cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1601892
title: Autophagy mediated CoCrMo particle-induced peri-implant osteolysis by promoting osteoblast apoptosis

description: Wear particle-induced osteolysis is the leading cause of aseptic loosening, which is the most common reason for THA (total hip arthroplasty) failure and revision surgery. Although existing studies suggest that osteoblast apoptosis induced by wear debris is involved in aseptic loosening, the underlying mechanism linking wear particles to osteoblast apoptosis remains almost totally unknown. In the present study, we investigated the effect of autophagy on osteoblast apoptosis induced by CoCrMo metal particles (CoPs) in vitro and in a calvarial resorption animal model. Our study demonstrated that CoPs stimulated autophagy in osteoblasts and PIO (particle-induced osteolysis) animal models. Both autophagy inhibitor 3-MA (3-methyladenine) and <i>siRNA</i> of <i>Atg5</i> could dramatically reduce CoPs-induced apoptosis in osteoblasts. Further, inhibition of autophagy with 3-MA ameliorated the severity of osteolysis in PIO animal models. Moreover, 3-MA also prevented osteoblast apoptosis in an antiautophagic way when tested in PIO model. Collectively, these results suggest that autophagy plays a key role in CoPs-induced osteolysis and that targeting autophagy-related pathways may represent a potential therapeutic approach for treating particle-induced peri-implant osteolysis.
DOI: 10.6084/m9.figshare.1601892.v1
title: Autophagy mediated CoCrMo particle-induced peri-implant osteolysis by promoting osteoblast apoptosis

description: Wear particle-induced osteolysis is the leading cause of aseptic loosening, which is the most common reason for THA (total hip arthroplasty) failure and revision surgery. Although existing studies suggest that osteoblast apoptosis induced by wear debris is involved in aseptic loosening, the underlying mechanism linking wear particles to osteoblast apoptosis remains almost totally unknown. In the present study, we investigated the effect of autophagy on osteoblast apoptosis induced by CoCrMo metal particles (CoPs) in vitro and in a calvarial resorption animal model. Our study demonstrated that CoPs stimulated autophagy in osteoblasts and PIO (particle-induced osteolysis) animal models. Both autophagy inhibitor 3-MA (3-methyladenine) and <i>siRNA</i> of <i>Atg5</i> could dramatically reduce CoPs-induced apoptosis in osteoblasts. Further, inhibition of autophagy with 3-MA ameliorated the severity of osteolysis in PIO animal models. Moreover, 3-MA also prevented osteoblast apoptosis in an antiautophagic way when tested in PIO model. Collectively, these results suggest that autophagy plays a key role in CoPs-induced osteolysis and that targeting autophagy-related pathways may represent a potential therapeutic approach for treating particle-induced peri-implant osteolysis.
DOI: 10.6084/m9.figshare.14184742.v1
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.1601938
title: Autophagy contributes to regulation of the hypoxia response during submergence in <i>Arabidopsis thaliana</i>

description: Autophagy involves massive degradation of intracellular components and functions as a conserved system that helps cells to adapt to adverse conditions. In mammals, hypoxia rapidly stimulates autophagy as a cell survival response. Here, we examine the function of autophagy in the regulation of the plant response to submergence, an abiotic stress that leads to hypoxia and anaerobic respiration in plant cells. In <i>Arabidopsis thaliana</i>, submergence induces the transcription of autophagy-related (<i>ATG</i>) genes and the formation of autophagosomes. Consistent with this, the autophagy-defective (<i>atg</i>) mutants are hypersensitive to submergence stress and treatment with ethanol, the end product of anaerobic respiration. Upon submergence, the <i>atg</i> mutants have increased levels of transcripts of anaerobic respiration genes (<i>alcohol dehydrogenase 1, ADH1</i> and <i>pyruvate decarboxylase 1, PDC1</i>), but reduced levels of transcripts of other hypoxia- and ethylene-responsive genes. Both submergence and ethanol treatments induce the accumulation of reactive oxygen species (ROS) in the rosettes of <i>atg</i> mutants more than in the wild type. Moreover, the production of ROS by the nicotinamide adenine dinucleotide phosphate (NADPH) oxidases is necessary for plant tolerance to submergence and ethanol, submergence-induced expression of <i>ADH1</i> and <i>PDC1</i>, and activation of autophagy. The submergence- and ethanol-sensitive phenotypes in the <i>atg</i> mutants depend on a complete salicylic acid (SA) signaling pathway. Together, our findings demonstrate that submergence-induced autophagy functions in the hypoxia response in <i>Arabidopsis</i> by modulating SA-mediated cellular homeostasis.
DOI: 10.6084/m9.figshare.7369106
title: Additional file 1: of Prediction of pathogenesis-related secreted proteins from Stemphylium lycopersici

description: Sequences of 511 predicted secreted proteins. (FASTA 249 kb)
DOI: 10.6084/m9.figshare.7369073
title: Additional file 2: of Natural variation in a CENTRORADIALIS homolog contributed to cluster fruiting and early maturity in cotton

description: Data S1. All primers used in this study. Data S2. The list of significant differentially expressed genes in Gh_VIGSvsGh_WT_Gb_VIGSvsGb_WT.venn. Data S3. 174 transcription factors in Gh_VIGSvsGh_WT_Gb_VIGSvsGb_WT.venn. Data S4. The 58 cultivars bred in Xinjiang Province. Data S5. The information of the expermental material of G. barbadense. (XLSX 167 kb)
DOI: 10.6084/m9.figshare.7369121.v1
title: Additional file 2: of Prediction of pathogenesis-related secreted proteins from Stemphylium lycopersici

description: Blast2go details. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7369073.v1
title: Additional file 2: of Natural variation in a CENTRORADIALIS homolog contributed to cluster fruiting and early maturity in cotton

description: Data S1. All primers used in this study. Data S2. The list of significant differentially expressed genes in Gh_VIGSvsGh_WT_Gb_VIGSvsGb_WT.venn. Data S3. 174 transcription factors in Gh_VIGSvsGh_WT_Gb_VIGSvsGb_WT.venn. Data S4. The 58 cultivars bred in Xinjiang Province. Data S5. The information of the expermental material of G. barbadense. (XLSX 167 kb)
DOI: 10.6084/m9.figshare.7369139.v1
title: Additional file 4: of Prediction of pathogenesis-related secreted proteins from Stemphylium lycopersici

description: CAZyme details. (XLSX 74 kb)
DOI: 10.6084/m9.figshare.7369106.v1
title: Additional file 1: of Prediction of pathogenesis-related secreted proteins from Stemphylium lycopersici

description: Sequences of 511 predicted secreted proteins. (FASTA 249 kb)
DOI: 10.6084/m9.figshare.7369121
title: Additional file 2: of Prediction of pathogenesis-related secreted proteins from Stemphylium lycopersici

description: Blast2go details. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7369127
title: Additional file 3: of Prediction of pathogenesis-related secreted proteins from Stemphylium lycopersici

description: PHI details. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7369127.v1
title: Additional file 3: of Prediction of pathogenesis-related secreted proteins from Stemphylium lycopersici

description: PHI details. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7369139
title: Additional file 4: of Prediction of pathogenesis-related secreted proteins from Stemphylium lycopersici

description: CAZyme details. (XLSX 74 kb)
DOI: 10.6084/m9.figshare.7369142
title: Additional file 1 of Comprehensive study of instable regions in Pseudomonas aeruginosa and Mycobacterium tuberculosis

description: Additional file 1: Table S1. Sca_olds for the 25 Pseudomonas aeruginosa genomes. Table S2. The 25 Pseudomonas aeruginosa strains used for studying instable regions. Table S3. 134 distinct pairs of core blocks between which instable region existed in Pseudomonas aeruginosa strains. Table S4. Sca_olds for the 28 Mycobacterium tuberculosis genomes. Table S5. The 28 Mycobacterium tuberculosis strains used for studying instable regions. Table S6. 82 distinct pairs of core blocks between which instable region existed in Mycobacterium tuberculosis strains. Table Rn. For every achieved DR pair Rn, we showed the 25 Pseudomonas aeruginosa strains' partial sca_olds covering Rn, where n is the ID of this DR pair.
DOI: 10.6084/m9.figshare.1602002
title: Disruption of microtubules in plants suppresses macroautophagy and triggers starch excess-associated chloroplast autophagy

description: Microtubules, the major components of cytoskeleton, are involved in various fundamental biological processes in plants. Recent studies in mammalian cells have revealed the importance of microtubule cytoskeleton in autophagy. However, little is known about the roles of microtubules in plant autophagy. Here, we found that ATG6 interacts with TUB8/β-tubulin 8 and colocalizes with microtubules in <i>Nicotiana benthamiana</i>. Disruption of microtubules by either silencing of tubulin genes or treatment with microtubule-depolymerizing agents in <i>N. benthamiana</i> reduces autophagosome formation during upregulation of nocturnal or oxidation-induced macroautophagy. Furthermore, a blockage of leaf starch degradation occurred in microtubule-disrupted cells and triggered a distinct ATG6-, ATG5- and ATG7-independent autophagic pathway termed starch excess-associated chloroplast autophagy (SEX chlorophagy) for clearance of dysfunctional chloroplasts. Our findings reveal that an intact microtubule network is important for efficient macroautophagy and leaf starch degradation.
DOI: 10.6084/m9.figshare.7369142.v2
title: Additional file 1 of Comprehensive study of instable regions in Pseudomonas aeruginosa and Mycobacterium tuberculosis

description: Additional file 1: Table S1. Sca_olds for the 25 Pseudomonas aeruginosa genomes. Table S2. The 25 Pseudomonas aeruginosa strains used for studying instable regions. Table S3. 134 distinct pairs of core blocks between which instable region existed in Pseudomonas aeruginosa strains. Table S4. Sca_olds for the 28 Mycobacterium tuberculosis genomes. Table S5. The 28 Mycobacterium tuberculosis strains used for studying instable regions. Table S6. 82 distinct pairs of core blocks between which instable region existed in Mycobacterium tuberculosis strains. Table Rn. For every achieved DR pair Rn, we showed the 25 Pseudomonas aeruginosa strains' partial sca_olds covering Rn, where n is the ID of this DR pair.
DOI: 10.6084/m9.figshare.7369142.v1
title: MOESM1 of Comprehensive study of instable regions in Pseudomonas aeruginosa and Mycobacterium tuberculosis

description: Additional file 1: Table S1. Sca_olds for the 25 Pseudomonas aeruginosa genomes. Table S2. The 25 Pseudomonas aeruginosa strains used for studying instable regions. Table S3. 134 distinct pairs of core blocks between which instable region existed in Pseudomonas aeruginosa strains. Table S4. Sca_olds for the 28 Mycobacterium tuberculosis genomes. Table S5. The 28 Mycobacterium tuberculosis strains used for studying instable regions. Table S6. 82 distinct pairs of core blocks between which instable region existed in Mycobacterium tuberculosis strains. Table Rn. For every achieved DR pair Rn, we showed the 25 Pseudomonas aeruginosa strains' partial sca_olds covering Rn, where n is the ID of this DR pair.
DOI: 10.6084/m9.figshare.7369181
title: Additional file 3: of Mitochondrial genomes of two diplectanids (Platyhelminthes: Monogenea) expose paraphyly of the order Dactylogyridea and extensive tRNA gene rearrangements

description: Table S2. General statistics for the protein-coding and rRNA genes of the two diplectanids and 18 other available monogeneans. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7369160
title: Additional file 2: of Mitochondrial genomes of two diplectanids (Platyhelminthes: Monogenea) expose paraphyly of the order Dactylogyridea and extensive tRNA gene rearrangements

description: Table S1. Monogenean species and outgroups used for comparative mitogenomic and phylogenetic analyses. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7369160.v1
title: Additional file 2: of Mitochondrial genomes of two diplectanids (Platyhelminthes: Monogenea) expose paraphyly of the order Dactylogyridea and extensive tRNA gene rearrangements

description: Table S1. Monogenean species and outgroups used for comparative mitogenomic and phylogenetic analyses. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.14184906
title: Association between atherosclerotic cardiovascular diseases risk and renal outcome in patients with type 2 diabetes mellitus

description: Chronic kidney disease (CKD) and diabetes mellitus increase atherosclerotic cardiovascular diseases (ASCVD) risk. However, the association between renal outcome of diabetic kidney disease (DKD) and ASCVD risk is unclear. This retrospective study enrolled 218 type 2 diabetic patients with biopsy-proven DKD, and without known cardiovascular diseases. Baseline characteristics were obtained and the 10-year ASCVD risk score was calculated using the Pooled Cohort Equation (PCE). Renal outcome was defined as progression to end-stage renal disease (ESRD). The association between ASCVD risk and renal function and outcome was analyzed with logistic regression and Cox analysis. Among all patients, the median 10-year ASCVD risk score was 14.1%. The median of ASCVD risk score in CKD stage 1, 2, 3, and 4 was 10.9%, 12.3%, 16.5%, and 14.8%, respectively (<i>p</i> = 0.268). Compared with patients with lower ASCVD risk (＜14.1%), those with higher ASCVD risk had lower eGFR, higher systolic blood pressure, and more severe renal interstitial inflammation. High ASCVD risk (&gt;14.1%) was an independent indicator of renal dysfunction in multivariable-adjusted logistic analysis (OR, 3.997; 95%CI, 1.385–11.530; <i>p</i> = 0.010), though failed to be an independent risk factor for ESRD in patients with DKD in univariate and multivariate Cox analysis. DKD patients even in CKD stage 1 had comparable ASCVD risk score to patients in CKD stage 2, 3, and 4. Higher ASCVD risk indicated severe renal insufficiency, while no prognostic value of ASVCD risk for renal outcome was observed, which implied macroangiopathy and microangiopathy in patients with DKD were related, but relatively independent.
DOI: 10.6084/m9.figshare.7369181.v1
title: Additional file 3: of Mitochondrial genomes of two diplectanids (Platyhelminthes: Monogenea) expose paraphyly of the order Dactylogyridea and extensive tRNA gene rearrangements

description: Table S2. General statistics for the protein-coding and rRNA genes of the two diplectanids and 18 other available monogeneans. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.12612068
title: Source Data and Code for "Determinants of genome-wide distribution and evolution of uORFs in eukaryotes"

description: This dataset contains the Source Data underlying all the data figures, and the custom scripts used to prepare data and perform analyses. See README.md for details.
DOI: 10.6084/m9.figshare.14184906.v1
title: Association between atherosclerotic cardiovascular diseases risk and renal outcome in patients with type 2 diabetes mellitus

description: Chronic kidney disease (CKD) and diabetes mellitus increase atherosclerotic cardiovascular diseases (ASCVD) risk. However, the association between renal outcome of diabetic kidney disease (DKD) and ASCVD risk is unclear. This retrospective study enrolled 218 type 2 diabetic patients with biopsy-proven DKD, and without known cardiovascular diseases. Baseline characteristics were obtained and the 10-year ASCVD risk score was calculated using the Pooled Cohort Equation (PCE). Renal outcome was defined as progression to end-stage renal disease (ESRD). The association between ASCVD risk and renal function and outcome was analyzed with logistic regression and Cox analysis. Among all patients, the median 10-year ASCVD risk score was 14.1%. The median of ASCVD risk score in CKD stage 1, 2, 3, and 4 was 10.9%, 12.3%, 16.5%, and 14.8%, respectively (<i>p</i> = 0.268). Compared with patients with lower ASCVD risk (＜14.1%), those with higher ASCVD risk had lower eGFR, higher systolic blood pressure, and more severe renal interstitial inflammation. High ASCVD risk (&gt;14.1%) was an independent indicator of renal dysfunction in multivariable-adjusted logistic analysis (OR, 3.997; 95%CI, 1.385–11.530; <i>p</i> = 0.010), though failed to be an independent risk factor for ESRD in patients with DKD in univariate and multivariate Cox analysis. DKD patients even in CKD stage 1 had comparable ASCVD risk score to patients in CKD stage 2, 3, and 4. Higher ASCVD risk indicated severe renal insufficiency, while no prognostic value of ASVCD risk for renal outcome was observed, which implied macroangiopathy and microangiopathy in patients with DKD were related, but relatively independent.
DOI: 10.6084/m9.figshare.14184915
title: Clinical significance of long noncoding RNA MNX1-AS1 in human cancers: a meta-analysis of cohort studies and bioinformatics analysis based on TCGA datasets

description: MNX1-AS1 expression has been proposed to be abnormally upregulated in multiple human malignancies and be linked with the survival outcome of patients. However, relevant conclusions were yielded based on the limited samples. Therefore, we herein implemented a meta-analysis of the published cohort studies to further decipher the relationship of MNX1-AS1 level to prognosis and clinicopathological features in various cancers. Additionally, using The Cancer Genome Atlas (TCGA) datasets we carried out a bioinformatics analysis to make a further evaluation on the prognostic value of MNX1-AS1 expression. The results of meta-analysis indicated elevated MNX1-AS1 level closely correlated with poorer overall survival (OS) (HR = 1.97, 95% CI, 1.73–2.24; P &lt; 0.00001), and disease-free survival (DFS) (HR = 2.24, 95% CI, 1.48–3.38; P = 0.0001) in cancers, which was confirmed by the bioinformatics analysis. Besides, it was observed the upregulated MNX1-AS1 level was significantly related to invasion depth, disease stage, tumor metastasis, and differentiation. Collectively, high MNX1-AS1 level correlated with poor survival outcome and aggressive clinicopathological characteristics in various cancers, suggesting that MNX1-AS1 may be applied as a prognostic marker and even a therapeutic target. Nevertheless, more high-quality studies designed with a large sample size should be conducted to further determine the clinical role of MNX1-AS1 in specific cancer types.
DOI: 10.6084/m9.figshare.14184915.v1
title: Clinical significance of long noncoding RNA MNX1-AS1 in human cancers: a meta-analysis of cohort studies and bioinformatics analysis based on TCGA datasets

description: MNX1-AS1 expression has been proposed to be abnormally upregulated in multiple human malignancies and be linked with the survival outcome of patients. However, relevant conclusions were yielded based on the limited samples. Therefore, we herein implemented a meta-analysis of the published cohort studies to further decipher the relationship of MNX1-AS1 level to prognosis and clinicopathological features in various cancers. Additionally, using The Cancer Genome Atlas (TCGA) datasets we carried out a bioinformatics analysis to make a further evaluation on the prognostic value of MNX1-AS1 expression. The results of meta-analysis indicated elevated MNX1-AS1 level closely correlated with poorer overall survival (OS) (HR = 1.97, 95% CI, 1.73–2.24; P &lt; 0.00001), and disease-free survival (DFS) (HR = 2.24, 95% CI, 1.48–3.38; P = 0.0001) in cancers, which was confirmed by the bioinformatics analysis. Besides, it was observed the upregulated MNX1-AS1 level was significantly related to invasion depth, disease stage, tumor metastasis, and differentiation. Collectively, high MNX1-AS1 level correlated with poor survival outcome and aggressive clinicopathological characteristics in various cancers, suggesting that MNX1-AS1 may be applied as a prognostic marker and even a therapeutic target. Nevertheless, more high-quality studies designed with a large sample size should be conducted to further determine the clinical role of MNX1-AS1 in specific cancer types.
DOI: 10.6084/m9.figshare.7369256
title: Additional file 2: of Seedless mutant ‘Wuzi Ougan’ (Citrus suavissima Hort. ex Tanaka ‘seedless’) and the wild type were compared by iTRAQ-based quantitative proteomics and integratedly analyzed with transcriptome to improve understanding of male sterility

description: Table S2. Annotated DEPs and their expression ratio (N/Y). “N” and “Y” indicate MT and WT, respectively. (XLS 181 kb)
DOI: 10.6084/m9.figshare.7369241
title: Additional file 1: of Seedless mutant ‘Wuzi Ougan’ (Citrus suavissima Hort. ex Tanaka ‘seedless’) and the wild type were compared by iTRAQ-based quantitative proteomics and integratedly analyzed with transcriptome to improve understanding of male sterility

description: Table S1. All identification proteins in three stages. “N” indicates MT in three stages, and “Y” indicates WT in three stages. (XLSX 2862 kb)
DOI: 10.6084/m9.figshare.7369259
title: Additional file 8: of Mitochondrial genomes of two diplectanids (Platyhelminthes: Monogenea) expose paraphyly of the order Dactylogyridea and extensive tRNA gene rearrangements

description: Table S4. Pairwise comparison of mitochondrial DNA gene orders among 13 monogenean species based on the order of all 36 genes. Scores correspond to the similarity between gene orders, where â 1254â represents an identical gene order. N is the number identifying the taxon in the pairwise comparisons. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7369241.v1
title: Additional file 1: of Seedless mutant ‘Wuzi Ougan’ (Citrus suavissima Hort. ex Tanaka ‘seedless’) and the wild type were compared by iTRAQ-based quantitative proteomics and integratedly analyzed with transcriptome to improve understanding of male sterility

description: Table S1. All identification proteins in three stages. “N” indicates MT in three stages, and “Y” indicates WT in three stages. (XLSX 2862 kb)
DOI: 10.6084/m9.figshare.7369259.v1
title: Additional file 8: of Mitochondrial genomes of two diplectanids (Platyhelminthes: Monogenea) expose paraphyly of the order Dactylogyridea and extensive tRNA gene rearrangements

description: Table S4. Pairwise comparison of mitochondrial DNA gene orders among 13 monogenean species based on the order of all 36 genes. Scores correspond to the similarity between gene orders, where â 1254â represents an identical gene order. N is the number identifying the taxon in the pairwise comparisons. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7369277
title: Additional file 3: of Seedless mutant ‘Wuzi Ougan’ (Citrus suavissima Hort. ex Tanaka ‘seedless’) and the wild type were compared by iTRAQ-based quantitative proteomics and integratedly analyzed with transcriptome to improve understanding of male sterility

description: Table S3. GO term of DEPs. (XLS 127 kb)