cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14912373.v1
title: Hsa_circ_0008360 sponges miR-186-5p to target CCND2 to modulate high glucose-induced vascular endothelial dysfunction

description: Vascular endothelial dysfunction is associated with the progress of many diseases. Circular RNAs (circRNAs) take part in the dysfunction of vascular endothelium. CircRNA hsa_circ_0008360 (circ_0008360) is dysregulated in high glucose-treated vascular endothelium, while the role and mechanism of circ_0008360 in high glucose-induced dysfunction remain unknown. Human umbilical vascular endothelium cells (HUVEC) were stimulated via high glucose. The abundances of circ_0008360, miR-186-5p and cyclin D2 (CCND2) were examined via quantitative real-time polymerase chain reaction or western blot. Vascular endothelial dysfunction was assessed via cell viability, apoptosis, migration and tube formation. The target relationship between miR-186-5p and circ_0008360 or CCND2 was analyzed via dual-luciferase reporter, RNA pull-down and RNA immunoprecipitation analyses. Circ_0008360 expression was enhanced in high-glucose-treated HUVEC. Circ_0008360 silence mitigated high glucose-induced suppression of viability, migration, tube formation, and increase in apoptosis in HUVEC. MiR-186-5p was sponged by circ_0008360, and miR-186-5p inhibition reversed the effect of circ_0008360 silence on high glucose-induced vascular endothelial dysfunction. MiR-186-5p alleviated high glucose-induced vascular endothelial dysfunction via targeting CCND2. CCND2 interference abolished the aggravated effect of circ_0008360 on high glucose-induced vascular endothelial dysfunction. Circ_0008360 knockdown attenuated high glucose-induced vascular endothelial dysfunction via regulating miR-186-5p and CCND2, indicating circ_0008360 might act as a target for the treatment of vascular endothelial dysfunction. <b>Abbreviations:</b> circRNAs, circular RNAs; HUVEC, human umbilical vascular endothelium cells; CCND2, cyclin D2; XPNPEP3, X-prolyl aminopeptidase 3; ceRNAs, competing endogenous RNAs; miRNAs, microRNAs; qRT-PCR, quantitative real-time polymerase chain reaction; RIP, RNA immunoprecipitation; HIF-1α, hypoxia inducible factor 1 alpha; TLR3, toll-like receptor 3; AKAP12, A-Kinase Anchoring Protein 12; ox-LDL, oxidized low-density lipoprotein; HG, high glucose; NG, normal glucose.
DOI: 10.6084/m9.figshare.24873961.v2
title: Supplementary Data S6. Ancestral State Reconstruction from Bare parts in the Galliformes: the evolution of a multifunctional structure

description: A morphological trait can have multiple functions shaped by varying selective forces. Bare parts in birds, such as wattles, casques and combs, are known to function in both signalling and thermoregulation. Studies have demonstrated such structures are targets of sexual selection via female choice in several species of Galliformes (junglefowl, turkeys and grouse), though other studies have shown some role in thermoregulation (guineafowl). Here, we tested fundamental hypotheses regarding the evolution and maintenance of bare parts in Galliformes. Using a phylogeny that included nearly 90% of species in the order, we evaluated the role of both sexual and natural selection in shaping the function of bare parts across different clades. We found a combination of both environmental and putative sexually selected traits strongly predicted the variation of bare parts for both males and females across Galliformes. When the analysis is restricted to the largest family, Phasianidae (pheasants, junglefowl and allies), sexually selected traits were the primary predictors of bare parts. Our results suggest that bare parts are important for both thermoregulation and sexual signalling across Galliformes but are primarily under strong sexual selection within the Phasianidae.
DOI: 10.6084/m9.figshare.24873982.v2
title: Supplementary Data S1. scores of bare parts.xlsx from Bare parts in the Galliformes: the evolution of a multifunctional structure

description: A morphological trait can have multiple functions shaped by varying selective forces. Bare parts in birds, such as wattles, casques and combs, are known to function in both signalling and thermoregulation. Studies have demonstrated such structures are targets of sexual selection via female choice in several species of Galliformes (junglefowl, turkeys and grouse), though other studies have shown some role in thermoregulation (guineafowl). Here, we tested fundamental hypotheses regarding the evolution and maintenance of bare parts in Galliformes. Using a phylogeny that included nearly 90% of species in the order, we evaluated the role of both sexual and natural selection in shaping the function of bare parts across different clades. We found a combination of both environmental and putative sexually selected traits strongly predicted the variation of bare parts for both males and females across Galliformes. When the analysis is restricted to the largest family, Phasianidae (pheasants, junglefowl and allies), sexually selected traits were the primary predictors of bare parts. Our results suggest that bare parts are important for both thermoregulation and sexual signalling across Galliformes but are primarily under strong sexual selection within the Phasianidae.
DOI: 10.6084/m9.figshare.24873982.v1
title: Supplementary Data S1 from Bare parts in the Galliformes: the evolution of a multifunctional structure

description: scores of bare parts.xlsx
DOI: 10.6084/m9.figshare.14912373
title: RETRACTED ARTICLE: Hsa_circ_0008360 sponges miR-186-5p to target CCND2 to modulate high glucose-induced vascular endothelial dysfunction

description: We, the Editors and Publisher of the journal <i>Cell Cycle</i>, have retracted the following article: Qian-Qian Zhu, Xi-Bin Pu, Tian-Chi Chen, Chen-Yang Qiu, Zi-Heng Wu, Lu Tian, Yang-Yan He, Xiao-Hui Wang, Tao Shang, Xun Wang, Yi-Lang Xiang, Dong-Lin Li, and Hong-Kun Zhang. Hsa_circ_0008360 sponges miR-186-5p to target CCND2 to modulate high glucose-induced vascular endothelial dysfunction. Cell Cycle. 2021;20(14):1389-1401. doi: 10.1080/15384101.2021.1918877 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 all the concerns raised. 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.23300595
title: IMP-1 inhibits renal cell carcinoma 786-O cell growth by targeting EphrinB2 signaling pathway

description: Abstract EphrinB2 plays a critical role in tumor growth. In this study, we studied the antitumor activity of imperatorin derivative IMP-1 in renal cell carcinoma (RCC) by regulating EphrinB2 pathway.. Results showed that IMP-1 inhibited the proliferation of 786-O cells in a dose- and time-dependent manner. More importantly, knockdown and transfection of EphrinB2 altered the inhibitory effect of IMP-1 on the activity of 786-O cells. IMP-1 arrested 786-O cell cycle at G0/G1 phase by decreasing the expression of cyclin D1 and cyclin E. Moreover, IMP-1 regulated Bcl-2 family proteins’ expression, thus inducing apoptosis of 786-O cells. IMP-1 down-regulated the expression of EphrinB2, Syntenin1 and PICK1. Then, IMP-1 decreased the phosphorylation of Erk1/2 and AKT. In all, IMP-1 could regulate the EphrinB2 pathway in order to inhibit 786-O cell growth by arresting the cell cycle at G0/G1 phase and inducing cell apoptosis. Thus, IMP-1 may present as a potential strategy for RCC treatment.
DOI: 10.6084/m9.figshare.24873964.v1
title: Supplementary Data S2 from Bare parts in the Galliformes: the evolution of a multifunctional structure

description: validation of bare part scores
DOI: 10.6084/m9.figshare.9145193.v1
title: Atorvastatin attenuates cardiac hypertrophy through AMPK/miR-143-3p/Bcl2 axis

description: Atorvastatin is employed as a lipid lowering agent and its heart protective effect has been recently reported as well. However, the mechanism of atorvastatin in attenuating cardiac hypertrophy and inhibiting cardiac failure is unclear. In our study, cardiac hypertrophy was induced in rats using transverse aortic constriction (TAC) method and in cardiomyocytes using angiotensin II (Ang II). Atorvastatin significantly suppressed TAC-induced heart weight increase and cardiomyocytes apoptosis in rats. At a molecular level, we found that miR-143-3p was significantly up-regulated, and the up-regulation could be inhibited by atorvastatin via activating AMPK pathway. Furthermore, it was validated that Bcl2 was one of the target genes of miR-143-3p. Taken together, the data indicated that miR-143-3p aggravated cardiac hypertrophy by inducing cardiomyocytes apoptosis through inhibiting Bcl2 expression. This study demonstrated the effects of atorvastatin in attenuating cardiac hypertrophy and inhibiting cardiac failure, which is depending on Bcl2 expression via miR-143-3p inhibition by AMPK activation.
DOI: 10.6084/m9.figshare.24873967.v2
title: Supplementary Data S8. PGLS models - sage-grouse removed from Bare parts in the Galliformes: the evolution of a multifunctional structure

description: A morphological trait can have multiple functions shaped by varying selective forces. Bare parts in birds, such as wattles, casques and combs, are known to function in both signalling and thermoregulation. Studies have demonstrated such structures are targets of sexual selection via female choice in several species of Galliformes (junglefowl, turkeys and grouse), though other studies have shown some role in thermoregulation (guineafowl). Here, we tested fundamental hypotheses regarding the evolution and maintenance of bare parts in Galliformes. Using a phylogeny that included nearly 90% of species in the order, we evaluated the role of both sexual and natural selection in shaping the function of bare parts across different clades. We found a combination of both environmental and putative sexually selected traits strongly predicted the variation of bare parts for both males and females across Galliformes. When the analysis is restricted to the largest family, Phasianidae (pheasants, junglefowl and allies), sexually selected traits were the primary predictors of bare parts. Our results suggest that bare parts are important for both thermoregulation and sexual signalling across Galliformes but are primarily under strong sexual selection within the Phasianidae.
DOI: 10.6084/m9.figshare.9145193
title: Atorvastatin attenuates cardiac hypertrophy through AMPK/miR-143-3p/Bcl2 axis

description: Atorvastatin is employed as a lipid lowering agent and its heart protective effect has been recently reported as well. However, the mechanism of atorvastatin in attenuating cardiac hypertrophy and inhibiting cardiac failure is unclear. In our study, cardiac hypertrophy was induced in rats using transverse aortic constriction (TAC) method and in cardiomyocytes using angiotensin II (Ang II). Atorvastatin significantly suppressed TAC-induced heart weight increase and cardiomyocytes apoptosis in rats. At a molecular level, we found that miR-143-3p was significantly up-regulated, and the up-regulation could be inhibited by atorvastatin via activating AMPK pathway. Furthermore, it was validated that Bcl2 was one of the target genes of miR-143-3p. Taken together, the data indicated that miR-143-3p aggravated cardiac hypertrophy by inducing cardiomyocytes apoptosis through inhibiting Bcl2 expression. This study demonstrated the effects of atorvastatin in attenuating cardiac hypertrophy and inhibiting cardiac failure, which is depending on Bcl2 expression via miR-143-3p inhibition by AMPK activation.
DOI: 10.6084/m9.figshare.24873973.v2
title: Supplementary Data S7. PGLS models - original output from Bare parts in the Galliformes: the evolution of a multifunctional structure

description: A morphological trait can have multiple functions shaped by varying selective forces. Bare parts in birds, such as wattles, casques and combs, are known to function in both signalling and thermoregulation. Studies have demonstrated such structures are targets of sexual selection via female choice in several species of Galliformes (junglefowl, turkeys and grouse), though other studies have shown some role in thermoregulation (guineafowl). Here, we tested fundamental hypotheses regarding the evolution and maintenance of bare parts in Galliformes. Using a phylogeny that included nearly 90% of species in the order, we evaluated the role of both sexual and natural selection in shaping the function of bare parts across different clades. We found a combination of both environmental and putative sexually selected traits strongly predicted the variation of bare parts for both males and females across Galliformes. When the analysis is restricted to the largest family, Phasianidae (pheasants, junglefowl and allies), sexually selected traits were the primary predictors of bare parts. Our results suggest that bare parts are important for both thermoregulation and sexual signalling across Galliformes but are primarily under strong sexual selection within the Phasianidae.
DOI: 10.6084/m9.figshare.14387700.v1
title: The first-line cluster headache medication verapamil alters the circadian period and elicits sex-specific sleep changes in mice

description: Verapamil is the first-line preventive medication for cluster headache, an excruciating disorder with strong circadian features. Whereas second- and third-line preventives include known circadian modulators, such as melatonin, corticosteroids, and lithium, the circadian effects of verapamil are poorly understood. Here, we characterize the circadian features of verapamil using both in vitro and in vivo models. In <i>Per2::LucSV</i> reporter fibroblasts, treatment with verapamil (0.03–10 µM) showed a dose-dependent period shortening of the reporter rhythm which reached a nadir at 1 µM, and altered core clock gene expression at 10 µM. Mouse wheel-running activity with verapamil (1 mg/mL added to the drinking water) also resulted in significant period shortening and activity reduction in both male and female free-running wild-type C57BL6/J mice. The temporal patterns of activity reduction, however, differ between the two sexes. Importantly, piezo sleep recording revealed sexual dimorphism in the effects of verapamil on sleep timing and bout duration, with more pronounced adverse effects in female mice. We also found altered circadian clock gene expression in the cerebellum, hypothalamus, and trigeminal ganglion of verapamil-treated mice. Verapamil did not affect reporter rhythms in ex vivo suprachiasmatic nucleus (SCN) slices from <i>Per2:Luc</i> reporter mice, perhaps due to the exceptionally tight coupling in the SCN. Thus, verapamil affects both peripheral (trigeminal ganglion) and central (hypothalamus and cerebellum) nervous system structures involved in cluster headache pathophysiology, possibly with network effects instead of isolated SCN effects. These studies suggest that verapamil is a circadian modulator in laboratory models at both molecular and behavioral levels, and sex is an important biological variable for cluster headache medications. These observations highlight the circadian system as a potential convergent target for cluster headache medications with different primary mechanisms of action.
DOI: 10.6084/m9.figshare.20147091
title: Additional file 7 of A promising Prognostic risk model for advanced renal cell carcinoma (RCC) with immune-related genes

description: Additional file 7: Supplementary Table 5. _landscape_high risk group.
DOI: 10.6084/m9.figshare.24873973.v1
title: Supplementary Data S7 from Bare parts in the Galliformes: the evolution of a multifunctional structure

description: PGLS models - original output
DOI: 10.6084/m9.figshare.14912676.v1
title: Long non-coding RNA LINC00511 regulates the expression of microRNA-625-5p and activates signal transducers and activators of transcription 3 (STAT3) to accelerate the progression of gastric cancer

description: This study aimed to investigate the expression, biological function, and downstream mechanism of LINC00511 in gastric cancer (GC). In paired GC samples, LINC00511, miR-625-5p and STAT3 mRNA expression levels were detected by quantitative real-time polymerase chain reaction (qRT-PCR); STAT3 protein expression was detected by immunohistochemical (IHC). The gain-of-function and loss-of-function models were established, and the proliferative and migrative ability of GC cells were measured by CCK-8 and transwell assays, respectively. The regulatory relationship between miR-625-5p and LINC00511 or STAT3 was examined by bioinformatics analysis, luciferase reporter gene assay, qRT-PCR, and western blot. We reported that LINC00511 and STAT3 expressions in GC tissues and cell lines were observably up-regulated, while miR-625-5p expression was inhibited. High expression of LINC00511 could facilitate the proliferation and promote the migration of GC cells. miR-625-5p was proved to be a downstream target of LINC00511, and LINC00511 could induce the expression of STAT3 by inhibiting the expression of miR-625-5p. Additionally, knockdown of LINC00511 suppressed the growth and lung metastases of CRC cells in nude mice. In conclusion, LINC00511 promotes the GC cell proliferation and migration via targeting the miR-625-5p/STAT3 axis, implying that LINC00511 can function as a target for GC therapy.
DOI: 10.6084/m9.figshare.20147091.v1
title: Additional file 7 of A promising Prognostic risk model for advanced renal cell carcinoma (RCC) with immune-related genes

description: Additional file 7: Supplementary Table 5. _landscape_high risk group.
DOI: 10.6084/m9.figshare.14912717
title: Multi-omics landscape of circadian rhythm pathway alterations in Glioma

description: Circadian rhythm pathway was demonstrated pathological functions in glioma on single-gene level. We aim to depict the multi-omics landscape of circadian rhythm pathway alteration in glioma using bioinformatic analyses. Multi-omics data were obtained from “cBioPortal” database. Comparisons were done regarding clinical parameters, differential-expressed genes and functional annotations. A pathway index was generated using the expression data from TCGA and GTEx to quantify the general alteration level of the pathway with clinical association of circadian rhythm pathway index explored. A total of 30 genes were mapped on the circadian rhythm pathway. Genomic profile ofcircadian rhythm pathway genes exhibited distinct characteristics on multiple levels between lower grade glioma (LGG) and glioblastoma multiforme (GBM) patients. LGG patients presented significantly higher frequencies of multi-omics mutations, as well as significant clinical relevance, on single-gene level. Differential-expressed genes between LGG and GBM patients revealed different functions between subtypes that related to the alteration of circadian rhythm pathway. LGG have significantly higher pathway index than normal brain tissue, while GBM significantly lower than normal tissue (P &lt; 0.01), indicating distinctly altered circadian pathway in LGG. Circadian rhythm pathway index correlated with the prognosis of LGG, but not GBM, patients, with higher score indicating better survival outcome (LGG: HR = 0.39, 95% CI: 0.26 − 0.59, P &lt; 0.001). In conclusion, LGG have more multi-omics alterations of circadian rhythm pathway than GBM. Quantification of circadian rhythm pathway using pathway index demonstrated hyperactivated pathway status in LGG and correlated with the prognosis of LGG patients.
DOI: 10.6084/m9.figshare.24873976.v2
title: Supplementary Data S3. All life history traits and respective references from Bare parts in the Galliformes: the evolution of a multifunctional structure

description: A morphological trait can have multiple functions shaped by varying selective forces. Bare parts in birds, such as wattles, casques and combs, are known to function in both signalling and thermoregulation. Studies have demonstrated such structures are targets of sexual selection via female choice in several species of Galliformes (junglefowl, turkeys and grouse), though other studies have shown some role in thermoregulation (guineafowl). Here, we tested fundamental hypotheses regarding the evolution and maintenance of bare parts in Galliformes. Using a phylogeny that included nearly 90% of species in the order, we evaluated the role of both sexual and natural selection in shaping the function of bare parts across different clades. We found a combination of both environmental and putative sexually selected traits strongly predicted the variation of bare parts for both males and females across Galliformes. When the analysis is restricted to the largest family, Phasianidae (pheasants, junglefowl and allies), sexually selected traits were the primary predictors of bare parts. Our results suggest that bare parts are important for both thermoregulation and sexual signalling across Galliformes but are primarily under strong sexual selection within the Phasianidae.
DOI: 10.6084/m9.figshare.14904062.v1
title: Additional file 3 of Genetic relationships and identification of core germplasm among rice photoperiod- and thermo-sensitive genic male sterile lines

description: Additional file 3: Table 1. The list of 118 two-line hybrid environment sensitive genetically male sterile (ESGMS) lines of rice.
DOI: 10.6084/m9.figshare.14904065
title: Additional file 4 of Genetic relationships and identification of core germplasm among rice photoperiod- and thermo-sensitive genic male sterile lines

description: Additional file 4: Table 2. Chromosome wise values of various genetic diversity parameters for four populations.
DOI: 10.6084/m9.figshare.14904071
title: Additional file 6 of Genetic relationships and identification of core germplasm among rice photoperiod- and thermo-sensitive genic male sterile lines

description: Additional file 6: Table 4. The genome wide selection sweeps indicating the genetic differentiation between the conventional breeding lines and the pedigree groups A, B, and C evaluated by Fst values at the threshold of top 5%.
DOI: 10.6084/m9.figshare.21215030
title: data

description: Scientific and practical identification and analysis of the differences in the spatial structure of metropolitan areas are of great significance to the long-term development of metropolitan areas and urban agglomerations. Because the current research focuses more on the external spatial structure of the metropolitan area and less on the internal spatial differences, this study is based on remote sensing data, POI data, and road vector data combined with a spatial clustering algorithm with location constraints. Multi-level analysis of spatial clustering and differences within the circle. Theresearch results show that compared with the traditional algorithm, spatial clustering with location constraints can identify the group structure within the metropolitan area to a large extent. At the same time, the single-factor and multi- factorclustering results show that the Changsha-Zhuzhou-Xiangtan metropolitan area currently has large internal spatial differences; Except for Changsha, Zhuzhou, and Xiangtan core urban areas, no apparent cluster structure has been formed. This study can well reflect the current heterogeneity of the internal spatial structure of the Chang-Zhu-Tan metropolitan area and provide a solid reference for the future developmentof the metropolitan area