cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6443588.v1
title: Additional file 11: of Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease

description: Table S7. GO and KEGG analysis of DMRs located in upstream region. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.7492235.v1
title: Downregulation of NEAT1 reverses the radioactive iodine resistance of papillary thyroid carcinoma cell via miR-101-3p/<i>FN1</i>/PI3K-AKT signaling pathway

description: Considering the resistance of papillary thyroid cancer (PTC) <sup>131</sup>I therapy, this study was designed to find a solution at molecular respect. By probing into lncRNA-NEAT1/miR-101-3p/<i>FN1</i> axis and PI3K/AKT signaling pathway, this study provided a potential target for PTC therapy. <sup>131</sup>I-resistant cell lines were established by continuous treatment with median-lethal <sup>131</sup>I. Bioinformatic analysis was applied to filtrate possible lncRNA/miRNA/mRNA and related signaling pathway. Luciferase reporter assay was employed in the verification of the targeting relationship between lncRNA and miRNA as well as miRNA and mRNA. MTT assay and flow cytometry assay were performed to observe the impact of NEAT1/miR-101-3p/<i>FN1</i> on cell viability and apoptosis in radioactivity iodine (RAI)-resistant PTC cell lines, respectively. Western blot and qRT-PCR were conducted to measure the expression of proteins and mRNAs in RAI-resistant PTC tissues and cells. Meanwhile, endogenous PTC mice model were constructed, in order to verify the relation between NEAT1 and RAI-resistance <i>in vivo</i>. NEAT1 was over-expressed in RAI-resistant PTC tissues and cell lines and could resist RAI by accelerating proliferation accompanied by suppressing apoptosis. It indicated that overexpressed NEAT1 restrained the damage of RAI to tumor in both macroscopic and microcosmic. Besides, NEAT1/miR-101-3p exhibited a negative correlation by directly targeting each other. The expression of <i>FN1</i>, an overexpressed downstream protein in RAI-resistance PTC tissues, could be tuned down by miR-101-3p, while the decrease could be restored by NEAT1. In conclusion, both <i>in vitro</i> and <i>in vivo</i>, NEAT1 suppression could inhibit <sup>131</sup>I resistance of PTC by upregulating miR-101-3p/<i>FN1</i> expression and inactivated PI3K/AKT signaling pathway both <i>in vitro</i> and <i>in vivo</i>.
DOI: 10.6084/m9.figshare.6443696.v1
title: Additional file 9: of Distinct sperm nucleus behaviors between genotypic and temperature-dependent sex determination males are associated with replication and expression-related pathways in a gynogenetic fish

description: Table S9. Subcellular location of down-regulated DEPs assigned to the process of “Replication and repair”, “Translation” and “Transcription”. (XLS 35 kb)
DOI: 10.6084/m9.figshare.6443564.v1
title: Additional file 10: of Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease

description: Table S6. DMRs between two samples. (XLSX 580 kb)
DOI: 10.6084/m9.figshare.6443588
title: Additional file 11: of Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease

description: Table S7. GO and KEGG analysis of DMRs located in upstream region. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.6443741
title: Additional file 1: of Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease

description: Table S1. Overview of WGS data. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.6443564
title: Additional file 10: of Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease

description: Table S6. DMRs between two samples. (XLSX 580 kb)
DOI: 10.6084/m9.figshare.6443813
title: Additional file 2: of Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease

description: Table S2. D3 specific SNVs and short InDels (XLSX 82 kb)
DOI: 10.6084/m9.figshare.6443813.v1
title: Additional file 2: of Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease

description: Table S2. D3 specific SNVs and short InDels (XLSX 82 kb)
DOI: 10.6084/m9.figshare.6443741.v1
title: Additional file 1: of Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease

description: Table S1. Overview of WGS data. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.6443684
title: Additional file 8: of Distinct sperm nucleus behaviors between genotypic and temperature-dependent sex determination males are associated with replication and expression-related pathways in a gynogenetic fish

description: Table S8. DEPs assigned to the process of â Transcriptionâ , related to Fig. 6e (XLS 27 kb)
DOI: 10.6084/m9.figshare.6443684.v1
title: Additional file 8: of Distinct sperm nucleus behaviors between genotypic and temperature-dependent sex determination males are associated with replication and expression-related pathways in a gynogenetic fish

description: Table S8. DEPs assigned to the process of â Transcriptionâ , related to Fig. 6e (XLS 27 kb)
DOI: 10.6084/m9.figshare.6443696
title: Additional file 9: of Distinct sperm nucleus behaviors between genotypic and temperature-dependent sex determination males are associated with replication and expression-related pathways in a gynogenetic fish

description: Table S9. Subcellular location of down-regulated DEPs assigned to the process of “Replication and repair”, “Translation” and “Transcription”. (XLS 35 kb)
DOI: 10.6084/m9.figshare.6443822.v1
title: Additional file 2: of Identification of QTL hot spots for malting quality in two elite breeding lines with distinct tolerance to abiotic stress

description: Table S1. Genetic positions of markers. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.13257720.v1
title: Additional file 1 of TruNeo: an integrated pipeline improves personalized true tumor neoantigen identification

description: Additional file 1. Median rank of epitopes with pre-existing CD8 immune response.
DOI: 10.6084/m9.figshare.13257681
title: Additional file 2 of Integrated metabolomics and transcriptomics study of traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao reveals global metabolic profile and novel phytochemical ingredients

description: Additional file 2. The metabolites from AMM, containing 5435 metabolites with 3985 tagged with MS2 data.
DOI: 10.6084/m9.figshare.21647927
title: Adaptive Algorithm for Multi-Armed Bandit Problem with High-Dimensional Covariates

description: This article studies an important sequential decision making problem known as the multi-armed stochastic bandit problem with covariates. Under a linear bandit framework with high-dimensional covariates, we propose a general multi-stage arm allocation algorithm that integrates both arm elimination and randomized assignment strategies. By employing a class of high-dimensional regression methods for coefficient estimation, the proposed algorithm is shown to have near optimal finite-time regret performance under a new study scope that requires neither a margin condition nor a reward gap condition for competitive arms. Based on the synergistically verified benefit of the margin, our algorithm exhibits adaptive performance that automatically adapts to the margin and gap conditions, and attains optimal regret rates simultaneously for both study scopes, without or with the margin, up to a logarithmic factor. Besides the desirable regret performance, the proposed algorithm simultaneously generates useful coefficient estimation output for competitive arms and is shown to achieve both estimation consistency and variable selection consistency. Promising empirical performance is demonstrated through extensive simulation and two real data evaluation examples. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6443834
title: Additional file 3: of Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease

description: Table S3. Sequence variations reported related to VSD. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.6443579
title: Additional file 3: of Distinct sperm nucleus behaviors between genotypic and temperature-dependent sex determination males are associated with replication and expression-related pathways in a gynogenetic fish

description: Table S3. Up-regulated DEPs (males of TSD vs males of GSD). (XLS 235 kb)
DOI: 10.6084/m9.figshare.6968078.v1
title: Effects of baicalin on inflammatory reaction, oxidative stress and PKDl and NF-kB protein expressions in rats with severe acute pancreatitis

description: Abstract Purpose: To investigate the effects of baicalin on inflammatory reaction, oxidative stress and protein kinase D1 (PKD1) and nuclear factor-kappa B (NF-κB) protein expressions in severe acute pancreatitis (SAP) rats. Methods: Sixty rats were divided into sham operation, model, and low-, medium- and high-dose baicalin group. SAP model was established in later 4 groups. The later 3 groups were injected with 0.1, 0.2 and 0.4 ml/100 g 5% baicalin injection, respectively. At 12 h, the serum SAP related indexes and inflammatory factors, peripheral blood CD3 and γδT cell percentages, wet/dry ratio and pancreas ascites volume, oxidative stress indexes and PKD1 and NF-κB protein expressions in pancreatic tissue were determined. Results: Compared with model group, in high-dose baicalin group the wet/dry ratio and ascites volume, serum amylase level, phospholipase A2 activity, TNF-α, IL-1 and IL-6 levels, and pancreatic malondialdehyde level and PKD1 and NF-κB protein expression were significantly decreased (P &lt; 0.05), and peripheral blood CD3 and γδT cell percentages and pancreatic superoxide dismutase and glutathione peroxidase levels were significantly increased (P &lt; 0.05). Conclusion: Baicalin can resist the inflammatory reaction and oxidative stress, and down-regulate protein kinase D1 and nuclear factor-kappa B protein expressions, thus exerting the protective effects on severe acute pancreatitis in rats.
DOI: 10.6084/m9.figshare.13257681.v1
title: Additional file 2 of Integrated metabolomics and transcriptomics study of traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao reveals global metabolic profile and novel phytochemical ingredients

description: Additional file 2. The metabolites from AMM, containing 5435 metabolites with 3985 tagged with MS2 data.
DOI: 10.6084/m9.figshare.6443870
title: Additional file 5: of Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease

description: Table S4. Analysis of CNVs two samples. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.6443870.v1
title: Additional file 5: of Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease

description: Table S4. Analysis of CNVs two samples. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.6443873
title: Additional file 5: of Identification of QTL hot spots for malting quality in two elite breeding lines with distinct tolerance to abiotic stress

description: Table S3. The list of candidate genes associated with largest QTL cluster on chromosome 3H. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.6443603
title: Additional file 4: of Distinct sperm nucleus behaviors between genotypic and temperature-dependent sex determination males are associated with replication and expression-related pathways in a gynogenetic fish

description: Table S4. Down-regulated DEPs (males of TSD vs males of GSD). (XLS 243 kb)
DOI: 10.6084/m9.figshare.6443822
title: Additional file 2: of Identification of QTL hot spots for malting quality in two elite breeding lines with distinct tolerance to abiotic stress

description: Table S1. Genetic positions of markers. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.6443873.v1
title: Additional file 5: of Identification of QTL hot spots for malting quality in two elite breeding lines with distinct tolerance to abiotic stress

description: Table S3. The list of candidate genes associated with largest QTL cluster on chromosome 3H. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.6443903.v1
title: Additional file 7: of Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease

description: Table S5. Overview of RRBS data. (XLS 26 kb)
DOI: 10.6084/m9.figshare.6968048
title: Clinical features of carriers of reciprocal chromosomal translocations involving chromosome 2: report of nine cases and review of the literature

description: ABSTRACT Objective: To explore the clinical features of carriers of chromosome 2 translocations, enabling informed genetic counseling of these patients. Materials and Methods: Eighty-two male carriers of a translocation who were infertile or receiving fertility counseling were recruited. Cytogenetic analyses were performed using G-banding. A search of PubMed was performed to determine whether the identified translocations on chromosome 2 are involved in male infertility. The relationships of translocation breakpoints with male infertility and recurrent pregnancy loss were analyzed. Results: Of the 82 translocation carriers, 9 (11%) were carriers of a chromosome 2 translocation. Four cases had oligozoospermia or infertility, while five had normal semen. In an analysis of the literature, 55 patients who were carriers of chromosome 2 translocations were also reviewed. Breakpoints at 2p13 and 2q31 were observed in six patients each, and were the most common. Breakpoints at 2p23, 2p13, 2p11.2, 2q31, and 2q37 were associated to both pre-gestational and gestational infertility, while other breakpoints were associated with gestational infertility. Conclusions: All breakpoints at chromosome 2 were correlated with gestational infertility. Carriers of chromosome 2 translocations should therefore receive counseling to continue with natural conception and use of different technologies available via assisted reproductive technology, such as preimplantation genetic diagnosis.
DOI: 10.6084/m9.figshare.13257693.v1
title: Additional file 6 of Integrated metabolomics and transcriptomics study of traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao reveals global metabolic profile and novel phytochemical ingredients

description: Additional file 6. Unigenes differentially expressed in leaf and stem in comparison of root transcriptome.
DOI: 10.6084/m9.figshare.6443606
title: Additional file 12: of Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease

description: Table S8. GO and KEGG analysis of DMRs located in gene body. (XLSX 99 kb)
DOI: 10.6084/m9.figshare.6968078
title: Effects of baicalin on inflammatory reaction, oxidative stress and PKDl and NF-kB protein expressions in rats with severe acute pancreatitis

description: Abstract Purpose: To investigate the effects of baicalin on inflammatory reaction, oxidative stress and protein kinase D1 (PKD1) and nuclear factor-kappa B (NF-κB) protein expressions in severe acute pancreatitis (SAP) rats. Methods: Sixty rats were divided into sham operation, model, and low-, medium- and high-dose baicalin group. SAP model was established in later 4 groups. The later 3 groups were injected with 0.1, 0.2 and 0.4 ml/100 g 5% baicalin injection, respectively. At 12 h, the serum SAP related indexes and inflammatory factors, peripheral blood CD3 and γδT cell percentages, wet/dry ratio and pancreas ascites volume, oxidative stress indexes and PKD1 and NF-κB protein expressions in pancreatic tissue were determined. Results: Compared with model group, in high-dose baicalin group the wet/dry ratio and ascites volume, serum amylase level, phospholipase A2 activity, TNF-α, IL-1 and IL-6 levels, and pancreatic malondialdehyde level and PKD1 and NF-κB protein expression were significantly decreased (P &lt; 0.05), and peripheral blood CD3 and γδT cell percentages and pancreatic superoxide dismutase and glutathione peroxidase levels were significantly increased (P &lt; 0.05). Conclusion: Baicalin can resist the inflammatory reaction and oxidative stress, and down-regulate protein kinase D1 and nuclear factor-kappa B protein expressions, thus exerting the protective effects on severe acute pancreatitis in rats.
DOI: 10.6084/m9.figshare.13257713
title: Additional file 3 of Systemic elucidation on the potential bioactive compounds and hypoglycemic mechanism of Polygonum multiflorum based on network pharmacology

description: Additional file 3. The specific values of docking energy between ligands and receptors.
DOI: 10.6084/m9.figshare.13257720
title: Additional file 1 of TruNeo: an integrated pipeline improves personalized true tumor neoantigen identification

description: Additional file 1. Median rank of epitopes with pre-existing CD8 immune response.
DOI: 10.6084/m9.figshare.6443876
title: MOESM3 of Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating Î˛-proteobacterium Pandoraea sp. ISTKB

description: Additional file 3: Table S10. Other differentially expressed proteins (related to PHA metabolism, dehydrogenase, reductases, transferases, esterases and hydrolases) on kraft lignin.
DOI: 10.6084/m9.figshare.6968003.v1
title: Numerical modeling of preloaded filling spiral case structure

description: Abstract A spiral case with its steel spiral case (SSC) being embedded in reinforced concrete under a pressurized condition is called a preloaded filling spiral case structure (PFSCS) in a hydropower plant. As a steel-concrete composite structure, a PFSCS is designed to work reliably. The non-uniform gap and contact nonlinearity between the SSC and the surrounding mass concrete have a great effect on the bearing mechanism of the composite structure. However, the description of the gap and contact nonlinearity in a PFSCS is a tough work. With the aim of efficiently describing the evolution process of the non-uniform gap and contact nonlinearity, we performed an experimental investigation and proposed a novel numerical simulation technique for structural finite element analyses (FEA) of PFSCSs. In the technique, the gap and contact nonlinearity as well as the construction process and operation process of a PFSCS are taken into account. A friction-contact model is used to simulate the sliding of the SSC against the concrete. A plasticity damage model is employed to describe the concrete. The development of the gap, contact status between the steel liner and the surrounding concrete, stresses of the steel liner and the steel bars, as well as the concrete cracking time and crack pattern, are presented in this work. The FEA results agree well with the experimental results. The agreement provides evidence that the applicability and competence of the proposed technique are valid and satisfactory.
DOI: 10.6084/m9.figshare.6443765.v1
title: Additional file 21: of Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease

description: Table S10. Expression profiling data of embryo and adult heart. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.6443858.v1
title: MOESM2 of Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating Î˛-proteobacterium Pandoraea sp. ISTKB

description: Additional file 2: Table S9. Detail of genomic islands identified in Pandoraea sp. ISTKB genome.
DOI: 10.6084/m9.figshare.12210836
title: Expression of a short antibody heavy chain peptide effectively antagonizes adenosine 2A receptor in vitro and in vivo

description: Adenosine 2A receptor (A<sub>2A</sub>R) is involved in many physiological and pathological functions and serves as an important drug target. Inhibition of A<sub>2A</sub>R may alleviate symptoms associated with a variety of neuropsychiatric disorders. However, the currently used A<sub>2A</sub>R antagonists have specificity limitations. A Fab fragment (Fab2838) of an A<sub>2A</sub>R mouse monoclonal antibody can specifically bind to A<sub>2A</sub>R to form a complex and inhibit the activity of its receptor. We constructed the vector AntiA<sub>2A</sub>R, a small-molecule peptide that binds to and inhibits A<sub>2A</sub>R based on Fab2838. Experiments in HEK293T cells showed that peptide AntiA<sub>2A</sub>R of 29 peptides was the most effective among the synthesized peptides in inhibiting the A<sub>2A</sub>R downstream signal cAMP/PKA/CREB. In neurons, the AntiA<sub>2A</sub>R reversed the calcium flow change induced by the A<sub>2A</sub>R agonist CGS21680 (1 μM). Furthermore, AntiA<sub>2A</sub>R expression in the mice striatum weakened the p-PKA/p-CREB signal, enhanced locomotor abilities and increased time spent in the center area in the home-cage observation experiment and increased anxiolytic behavior in the elevated-plus maze test. Antagonistic peptide AntiA<sub>2A</sub>R can effectively block the A<sub>2A</sub>R signaling pathway. This provides a new strategy for the specific inhibition of A<sub>2A</sub>R and provides information needed for drug development.
DOI: 10.6084/m9.figshare.7492235.v2
title: RETRACTED ARTICLE: Downregulation of NEAT1 reverses the radioactive iodine resistance of papillary thyroid carcinoma cell via miR-101-3p/FN1/PI3K-AKT signaling pathway

description: We, the Editors and Publisher of the journal <i>Cell Cycle</i>, have retracted the following article Chao Liu, Zhiping Feng, Ting Chen, Juan Lv, Pengjie Liu, Li Jia, Jialun Zhu, Fukun Chen, Chuanzhou Yang, and Zhiyong Deng. Downregulation of NEAT1 reverses the radioactive iodine resistance of papillary thyroid carcinoma cell via miR-101-3p/FN1/PI3K-AKT signaling pathway. Cell Cycle. 2018;18(2):167–203. doi: 10.1080/15384101.2018.1560203. Since publication, concerns have been raised about the integrity of the data in the article. When approached for an explanation, the authors checked their data and confirmed there are fundamental errors present. Therefore, they have agreed to the retraction of this article. The authors apologise for this oversight.    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.6444086.v1
title: Additional file 1: of Comparative transcriptomic and proteomic analyses reveal upregulated expression of virulence and iron transport factors of Aeromonas hydrophila under iron limitation

description: Excel S1. The results of differentially expressed transcripts and proteins to find the corresponding genes and proteins. (XLSX 87Â kb)
DOI: 10.6084/m9.figshare.6444098
title: Additional file 2: of Comparative transcriptomic and proteomic analyses reveal upregulated expression of virulence and iron transport factors of Aeromonas hydrophila under iron limitation

description: Excel S2. The enriched DEGs GO terms between control and iron-limitation groups using bioinformatics methods. (XLSX 42Â kb)
DOI: 10.6084/m9.figshare.6444113
title: Additional file 3: of Comparative transcriptomic and proteomic analyses reveal upregulated expression of virulence and iron transport factors of Aeromonas hydrophila under iron limitation

description: Excel S3. The enriched DEPs GO terms between control and iron-limitation groups using bioinformatics methods. (XLSX 42Â kb)
DOI: 10.6084/m9.figshare.13257453
title: Additional file 2 of Transcriptome analysis identifies genes involved in the somatic embryogenesis of Eucalyptus

description: Additional file 2. Differentially expressed genes in the dedifferentiated tissues compared to the differentiated tissues of E. camaldulensis and E. grandis x urophylla.
DOI: 10.6084/m9.figshare.6444086
title: Additional file 1: of Comparative transcriptomic and proteomic analyses reveal upregulated expression of virulence and iron transport factors of Aeromonas hydrophila under iron limitation

description: Excel S1. The results of differentially expressed transcripts and proteins to find the corresponding genes and proteins. (XLSX 87Â kb)