cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7975778.v1
title: Small molecule-driven NLRP3 inflammation inhibition via interplay between ubiquitination and autophagy: implications for Parkinson disease

description: Aging-related, nonresolving inflammation in both the central nervous system (CNS) and periphery predisposes individuals to the development of neurodegenerative disorders (NDDs). Inflammasomes are thought to be especially relevant to immune homeostasis, and their dysregulation contributes to inflammation and NDDs. However, few agents have been clinically shown to reduce NDD incidence by targeting inflammasomes. Our study indicated that NLRP3 (NLR family, pyrin domain containing 3) inflammasome is involved in Parkinson disease (PD) progression in patients and various murine models. In addition, the small molecule kaempferol (Ka) protected mice against LPS- and SNCA-induced neurodegeneration by inhibiting NLRP3 inflammasome activation as evidenced by the fact that Ka reduced cleaved CASP1 expression and disrupted NLRP3-PYCARD-CASP1 complex assembly with concomitant decreased IL1B secretion. Mechanically, Ka promoted macroautophagy/autophagy in microglia, leading to reduced NLRP3 protein expression, which in turn deactivated the NLRP3 inflammasome. Intriguingly, ubiquitination was involved in Ka-induced autophagic NLRP3 degradation. These findings were further confirmed <i>in vivo</i> as knockdown of <i>Atg5</i> expression or autophagy inhibitor treatment significantly inhibited the Ka-mediated NLRP3 inflammasome inhibition and neurodegeneration amelioration. Thus, we demonstrated that Ka promotes neuroinflammatory inhibition via the cooperation of ubiquitination and autophagy, suggesting that Ka is a promising therapeutic strategy for the treatment of NDDs. <b>Abbreviations:</b> 3-MA: 3-methyladenine; AAV: adeno-associated virus; ACTB: actin, beta; AIF1/IBA1: allograft inflammatory factor 1; ATG5: autophagy related 5; ATG7: autophagy related 7; BafA1: bafilomycin A<sub>1;</sub> BECN1: beclin 1, autophagy related; CASP1: caspase 1; CNS: central nervous system; CQ: chloroquine; DA neurons: dopaminergic neurons; DAMPS: damage-associated molecular patterns; DAPI: 4’,6-diamidino-2-phenylindole; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; GFAP: glial fibrillary acidic protein; IP: immunoprecipitation; i.p.: intraperitoneally; Ka: kaempferol; KD: knockdown; KO: knockout; LPS: lipopolysaccharide; IL1B: interleukin 1 beta; IL6: interleukin 6; Ly: lysate; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; MPTP: 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine; NC: negative control; NDD: neurodegenerative diseases; NLRP3: NLR family, pyrin domain containing 3; OE: overexpression; PD: Parkinson disease; poly-Ub: poly-ubiquitin; PTM: post-translational modification; PYCARD/ASC: PYD and CARD domain containing; Rapa: rapamycin; RFP: red fluorescent protein; SN: supernatant; SNCA: synuclein alpha; SNpc: substantia nigra pars compacta; SQSTM1: sequestosome 1; TH: tyrosine hydroxylase; TNF/TNF-alpha: tumor necrosis factor; Ub: ubiquitin; WT: wild type
DOI: 10.6084/m9.figshare.23700869
title: Additional file 5 of Genomic alterations related to HPV infection status in a cohort of Chinese prostate cancer patients

description: Additional file 5: Table S2. The summary of somatic SNV and InDel.
DOI: 10.6084/m9.figshare.23700734
title: Additional file 2 of Whole-genome sequencing and functional annotation of pathogenic Paraconiothyrium brasiliense causing human cellulitis

description: Additional file 2: Table S2. The secretome of P. brasiliense GGX 413
DOI: 10.6084/m9.figshare.23700875.v1
title: Additional file 7 of Genomic alterations related to HPV infection status in a cohort of Chinese prostate cancer patients

description: Additional file 7: Table S4. The summary of differentially altered genes between HPV-positvie and HPV-negative groups.
DOI: 10.6084/m9.figshare.13212635.v1
title: Additional file 2 of Temporal transcriptomic differences between tolerant and susceptible genotypes contribute to rice drought tolerance

description: Additional file 2: Supplementary Table S1. Basic information of RNA-seq for all samples. Supplementary Table S2. Total expressed genes (FPKM&gt; 0.001) detected in twelve rice genotypes. Supplementary Table S3. Function-studied drought-tolerant genes, their correlation with drought-tolerance index by biomass (DTIB) and biomass measured in well-watered fields. Supplementary Table S4. Number of enriched GOBPs by upregulated and downregulated DRGs in various classifications of biological processes. Number in shade indicates the GO classification preferred by upregulated or downregulated DRGs. Supplementary Table S5. Correlations of fold changes from common drought-responsive genes between the tolerant and the susceptible groups during drought. Supplementary Table S6. Number of biological processes in various GO classifications enriched by recovery related genes in different clusters. Supplementary Table S7. Distributions of GO biological processes of different types in various GO classifications. Percentage in shade indicates the GO classification preferred by the type of GO biological processes. Supplementary Table S8. Enrichments of GO biological processes by osmolality- and H2O2-correlated drought responsive genes. Supplementary Table S9. Distribution of biological processes enriched by osmolality- and H2O2-correlated drought responsive genes in various GO classification. Supplementary Table S10. The enrichment of DT-featured biological processes in Gene Ontology for nine modules. Supplementary Table S11. Distribution of genes relevant to photosynthesis and phytohormones in the modules. Supplementary Table S12. Information of candidate genes of drought-tolerance. Supplementary Table S13. Information of candidate genes for drought-recovery.
DOI: 10.6084/m9.figshare.25195514
title: Files used to create the sourmash lca database from reference sequences of the Genome Taxonomy Database release 214.1

description: Files used to create the sourmash lca database from reference sequences of the Genome Taxonomy Database release 214.1 - GTDB Data - /releases/release214/214.1/ (ecogenomic.org)
DOI: 10.6084/m9.figshare.25195514.v1
title: Files used to create the sourmash lca database from reference sequences of the Genome Taxonomy Database release 214.1

description: Files used to create the sourmash lca database from reference sequences of the Genome Taxonomy Database release 214.1 - GTDB Data - /releases/release214/214.1/ (ecogenomic.org)
DOI: 10.6084/m9.figshare.10069796.v2
title: Metadata record for: A chromosome-level genome assembly of the Chinese tupelo Nyssa sinensis

description: This dataset contains key characteristics about the data described in the Data Descriptor A chromosome-level genome assembly of the Chinese tupelo Nyssa sinensis. <br>
 Contents: <br>
 
 1. human readable metadata summary table in CSV format
 
 
 2. machine readable metadata file in JSON format<br><br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.14791693
title: Genetic polymorphisms of 16 X-STR loci in the Hani population from Southwest China

description: X chromosomal short tandem repeats (X-STRs) have the characteristics of both autosomal and uniparental genetic markers and have been shown to be particularly useful in forensic casework. However, relevant research or reports have not focused on X-STRs in the Hani population. To investigate the genetic variation and forensic efficiency of 16 X-STR loci in the Hani ethnic minority, we calculated the allele frequencies and forensic parameters of 451 (116 males and 335 females) unrelated healthy Hani individuals from Yunnan Province, Southwest China. All these loci are highly polymorphic in Hani individuals in Yunnan Province except DXS6800. The combined power of discrimination in males (PD<sub>M</sub>) and power of discrimination in females (PD<sub>F</sub>) were found to be 0.999 999 998 433 993 and 0.999 999 999 999 998, respectively. Furthermore, a population genetic structure investigation between the Yunnan Hani population and another 18 populations was performed using a principal component analysis, multidimensional scaling plot and neighbouring-joining phylogenetic tree and the findings illustrated that neighbouring populations and different nationalities in the same area appeared to have a closer evolutionary relationship. This study provides the first batch of X chromosome genetic polymorphism data of the Hani population in Yunnan Province, Southwest China and enriches the reference database of the Chinese minority population. This is the first study of X-STR in the Hani population. We calculated the allele frequencies and forensic parameters of 451 unrelated healthy Hani individuals from Yunnan Province, Southwest China. All these loci are highly polymorphic in Hani individuals in Yunnan Province except DXS6800. The genetic relationship between the Hani and the other 18 nationalities was analyzed. This study provides the first batch of X chromosome genetic polymorphism data of the Hani population in Yunnan Province, Southwest China and enriches the reference database of the Chinese minority population.
DOI: 10.6084/m9.figshare.12170340
title: Author_List

description: CSV file containing PubMed authors and AND_IDs. It correspond to the Table 5 in the article.
DOI: 10.6084/m9.figshare.12170340.v1
title: Author_List

description: CSV file containing PubMed authors and AND_IDs. It correspond to the Table 5 in the article.
DOI: 10.6084/m9.figshare.23700710
title: Additional file 3 of Ancestry-driven metabolite variation provides insights into disease states in admixed populations

description: Additional file 3: Extended Data Table S1. Significant independent local ancestry regions from admixture mapping. Extended Data Table S2. Genetic variants that do not explain association between local ancestry regions and metabolites. Extended Data Table S3. Replication of significant independent local ancestry regions from admixture mapping for 64 metabolites avaialble in the replication dataset.
DOI: 10.6084/m9.figshare.12170343
title: Researcher_Employment

description: CSV file containing employment history from ORCID. It correspond to the Table 9 in the article.
DOI: 10.6084/m9.figshare.12170343.v1
title: Researcher_Employment

description: CSV file containing employment history from ORCID. It correspond to the Table 9 in the article.
DOI: 10.6084/m9.figshare.12170346
title: Researcher_Education

description: CSV file containing educational background from ORCID. It correspond to the Table 10 in the article.
DOI: 10.6084/m9.figshare.12170346.v1
title: Researcher_Education

description: CSV file containing educational background from ORCID. It correspond to the Table 10 in the article.
DOI: 10.6084/m9.figshare.13215441
title: A holistic strategy for discovering structural analogues of drug residues in meat using characteristic structural fragments filtering by high-resolution Orbitrap mass spectrometry

description: A holistic strategy for discovering structural analogs was established using characteristic structural fragments filtering by high-resolution Orbitrap mass spectrometry and successfully employed for discovering potential hazards in meat. The mass spectrometry fragmentation mechanisms of 113 compounds (including sulphonamides, tetracyclines, benzimidazoles, steroid hormones, cephalosporins, β-blockers) were investigated and a new strategy for screening of characteristic fragment ions was proposed. To process the data acquired by two scan modes, firstly an integrated filtering strategy was conducted to facilitate the characterisation of multi-class drugs. The integrated filtering strategy was applied to reduce interference in the raw data, which could help extracting the MS1 characteristics of the homolog-type chemical substances and expand the screening of the compounds as effectively as possible. This strategy was based on a combination of nitrogen rule, neutral loss and multiple characteristic fragment ions filtering. The method was validated by rapid screening and identification of targeted compounds in spiked samples. Particularly, the successful detection of several new compounds indicated that this strategy had significant advantages over individual filtration methods and could be a promising method for screening and identifying newly homolog-type drug residues in complex samples.
DOI: 10.6084/m9.figshare.12170352
title: Bio-entities_Mutation

description: CSV file containing additional items of mutations from Bio-entities_Main file. It correspond to the Table 7 in the article.
DOI: 10.6084/m9.figshare.12170352.v1
title: Bio-entities_Mutation

description: CSV file containing additional items of mutations from Bio-entities_Main file. It correspond to the Table 7 in the article.
DOI: 10.6084/m9.figshare.25195505
title: gtdb_rs214_1_k31.lca.json.gz file for use with sourmash lca

description: Follow instructions available at Using sourmash LCA to do taxonomic classification — sourmash 4.8.6.dev0 documentation to use the database in your analyses.
DOI: 10.6084/m9.figshare.25195505.v1
title: gtdb_rs214_1_k31.lca.json.gz file for use with sourmash lca

description: Follow instructions available at Using sourmash LCA to do taxonomic classification — sourmash 4.8.6.dev0 documentation to use the database in your analyses.
DOI: 10.6084/m9.figshare.18461906
title: Additional file 1 of EWSR1-induced circNEIL3 promotes glioma progression and exosome-mediated macrophage immunosuppressive polarization via stabilizing IGF2BP3

description: Additional file 1: Table S1. Genes positively correlated with circNEIL3. Table S2. Interacting proteins identified by circNEIL3 pulldown assays. Table S3. Interacting proteins identified by IGF2BP3 Co-IP assays. Table S4. Genes differentially expressed in circNEIL3 high group. Compared with low group. Table S5. Enriched terms across upregulated genes in circNEIL3 high group. Table S6. Genes differentially expressed in IGF2BP3 high group. Compared with low group in TCGA glioma cohort. Table S7. Enriched terms across upregulated genes in IGF2BP3 high group. Table S8. The detailed clinicopathological characteristics of glioma patients in our local cohort. Table S9. The detailed qRT-PCR primers used in this study. Table S10. The detailed siRNA sequences used in this study. Table S11. The detailed antibody information used in this study.
DOI: 10.6084/m9.figshare.10073405
title: Hesperidin inhibits the epithelial to mesenchymal transition induced by transforming growth factor-β1 in A549 cells through Smad signaling in the cytoplasm

description: Hesperidin, a natural compound, suppresses the epithelial-to-mesenchymal transition through the TGF-β1/Smad signaling pathway. However, studies on the detailed effects and mechanisms of hesperidin are rare. The present study showed that, for A549 alveolar epithelial cells, the anti-proliferative effects of hesperidin occurred in a dose-dependent manner, with an IC50= 216.8 µM at 48 h. TGF-β1 was used to activate the Smad signaling pathway and induce the epithelial to mesenchymal transition in cells. Treatment with hesperidin or SB431542 was used for antagonism of Smad pathway activation. Hesperidin inhibited the increase in ɑ-SMA and Col1ɑ-1 and the decrease in E-cadherin in a dose-dependent manner from concentration of 20 µM to 60 µM, as assessed by both ELISA and Western blotting assays; however, there was no significant effect on cellular morphological alterations. Moreover, the Western blotting assay showed that, in the cytoplasm, hesperidin and SB431542 had no significant effect on the protein expression of Smad 2, 3, 4, or 7 as well as 2/3. However, 60 µM hesperidin and SB431542 significantly decreased p-Smad2/3 protein expression. From the above results, it is concluded that hesperidin can partly inhibit the epithelial to mesenchymal transition in human alveolar epithelial cells; the effect accounts for the blockage of the phosphorylation of Smad2/3 in the cytoplasm rather than a change in Smad protein production in the cytoplasm.
DOI: 10.6084/m9.figshare.10073405.v1
title: Hesperidin inhibits the epithelial to mesenchymal transition induced by transforming growth factor-β1 in A549 cells through Smad signaling in the cytoplasm

description: Hesperidin, a natural compound, suppresses the epithelial-to-mesenchymal transition through the TGF-β1/Smad signaling pathway. However, studies on the detailed effects and mechanisms of hesperidin are rare. The present study showed that, for A549 alveolar epithelial cells, the anti-proliferative effects of hesperidin occurred in a dose-dependent manner, with an IC50= 216.8 µM at 48 h. TGF-β1 was used to activate the Smad signaling pathway and induce the epithelial to mesenchymal transition in cells. Treatment with hesperidin or SB431542 was used for antagonism of Smad pathway activation. Hesperidin inhibited the increase in ɑ-SMA and Col1ɑ-1 and the decrease in E-cadherin in a dose-dependent manner from concentration of 20 µM to 60 µM, as assessed by both ELISA and Western blotting assays; however, there was no significant effect on cellular morphological alterations. Moreover, the Western blotting assay showed that, in the cytoplasm, hesperidin and SB431542 had no significant effect on the protein expression of Smad 2, 3, 4, or 7 as well as 2/3. However, 60 µM hesperidin and SB431542 significantly decreased p-Smad2/3 protein expression. From the above results, it is concluded that hesperidin can partly inhibit the epithelial to mesenchymal transition in human alveolar epithelial cells; the effect accounts for the blockage of the phosphorylation of Smad2/3 in the cytoplasm rather than a change in Smad protein production in the cytoplasm.
DOI: 10.6084/m9.figshare.22656418
title: Detailed information on single-copy orthologous PCGs across 15 vertebrate species.

description: Detailed information on single-copy orthologous PCGs across 15 vertebrate species.
DOI: 10.6084/m9.figshare.10073519
title: Fluorofenidone inhibits apoptosis of renal tubular epithelial cells in rats with renal interstitial fibrosis

description: This study aimed to investigate the mechanism of fluorofenidone (AKF-PD) in treating renal interstitial fibrosis in rats with unilateral urinary obstruction (UUO). Thirty-two male Sprague-Dawley rats were randomly divided into sham, UUO, UUO + enalapril, and UUO + AKF-PD groups. All rats, except sham, underwent left urethral obstruction surgery to establish the animal model. Rats were sacrificed 14 days after surgery, and serum was collected for renal function examination. Kidneys were collected to observe pathological changes. Immunohistochemistry was performed to assess collagen I (Col I) protein expression, and terminal deoxynucleotidyl transferase-mediated nick end-labeling staining to observe the apoptosis of renal tubular epithelial cells. The expression of Fas-associated death domain (FADD), apoptotic protease activating factor-1 (Apaf-1), and C/EBP homologous protein (CHOP) proteins was evaluated by immunohistochemistry and western blot analysis. AKF-PD showed no significant effect on renal function in UUO rats. The pathological changes were alleviated significantly after enalapril or AKF-PD treatment, but with no significant differences between the two groups. Col I protein was overexpressed in the UUO group, which was inhibited by both enalapril and AKF-PD. The number of apoptotic renal tubular epithelial cells was much higher in the UUO group, and AKF-PD significantly inhibited epithelial cells apoptosis. The expression of FADD, Apaf-1, and CHOP proteins was significantly upregulated in the UUO group and downregulated by enalapril and AKF-PD. In conclusion, AKF-PD improved renal interstitial fibrosis by inhibiting apoptosis of renal tubular epithelial cells in rats with UUO.
DOI: 10.6084/m9.figshare.10073519.v1
title: Fluorofenidone inhibits apoptosis of renal tubular epithelial cells in rats with renal interstitial fibrosis

description: This study aimed to investigate the mechanism of fluorofenidone (AKF-PD) in treating renal interstitial fibrosis in rats with unilateral urinary obstruction (UUO). Thirty-two male Sprague-Dawley rats were randomly divided into sham, UUO, UUO + enalapril, and UUO + AKF-PD groups. All rats, except sham, underwent left urethral obstruction surgery to establish the animal model. Rats were sacrificed 14 days after surgery, and serum was collected for renal function examination. Kidneys were collected to observe pathological changes. Immunohistochemistry was performed to assess collagen I (Col I) protein expression, and terminal deoxynucleotidyl transferase-mediated nick end-labeling staining to observe the apoptosis of renal tubular epithelial cells. The expression of Fas-associated death domain (FADD), apoptotic protease activating factor-1 (Apaf-1), and C/EBP homologous protein (CHOP) proteins was evaluated by immunohistochemistry and western blot analysis. AKF-PD showed no significant effect on renal function in UUO rats. The pathological changes were alleviated significantly after enalapril or AKF-PD treatment, but with no significant differences between the two groups. Col I protein was overexpressed in the UUO group, which was inhibited by both enalapril and AKF-PD. The number of apoptotic renal tubular epithelial cells was much higher in the UUO group, and AKF-PD significantly inhibited epithelial cells apoptosis. The expression of FADD, Apaf-1, and CHOP proteins was significantly upregulated in the UUO group and downregulated by enalapril and AKF-PD. In conclusion, AKF-PD improved renal interstitial fibrosis by inhibiting apoptosis of renal tubular epithelial cells in rats with UUO.
DOI: 10.5281/zenodo.10518008
title: Skyrmion motion in magnetic anisotropy gradients: Acceleration caused by deformation

description: Data used in the publication
DOI: 10.5281/zenodo.10518009
title: Skyrmion motion in magnetic anisotropy gradients: Acceleration caused by deformation

description: Data used in the publication
DOI: 10.6084/m9.figshare.13215441.v1
title: A holistic strategy for discovering structural analogues of drug residues in meat using characteristic structural fragments filtering by high-resolution Orbitrap mass spectrometry

description: A holistic strategy for discovering structural analogs was established using characteristic structural fragments filtering by high-resolution Orbitrap mass spectrometry and successfully employed for discovering potential hazards in meat. The mass spectrometry fragmentation mechanisms of 113 compounds (including sulphonamides, tetracyclines, benzimidazoles, steroid hormones, cephalosporins, β-blockers) were investigated and a new strategy for screening of characteristic fragment ions was proposed. To process the data acquired by two scan modes, firstly an integrated filtering strategy was conducted to facilitate the characterisation of multi-class drugs. The integrated filtering strategy was applied to reduce interference in the raw data, which could help extracting the MS1 characteristics of the homolog-type chemical substances and expand the screening of the compounds as effectively as possible. This strategy was based on a combination of nitrogen rule, neutral loss and multiple characteristic fragment ions filtering. The method was validated by rapid screening and identification of targeted compounds in spiked samples. Particularly, the successful detection of several new compounds indicated that this strategy had significant advantages over individual filtration methods and could be a promising method for screening and identifying newly homolog-type drug residues in complex samples.