cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11769891.v1
title: Colistin-resistance gene <i>mcr</i> in clinical carbapenem-resistant <i>Enterobacteriaceae</i> strains in China, 2014–2019

description: To investigate whether introduction of colistin into the clinical settings selected colistin-resistant CRE, we performed molecular epidemiological study of 1868 CRE strains collected from different geographical locales in China during the period 2014–2019. 1755 (96.18%) isolates carried the carbapenemase genes <i>bla</i><sub>KPC</sub> and <i>bla</i><sub>NDM</sub>; 14 <i>Escherichia coli</i> isolates (0.75%) carrying <i>mcr-1</i> and <i>bla</i><sub>NDM</sub> (MCR-CREC) were also identified. Importantly, the number and relative prevalence of MCR-CREC isolates increased from 5 (0.41%) to 9 (1.38%) after introduction of polymyxin into clinical practice. Consistently, results of genetic analysis indicated that MCR-CREC strains collected before December 2017 were genetically diverse, yet those collected after that date exhibited more closely related genetic profiles, indicating that specific MCR-CREC strains were rapidly selected as a result of increased usage of colistin in clinical settings. The resistance level of MCR-CREC isolates to colistin increased after the introduction of polymyxin into clinical use with the MIC to colistin from &lt;2 mg/L in 80% strains to 2 mg/L in 100% strains. Further dissemination of MCR-CREC strains, which exhibit resistance to the last-line drugs of carbapenems and colistin, is expected to pose a severe threat to human health.
DOI: 10.6084/m9.figshare.19619498.v1
title: Additional file 3 of Small HSPs play an important role in crosstalk between HSF-HSP and ROS pathways in heat stress response through transcriptomic analysis in lilies (Lilium longiflorum)

description: Additional file 3. 436 common genes enriched in of the top 40 GO terms and the 20 KEGG pathways.
DOI: 10.6084/m9.figshare.19619489.v1
title: Additional file 1 of Small HSPs play an important role in crosstalk between HSF-HSP and ROS pathways in heat stress response through transcriptomic analysis in lilies (Lilium longiflorum)

description: Additional file 1. The information of all the annotated 55,044 unigenes in this RNA-seq data.
DOI: 10.6084/m9.figshare.19619489
title: Additional file 1 of Small HSPs play an important role in crosstalk between HSF-HSP and ROS pathways in heat stress response through transcriptomic analysis in lilies (Lilium longiflorum)

description: Additional file 1. The information of all the annotated 55,044 unigenes in this RNA-seq data.
DOI: 10.6084/m9.figshare.11769900.v1
title: Discovery of a subgenotype of human coronavirus NL63 associated with severe lower respiratory tract infection in China, 2018

description: Human coronavirus NL63 (HCoV-NL63) is primarily associated with common cold in children, elderly and immunocompromised individuals. Outbreaks caused by HCoV-NL63 are rare. Here we report a cluster of HCoV-NL63 cases with severe lower respiratory tract infection that arose in Guangzhou, China, in 2018. Twenty-three hospitalized children were confirmed to be HCoV-NL63 positive, and most of whom were hospitalized with severe pneumonia or acute bronchitis. Whole genomes of HCoV-NL63 were obtained using next-generation sequencing. Phylogenetic and single amino acid polymorphism analyses showed that this outbreak was associated with two subgenotypes (C3 and B) of HCoV-NL63. Half of patients were identified to be related to a new subgenotype C3. One unique amino acid mutation at I507 L in spike protein receptor binding domain (RBD) was detected, which segregated this subgenotype C3 from other known subgenotypes. Pseudotyped virus bearing the I507 L mutation in RBD showed enhanced entry into host cells as compared to the prototype virus. This study proved that HCoV-NL63 was undergoing continuous mutation and has the potential to cause severe lower respiratory disease in humans.
DOI: 10.6084/m9.figshare.23828526
title: Data from: Genetic connectivity constrained by natural barriers in a key agricultural pest: Insights from mitochondrial DNA analysis

description: The original mtDNA data and the R code for random forest model used in the study 'Genetic connectivity constrained by natural barriers in a key agricultural pest: Insights from mitochondrial DNA analysis'.
DOI: 10.6084/m9.figshare.19625579
title: Additional file 6 of Genome-wide analysis and functional characterization of CHYR gene family associated with abiotic stress tolerance in bread wheat (Triticum aestivum L.)

description: Additional file 6: Table S3. Paralogous CHYR gene pairs among T.aestivum
DOI: 10.6084/m9.figshare.19625582.v1
title: Additional file 7 of Genome-wide analysis and functional characterization of CHYR gene family associated with abiotic stress tolerance in bread wheat (Triticum aestivum L.)

description: Additional file 7: Table S4. Orthologous relationships between TaCHYR genes in T. aestivum with other CHYR genes in T. urartu, Ae.tauschii, B. distachyon, and O. sativa
DOI: 10.6084/m9.figshare.19625585.v1
title: Additional file 8 of Genome-wide analysis and functional characterization of CHYR gene family associated with abiotic stress tolerance in bread wheat (Triticum aestivum L.)

description: Additional file 8: Table S5. The cis-elements analysis in the promoter regions of TaCHYR genes
DOI: 10.6084/m9.figshare.19625555
title: Additional file 10 of Genome-wide analysis and functional characterization of CHYR gene family associated with abiotic stress tolerance in bread wheat (Triticum aestivum L.)

description: Additional file 10: Table S7. The protein-protein interaction network between TaCHYRs and other proteins in wheat
DOI: 10.6084/m9.figshare.19625561.v1
title: Additional file 12 of Genome-wide analysis and functional characterization of CHYR gene family associated with abiotic stress tolerance in bread wheat (Triticum aestivum L.)

description: Additional file 12: Table S9. Specific primers used in the study
DOI: 10.6084/m9.figshare.19625501
title: Additional file 8 of Identification of a pyroptosis-related prognostic signature in breast cancer

description: Additional file 8.
DOI: 10.6084/m9.figshare.19625495.v1
title: Additional file 6 of Identification of a pyroptosis-related prognostic signature in breast cancer

description: Additional file 6.
DOI: 10.6084/m9.figshare.19625489.v1
title: Additional file 4 of Identification of a pyroptosis-related prognostic signature in breast cancer

description: Additional file 4.
DOI: 10.6084/m9.figshare.19625489
title: Additional file 4 of Identification of a pyroptosis-related prognostic signature in breast cancer

description: Additional file 4.
DOI: 10.6084/m9.figshare.19625498
title: Additional file 7 of Identification of a pyroptosis-related prognostic signature in breast cancer

description: Additional file 7.
DOI: 10.6084/m9.figshare.19619501
title: Additional file 4 of Small HSPs play an important role in crosstalk between HSF-HSP and ROS pathways in heat stress response through transcriptomic analysis in lilies (Lilium longiflorum)

description: Additional file 4. primers sequence used in this study.
DOI: 10.6084/m9.figshare.19625495
title: Additional file 6 of Identification of a pyroptosis-related prognostic signature in breast cancer

description: Additional file 6.
DOI: 10.6084/m9.figshare.19625588
title: Additional file 9 of Genome-wide analysis and functional characterization of CHYR gene family associated with abiotic stress tolerance in bread wheat (Triticum aestivum L.)

description: Additional file 9: Table S6. Gene ontology (GO) annotation of TaCHYR genes in T. aestivum
DOI: 10.6084/m9.figshare.19625588.v1
title: Additional file 9 of Genome-wide analysis and functional characterization of CHYR gene family associated with abiotic stress tolerance in bread wheat (Triticum aestivum L.)

description: Additional file 9: Table S6. Gene ontology (GO) annotation of TaCHYR genes in T. aestivum
DOI: 10.6084/m9.figshare.19625514.v1
title: Additional file 2 of Genome sequencing of Inonotus obliquus reveals insights into candidate genes involved in secondary metabolite biosynthesis

description: Additional file 2.
DOI: 10.6084/m9.figshare.23304395
title: <strong>Measurements in the Changjiang Estuary by a bottom-mounted tripod system</strong>

description: This collection shares the data used in the paper entitled " A Novel Approach for Wave-Turbulence Decomposition ", including obseration conditions (e.g., water depth, flow velocity, wind velocity, wave height and period) and velocity fluctuations.
DOI: 10.6084/m9.figshare.19625561
title: Additional file 12 of Genome-wide analysis and functional characterization of CHYR gene family associated with abiotic stress tolerance in bread wheat (Triticum aestivum L.)

description: Additional file 12: Table S9. Specific primers used in the study
DOI: 10.6084/m9.figshare.19619495
title: Additional file 2 of Small HSPs play an important role in crosstalk between HSF-HSP and ROS pathways in heat stress response through transcriptomic analysis in lilies (Lilium longiflorum)

description: Additional file 2. DEGs for GO and KEGG enrichment analysis.
DOI: 10.6084/m9.figshare.19619498
title: Additional file 3 of Small HSPs play an important role in crosstalk between HSF-HSP and ROS pathways in heat stress response through transcriptomic analysis in lilies (Lilium longiflorum)

description: Additional file 3. 436 common genes enriched in of the top 40 GO terms and the 20 KEGG pathways.
DOI: 10.6084/m9.figshare.19625555.v1
title: Additional file 10 of Genome-wide analysis and functional characterization of CHYR gene family associated with abiotic stress tolerance in bread wheat (Triticum aestivum L.)

description: Additional file 10: Table S7. The protein-protein interaction network between TaCHYRs and other proteins in wheat
DOI: 10.34740/kaggle/dsv/7624080
title: 2021 World Population (updated daily)
DOI: 10.6084/m9.figshare.17004210.v1
title: Additional file 4 of CRPGCN: predicting circRNA-disease associations using graph convolutional network based on heterogeneous network

description: Additional file 4: circRNA feature matrix.
DOI: 10.6084/m9.figshare.17004213.v1
title: Additional file 5 of CRPGCN: predicting circRNA-disease associations using graph convolutional network based on heterogeneous network

description: Additional file 5: Disease feature matrix.
DOI: 10.6084/m9.figshare.8091344.v1
title: Artesunate promotes Th1 differentiation from CD4+ T cells to enhance cell apoptosis in ovarian cancer via miR-142

description: The aim of this study was to evaluate the influence of artesunate on Th1 differentiation and its anti-tumor effect on ovarian cancer. A Murine ovarian cancer model was established by ID8 cells transplantation. The expression of miR-142 and Sirt1 proteins in peripheral CD4+ T cells were quantified with qRT-PCR and western blot, respectively. Peripheral CD4+ T cells were induced for Th1 differentiation. The percentages of apoptosis of Th1/CD4+ T cells and ovarian cancer cells were analyzed by flow cytometry. The IFN-γ level was examined through enzyme-linked immunosorbent assay. Artesunate promoted miR-142 expression in peripheral CD4+ T cells and Th1 differentiation from CD4+ T cells. Artesunate promoted cell apoptosis of ovarian cancer cells by inducing Th1 differentiation. By up-regulating miR-142, artesunate suppressed Sirt1 level and promoted Th1 differentiation. Artesunate enhanced the pro-apoptotic effects of Th1 cells on ovarian cancer via the miR-142/Sirt1 pathway. Artesunate promoted Th1 differentiation from CD4+ T cells by down-regulating Sirt1 through miR-142, thereby enhancing cell apoptosis in ovarian cancer.
DOI: 10.6084/m9.figshare.19625558
title: Additional file 11 of Genome-wide analysis and functional characterization of CHYR gene family associated with abiotic stress tolerance in bread wheat (Triticum aestivum L.)

description: Additional file 11: Table S8. The regulatory network between the putative miRNAs and their targeted wheat CHYR genes
DOI: 10.6084/m9.figshare.19625573
title: Additional file 4 of Genome-wide analysis and functional characterization of CHYR gene family associated with abiotic stress tolerance in bread wheat (Triticum aestivum L.)

description: Additional file 4: Table S1. The characteristics of CHYR genes in wheat
DOI: 10.6084/m9.figshare.17004201
title: Additional file 1 of CRPGCN: predicting circRNA-disease associations using graph convolutional network based on heterogeneous network

description: Additional file 1: Adjacency matrix A. The adjacency matrix A constructed from circR2Disease.
DOI: 10.6084/m9.figshare.19619501.v1
title: Additional file 4 of Small HSPs play an important role in crosstalk between HSF-HSP and ROS pathways in heat stress response through transcriptomic analysis in lilies (Lilium longiflorum)

description: Additional file 4. primers sequence used in this study.
DOI: 10.6084/m9.figshare.19625573.v1
title: Additional file 4 of Genome-wide analysis and functional characterization of CHYR gene family associated with abiotic stress tolerance in bread wheat (Triticum aestivum L.)

description: Additional file 4: Table S1. The characteristics of CHYR genes in wheat
DOI: 10.6084/m9.figshare.8091353
title: Skp2 inhibitor SKPin C1 decreased viability and proliferation of multiple myeloma cells and induced apoptosis

description: Multiple myeloma (MM) is a malignant neoplasm of plasma, and exhibits several harmful effects including osteolytic injuries, hypercalcemia, and immune dysfunction. Many patients with MM succumb to the underlying malignancy. An S-phase kinase-related protein 2 (Skp2) inhibitor, designated SKPin C1, has been developed and confirmed to have an inhibitory effect on metastatic melanoma cells. This study aimed to determine the effect of SKPin C1 on MM. Normal B lymphocytes, THP-1 cells, and MM U266 and RPMI 8226 cells were exposed to various dosages of SKPin C1 for 48 h. Cell proliferation was determined by MTT, EdU staining, and cell cycle assays. Western blot assays were performed to assess intracellular protein levels of Skp2, p27, and cleaved caspase-3. The amount of ubiquitin attached to p27 was determined using an immunoprecipitation assay. The viability of U266 and RPMI 8226 cells was significantly inhibited by 10 μM SKPin C1 and the inhibitory effect was enhanced with increasing doses of SKPin C1. In contrast, 50 μM SKPin C1 only marginally decreased viability of normal B lymphocytes in 12 h. Skp2 and p27 expression in U266 and RPMI 8226 cells was higher and lower, respectively, than that in the normal B lymphocytes. Treatment with SKPin C1 or Skp2 knockdown increased p27 protein levels in U266 and RPMI 8226 cells by preventing p27 from being ubiquitinated, which slowed the cell cycle, inhibited cell proliferation, and triggered apoptosis. Therefore, this study suggested SKPin C1 as a potent inhibitor against aberrant proliferation and immortalization of MM.
DOI: 10.6084/m9.figshare.8091377.v1
title: A biomechanical study on proximal junctional kyphosis following long-segment posterior spinal fusion

description: Posterior long-segment spinal fusion may lead to proximal junctional kyphosis (PJK). The present study sought to identify the appropriate fusion levels required in order to prevent PJK using finite element analysis. A finite element model was constructed based on the whole-spine computed tomography findings of a healthy adult. Nine commonly used posterior spinal fusion methods were selected. Stress on the annulus fibrosis fibers, the posterior ligamentous complex, and the vertebrae after various spinal fusions in the upright position were compared. This study was divided into two groups: non-fusion and fusion. In the former, the stress between the T10 and the upper thoracic vertebrae was higher. Comparing thoracic and lumbar segments in the fusion group, the peak stress values of the upper instrumented vertebrae (UIV) were mainly observed in T2 and L2 whilst those of the UIV+1 were observed in T10 and L2. After normalization, the peak stress values of the UIV and UIV+1 were located in T2 and L2. Similarly, the peak stress values of the annulus fibrosus at the upper adjacent level were on T10 and L2 after normalization. However, the peak stress values of the interspinal/supraspinal complex forces were concentrated on T11, T12, and L1 after normalization whilst the peak stress value of the pedicle screw was on T2. Controversy remains over the fusion of T10, and this study simulated testing conditions with gravitational loading only. However, further assessment is needed prior to reaching definitive conclusions.
DOI: 10.6084/m9.figshare.21207488
title: Data File for "Measuring A Contract's Breadth: A Textual Analysis"

description: Data file for "Measuring a Contract's Breadth: A Text Analysis"
DOI: 10.6084/m9.figshare.21731810
title: Hyperosmolar Potassium Inhibits Corneal Myofibroblast Transformation and Prevent Corneal Scar

description: Corneal myofibroblasts play a crucial role in the process of corneal scarring. Potassium has been documented to reduce skin scar tissue formation. Herein, we investigated the ability of potassium to prevent corneal fibrosis in cell culture and <i>in vivo</i>. Corneal fibroblasts (CFs) were isolated from the corneal limbus and treated with TGF-β1 to transform into corneal myofibroblasts. Corneal myofibroblast markers were detected by quantitative real-time PCR, Western blot, and immunofluorescence. The contractive functions of corneal myofibroblast were evaluated by the scratch assay and the collagen gel contraction assay. RNA sequencing in corneal fibroblasts was performed to explore the mechanisms underlying hyperosmolar potassium treatment. GO and KEGG analysis were performed to explore the underlying mechanism by hyperosmolar potassium treatment. The ATP detection assay assessed the level of cell metabolism. KCl eye drops four times per day were administered to mice models of corneal injury to evaluate the ability to prevent corneal scar formation. Corneal opacity area was evaluated by Image J software. Treatment with hyperosmolar potassium could suppress corneal myofibroblast transformation and collagen I synthesis induced by TGF-β1 in cell culture. Hyperosmolar potassium could inhibit wound healing and gel contraction in CFs. RNA sequencing results suggested that genes involved in the metabolic pathway were downregulated after KCl treatment. ATP levels were significantly decreased in the KCl group compared with the control group. Hyperosmolar potassium could prevent corneal myofibroblast transformation after corneal injury and corneal scar formation in mice. Potassium can suppress corneal myofibroblast transformation and collagen I protein synthesis. Moreover, given that KCl eye drops can prevent corneal scar formation, it has been suggested to have huge prospects as a novel treatment approach during clinical practice.
DOI: 10.6084/m9.figshare.21731810.v1
title: Hyperosmolar Potassium Inhibits Corneal Myofibroblast Transformation and Prevent Corneal Scar

description: Corneal myofibroblasts play a crucial role in the process of corneal scarring. Potassium has been documented to reduce skin scar tissue formation. Herein, we investigated the ability of potassium to prevent corneal fibrosis in cell culture and <i>in vivo</i>. Corneal fibroblasts (CFs) were isolated from the corneal limbus and treated with TGF-β1 to transform into corneal myofibroblasts. Corneal myofibroblast markers were detected by quantitative real-time PCR, Western blot, and immunofluorescence. The contractive functions of corneal myofibroblast were evaluated by the scratch assay and the collagen gel contraction assay. RNA sequencing in corneal fibroblasts was performed to explore the mechanisms underlying hyperosmolar potassium treatment. GO and KEGG analysis were performed to explore the underlying mechanism by hyperosmolar potassium treatment. The ATP detection assay assessed the level of cell metabolism. KCl eye drops four times per day were administered to mice models of corneal injury to evaluate the ability to prevent corneal scar formation. Corneal opacity area was evaluated by Image J software. Treatment with hyperosmolar potassium could suppress corneal myofibroblast transformation and collagen I synthesis induced by TGF-β1 in cell culture. Hyperosmolar potassium could inhibit wound healing and gel contraction in CFs. RNA sequencing results suggested that genes involved in the metabolic pathway were downregulated after KCl treatment. ATP levels were significantly decreased in the KCl group compared with the control group. Hyperosmolar potassium could prevent corneal myofibroblast transformation after corneal injury and corneal scar formation in mice. Potassium can suppress corneal myofibroblast transformation and collagen I protein synthesis. Moreover, given that KCl eye drops can prevent corneal scar formation, it has been suggested to have huge prospects as a novel treatment approach during clinical practice.
DOI: 10.6084/m9.figshare.25218530
title: 12-PRISMA-2020-Checklist.docx

description: PRISMA Checklist
DOI: 10.6084/m9.figshare.25218530.v1
title: 12-PRISMA-2020-Checklist.docx

description: PRISMA Checklist
DOI: 10.6084/m9.figshare.22256130
title: Structural insight into TIPE1 functioning as a lipid transfer protein

description: As a member of the tumor necrosis factor-α-induced protein 8 (TNFAIP8/TIPE) family, TIPE1 has been found to be associated with many cellular signaling pathways in regulating apoptosis, autophagy, and tumorigenesis. However, the position of TIPE1 in the signaling network remains elusive. Here we present the crystal structure of zebrafish TIPE1 in complex with phosphatidylethanolamine (PE) at a resolution of 1.38 Å. By comparison with structures of other three TIPE family proteins, a universal phospholipid-binding mode was proposed. Namely, the hydrophobic cavity binds to fatty acid tails, while ‘X-R-R’ triad nearby the entrance of cavity recognizes the phosphate group head. Using molecular dynamics (MD) simulations, we further elaborated the mechanism of how the lysine-rich N-terminal domain assisting TIPE1 to favorably bind to phosphatidylinositol (PI). Beside small molecule substrate, we identified Gαi3 as a direct-binding partner of TIPE1 using GST pull-down assay and size-exclusion chromatography. Analyses of key-residue mutations and predicted complex structure revealed that the binding mode of TIPE1 to Gαi3 could be non-canonical. In summary, our findings narrowed down TIPE1’s position in Gαi3-related and PI-inducing signaling pathways. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22256130.v1
title: Structural insight into TIPE1 functioning as a lipid transfer protein

description: As a member of the tumor necrosis factor-α-induced protein 8 (TNFAIP8/TIPE) family, TIPE1 has been found to be associated with many cellular signaling pathways in regulating apoptosis, autophagy, and tumorigenesis. However, the position of TIPE1 in the signaling network remains elusive. Here we present the crystal structure of zebrafish TIPE1 in complex with phosphatidylethanolamine (PE) at a resolution of 1.38 Å. By comparison with structures of other three TIPE family proteins, a universal phospholipid-binding mode was proposed. Namely, the hydrophobic cavity binds to fatty acid tails, while ‘X-R-R’ triad nearby the entrance of cavity recognizes the phosphate group head. Using molecular dynamics (MD) simulations, we further elaborated the mechanism of how the lysine-rich N-terminal domain assisting TIPE1 to favorably bind to phosphatidylinositol (PI). Beside small molecule substrate, we identified Gαi3 as a direct-binding partner of TIPE1 using GST pull-down assay and size-exclusion chromatography. Analyses of key-residue mutations and predicted complex structure revealed that the binding mode of TIPE1 to Gαi3 could be non-canonical. In summary, our findings narrowed down TIPE1’s position in Gαi3-related and PI-inducing signaling pathways. Communicated by Ramaswamy H. Sarma