cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8019623
title: MTORC1 coordinates the autophagy and apoptosis signaling in articular chondrocytes in osteoarthritic temporomandibular joint

description: A switch from autophagy to apoptosis is implicated in chondrocytes during the osteoarthritis (OA) progression with currently unknown mechanism(s). In this study we utilized a flow fluid shear stress (FFSS) model in cultured chondrocytes and a unilateral anterior crossbite (UAC) animal model. We found that both FFSS and UAC actively induced endoplasmic reticulum stress (ERS) in the temporomandibular joints (TMJ) chondrocytes, as demonstrated by dramatic increases in expression of HSPA5, p-EIF2AK3, p-ERN1 and ATF6. Interestingly, both FFSS and UAC activated not only pro-death p-EIF2AK3-mediated ERS-apoptosis programs but also pro-survival p-ERN1-mediated autophagic flux in chondrocytes. Data from FFSS demonstrated that MTORC1, a downstream of p-ERN1, suppressed autophagy but promoted p-EIF2AK3 mediated ERS-apoptosis. Data from UAC model demonstrated that at early stage both the p-ERN1 and p-EIF2AK3 were activated and MTORC1 was inhibited in TMJ chondrocytes. At late stage, MTORC1-p-EIF2AK3-mediated ERS apoptosis were predominant, while p-ERN1 and autophagic flux were inhibited. Inhibition of MTORC1 by TMJ local injection of rapamycin in rats or inducible ablation of MTORC1 expression selectively in chondrocytes in mice promoted chondrocyte autophagy and suppressed apoptosis, and reduced TMJ cartilage loss induced by UAC. In contrast, MTORC1 activation by TMJ local administration of MHY1485 or genetic deletion of <i>Tsc1</i>, an upstream MTORC1 suppressor, resulted in opposite effects. Collectively, our results establish that aberrant mechanical loading causes cartilage degeneration by activating, at least in part, the MTORC1 signaling which modulates the autophagy and apoptosis programs in TMJ chondrocytes. Thus, inhibition of MTORC1 provides a novel therapeutic strategy for prevention and treatment of OA. <b>Abbreviations</b> : ACTB: actin beta; ATF6: activating transcription factor 6; BECN1: beclin 1; BFL: bafilomycin A<sub>1</sub>; CASP12: caspase 12; CASP3: caspase 3; DAPI: 4ʹ,6-diamidino-2-phenylindole; DDIT3: DNA-damage inducible transcript 3; EIF2AK3/PERK: eukaryotic translation initiation factor 2 alpha kinase 3; ER: endoplasmic reticulum; ERS: endoplasmic reticulum stress; ERN1/IRE1: endoplasmic reticulum to nucleus signaling 1; FFSS: flow fluid shear stress; HSPA5/GRP78/BiP: heat shock protein 5; LAMP2: lysosome-associated membrane protein 2; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MTOR: mechanistic target of rapamycin kinase; MTORC1: mechanistic target of rapamycin complex 1; OA: osteoarthritis; PRKAA1/2/AMPK1/2: protein kinase, AMP-activated, alpha 1/2 catalytic subunit; RPS6: ribosomal protein S6; Rapa: rapamycin; SQSTM1/p62: sequestosome 1; TEM: transmission electron microscopy; TG: thapsigargin; TMJ: temporomandibular joints; TSC1/2: tuberous sclerosis complex 1/2; UAC: unilateral anterior crossbite; UPR: unfolded protein response; XBP1: x-box binding protein 1.
DOI: 10.6084/m9.figshare.8019623.v2
title: MTORC1 coordinates the autophagy and apoptosis signaling in articular chondrocytes in osteoarthritic temporomandibular joint

description: A switch from autophagy to apoptosis is implicated in chondrocytes during the osteoarthritis (OA) progression with currently unknown mechanism(s). In this study we utilized a flow fluid shear stress (FFSS) model in cultured chondrocytes and a unilateral anterior crossbite (UAC) animal model. We found that both FFSS and UAC actively induced endoplasmic reticulum stress (ERS) in the temporomandibular joints (TMJ) chondrocytes, as demonstrated by dramatic increases in expression of HSPA5, p-EIF2AK3, p-ERN1 and ATF6. Interestingly, both FFSS and UAC activated not only pro-death p-EIF2AK3-mediated ERS-apoptosis programs but also pro-survival p-ERN1-mediated autophagic flux in chondrocytes. Data from FFSS demonstrated that MTORC1, a downstream of p-ERN1, suppressed autophagy but promoted p-EIF2AK3 mediated ERS-apoptosis. Data from UAC model demonstrated that at early stage both the p-ERN1 and p-EIF2AK3 were activated and MTORC1 was inhibited in TMJ chondrocytes. At late stage, MTORC1-p-EIF2AK3-mediated ERS apoptosis were predominant, while p-ERN1 and autophagic flux were inhibited. Inhibition of MTORC1 by TMJ local injection of rapamycin in rats or inducible ablation of MTORC1 expression selectively in chondrocytes in mice promoted chondrocyte autophagy and suppressed apoptosis, and reduced TMJ cartilage loss induced by UAC. In contrast, MTORC1 activation by TMJ local administration of MHY1485 or genetic deletion of <i>Tsc1</i>, an upstream MTORC1 suppressor, resulted in opposite effects. Collectively, our results establish that aberrant mechanical loading causes cartilage degeneration by activating, at least in part, the MTORC1 signaling which modulates the autophagy and apoptosis programs in TMJ chondrocytes. Thus, inhibition of MTORC1 provides a novel therapeutic strategy for prevention and treatment of OA. <b>Abbreviations</b> : ACTB: actin beta; ATF6: activating transcription factor 6; BECN1: beclin 1; BFL: bafilomycin A<sub>1</sub>; CASP12: caspase 12; CASP3: caspase 3; DAPI: 4ʹ,6-diamidino-2-phenylindole; DDIT3: DNA-damage inducible transcript 3; EIF2AK3/PERK: eukaryotic translation initiation factor 2 alpha kinase 3; ER: endoplasmic reticulum; ERS: endoplasmic reticulum stress; ERN1/IRE1: endoplasmic reticulum to nucleus signaling 1; FFSS: flow fluid shear stress; HSPA5/GRP78/BiP: heat shock protein 5; LAMP2: lysosome-associated membrane protein 2; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MTOR: mechanistic target of rapamycin kinase; MTORC1: mechanistic target of rapamycin complex 1; OA: osteoarthritis; PRKAA1/2/AMPK1/2: protein kinase, AMP-activated, alpha 1/2 catalytic subunit; RPS6: ribosomal protein S6; Rapa: rapamycin; SQSTM1/p62: sequestosome 1; TEM: transmission electron microscopy; TG: thapsigargin; TMJ: temporomandibular joints; TSC1/2: tuberous sclerosis complex 1/2; UAC: unilateral anterior crossbite; UPR: unfolded protein response; XBP1: x-box binding protein 1.
DOI: 10.6084/m9.figshare.10117028
title: MOESM2 of Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

description: Additional file 2:Table S6. Identified fungi from ITS1 sequencing.
DOI: 10.6084/m9.figshare.10117028.v1
title: MOESM2 of Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

description: Additional file 2:Table S6. Identified fungi from ITS1 sequencing.
DOI: 10.6084/m9.figshare.10117064
title: MOESM1 of Suppressed N fixation and diazotrophs after four decades of fertilization

description: Additional file 1: Table S1. Physicochemical soil properties in bulk soil and rhizosphere soil among different fertilization treatments. Table S2. The relative abundance of dominant diazotrophic genera among different treatments. Table S3. Pairwise t-tests for the relative abundance of dominant diazotrophic genera between bulk soil and rhizosphere soil in different fertilization treatments. Table S4. Comparison of diazotrophic alpha-diversity indexes among different fertilization treatments. Table S5. Pairwise t-testing of diazotrophic alpha-diversity in bulk soil and rhizosphere soil. Table S6. Pairwise t-tests of nitrogen fixation rates in bulk soil and rhizosphere soil in different fertilization treatments. Table S7. ADONIS double factor analysis for the diazotrophic community. Table S8. Pairwise t-tests of relative abundance of main ecological clusters within the diazotrophic community in bulk soil and rhizosphere soil under different fertilization treatments. Table S9. The network properties for the main ecological clusters of the diazotrophic community. Table S10. Operational taxonomic unit (OTU) count properties of important species for nitrogen fixation rates found by the Random Forest model in the three main ecological clusters. Table S11. The correlations (r) and significance (p) were determined using a Mantel test between the diazotrophic community and environmental variables in bulk soil and rhizosphere soil. Table S12. Spearman correlation between physicochemical soil properties and diazotrophic alpha-diversity. Table S13. Spearman correlation between physicochemical soil properties and relative abundance of the main diazotrophic ecological clusters.
DOI: 10.6084/m9.figshare.10117064.v1
title: MOESM1 of Suppressed N fixation and diazotrophs after four decades of fertilization

description: Additional file 1: Table S1. Physicochemical soil properties in bulk soil and rhizosphere soil among different fertilization treatments. Table S2. The relative abundance of dominant diazotrophic genera among different treatments. Table S3. Pairwise t-tests for the relative abundance of dominant diazotrophic genera between bulk soil and rhizosphere soil in different fertilization treatments. Table S4. Comparison of diazotrophic alpha-diversity indexes among different fertilization treatments. Table S5. Pairwise t-testing of diazotrophic alpha-diversity in bulk soil and rhizosphere soil. Table S6. Pairwise t-tests of nitrogen fixation rates in bulk soil and rhizosphere soil in different fertilization treatments. Table S7. ADONIS double factor analysis for the diazotrophic community. Table S8. Pairwise t-tests of relative abundance of main ecological clusters within the diazotrophic community in bulk soil and rhizosphere soil under different fertilization treatments. Table S9. The network properties for the main ecological clusters of the diazotrophic community. Table S10. Operational taxonomic unit (OTU) count properties of important species for nitrogen fixation rates found by the Random Forest model in the three main ecological clusters. Table S11. The correlations (r) and significance (p) were determined using a Mantel test between the diazotrophic community and environmental variables in bulk soil and rhizosphere soil. Table S12. Spearman correlation between physicochemical soil properties and diazotrophic alpha-diversity. Table S13. Spearman correlation between physicochemical soil properties and relative abundance of the main diazotrophic ecological clusters.
DOI: 10.6084/m9.figshare.12737535
title: Additional file 3 of Insights into the phylogenetic relationships and drug targets of Babesia isolates infective to small ruminants from the mitochondrial genomes

description: Additional file 3: Table S2. Comparison of six ovine Babesia mitochondrial genomes.
DOI: 10.6084/m9.figshare.12737535.v1
title: Additional file 3 of Insights into the phylogenetic relationships and drug targets of Babesia isolates infective to small ruminants from the mitochondrial genomes

description: Additional file 3: Table S2. Comparison of six ovine Babesia mitochondrial genomes.
DOI: 10.6084/m9.figshare.10117172
title: MOESM5 of Circ-AKT3 inhibits clear cell renal cell carcinoma metastasis via altering miR-296-3p/E-cadherin signals

description: Additional file 5: Table S4. Differently expressed circRNAs expression profiles in ccRCC via microarray.
DOI: 10.6084/m9.figshare.10117172.v1
title: MOESM5 of Circ-AKT3 inhibits clear cell renal cell carcinoma metastasis via altering miR-296-3p/E-cadherin signals

description: Additional file 5: Table S4. Differently expressed circRNAs expression profiles in ccRCC via microarray.
DOI: 10.6084/m9.figshare.20078678
title: Dataset for Competing effects of proppant and surface roughness on the frictional stability of propped rock fractures

description: This is the dataset for the manuscript titled "Competing effects of proppant and surface roughness on the frictional stability of propped rock fractures"
DOI: 10.6084/m9.figshare.19028918
title: Additional file 1 of Physiological response of Kobresia pygmaea to temperature changes on the Qinghai-Tibet Plateau

description: Additional file 1.
DOI: 10.6084/m9.figshare.12736863
title: Additional file 2 of Intermittent theta burst stimulation (iTBS) combined with working memory training to improve cognitive function in schizophrenia: study protocol for a randomized controlled trial

description: Additional file 2. Funding Documentation: National Natural Science Foundation of China General Projects.
DOI: 10.6084/m9.figshare.12737823
title: Additional file 4 of Splicing-accessible coding 3′UTRs control protein stability and interaction networks

description: Additional file 4: Table S3. Correlation of protein half-life and proline content of frameshift-proteins.
DOI: 10.6084/m9.figshare.12737645.v1
title: Additional file 1 of Population structure, genetic diversity, and selective signature of Chaka sheep revealed by whole genome sequencing

description: Additional file 1: Supplementary Table 1. The genetic variation information of SNPs and indels in sheep breeds. Supplementary Table 2. The level of genetic diversity in the four populations. Supplementary Table 3. Amount of ROH at different lengths. Supplementary Table 4. Host genes of CKA Specific missense mutations for GO and KEGG analysis. Supplementary Table 5. Summary of candidate genes in the Chaka sheep population detected by XP-CLR statistics. Supplementary Table 6. The list of GO and KEGG analyses for genes with high selection signature by XP-CLR. Supplementary Table 7. Summary of candidate genes in four sheep populations detected by Fst statistics. Supplementary Table 8. The list of GO and KEGG analyses for genes with high selection signature by Fst. Supplementary Table 9. The range and amount of sequence data. Supplementary Table 10. Sample collection and sequencing information. Supplementary Table 11. Optimum for population differentiation according to CV errors.
DOI: 10.6084/m9.figshare.12737823.v1
title: Additional file 4 of Splicing-accessible coding 3′UTRs control protein stability and interaction networks

description: Additional file 4: Table S3. Correlation of protein half-life and proline content of frameshift-proteins.
DOI: 10.6084/m9.figshare.12737826.v1
title: Additional file 5 of Splicing-accessible coding 3′UTRs control protein stability and interaction networks

description: Additional file 5: Table S4. Potential extended frames allowing translation into the 3’UTR of all mammalian species harboring a U2af26 gene.
DOI: 10.6084/m9.figshare.12737829.v1
title: Additional file 6 of Splicing-accessible coding 3′UTRs control protein stability and interaction networks

description: Additional file 6: Table S5. Interactions of U2AF26fl and U2AF26fs analyzed by mass spec.
DOI: 10.6084/m9.figshare.19029144
title: Additional file 3 of Integrated 5-hydroxymethylcytosine and fragmentation signatures as enhanced biomarkers in lung cancer

description: Additional file 3: Table S2: GREAT enrichment analysis result of different 3718 loci from cfDNA 5hmC data.
DOI: 10.6084/m9.figshare.19029144.v1
title: Additional file 3 of Integrated 5-hydroxymethylcytosine and fragmentation signatures as enhanced biomarkers in lung cancer

description: Additional file 3: Table S2: GREAT enrichment analysis result of different 3718 loci from cfDNA 5hmC data.
DOI: 10.6084/m9.figshare.19029147
title: Additional file 4 of Integrated 5-hydroxymethylcytosine and fragmentation signatures as enhanced biomarkers in lung cancer

description: Additional file 4: Table S3: List of 5hmC markers used in model construction.
DOI: 10.6084/m9.figshare.19029141
title: Additional file 2 of Integrated 5-hydroxymethylcytosine and fragmentation signatures as enhanced biomarkers in lung cancer

description: Additional file 2: Table S1: Mapping summary of cfDNA 5hmC sequencing data.
DOI: 10.6084/m9.figshare.19029141.v1
title: Additional file 2 of Integrated 5-hydroxymethylcytosine and fragmentation signatures as enhanced biomarkers in lung cancer

description: Additional file 2: Table S1: Mapping summary of cfDNA 5hmC sequencing data.
DOI: 10.6084/m9.figshare.19029153.v1
title: Additional file 6 of Integrated 5-hydroxymethylcytosine and fragmentation signatures as enhanced biomarkers in lung cancer

description: Additional file 6: Table S5: Wd-scores of 189 healthy controls, 157 lung cancer patients and 133 external validation samples derived from distinct models.
DOI: 10.6084/m9.figshare.19029150
title: Additional file 5 of Integrated 5-hydroxymethylcytosine and fragmentation signatures as enhanced biomarkers in lung cancer

description: Additional file 5: Table S4: List of fragmentation markers used in model construction.
DOI: 10.6084/m9.figshare.19029150.v1
title: Additional file 5 of Integrated 5-hydroxymethylcytosine and fragmentation signatures as enhanced biomarkers in lung cancer

description: Additional file 5: Table S4: List of fragmentation markers used in model construction.
DOI: 10.6084/m9.figshare.12737645
title: Additional file 1 of Population structure, genetic diversity, and selective signature of Chaka sheep revealed by whole genome sequencing

description: Additional file 1: Supplementary Table 1. The genetic variation information of SNPs and indels in sheep breeds. Supplementary Table 2. The level of genetic diversity in the four populations. Supplementary Table 3. Amount of ROH at different lengths. Supplementary Table 4. Host genes of CKA Specific missense mutations for GO and KEGG analysis. Supplementary Table 5. Summary of candidate genes in the Chaka sheep population detected by XP-CLR statistics. Supplementary Table 6. The list of GO and KEGG analyses for genes with high selection signature by XP-CLR. Supplementary Table 7. Summary of candidate genes in four sheep populations detected by Fst statistics. Supplementary Table 8. The list of GO and KEGG analyses for genes with high selection signature by Fst. Supplementary Table 9. The range and amount of sequence data. Supplementary Table 10. Sample collection and sequencing information. Supplementary Table 11. Optimum for population differentiation according to CV errors.
DOI: 10.6084/m9.figshare.12737829
title: Additional file 6 of Splicing-accessible coding 3′UTRs control protein stability and interaction networks

description: Additional file 6: Table S5. Interactions of U2AF26fl and U2AF26fs analyzed by mass spec.
DOI: 10.6084/m9.figshare.19029147.v1
title: Additional file 4 of Integrated 5-hydroxymethylcytosine and fragmentation signatures as enhanced biomarkers in lung cancer

description: Additional file 4: Table S3: List of 5hmC markers used in model construction.
DOI: 10.6084/m9.figshare.19029153
title: Additional file 6 of Integrated 5-hydroxymethylcytosine and fragmentation signatures as enhanced biomarkers in lung cancer

description: Additional file 6: Table S5: Wd-scores of 189 healthy controls, 157 lung cancer patients and 133 external validation samples derived from distinct models.
DOI: 10.6084/m9.figshare.12737915
title: Additional file 1 of Constructing a novel expression system by specific activation of amylase expression pathway in Penicillium

description: Additional file 1: Table S1. Quality control statistics of transcriptomics sequences.
DOI: 10.6084/m9.figshare.12737918
title: Additional file 2 of Constructing a novel expression system by specific activation of amylase expression pathway in Penicillium

description: Additional file 2: Table S2. Gene list of the 680 genes showed increase in strain Δ13A-OamyR as compared to strain Δ13A.
DOI: 10.6084/m9.figshare.12737921
title: Additional file 3 of Constructing a novel expression system by specific activation of amylase expression pathway in Penicillium

description: Additional file 3: Table S3. Gene list of the 1042 genes showed decrease in strain Δ13A-OamyR as compared to strain Δ13A.
DOI: 10.6084/m9.figshare.12736850
title: Additional file 1 of Impact of initial dialysis modality on the survival of patients with ESRD in eastern China: a propensity-matched study

description: Additional file 1: Table S1. Baseline characteristics of 7761 excluded hemodialysis (HD) and 541 excluded peritoneal dialysis (PD) patients.
DOI: 10.6084/m9.figshare.12737817
title: Additional file 2 of Splicing-accessible coding 3′UTRs control protein stability and interaction networks

description: Additional file 2: Table S1. List of mouse and human candidates with extended frames in the 3’UTR as well as conservation of frameshift-inducing alternative splicing of the penultimate exon between mouse and human.
DOI: 10.6084/m9.figshare.12737915.v1
title: Additional file 1 of Constructing a novel expression system by specific activation of amylase expression pathway in Penicillium

description: Additional file 1: Table S1. Quality control statistics of transcriptomics sequences.
DOI: 10.6084/m9.figshare.12737921.v1
title: Additional file 3 of Constructing a novel expression system by specific activation of amylase expression pathway in Penicillium

description: Additional file 3: Table S3. Gene list of the 1042 genes showed decrease in strain Δ13A-OamyR as compared to strain Δ13A.
DOI: 10.6084/m9.figshare.12737817.v1
title: Additional file 2 of Splicing-accessible coding 3′UTRs control protein stability and interaction networks

description: Additional file 2: Table S1. List of mouse and human candidates with extended frames in the 3’UTR as well as conservation of frameshift-inducing alternative splicing of the penultimate exon between mouse and human.
DOI: 10.6084/m9.figshare.12736866.v1
title: Additional file 3 of Intermittent theta burst stimulation (iTBS) combined with working memory training to improve cognitive function in schizophrenia: study protocol for a randomized controlled trial

description: Additional file 3. Ethical review approval
DOI: 10.6084/m9.figshare.20076701
title: Additional file 1 of SARS-CoV-2 productively infects human brain microvascular endothelial cells

description: Additional file 1: Table S1. Primers used for qPCR in this study.
DOI: 10.17632/f25py6tjyp.1
title: Future-projected One-day PMP dataset across India based on CMIP6

description: This multi-model multi-scenario dataset presents high-resolution (0.25° latitude x 0.25° longitude) one-day Probable Maximum Precipitation (PMP) estimates across Indian mainland ocer the future (2021-2100). Towards this, a total of 14 state-of-the-art General Circulation Models (GCMs), participating in Coupled Model Intercomparison Project version 6 (CMIP6) are considered, following two possible emission scenarios (SSP 245 and SSP 585). These estimates are determined following the research article entitled “Increase in Probable Maximum Precipitation in a Changing Climate over India," published in Journal of Hydrology by Sarkar and Maity (2020). It is worthwhile to mention here that, this future projection is done after suitably correcting the inherent bias present in the simulated output from the GCMs. We expect, this future-projected PMP dataset will serve as an important information for the design engineers and hydro-meteorologists for planning and designing various water-energy infrastructures such as dams and other major water resources engineering applications.
DOI: 10.6084/m9.figshare.12737820
title: Additional file 3 of Splicing-accessible coding 3′UTRs control protein stability and interaction networks

description: Additional file 3: Table S2. Frameshift peptides identified by mass spectrometric analysis of mouse brain lysate and PxxP motif frequency in mouse and human candidates.
DOI: 10.6084/m9.figshare.12737820.v1
title: Additional file 3 of Splicing-accessible coding 3′UTRs control protein stability and interaction networks

description: Additional file 3: Table S2. Frameshift peptides identified by mass spectrometric analysis of mouse brain lysate and PxxP motif frequency in mouse and human candidates.
DOI: 10.6084/m9.figshare.12737918.v1
title: Additional file 2 of Constructing a novel expression system by specific activation of amylase expression pathway in Penicillium

description: Additional file 2: Table S2. Gene list of the 680 genes showed increase in strain Δ13A-OamyR as compared to strain Δ13A.