cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23621424.v1
title: Additional file 11 of Time interval between hCG administration and oocyte retrieval and ART outcomes: an updated systematic review and meta-analysis

description: Additional file 11: Appendix 1. Justifications in ROB.
DOI: 10.6084/m9.figshare.21524276
title: Additional file 2 of Transcriptome analysis of intestine from alk-SMase knockout mice reveals the effect of alk-SMase

description: Additional file 2. The original experimental data of qPCR
DOI: 10.6084/m9.figshare.21524276.v1
title: Additional file 2 of Transcriptome analysis of intestine from alk-SMase knockout mice reveals the effect of alk-SMase

description: Additional file 2. The original experimental data of qPCR
DOI: 10.6084/m9.figshare.21524391
title: Weibo sentiment analysis validation dataset

description:   
Humans spend most of their time in settlements, and the built environment of settlements may affect the residents’ sentiments. Research in this field is interdisciplinary, integrating urban planning and public health. However, it has been limited by the difficulty of quantifying subjective sentiments and the small sample size. This study uses 147,613 Weibo text check-ins in Xiamen from 2017 to quantify residents' sentiments in 1,096 neighborhoods in the city. A multilevel regression model and gradient boosting decision tree (GBDT) model are used to investigate the multilevel and nonlinear effects of the built environment of neighborhoods and subdistricts on residents' sentiments. The results show the following: 1) The multilevel regression model indicates that at the neighborhood level, a high land value, low plot ratio, low population density, more security facilities, and neighborhoods close to water are more likely to improve the residents’ sentiments. At the subdistrict level, more green space and commercial land, less industry, higher building density and road density, and a smaller migrant population are more likely to promote positive sentiments. Approximately 19% of the total variance in the sentiments occurred among subdistricts. 2) The number of security facilities, the proportion of green space and commercial land, and the density of buildings and roads are linearly correlated with residents' sentiments. The land value and the number of security facilities are basic needs and exhibit nonlinear correlations with sentiments. The plot ratio, population density, and the proportions of industrial land and the migrant population are advanced needs and are nonlinearly correlated with sentiments. The quantitative analysis of sentiments enables setting a threshold of the influence of the built environment on residents' sentiments in neighborhoods and surrounding areas. Our results provide data support for urban planning and implementing targeted measures to improve the living environment of residents.
DOI: 10.6084/m9.figshare.13135797
title: Asymptotic Theory of Eigenvectors for Random Matrices With Diverging Spikes

description: Characterizing the asymptotic distributions of eigenvectors for large random matrices poses important challenges yet can provide useful insights into a range of statistical applications. To this end, in this article we introduce a general framework of asymptotic theory of eigenvectors for large spiked random matrices with diverging spikes and heterogeneous variances, and establish the asymptotic properties of the spiked eigenvectors and eigenvalues for the scenario of the generalized Wigner matrix noise. Under some mild regularity conditions, we provide the asymptotic expansions for the spiked eigenvalues and show that they are asymptotically normal after some normalization. For the spiked eigenvectors, we establish asymptotic expansions for the general linear combination and further show that it is asymptotically normal after some normalization, where the weight vector can be arbitrary. We also provide a more general asymptotic theory for the spiked eigenvectors using the bilinear form. Simulation studies verify the validity of our new theoretical results. Our family of models encompasses many popularly used ones such as the stochastic block models with or without overlapping communities for network analysis and the topic models for text analysis, and our general theory can be exploited for statistical inference in these large-scale applications. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.13135797.v2
title: Asymptotic Theory of Eigenvectors for Random Matrices With Diverging Spikes

description: Characterizing the asymptotic distributions of eigenvectors for large random matrices poses important challenges yet can provide useful insights into a range of statistical applications. To this end, in this article we introduce a general framework of asymptotic theory of eigenvectors for large spiked random matrices with diverging spikes and heterogeneous variances, and establish the asymptotic properties of the spiked eigenvectors and eigenvalues for the scenario of the generalized Wigner matrix noise. Under some mild regularity conditions, we provide the asymptotic expansions for the spiked eigenvalues and show that they are asymptotically normal after some normalization. For the spiked eigenvectors, we establish asymptotic expansions for the general linear combination and further show that it is asymptotically normal after some normalization, where the weight vector can be arbitrary. We also provide a more general asymptotic theory for the spiked eigenvectors using the bilinear form. Simulation studies verify the validity of our new theoretical results. Our family of models encompasses many popularly used ones such as the stochastic block models with or without overlapping communities for network analysis and the topic models for text analysis, and our general theory can be exploited for statistical inference in these large-scale applications. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12611621
title: Results of multimodal evaluation approaches for Angel’s Eyes

description: Results of multimodal evaluation approaches （questionnaire, probability distribution of brush tip, trajectory of brush tip, task completion, task completion time, etc.） for Angel Girl of Visually Impaired Artists is used for the conference paper （the extended version has been submitted to the journal for peer review）: Liu Hang, Menghan Hu, Guangtao Zhai, Huijing Huang, Wa Zhang, Qingli Li, Yinghong Tian, Yanling Shi. Angel Girl of Visually Impaired Artists: Painting Navigation System for Blind or Visually Impaired Painters. In 2019 IEEE International Conference on Visual Communications and Image Processing.If you have any questions, you can send a request to: humenghan89@163.com
DOI: 10.6084/m9.figshare.6844466
title: Inhibition of glioma growth by flavokawain B is mediated through endoplasmic reticulum stress induced autophagy

description: Flavokawain B (FKB), a natural kava chalcone, displays potent antitumor activity in various types of cancer. The mechanism of action, however, remains unclear. Here, we evaluated the efficacy of FKB in the treatment of human glioblastoma multiforme (GBM) as well as the molecular basis for its inhibitory effects in cancer. Approximately 60% of GBM cells became senescent after treatment with FKB as assessed in the senescence-associated (SA)-GLB1/SA-β-galactosidase assay. The cellular process of autophagy potentially contributed to the establishment of senescence. Transmission electron microscopy revealed the formation of autophagic vesicles under FKB treatment, and MAP1LC3B (microtubule associated protein 1 light chain 3 beta)-II was increased. Transfection of <i>ATG5</i> or <i>ATG7</i> small interfering RNAs (siRNAs) inhibited FKB-induced autophagy in U251 cells. Western blot revealed that molecular components of the endoplasmic reticulum stress pathway were activated, including ATF4 (activating transcription factor 4) and DDIT3 (DNA damage inducible transcript 3), while levels of TRIB3 (tribbles pseudokinase 3) increased. In addition, based on the phosphorylation status, the AKT-MTOR-RPS6KB1 pathway was inhibited, which induced autophagy in GBM cells. Inhibition of autophagy by autophagy inhibitors 3-methyladenine and chloroquine or knockdown of <i>ATG5</i> or <i>ATG7</i> caused FKB-treated U251 cells to switch from senescence to apoptosis. Finally, knockdown of ATG5 or treatment with chloroquine in combination with FKB, significantly inhibited tumor growth <i>in vivo</i>. Our results demonstrated that FKB induced protective autophagy through the ATF4-DDIT3-TRIB3-AKT-MTOR-RPS6KB1 signaling pathway in GBM cells, indicating that the combination treatment of FKB with autophagy inhibitors may potentially be an effective therapeutic strategy for GBM. <b>Abbreviations:</b> 3-MA: 3-methyladenine; 4-PBA: 4-phenylbutyrate; AKT: AKT serine/threonine kinase; ATF4: activating transcription factor 4; ATG: autophagy related; CASP3: caspase 3; CCK-8: cell counting kit-8; CDKN1A: cyclin-dependent kinase inhibitor 1A; CQ: chloroquine; DDIT3: DNA damage inducible transcript 3; DMEM: Dulbecco’s modified Eagle’s medium; EIF2A: eukaryotic translation initiation factor 2A; EIF2AK3: eukaryotic translation initiation factor 2 alpha kinase 3; ER: endoplasmic reticulum; FKB: flavokawain B; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GBM: glioblastoma multiforme; GFP: green fluorescent protein; HSPA5: heat shock protein family A (Hsp70) member 5; MAP1LC3B: microtubule associated protein 1 light chain 3 beta; MTOR: mechanistic target of rapamycin kinase; PARP1: poly(ADP-ribose) polymerase; 1RPS6KB1: ribosomal protein S6 kinase B1; SA-GLB1: senescence-associated galactosidase beta 1; siRNA: short interfering RNA; SQSTM1: sequestosome 1; TEM: transmission electron microscopy; TRIB3: tribbles pseudokinase 3; TUNEL: deoxynucleotidyl transferase-mediated dUTP nick-end labeling
DOI: 10.6084/m9.figshare.6844466.v1
title: Inhibition of glioma growth by flavokawain B is mediated through endoplasmic reticulum stress induced autophagy

description: Flavokawain B (FKB), a natural kava chalcone, displays potent antitumor activity in various types of cancer. The mechanism of action, however, remains unclear. Here, we evaluated the efficacy of FKB in the treatment of human glioblastoma multiforme (GBM) as well as the molecular basis for its inhibitory effects in cancer. Approximately 60% of GBM cells, U251, U87, and T98, became senescent after treatment with FKB (3 μg/mL for 48 h) as assessed in the senescence-associated (SA)-GLB1/SA-β-galactosidase assay. The cellular process of macroautophagy/autophagy potentially contributed to the establishment of senescence. Transmission electron microscopy revealed the formation of autophagic vesicles under FKB treatment, and MAP1LC3B (microtubule associated protein 1 light chain 3 beta)-II, a protein associated with autophagy, was increased. Transfection of <i>ATG5</i> or <i>ATG7</i> small interfering RNAs (siRNAs) inhibited FKB-induced autophagy in U251 cells. Western blot analysis revealed that molecular components of the endoplasmic reticulum stress pathway were activated, including ATF4 (activating transcription factor 4) and DDIT3 (DNA damage inducible transcript 3), while levels of TRIB3 (tribbles pseudokinase 3) increased. In addition, based on the phosphorylation status, the AKT-MTOR-RPS6KB1 pathway was inhibited, which induced autophagy in GBM cells. Inhibition of autophagy by pharmacological autophagy inhibitors 3-methyladenine and chloroquine or knockdown of <i>ATG5</i> or <i>ATG7</i> caused FKB-treated U251 cells to switch from senescence to apoptosis. Finally, in orthotopic implantations of luciferase-transduced U251 cells in mice, knockdown of ATG5 or treatment with chloroquine in combination with FKB, significantly inhibited tumor growth. Our results demonstrated that FKB induced protective autophagy through the ATF4-DDIT3-TRIB3-AKT-MTOR-RPS6KB1 signaling pathway in GBM cells, indicating that the combination treatment of FKB with autophagy inhibitors may potentially be an effective therapeutic strategy for GBM.
DOI: 10.6084/m9.figshare.23621482
title: Additional file 4 of Characteristics of glucose and lipid metabolism and the interaction between gut microbiota and colonic mucosal immunity in pigs during cold exposure

description: Additional file 4: Table S4. Details of primary and secondary antibodies involved in Western blot.
DOI: 10.6084/m9.figshare.23621488
title: Additional file 6 of Characteristics of glucose and lipid metabolism and the interaction between gut microbiota and colonic mucosal immunity in pigs during cold exposure

description: Additional file 6: Table S6. Differential metabolites enriched in the plasma metabolome.
DOI: 10.6084/m9.figshare.7368923
title: Additional file 1: of LncRNA MIR31HG targets HIF1A and P21 to facilitate head and neck cancer cell proliferation and tumorigenesis by promoting cell-cycle progression

description: Figure S1. Relative gene expression of MIR31HG in LSCC cancer tissues and plasma. Figure S2. IHC of HIF1A and p21 proteins in LSCC tissues. Figure S3. MIR31HG KD lentivirus transfected Fadu and Cal-27 cells. Table S1. Association between MIR31HG and clinicopathological characteristics of LSCC patients. Table S2 Multivariate analyses of factors associated with OS in LSCC patients. Table S3. Relationship of HIF1A expression and clinicopathological parameters in LSCC patients. Table S4. Relationship of p21 expression and clinicopathological parameters in LSCC patients. Table S5. The correlation of HIF1A with p21 expression in LSCC. Table S6. Multivariate analyses for recurrence free survival of the postoperative LSCC by COX regression. (RAR 8552 kb)
DOI: 10.6084/m9.figshare.7893182.v1
title: Nonlinear response surface in the study of aqueous two-phase system and ionic liquid extraction of lignans from <i>Schisandrae chinensis</i> and mechanism clarification

description: Nonlinear response surface methodology was adopted to investigate complicated interactions of the extraction parameters of aqueous two-phase system and ionic liquids (ILs) to determine their optimum conditions for enhancing the extraction yield and antioxidant activity. Using statistical optimizations of ultrasound-assisted ionic liquid (UAE-ILs), the yield was increased from 8.73 to 10.44 mg g<sup>−1</sup>, and IC<sub>50</sub> value of DPPH was decreased from 0.49 to 0.36 mg mL<sup>−1</sup> with minimum cost and pollution. Additionally, the extraction mechanism of different methods was in-depth assessment. Experimental results showed that UAE-ILs in the extraction of lignans from plants can show a great promising prospect.
DOI: 10.6084/m9.figshare.23621482.v1
title: Additional file 4 of Characteristics of glucose and lipid metabolism and the interaction between gut microbiota and colonic mucosal immunity in pigs during cold exposure

description: Additional file 4: Table S4. Details of primary and secondary antibodies involved in Western blot.
DOI: 10.6084/m9.figshare.23621485.v1
title: Additional file 5 of Characteristics of glucose and lipid metabolism and the interaction between gut microbiota and colonic mucosal immunity in pigs during cold exposure

description: Additional file 5: Table S5. Differential metabolites enriched in the plasma metabolome.
DOI: 10.6084/m9.figshare.7368923.v1
title: Additional file 1: of LncRNA MIR31HG targets HIF1A and P21 to facilitate head and neck cancer cell proliferation and tumorigenesis by promoting cell-cycle progression

description: Figure S1. Relative gene expression of MIR31HG in LSCC cancer tissues and plasma. Figure S2. IHC of HIF1A and p21 proteins in LSCC tissues. Figure S3. MIR31HG KD lentivirus transfected Fadu and Cal-27 cells. Table S1. Association between MIR31HG and clinicopathological characteristics of LSCC patients. Table S2 Multivariate analyses of factors associated with OS in LSCC patients. Table S3. Relationship of HIF1A expression and clinicopathological parameters in LSCC patients. Table S4. Relationship of p21 expression and clinicopathological parameters in LSCC patients. Table S5. The correlation of HIF1A with p21 expression in LSCC. Table S6. Multivariate analyses for recurrence free survival of the postoperative LSCC by COX regression. (RAR 8552 kb)
DOI: 10.6084/m9.figshare.7893182
title: Nonlinear response surface in the study of aqueous two-phase system and ionic liquid extraction of lignans from <i>Schisandrae chinensis</i> and mechanism clarification

description: Nonlinear response surface methodology was adopted to investigate complicated interactions of the extraction parameters of aqueous two-phase system and ionic liquids (ILs) to determine their optimum conditions for enhancing the extraction yield and antioxidant activity. Using statistical optimizations of ultrasound-assisted ionic liquid (UAE-ILs), the yield was increased from 8.73 to 10.44 mg g<sup>−1</sup>, and IC<sub>50</sub> value of DPPH was decreased from 0.49 to 0.36 mg mL<sup>−1</sup> with minimum cost and pollution. Additionally, the extraction mechanism of different methods was in-depth assessment. Experimental results showed that UAE-ILs in the extraction of lignans from plants can show a great promising prospect.
DOI: 10.6084/m9.figshare.23621485
title: Additional file 5 of Characteristics of glucose and lipid metabolism and the interaction between gut microbiota and colonic mucosal immunity in pigs during cold exposure

description: Additional file 5: Table S5. Differential metabolites enriched in the plasma metabolome.
DOI: 10.6084/m9.figshare.23621488.v1
title: Additional file 6 of Characteristics of glucose and lipid metabolism and the interaction between gut microbiota and colonic mucosal immunity in pigs during cold exposure

description: Additional file 6: Table S6. Differential metabolites enriched in the plasma metabolome.
DOI: 10.6084/m9.figshare.7368908
title: MOESM2 of Clostridium acetobutylicum grows vegetatively in a biofilm rich in heteropolysaccharides and cytoplasmic proteins

description: Additional file 2. Full list of the biofilm proteins and relevant gene expression data.
DOI: 10.6084/m9.figshare.7368947
title: Additional file 2: of LncRNA MIR31HG targets HIF1A and P21 to facilitate head and neck cancer cell proliferation and tumorigenesis by promoting cell-cycle progression

description: Materials and Methods. (RAR 18 kb)
DOI: 10.6084/m9.figshare.7368947.v1
title: Additional file 2: of LncRNA MIR31HG targets HIF1A and P21 to facilitate head and neck cancer cell proliferation and tumorigenesis by promoting cell-cycle progression

description: Materials and Methods. (RAR 18 kb)
DOI: 10.6084/m9.figshare.7368908.v1
title: MOESM2 of Clostridium acetobutylicum grows vegetatively in a biofilm rich in heteropolysaccharides and cytoplasmic proteins

description: Additional file 2. Full list of the biofilm proteins and relevant gene expression data.
DOI: 10.6084/m9.figshare.7368953
title: Additional file 3: of Invasion-related circular RNA circFNDC3B inhibits bladder cancer progression through the miR-1178-3p/G3BP2/SRC/FAK axis

description: The potential miRNAs targeted with circFNDC3B were predicted by CircInteractome. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7368953.v1
title: Additional file 3: of Invasion-related circular RNA circFNDC3B inhibits bladder cancer progression through the miR-1178-3p/G3BP2/SRC/FAK axis

description: The potential miRNAs targeted with circFNDC3B were predicted by CircInteractome. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7368965
title: Additional file 4: of Invasion-related circular RNA circFNDC3B inhibits bladder cancer progression through the miR-1178-3p/G3BP2/SRC/FAK axis

description: The differentially changed genes were screened in both T24 and UM-UC-3 cells treated with circFNDC3B siRNA1 and siRNA2. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.7368965.v1
title: Additional file 4: of Invasion-related circular RNA circFNDC3B inhibits bladder cancer progression through the miR-1178-3p/G3BP2/SRC/FAK axis

description: The differentially changed genes were screened in both T24 and UM-UC-3 cells treated with circFNDC3B siRNA1 and siRNA2. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.14184742
title: Mt-Keima detects PINK1-PRKN mitophagy <i>in vivo</i> with greater sensitivity than mito-QC

description: PINK1 and PRKN, which cause Parkinson disease when mutated, form a quality control mitophagy pathway that is well-characterized in cultured cells. The extent to which the PINK1-PRKN pathway contributes to mitophagy <i>in vivo</i>, however, is controversial. This is due in large part to conflicting results from studies using one of two mitophagy reporters: mt-Keima or mito-QC. Studies using mt-Keima have generally detected PINK1-PRKN mitophagy <i>in vivo</i>, whereas those using mito-QC generally have not. Here, we directly compared the performance of mito-QC and mt-Keima in cell culture and in mice subjected to a PINK1-PRKN activating stress. We found that mito-QC was less sensitive than mt-Keima for mitophagy, and that this difference was more pronounced for PINK1-PRKN mitophagy. These findings suggest that mito-QC’s poor sensitivity may account for conflicting reports of PINK1-PRKN mitophagy <i>in vivo</i> and caution against using mito-QC as a reporter for PINK1-PRKN mitophagy. <b>Abbreviations:</b> DFP: deferiprone; EE: exhaustive exercise; FBS: fetal bovine serum; OAQ: oligomycin, antimycin, and Q-VD-OPH; OMM: outer mitochondrial membrane; PBS: phosphate-buffered saline; PD: Parkinson disease; UPS: ubiquitin-proteasome system.
DOI: 10.6084/m9.figshare.1601869
title: <i>MIR517C</i> inhibits autophagy and the epithelial-to-mesenchymal (-like) transition phenotype in human glioblastoma through KPNA2-dependent disruption of TP53 nuclear translocation

description: The epithelial-to-mesenchymal (-like) transition (EMT), a crucial embryonic development program, has been linked to the regulation of glioblastoma (GBM) progression and invasion. Here, we investigated the role of <i>MIR517C/miR-517c</i>, which belongs to the <i>C19MC</i> microRNA cluster identified in our preliminary studies, in the pathogenesis of GBM. We found that <i>MIR517C</i> was associated with improved prognosis in patients with GBM. Furthermore, following treatment with the autophagy inducer temozolomide (TMZ) and low glucose (LG), <i>MIR517C</i> degraded <i>KPNA2</i> (karyopherin alpha 2 [RAG cohort 1, importin alpha 1]) and subsequently disturbed the nuclear translocation of TP53 in the GBM cell line U87 in vitro. Interestingly, this microRNA could inhibit autophagy and reduce cell migration and infiltration in U87 cells harboring wild-type (WT) <i>TP53</i>, but not in U251 cells harboring mutant (MU) <i>TP53</i>. Moreover, the expression of epithelial markers (i.e., CDH13/T-cadherin and CLDN1 [claudin 1]) increased, while the expression of mesenchymal markers (i.e., CDH2/N-cadherin, SNAI1/Snail, and VIM [vimentin]) decreased, indicating that the EMT status was blocked by <i>MIR517C</i> in U87 cells. Compared with <i>MIR517C</i> overexpression, <i>MIR517C</i> knockdown promoted infiltration of U87 cells to the surrounding structures in nude mice in vivo. The above phenotypic changes were also observed in <i>TP53</i><sup><i>+/+</i></sup> and <i>TP53</i><sup><i>-/-</i></sup> HCT116 colon cancer cells. In summary, our study provided support for a link between autophagy and EMT status in WT <i>TP53</i> GBM cells and provided evidence for the signaling pathway (<i>MIR517C</i>-KPNA2-cytoplasmic TP53) involved in attenuating autophagy and eliminating the increased migration and invasion during the EMT.