSF12 pathway in NSCLC. Cell Cycle. 2018;17(14):1772-1783. doi: 10.1080/15384101.2018.1496745 Since publication, concerns have been raised about the integrity of the data in the article. When approached for an explanation, the authors have been unable to address the concerns raised and have not been able to provide their original data. 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. The authors do not agree with the retraction. 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.21069659
title: Additional file 2 of Transcriptomic and alternative splicing analyses provide insights into the roles of exogenous salicylic acid ameliorating waxy maize seedling growth under heat stress

description: Additional file 3 Table S2. List of plant hormone signal transduction pathway related DEGs in different comparisons.
DOI: 10.6084/m9.figshare.21069662
title: Additional file 3 of Transcriptomic and alternative splicing analyses provide insights into the roles of exogenous salicylic acid ameliorating waxy maize seedling growth under heat stress

description: Additional file 2 Table S3. Primer sequences of DEGs encoding genes used for qRT-PCR.
DOI: 10.6084/m9.figshare.21069539
title: Additional file 2 of A transcriptomic map of EGFR-induced epithelial-to-mesenchymal transition identifies prognostic and therapeutic targets for head and neck cancer

description: Additional file 2: Supplementary Table 1. EGFR-mediated EMT.
DOI: 10.6084/m9.figshare.25193021
title: scd.lin_3.integrated.new.rds

description: Main object for MRV project.
DOI: 10.6084/m9.figshare.6913796.v2
title: RETRACTED ARTICLE: The lncRNA RHPN1-AS1 downregulation promotes gefitinib resistance by targeting miR-299-3p/TNFSF12 pathway in NSCLC

description: We, the Editors and Publisher of the journal <i>Cell Cycle</i>, have retracted the following article: Xuehao Li, Xin Zhang, Chunlu Yang, Sui Cui, Qiming Shen and Shun Xu. The lncRNA RHPN1-AS1 downregulation promotes gefitinib resistance by targeting miR-299-3p/TNFSF12 pathway in NSCLC. Cell Cycle. 2018;17(14):1772-1783. doi: 10.1080/15384101.2018.1496745 Since publication, concerns have been raised about the integrity of the data in the article. When approached for an explanation, the authors have been unable to address the concerns raised and have not been able to provide their original data. 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. The authors do not agree with the retraction. 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.6389549.v1
title: MOESM3 of Distinct mutations with different inheritance mode caused similar retinal dystrophies in one family: a demonstration of the importance of genetic annotations in complicated pedigrees

description: Additional file 3: Table S3. Overview of data production.
DOI: 10.6084/m9.figshare.6389564
title: MOESM4 of Distinct mutations with different inheritance mode caused similar retinal dystrophies in one family: a demonstration of the importance of genetic annotations in complicated pedigrees

description: Additional file 4: Table S4. Coverage for all exons in all known RP genes.
DOI: 10.6084/m9.figshare.6913796.v1
title: The lncRNA RHPN1-AS1 downregulation promotes gefitinib resistance by targeting miR-299-3p/TNFSF12 pathway in NSCLC

description: Although epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) gefitinib has exhibited notable clinical efficacy in non-small cell lung cancer (NSCLC) patients. However, its therapeutic efficacy is ultimately limited by the development of gefitinib resistance. The present study aimed to investigate the effects of the long non-coding RNA, RHPN1-AS1 on gefitinib resistance in NSCLC and explore the underlying mechanisms. In this study, RHPN1-AS1 was observed to be downregulated in gefitinib resistant patients and NSCLC cell lines. Besides, decreased expression of RHPN1-AS1 was found to be associated with poor prognosis of NSCLC patients. RHPN1-AS1 knockdown conferred gefitinib resistance to gefitinib sensitive NSCLC cells, whereas the overexpression of RHPN1-AS1 sensitized gefitinib resistant NSCLC cells to gefitinib treatment. Mechanistically, RHPN1-AS1 was found to positively regulate the expression of TNFSF12 by directly interacting with miR-299-3p. Collectively, RHPN1-AS1 modulates gefitinib resistance through miR-299-3p/TNFSF12 pathway in NSCLC. Our findings indicate that RHPN1-AS1 may serve as not only a prognostic biomarker for gefitinib resistance but also as a promising therapeutic biomarker and target for the treatment of NSCLC patients.
DOI: 10.6084/m9.figshare.13729543
title: Petrogenesis and tectonic setting of the early-middle triassic subduction-related granite in the eastern segment of East Kunlun: evidences from petrology, geochemistry, and zircon U-Pb-Hf isotopes

description: The subduction process of the Paleo-Tethyan Ocean is still under controversy. We report zircon U-Pb ages and geochemistry (major and trace elements, and Hf isotopic compositions) for the Xiangjiananshan granitic plutons in the eastern segment of the East Kunlun Orogenic Belt, northern Tibetan Plateau, to constrain the subduction-related granitoids in its petrogenesis and to reconstruct the subduction prosess of the Buqingshan-A’nyemaqing Ocean. Zircon U-Pb dating yields coeval ages of 246.6 ± 4.1 Ma for granodiorite and 246.4 ± 3.9 Ma for biotite monzogranite of the Xiangjiananshan granitoid pluton. The granitoids include granodiorites, biotite monzogranites, and pseudo-porphyritic monzogranites. The granitoids have high contents of SiO<sub>2</sub> (66.60–73.19 wt.%) and Al<sub>2</sub>O<sub>3</sub> (13.28–16.38 wt.%), consistent with the high-K calc-alkaline series. The A/CNK ratios range from 0.98 to 1.02, indicating that the granodiorite is metaluminous and weakly peraluminous. The mafic microgranular enclaves (MMEs) in granodiorite and biotite monzogranite have a restricted SiO<sub>2</sub> range (57.24–60.03 wt.%), and have higher Fe<sub>2</sub>O<sub>3</sub><sup>T</sup>, and MgO contents than the host granitoids, as well as higher total rare earth element (REE) concentrations. All samples are depleted in high field strength elements (HFSEs; e.g., Nb, Ta, Ti and P) and heavy rare earth elements (HREEs), and are enriched in large ion lithophile elements (LILEs; e.g., Rb, Nd and La) and light rare earth elements (LREEs). Zircons from the pseudoporphyritic monzogranite yield two-stage model ages of 1137.32 to 1588.12 Ma, together with ε<sub>Hf</sub>(t) values from −5.01 to +2.11. These results indicate that the parental magma of pseudoporphyritic monzogranite was generated by partial melting of Paleoproterozoic to Mesoproterozoic rocks of the lower crust with contamination of ancient crustal material. Field and petrological observations, together with elemental and Hf isotopic data, indicate that the Xiangjiananshan granitic plutons was formed by magma mixing of mafic and felsic magmas. The felsic magma was derived from partial melting of the lower crust, while the mafic magma was derived from partial melting of an enriched lithospheric mantle metasomatized by slab-derived fluid due to the subduction of the Buqingshan-A’nyemaqing Ocean. Therefore, we propose that the northward subduction of the Buqingshan-A’nyemaqing ocean north to the Bayan Hara block under East Kunlun initiated in the Middle Permian (ca. 270 Ma), yielding calcium metaluminous arc magmatic rocks with I-type granite characteristics at East Kunlun, including the XG pluton in this study. Subsequently, the Buqingshan-A’nyemaqing ocean closed and resulted in collision of the Bayan Hara and East Kunlun blocks from 240 to 230 Ma.
DOI: 10.6084/m9.figshare.13729543.v1
title: Petrogenesis and tectonic setting of the early-middle triassic subduction-related granite in the eastern segment of East Kunlun: evidences from petrology, geochemistry, and zircon U-Pb-Hf isotopes

description: The subduction process of the Paleo-Tethyan Ocean is still under controversy. We report zircon U-Pb ages and geochemistry (major and trace elements, and Hf isotopic compositions) for the Xiangjiananshan granitic plutons in the eastern segment of the East Kunlun Orogenic Belt, northern Tibetan Plateau, to constrain the subduction-related granitoids in its petrogenesis and to reconstruct the subduction prosess of the Buqingshan-A’nyemaqing Ocean. Zircon U-Pb dating yields coeval ages of 246.6 ± 4.1 Ma for granodiorite and 246.4 ± 3.9 Ma for biotite monzogranite of the Xiangjiananshan granitoid pluton. The granitoids include granodiorites, biotite monzogranites, and pseudo-porphyritic monzogranites. The granitoids have high contents of SiO<sub>2</sub> (66.60–73.19 wt.%) and Al<sub>2</sub>O<sub>3</sub> (13.28–16.38 wt.%), consistent with the high-K calc-alkaline series. The A/CNK ratios range from 0.98 to 1.02, indicating that the granodiorite is metaluminous and weakly peraluminous. The mafic microgranular enclaves (MMEs) in granodiorite and biotite monzogranite have a restricted SiO<sub>2</sub> range (57.24–60.03 wt.%), and have higher Fe<sub>2</sub>O<sub>3</sub><sup>T</sup>, and MgO contents than the host granitoids, as well as higher total rare earth element (REE) concentrations. All samples are depleted in high field strength elements (HFSEs; e.g., Nb, Ta, Ti and P) and heavy rare earth elements (HREEs), and are enriched in large ion lithophile elements (LILEs; e.g., Rb, Nd and La) and light rare earth elements (LREEs). Zircons from the pseudoporphyritic monzogranite yield two-stage model ages of 1137.32 to 1588.12 Ma, together with ε<sub>Hf</sub>(t) values from −5.01 to +2.11. These results indicate that the parental magma of pseudoporphyritic monzogranite was generated by partial melting of Paleoproterozoic to Mesoproterozoic rocks of the lower crust with contamination of ancient crustal material. Field and petrological observations, together with elemental and Hf isotopic data, indicate that the Xiangjiananshan granitic plutons was formed by magma mixing of mafic and felsic magmas. The felsic magma was derived from partial melting of the lower crust, while the mafic magma was derived from partial melting of an enriched lithospheric mantle metasomatized by slab-derived fluid due to the subduction of the Buqingshan-A’nyemaqing Ocean. Therefore, we propose that the northward subduction of the Buqingshan-A’nyemaqing ocean north to the Bayan Hara block under East Kunlun initiated in the Middle Permian (ca. 270 Ma), yielding calcium metaluminous arc magmatic rocks with I-type granite characteristics at East Kunlun, including the XG pluton in this study. Subsequently, the Buqingshan-A’nyemaqing ocean closed and resulted in collision of the Bayan Hara and East Kunlun blocks from 240 to 230 Ma.
DOI: 10.6084/m9.figshare.21069551
title: Additional file 5 of A transcriptomic map of EGFR-induced epithelial-to-mesenchymal transition identifies prognostic and therapeutic targets for head and neck cancer

description: Additional file 5: Supplementary Table 4. SCC1 cell line: DEGs overlapping with EGFR-mediated EMT signature.
DOI: 10.6084/m9.figshare.6389519.v1
title: MOESM1 of Distinct mutations with different inheritance mode caused similar retinal dystrophies in one family: a demonstration of the importance of genetic annotations in complicated pedigrees

description: Additional file 1: Table S1. Post-filtration variants in family A.
DOI: 10.6084/m9.figshare.6389549
title: MOESM3 of Distinct mutations with different inheritance mode caused similar retinal dystrophies in one family: a demonstration of the importance of genetic annotations in complicated pedigrees

description: Additional file 3: Table S3. Overview of data production.
DOI: 10.6084/m9.figshare.21069551.v1
title: Additional file 5 of A transcriptomic map of EGFR-induced epithelial-to-mesenchymal transition identifies prognostic and therapeutic targets for head and neck cancer

description: Additional file 5: Supplementary Table 4. SCC1 cell line: DEGs overlapping with EGFR-mediated EMT signature.
DOI: 10.6084/m9.figshare.6389564.v1
title: MOESM4 of Distinct mutations with different inheritance mode caused similar retinal dystrophies in one family: a demonstration of the importance of genetic annotations in complicated pedigrees

description: Additional file 4: Table S4. Coverage for all exons in all known RP genes.
DOI: 10.6084/m9.figshare.5340988.v1
title: Characterisation of the whole-genome wide hexokinase gene family unravels the functional divergence in pear (<i>Pyrus bretschneideri</i> Rehd.)

description: Hexokinase genes <i>(HXK</i>) encode enzymes that play an important role in fruit quality and plant development because they participate in the first step of the glycolytic pathway for sugar accumulation and metabolism. In this study, the authors conducted analysis of the phylogeny, gene structure, and expression of <i>HXK</i> genes in pear (<i>Pyrus bretschneideri</i> Rehd.), comparing them with 7 other plant species. A total of 10 <i>HXK</i> protein sequences from pear and 33 <i>HXK</i>s from 7 other species were identified and clustered into 4 groups, matching their motif classification. Duplication events and motif structure variation attributed the diversification of <i>HXK</i> genes, supported by differential expression pattern of <i>PbrHXKs</i> from pear fruit transcriptome data and qRT – PCR verification. Combining pear fruit soluble sugar content data and analyses above, <i>PbrHXK1</i>and <i>PbrHXK3</i> were identified as important candidate genes in sorbitol, fructose, and glucose accumulation during pear fruit development. <i>PbrHXK1</i>and <i>PbrHXK3</i> were identified as important candidate genes in sorbitol, fructose, and glucose accumulation during pear fruit development. Subsequent research on these highly expressed <i>PbrHXKs</i> will benefit the enhancement of sugar content and quality in pear.
DOI: 10.6084/m9.figshare.21069656
title: Additional file 1 of Transcriptomic and alternative splicing analyses provide insights into the roles of exogenous salicylic acid ameliorating waxy maize seedling growth under heat stress

description: Additional file 1 Table S1. Summary of 18 RNA-seq samples with QC quality.
DOI: 10.6084/m9.figshare.6389594.v1
title: Additional file 1: of A computational framework for complex disease stratification from multiple large-scale datasets

description: AUC of consensus clustering. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.5340988
title: Characterisation of the whole-genome wide hexokinase gene family unravels the functional divergence in pear (<i>Pyrus bretschneideri</i> Rehd.)

description: Hexokinase genes <i>(HXK</i>) encode enzymes that play an important role in fruit quality and plant development because they participate in the first step of the glycolytic pathway for sugar accumulation and metabolism. In this study, the authors conducted analysis of the phylogeny, gene structure, and expression of <i>HXK</i> genes in pear (<i>Pyrus bretschneideri</i> Rehd.), comparing them with 7 other plant species. A total of 10 <i>HXK</i> protein sequences from pear and 33 <i>HXK</i>s from 7 other species were identified and clustered into 4 groups, matching their motif classification. Duplication events and motif structure variation attributed the diversification of <i>HXK</i> genes, supported by differential expression pattern of <i>PbrHXKs</i> from pear fruit transcriptome data and qRT – PCR verification. Combining pear fruit soluble sugar content data and analyses above, <i>PbrHXK1</i>and <i>PbrHXK3</i> were identified as important candidate genes in sorbitol, fructose, and glucose accumulation during pear fruit development. <i>PbrHXK1</i>and <i>PbrHXK3</i> were identified as important candidate genes in sorbitol, fructose, and glucose accumulation during pear fruit development. Subsequent research on these highly expressed <i>PbrHXKs</i> will benefit the enhancement of sugar content and quality in pear.
DOI: 10.25549/usctheses-ouc11226487
title: 00001.tif
DOI: 10.6084/m9.figshare.13129037.v6
title: Arctic COSMO-CLM hindcast 1992

description: COSMO-CLM Russian Arctic climate dataset
DOI: 10.6084/m9.figshare.21593957
title: Additional file 2 of Quantifying substantial carcinogenesis of genetic and environmental factors from measurement error in the number of stem cell divisions

description: Additional file 2: Table S1. Ranked matrix of LCR in global scope and the contribution of the genetic and environmental factors on the variation in cancer risk. Table S2. Ranked matrix of LCR in national-wide of China and the contribution of the genetic and environmental factors on the variation in cancer risk. Table S3. Ranked matrix of LCR in counties of Shandong province, China and the contribution of the genetic and environmental factors on the variation in cancer risk. Table S4. Ranked matrix of LCR in global scope and R2 of LCRi on LTCD0. Table S5. Ranked matrix of LCR in global scope and R2 of LCRi on SMN0. Table S6. Ranked matrix of ACR in global scope and the contribution of genetic and environmental factors for each site-specific cancer. Table S7. Ranked matrix of ACR in Shandong province and the contribution of genetic and environmental factors for each site-specific cancer.