cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16571247.v1
title: Brachyericines (Erinaceidae, Eulipotyphla) from the early Miocene of central Nei Mongol, China

description: Brachyericinae is a subfamily of Erinaceidae (hedgehogs and moonrats) with a very short history and limited distribution. Fossil records of brachyericines, with rare materials, were confined to the Oligocene and early Miocene in Central Asia and to the Miocene in North America. Here, we report three forms of short-faced hedgehogs: <i>Synexallerix junggarensis</i>, Brachyericinae gen. et sp. indet. 1 and Brachyericinae gen. et sp. indet. 2 from Aoerban and Gashunyin Adege, localities of the early Miocene in Central Nei Mongol. <i>S. junggarensis</i> is the first discovery outside the Suosuoquan Formation in Xinjiang and detailed description of the new materials, including a nearly complete skull, clarifies its taxonomic position within the Brachyericinae. The new Nei Mongol material is important not only because they include a nearly complete skull of <i>S. junggarensis</i> (previously known by a rostral part of the skull) but also because of the presence of three taxa of the brachyericines from the same general area. The similarity of its morphological characteristics with the North American genera also further confirms the close affinities of brachyericines from the two continents during the early Miocene.
DOI: 10.6084/m9.figshare.16571330.v1
title: USP5 attenuates NLRP3 inflammasome activation by promoting autophagic degradation of NLRP3

description: The NLRP3 (NLR family pyrin domain containing 3) inflammasome is involved in diverse inflammatory diseases, thus strict control of its activation is necessary to prevent excessive inflammation. Protein ubiquitination has been reported to regulate the assembly, protein expression and activation of the NLRP3 inflammasome. Until now, several deubiquitinases (DUBs) have been reported to affect the degradation of NLRP3 through the proteasome pathway. However, there is no research on DUBs regulating NLRP3 degradation through macroautophagy/autophagy. Here, we demonstrated the pivotal function of USP5 (ubiquitin specific peptidase 5) in restraining the activation of the NLRP3 inflammasome independent of its deubiquitinating enzyme activity. USP5 selectively promoted K48-linked polyubiquitination of NLRP3 and mediated its degradation through the autophagy-lysosomal pathway by recruiting the E3 ligase MARCHF7/MARCH7. Knockdown of <i>USP5</i> facilitated the two-signal model of lipopolysaccharide and ATP-triggered IL1B/IL-1β production. Simultaneously, USP5 overexpression <i>in vivo</i> reduced IL1B and polymorphonuclear (PMN) infiltration in alum-induced peritonitis. Overall, the data revealed that USP5 is a key scaffold protein recruiting the E3 ligase MARCHF7 to NLRP3, and promoting autophagic degradation of NLRP3. The findings provide new insight into USP5 in the regulation of excessive activation of the NLRP3 inflammasome and inflammatory innate immune response. 3-MA: 3-methyladenine; AIM2: absent in melanoma 2; ATG5: autophagy related 5; BafA1: bafilomycin A<sub>1</sub>; CASP1: caspase 1; CHX: cycloheximide; Co-IP: co-immunoprecipitation; CQ: chloroquine; DUBs: deubiquitinases; IL1B/IL-1β: interleukin 1 beta; LAMP1: lysosomal associated membrane protein 1; LPS: lipopolysaccharide; MARCHF7/MARCH7: membrane associated RING-CH-type finger 7; NFKB/NF-κB: nuclear factor kappa B; Nig.: nigericin; NLRC4: NLR family CARD domain containing 4; NLRP3: NLR family pyrin domain containing 3; PECs: peritoneal exudate cells; PMN: polymorphonuclear; PMs: peritoneal macrophages; PYCARD/ASC: PYD and CARD domain containing; TLRs: toll like receptors; TNF/TNF-α: tumor necrosis factor; Ub: ubiquitin; USP5: ubiquitin specific peptidase 5; WT: wild type.
DOI: 10.6084/m9.figshare.16571351
title: Extremely low-Ni olivine as a tracer of carbonate-rich sediment recycling beneath the southwestern Okinawa Trough

description: Carbonate recycling in subduction zones has a strong influence on arc magmatism and carbon reservoirs in the mantle. However, geochemical evidence of carbonate recycling during subduction, especially at sub-arc depths, is rare and the related process is poorly understood. In this study, we document high-Mg olivines (81–91 mol.% forsterite) with extremely low Ni concentrations (mostly &lt;600 ppm), which occur in host dacites recovered from the southwestern Okinawa Trough (SWOT). The temperature–pressure of crystallization had a negligible effect on the Ni contents of the olivines, and reactions between primary basaltic magmas and the lithospheric mantle were also insignificant. Small sulphide droplets are present in the olivines, which suggest that sulphide–silicate melt immiscibility occurred during the early stages of magmatic evolution. Although early segregation of sulphide melts could reduce the Ni contents of the primitive magmas, our forward modelling suggests that sulphide segregation cannot solely explain the low Ni contents. Therefore, the most likely explanation for low Ni concentrations is the interaction between Ca-rich carbonate melts and the mantle wedge, forming an olivine-rich mantle source by consumption of orthopyroxene, as indicated by the extremely low Ni/Mg and high Ca/Fe ratios of magmatic olivines. Given that the SWOT is located just ~100 km above the Wadati–Benioff zone, our results provide rare evidence for carbonate recycling at sub-arc depths in an active subduction zone.
DOI: 10.6084/m9.figshare.16571351.v1
title: Extremely low-Ni olivine as a tracer of carbonate-rich sediment recycling beneath the southwestern Okinawa Trough

description: Carbonate recycling in subduction zones has a strong influence on arc magmatism and carbon reservoirs in the mantle. However, geochemical evidence of carbonate recycling during subduction, especially at sub-arc depths, is rare and the related process is poorly understood. In this study, we document high-Mg olivines (81–91 mol.% forsterite) with extremely low Ni concentrations (mostly &lt;600 ppm), which occur in host dacites recovered from the southwestern Okinawa Trough (SWOT). The temperature–pressure of crystallization had a negligible effect on the Ni contents of the olivines, and reactions between primary basaltic magmas and the lithospheric mantle were also insignificant. Small sulphide droplets are present in the olivines, which suggest that sulphide–silicate melt immiscibility occurred during the early stages of magmatic evolution. Although early segregation of sulphide melts could reduce the Ni contents of the primitive magmas, our forward modelling suggests that sulphide segregation cannot solely explain the low Ni contents. Therefore, the most likely explanation for low Ni concentrations is the interaction between Ca-rich carbonate melts and the mantle wedge, forming an olivine-rich mantle source by consumption of orthopyroxene, as indicated by the extremely low Ni/Mg and high Ca/Fe ratios of magmatic olivines. Given that the SWOT is located just ~100 km above the Wadati–Benioff zone, our results provide rare evidence for carbonate recycling at sub-arc depths in an active subduction zone.
DOI: 10.6084/m9.figshare.16571351.v2
title: Extremely low-Ni olivine as a tracer of carbonate-rich sediment recycling beneath the southwestern Okinawa Trough

description: Carbonate recycling in subduction zones has a strong influence on arc magmatism and carbon reservoirs in the mantle. However, geochemical evidence of carbonate recycling during subduction, especially at sub-arc depths, is rare and the related process is poorly understood. In this study, we document high-Mg olivines (81–91 mol.% forsterite) with extremely low Ni concentrations (mostly &lt;600 ppm), which occur in host dacites recovered from the southwestern Okinawa Trough (SWOT). The temperature–pressure of crystallization had a negligible effect on the Ni contents of the olivines, and reactions between primary basaltic magmas and the lithospheric mantle were also insignificant. Small sulphide droplets are present in the olivines, which suggest that sulphide–silicate melt immiscibility occurred during the early stages of magmatic evolution. Although early segregation of sulphide melts could reduce the Ni contents of the primitive magmas, our forward modelling suggests that sulphide segregation cannot solely explain the low Ni contents. Therefore, the most likely explanation for low Ni concentrations is the interaction between Ca-rich carbonate melts and the mantle wedge, forming an olivine-rich mantle source by consumption of orthopyroxene, as indicated by the extremely low Ni/Mg and high Ca/Fe ratios of magmatic olivines. Given that the SWOT is located just ~100 km above the Wadati–Benioff zone, our results provide rare evidence for carbonate recycling at sub-arc depths in an active subduction zone.
DOI: 10.6084/m9.figshare.25234051
title: Butterfly abundance along an urban gradient in Montréal, Quebec, Canada

description: This dataset consists of field data collected from 44 open sites located around Montréal, Quebec, Canada that were visited in rotation from May to August in 2017 or 2018. During each visit to a site, two observers walked a designated 300 m transect and collected data on the identity and abundance of all butterflies observed. Field data was analyzed to show that urban butterfly communities were dominated by a few, highly abundant, non-native species. The data also showed that for most of the butterfly community, species with longer flight periods were more common in urban areas. Finally, the data showed that urban butterfly communities tended to be more homogenized than rural communities at both the taxonomic and functional levels.
DOI: 10.6084/m9.figshare.16571369
title: Genome-wide screening for the G-protein-coupled receptor (GPCR) pathway-related therapeutic gene <i>RGS19</i> (regulator of G protein signaling 19) in bladder cancer

description: Bladder cancer is one of the most severe genitourinary cancers, causing high morbidity worldwide. However, the underlying molecular mechanism is not clear, and it is urgent to find target genes for treatment. G-protein-coupled receptors are currently a target of high interest for drug design. Thus, we aimed to identify a target gene-related to G-protein-coupled receptors for therapy. We used The Cancer Genome Atlas (TCGA) and DepMap databases to obtain the expression and clinical data of <i>RGS19</i>. The results showed that <i>RGS19</i> was overexpressed in a wide range of tumor, especially bladder cancer. We also explored its effect on various types of cancer. High expression of <i>RGS19</i> was also shown to be significantly associated with poor prognosis. Cell models were constructed for cell cycle detection. sh<i>RGS19</i> can halt the cell cycle at a polyploid point. <i>RGS19</i> is a G-protein-coupled receptor signaling pathway-related gene with a significant effect on survival. We chose <i>RGS19</i> as a therapeutic target gene in bladder cancer. The drug GSK1070916 was found to inhibit the effect of <i>RGS19</i> via cell rescue experiments <i>in vitro</i>.
DOI: 10.6084/m9.figshare.16571369.v1
title: Genome-wide screening for the G-protein-coupled receptor (GPCR) pathway-related therapeutic gene <i>RGS19</i> (regulator of G protein signaling 19) in bladder cancer

description: Bladder cancer is one of the most severe genitourinary cancers, causing high morbidity worldwide. However, the underlying molecular mechanism is not clear, and it is urgent to find target genes for treatment. G-protein-coupled receptors are currently a target of high interest for drug design. Thus, we aimed to identify a target gene-related to G-protein-coupled receptors for therapy. We used The Cancer Genome Atlas (TCGA) and DepMap databases to obtain the expression and clinical data of <i>RGS19</i>. The results showed that <i>RGS19</i> was overexpressed in a wide range of tumor, especially bladder cancer. We also explored its effect on various types of cancer. High expression of <i>RGS19</i> was also shown to be significantly associated with poor prognosis. Cell models were constructed for cell cycle detection. sh<i>RGS19</i> can halt the cell cycle at a polyploid point. <i>RGS19</i> is a G-protein-coupled receptor signaling pathway-related gene with a significant effect on survival. We chose <i>RGS19</i> as a therapeutic target gene in bladder cancer. The drug GSK1070916 was found to inhibit the effect of <i>RGS19</i> via cell rescue experiments <i>in vitro</i>.
DOI: 10.6084/m9.figshare.16571369.v2
title: Genome-wide screening for the G-protein-coupled receptor (GPCR) pathway-related therapeutic gene <i>RGS19</i> (regulator of G protein signaling 19) in bladder cancer

description: Bladder cancer is one of the most severe genitourinary cancers, causing high morbidity worldwide. However, the underlying molecular mechanism is not clear, and it is urgent to find target genes for treatment. G-protein-coupled receptors are currently a target of high interest for drug design. Thus, we aimed to identify a target gene-related to G-protein-coupled receptors for therapy. We used The Cancer Genome Atlas (TCGA) and DepMap databases to obtain the expression and clinical data of <i>RGS19</i>. The results showed that <i>RGS19</i> was overexpressed in a wide range of tumor, especially bladder cancer. We also explored its effect on various types of cancer. High expression of <i>RGS19</i> was also shown to be significantly associated with poor prognosis. Cell models were constructed for cell cycle detection. sh<i>RGS19</i> can halt the cell cycle at a polyploid point. <i>RGS19</i> is a G-protein-coupled receptor signaling pathway-related gene with a significant effect on survival. We chose <i>RGS19</i> as a therapeutic target gene in bladder cancer. The drug GSK1070916 was found to inhibit the effect of <i>RGS19</i> via cell rescue experiments <i>in vitro</i>.
DOI: 10.6084/m9.figshare.10279919
title: MOESM1 of Functional exploration of co-expression networks identifies a nexus for modulating protein and citric acid titres in Aspergillus niger submerged culture

description: Additional file 1. Multi-gene co-expression network reveals transcriptional coupling of the Golgi and TCA cycle with ArfA GEFs and GAPs.
DOI: 10.6084/m9.figshare.10279919.v1
title: MOESM1 of Functional exploration of co-expression networks identifies a nexus for modulating protein and citric acid titres in Aspergillus niger submerged culture

description: Additional file 1. Multi-gene co-expression network reveals transcriptional coupling of the Golgi and TCA cycle with ArfA GEFs and GAPs.
DOI: 10.6084/m9.figshare.16571378
title: Centromere protein E as a novel biomarker and potential therapeutic target for retinoblastoma

description: Retinoblastoma is the most common intraocular malignancy during childhood. Currently, there is no effective treatment for metastatic retinoblastoma. We investigated potential biomarkers of retinoblastoma by utilizing three datasets from a public database. Functional enrichment analysis, including gene ontology, Kyoto encyclopedia of genes and genomes, gene set enrichment analysis and variation analysis, suggested that differentially expressed genes in retinoblastoma were enriched in accelerated cell cycle events. Protein-protein interaction analysis constructed a network consisting of six hub genes, including <i>benzimidazoles 1 (BUB1), cyclin dependent kinase 1 (CDK1), centromere protein E (CENPE), kinesin family member 20A (KIF20A), PDZ binding kinase (PBK), and targeting protein for xklp2 (TPX2)</i>. Drug sensitivity analysis showed that nelarabine was positively correlated with five hub genes. All six genes were expressed differently in six immune subtypes and were positively correlated with stemness indices in most human cancer types. Since <i>CENPE</i> is the least known hub gene in retinoblastoma, we further analyzed the potential non-coding RNAs and transcription factors that regulate <i>CENPE</i> and built interaction networks of competing endogenous RNA and transcription factors. Immune cell infiltration, especially by plasma and B cells, was enhanced in samples with high <i>CENPE</i> expression. Pan-cancer analysis illustrated that <i>CENPE</i> was highly expressed in a wide range of human tumors. <i>In vitro</i> validation revealed that <i>CENPE</i> was significantly upregulated at both the mRNA and protein levels in retinoblastoma cells. In conclusion, <i>CENPE</i>, along with other hub genes, could serve as a potential biomarker and intervention target for retinoblastoma.
DOI: 10.6084/m9.figshare.16571378.v1
title: Centromere protein E as a novel biomarker and potential therapeutic target for retinoblastoma

description: Retinoblastoma is the most common intraocular malignancy during childhood. Currently, there is no effective treatment for metastatic retinoblastoma. We investigated potential biomarkers of retinoblastoma by utilizing three datasets from a public database. Functional enrichment analysis, including gene ontology, Kyoto encyclopedia of genes and genomes, gene set enrichment analysis and variation analysis, suggested that differentially expressed genes in retinoblastoma were enriched in accelerated cell cycle events. Protein-protein interaction analysis constructed a network consisting of six hub genes, including <i>benzimidazoles 1 (BUB1), cyclin dependent kinase 1 (CDK1), centromere protein E (CENPE), kinesin family member 20A (KIF20A), PDZ binding kinase (PBK), and targeting protein for xklp2 (TPX2)</i>. Drug sensitivity analysis showed that nelarabine was positively correlated with five hub genes. All six genes were expressed differently in six immune subtypes and were positively correlated with stemness indices in most human cancer types. Since <i>CENPE</i> is the least known hub gene in retinoblastoma, we further analyzed the potential non-coding RNAs and transcription factors that regulate <i>CENPE</i> and built interaction networks of competing endogenous RNA and transcription factors. Immune cell infiltration, especially by plasma and B cells, was enhanced in samples with high <i>CENPE</i> expression. Pan-cancer analysis illustrated that <i>CENPE</i> was highly expressed in a wide range of human tumors. <i>In vitro</i> validation revealed that <i>CENPE</i> was significantly upregulated at both the mRNA and protein levels in retinoblastoma cells. In conclusion, <i>CENPE</i>, along with other hub genes, could serve as a potential biomarker and intervention target for retinoblastoma.
DOI: 10.6084/m9.figshare.10279925
title: MOESM2 of Functional exploration of co-expression networks identifies a nexus for modulating protein and citric acid titres in Aspergillus niger submerged culture

description: Additional file 2. Predictions derived from gene co-expression network analysis of secG, ageB and geaB connect A. niger GEFs and GAPs with protein secretion and the TCA.
DOI: 10.6084/m9.figshare.10279925.v1
title: MOESM2 of Functional exploration of co-expression networks identifies a nexus for modulating protein and citric acid titres in Aspergillus niger submerged culture

description: Additional file 2. Predictions derived from gene co-expression network analysis of secG, ageB and geaB connect A. niger GEFs and GAPs with protein secretion and the TCA.
DOI: 10.6084/m9.figshare.10279931
title: MOESM10 of Molecular and transcriptional characterization of phosphatidyl ethanolamine-binding proteins in wild peanuts Arachis duranensis and Arachis ipaensis

description: Additional file 10. Primers used in this study.
DOI: 10.6084/m9.figshare.10279931.v1
title: MOESM10 of Molecular and transcriptional characterization of phosphatidyl ethanolamine-binding proteins in wild peanuts Arachis duranensis and Arachis ipaensis

description: Additional file 10. Primers used in this study.
DOI: 10.6084/m9.figshare.23911422
title: CircEpha5 regulates the synthesis and secretion of androgen in mouse preantral follicles by targeting miR-758-5p

description: Circular RNAs are involved in the pathogenesis of various diseases, although its expression pattern and role in polycystic ovary syndrome (PCOS), characterised by hyperandrogenism, are not very clear. This article assessed the circRNAs expression profile in the ovaries of PCOS mice by circRNAs high-throughput sequencing and explored the role of circEpha5 in hyperandrogenism. The results showed that the overexpression of circEpha5 in mouse preantral follicles could increase the expression of <i>Cyp17a1</i>, an androgen synthesis-related gene, which resulted in a higher serum level of testosterone. Dual-luciferase reporter gene studies identified miR-758-5p as a direct target of circEpha5. Consequently, miR-758-5p expression was downregulated upon circEpha5 overexpression. Ectopically expressed miR-758-5p reversed the stimulation effects of circEpha5 on steroidogenesis-related gene expression and testosterone release. Therefore, circEpha5 could sponge miR-758-5p to regulate the expression of <i>Cyp17a1</i>, thereby promoting the synthesis and secretion of androgen in the preantral follicles. This work is contributed to the understanding of the pathogenesis of hyperandrogenemia and lays the foundation for the development of therapeutic targets of PCOS hyperandrogenism. <b>What is already known on this subject?</b> PCOS is a complex endocrine and metabolic disorders with hyperandrogenism as the main clinical manifestation. There are a variety of abnormal expression circRNAs in PCOS, however, the relationship between circEpha5 and hyperandrogenism has yet to be fully elucidated. <b>What do the results of this study add?</b> We first found that expression levels of serum circEpha5 were significantly higher in PCOS than in a normal group. Using mouse preantral follicle culture model and the letrozole-induced PCOS mouse model, the mechanism of CircEpha5 regulating androgen secretion was studied. <b>What the implications are of these findings for clinical practice and/or further research?</b> It was revealed that CircEpha5 can absorb miR-758-5p in the sponge to regulate the expression of <i>Cyp17a1</i>, thereby promoting the synthesis and secretion of androgen in preantral follicles, which may become a key target for the screening and treatment of PCOS hyperandrogenism.