cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11315726.v1
title: MOESM4 of A novel target convergence set based random walk with restart for prediction of potential LncRNA-disease associations

description: Additional file 4. The known 98 human cancer,668 lncRNAs and 1103 confirmed associations between them from Lnc2Cancer database.
DOI: 10.6084/m9.figshare.21275744.v1
title: Additional file 2 of Identification and validation of a fatty acid metabolism-related lncRNA signature as a predictor for prognosis and immunotherapy in patients with liver cancer

description: Additional file2: Supplementary excel 2. The correlation analysis between FA scores and lncRNAs in the TCGA LIHC cohort.
DOI: 10.6084/m9.figshare.21275747.v1
title: Additional file 3 of Identification and validation of a fatty acid metabolism-related lncRNA signature as a predictor for prognosis and immunotherapy in patients with liver cancer

description: Additional file3: Supplementary excel 3. The correlation analysis between FA scores and lncRNAs in the GSE76427 cohort.
DOI: 10.6084/m9.figshare.21275753
title: Additional file 5 of Identification and validation of a fatty acid metabolism-related lncRNA signature as a predictor for prognosis and immunotherapy in patients with liver cancer

description: Additional file5: Supplementary excel 5. The KEGG analysis of TFs in the TCGA LIHC cohort.
DOI: 10.6084/m9.figshare.21275753.v1
title: Additional file 5 of Identification and validation of a fatty acid metabolism-related lncRNA signature as a predictor for prognosis and immunotherapy in patients with liver cancer

description: Additional file5: Supplementary excel 5. The KEGG analysis of TFs in the TCGA LIHC cohort.
DOI: 10.6084/m9.figshare.21275744
title: Additional file 2 of Identification and validation of a fatty acid metabolism-related lncRNA signature as a predictor for prognosis and immunotherapy in patients with liver cancer

description: Additional file2: Supplementary excel 2. The correlation analysis between FA scores and lncRNAs in the TCGA LIHC cohort.
DOI: 10.6084/m9.figshare.25232159
title: Brussels-based Think Tanks Behaviour and Brexit

description: The related datasets are to accompany the article 'Brussels-based Think Tanks in Times of Crises: Examining Think Tank Climate Behavior Before and After Brexit'. The primary dataset is an interrupted time-series analysis of think tank publications before and after Brexit. The network datasets (edge and node lists) are focusing on the think tank's co-authorship interactions with other organizations.
DOI: 10.6084/m9.figshare.5024420
title: SPHK1 (sphingosine kinase 1) induces epithelial-mesenchymal transition by promoting the autophagy-linked lysosomal degradation of CDH1/E-cadherin in hepatoma cells

description: SPHK1 (sphingosine kinase 1), a regulator of sphingolipid metabolites, plays a causal role in the development of hepatocellular carcinoma (HCC) through augmenting HCC invasion and metastasis. However, the mechanism by which SPHK1 signaling promotes invasion and metastasis in HCC remains to be clarified. Here, we reported that SPHK1 induced the epithelial-mesenchymal transition (EMT) by accelerating CDH1/E-cadherin lysosomal degradation and facilitating the invasion and metastasis of HepG2 cells. Initially, we found that SPHK1 promoted cell migration and invasion and induced the EMT process through decreasing the expression of CDH1, which is an epithelial marker. Furthermore, SPHK1 accelerated the lysosomal degradation of CDH1 to induce EMT, which depended on TRAF2 (TNF receptor associated factor 2)-mediated macroautophagy/autophagy activation. In addition, the inhibition of autophagy recovered CDH1 expression and reduced cell migration and invasion through delaying the degradation of CDH1 in SPHK1-overexpressing cells. Moreover, the overexpression of SPHK1 produced intracellular sphingosine-1-phosphate (S1P). In response to S1P stimulation, TRAF2 bound to BECN1/Beclin 1 and catalyzed the lysine 63-linked ubiquitination of BECN1 for triggering autophagy. The deletion of the RING domain of TRAF2 inhibited autophagy and the interaction of BECN1 and TRAF2. Our findings define a novel mechanism responsible for the regulation of the EMT via SPHK1-TRAF2-BECN1-CDH1 signal cascades in HCC cells. Our work indicates that the blockage of SPHK1 activity to attenuate autophagy may be a promising strategy for the prevention and treatment of HCC.
DOI: 10.6084/m9.figshare.5024420.v1
title: SPHK1 (sphingosine kinase 1) induces epithelial-mesenchymal transition by promoting the autophagy-linked lysosomal degradation of CDH1/E-cadherin in hepatoma cells

description: SPHK1 (sphingosine kinase 1), a regulator of sphingolipid metabolites, plays a causal role in the development of hepatocellular carcinoma (HCC) through augmenting HCC invasion and metastasis. However, the mechanism by which SPHK1 signaling promotes invasion and metastasis in HCC remains to be clarified. Here, we reported that SPHK1 induced the epithelial-mesenchymal transition (EMT) by accelerating CDH1/E-cadherin lysosomal degradation and facilitating the invasion and metastasis of HepG2 cells. Initially, we found that SPHK1 promoted cell migration and invasion and induced the EMT process through decreasing the expression of CDH1, which is an epithelial marker. Furthermore, SPHK1 accelerated the lysosomal degradation of CDH1 to induce EMT, which depended on TRAF2 (TNF receptor associated factor 2)-mediated macroautophagy/autophagy activation. In addition, the inhibition of autophagy recovered CDH1 expression and reduced cell migration and invasion through delaying the degradation of CDH1 in SPHK1-overexpressing cells. Moreover, the overexpression of SPHK1 produced intracellular sphingosine-1-phosphate (S1P). In response to S1P stimulation, TRAF2 bound to BECN1/Beclin 1 and catalyzed the lysine 63-linked ubiquitination of BECN1 for triggering autophagy. The deletion of the RING domain of TRAF2 inhibited autophagy and the interaction of BECN1 and TRAF2. Our findings define a novel mechanism responsible for the regulation of the EMT via SPHK1-TRAF2-BECN1-CDH1 signal cascades in HCC cells. Our work indicates that the blockage of SPHK1 activity to attenuate autophagy may be a promising strategy for the prevention and treatment of HCC.
DOI: 10.6084/m9.figshare.11315927
title: MOESM6 of Identification and analysis of long non-coding RNA related miRNA sponge regulatory network in bladder urothelial carcinoma

description: Additional file 6.Â R software, version 3.4.3.
DOI: 10.6084/m9.figshare.11315927.v1
title: MOESM6 of Identification and analysis of long non-coding RNA related miRNA sponge regulatory network in bladder urothelial carcinoma

description: Additional file 6.Â R software, version 3.4.3.
DOI: 10.6084/m9.figshare.21273841
title: Additional file 1 of Genetic liability to obesity and peptic ulcer disease: a Mendelian randomization study

description: Additional file 1. Tabel S1. Proxies for SNPs not found in the outcome dataset (Forward MR); Tabel S2. Characteristics of the genetic variants associated with body mass index; Tabel S3. Characteristics of the genetic variants associated with waist-to-hip ratio; Tabel S4. Characteristics of the genetic variants associated with body mass index in replication analyses; Tabel S5. Characteristics of the genetic variants associated with waist-to-hip ratio in replication analyses; Tabel S6. Proxies for SNPs not found in the outcome dataset (Reverse MR); Tabel S7. Characteristics of the genetic variants associated with peptic ulcer disease; Tabel S8. Evaluation of heterogeneity and directional pleiotropy using different methods (Forward MR); Tabel S9. Evaluation of heterogeneity and directional pleiotropy in replication analyses (Forward MR); Table S10. Associations of genetic predisposition to PUD with risk of obesity in complementary Mendelian Randomization analyses (Reverse MR); Tabel S11. Evaluation of heterogeneity and directional pleiotropy using different methods (Reverse MR); Tabel S12. Evaluation of heterogeneity and directional pleiotropy in replication analyses (Reverse MR).
DOI: 10.6084/m9.figshare.20227054
title: Additional file 3 of Transcriptome-wide characterization, evolutionary analysis, and expression pattern analysis of the NF-Y transcription factor gene family and salt stress response in Panax ginseng

description: Additional file 3: Table S3. The classification, annotation and GO functional categorization of the PgNF-Y gene transcripts
DOI: 10.6084/m9.figshare.21275741
title: Additional file 1 of Identification and validation of a fatty acid metabolism-related lncRNA signature as a predictor for prognosis and immunotherapy in patients with liver cancer

description: Additional file1: Supplementary excel 1. Detailed clinical features in the two HCC cohorts.
DOI: 10.6084/m9.figshare.21275750
title: Additional file 4 of Identification and validation of a fatty acid metabolism-related lncRNA signature as a predictor for prognosis and immunotherapy in patients with liver cancer

description: Additional file4: Supplementary excel 4. The mutation profiles in the TCGA LIHC cohort.
DOI: 10.6084/m9.figshare.20227018.v1
title: Additional file 7 of Integrated transcriptome and hormonal analysis of naphthalene acetic acid-induced adventitious root formation of tea cuttings (Camellia sinensis)

description: Additional file 7: Table S3. KEGG enrichment analysis of DEGs in the green-stem cutting groups.
DOI: 10.6084/m9.figshare.20227012.v1
title: Additional file 5 of Integrated transcriptome and hormonal analysis of naphthalene acetic acid-induced adventitious root formation of tea cuttings (Camellia sinensis)

description: Additional file 5: Table S1. KEGG enrichment analysis of DEGs in both the red- and green-stem cutting groups.
DOI: 10.6084/m9.figshare.20227015
title: Additional file 6 of Integrated transcriptome and hormonal analysis of naphthalene acetic acid-induced adventitious root formation of tea cuttings (Camellia sinensis)

description: Additional file 6: Table S2. KEGG enrichment analysis of DEGs in the red-stem cutting groups.
DOI: 10.6084/m9.figshare.20227021.v1
title: Additional file 8 of Integrated transcriptome and hormonal analysis of naphthalene acetic acid-induced adventitious root formation of tea cuttings (Camellia sinensis)

description: Additional file 8: Table S4. Hormone-related DEGs in both the red- and green-stem cutting groups.
DOI: 10.6084/m9.figshare.21275741.v1
title: Additional file 1 of Identification and validation of a fatty acid metabolism-related lncRNA signature as a predictor for prognosis and immunotherapy in patients with liver cancer

description: Additional file1: Supplementary excel 1. Detailed clinical features in the two HCC cohorts.
DOI: 10.6084/m9.figshare.21275747
title: Additional file 3 of Identification and validation of a fatty acid metabolism-related lncRNA signature as a predictor for prognosis and immunotherapy in patients with liver cancer

description: Additional file3: Supplementary excel 3. The correlation analysis between FA scores and lncRNAs in the GSE76427 cohort.
DOI: 10.6084/m9.figshare.11316020
title: The GID ubiquitin ligase complex is a regulator of AMPK activity and organismal lifespan

description: The AMP-activated protein kinase (AMPK) regulates cellular energy homeostasis by sensing the metabolic status of the cell. AMPK is regulated by phosphorylation and dephosphorylation as a result of changing AMP/ATP levels and by removal of inhibitory ubiquitin residues by USP10. In this context, we identified the GID-complex, an evolutionarily conserved ubiquitin-ligase-complex (E3), as a negative regulator of AMPK activity. Our data show that the GID-complex targets AMPK for ubiquitination thereby altering its activity. Cells depleted of GID-subunits mimic a state of starvation as shown by increased AMPK activity and macroautophagic/autophagic flux as well as reduced MTOR activation. Consistently, <i>gid</i>-genes knockdown in <i>C. elegans</i> results in increased organismal lifespan. This study may contribute to understand metabolic disorders such as type 2 diabetes mellitus and morbid obesity and implements alternative therapeutic approaches to alter AMPK activity. ACTB: actin, beta; ADP: adenosine diphosphate; AMP: adenosine monophosphate; AMPK: AMP-activated protein kinase; ARMC8: armadillo repeat containing 8; ATP: adenosine triphosphate; BafA1: bafilomycin A<sub>1</sub>; BCAA: branched chain amino acid; BICC1: BicC family RNA binding protein 1; BSA: bovine serum albumin; CAMKK2 kinase: calcium/calmodulin dependent protein kinase kinase 2, beta; CHX: cycloheximide; DMEM: Dulbecco’s modified Eagle’s medium; E1: ubiquitin-activating enzyme; E2: ubiquitin-conjugating enzyme; E3: ubiquitin ligase; ECAR: extracellular acidification rate; FACS: fluorescent associated cell sorter; FBP1: fructose-bisphosphatase 1; FCCP: carbonyl cyanide-4 (trifluoromethoxy) phenylhydrazone; G6P: glucose-6-phosphate; GDP: guanosine diphosphate; GFP: green fluorescent protein; GID: glucose induced degradation deficient; GMP: guanosine monophosphate; GTP: guanosine triphosphate; HBP1: high mobility group box transcription factor 1; HPRT: hypoxanthine guanine phosphoribosyl transferase; KO: knock out; LE: long exposure; MAEA: macrophage erythroblast attacher; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; MKLN1: muskelin 1; mRNA: messenger RNA; MTOR: mechanistic target of rapamycin; NES: normalized enrichment score; OCR: oxygen consumption rate; PBS: phosphate buffered saline; PCK1: phosphoenolpyruvate carboxykinase 1, cytosolic; PCR: polymerase chain reaction; PFA: paraformaldehyde; RANBP9: RAN binding protein 9; RING: really interesting new gene; RMND5: required for meiotic nuclear division5 homolog; RPS6: ribosomal protein S6; RPTOR: regulatory associated protein of MTOR, complex 1; SE: short exposure; SEM: standard error of the mean; SQSTM1/p62: sequestosome 1; TSC2: tuberous sclerosis complex 2; TUBA4A: tubulin; TUBE: tandem ubiquitin binding entities; Ub: ubiquitin; UPS: ubiquitin proteasome system; WDR26: WD repeat domain 26; WT: wild type.
DOI: 10.6084/m9.figshare.11316020.v1
title: The GID ubiquitin ligase complex is a regulator of AMPK activity and organismal lifespan

description: The AMP-activated protein kinase (AMPK) regulates cellular energy homeostasis by sensing the metabolic status of the cell. AMPK is regulated by phosphorylation and dephosphorylation as a result of changing AMP/ATP levels and by removal of inhibitory ubiquitin residues by USP10. In this context, we identified the GID-complex, an evolutionarily conserved ubiquitin-ligase-complex (E3), as a negative regulator of AMPK activity. Our data show that the GID-complex targets AMPK for ubiquitination thereby altering its activity. Cells depleted of GID-subunits mimic a state of starvation as shown by increased AMPK activity and macroautophagic/autophagic flux as well as reduced MTOR activation. Consistently, <i>gid</i>-genes knockdown in <i>C. elegans</i> results in increased organismal lifespan. This study may contribute to understand metabolic disorders such as type 2 diabetes mellitus and morbid obesity and implements alternative therapeutic approaches to alter AMPK activity. ACTB: actin, beta; ADP: adenosine diphosphate; AMP: adenosine monophosphate; AMPK: AMP-activated protein kinase; ARMC8: armadillo repeat containing 8; ATP: adenosine triphosphate; BafA1: bafilomycin A<sub>1</sub>; BCAA: branched chain amino acid; BICC1: BicC family RNA binding protein 1; BSA: bovine serum albumin; CAMKK2 kinase: calcium/calmodulin dependent protein kinase kinase 2, beta; CHX: cycloheximide; DMEM: Dulbecco’s modified Eagle’s medium; E1: ubiquitin-activating enzyme; E2: ubiquitin-conjugating enzyme; E3: ubiquitin ligase; ECAR: extracellular acidification rate; FACS: fluorescent associated cell sorter; FBP1: fructose-bisphosphatase 1; FCCP: carbonyl cyanide-4 (trifluoromethoxy) phenylhydrazone; G6P: glucose-6-phosphate; GDP: guanosine diphosphate; GFP: green fluorescent protein; GID: glucose induced degradation deficient; GMP: guanosine monophosphate; GTP: guanosine triphosphate; HBP1: high mobility group box transcription factor 1; HPRT: hypoxanthine guanine phosphoribosyl transferase; KO: knock out; LE: long exposure; MAEA: macrophage erythroblast attacher; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; MKLN1: muskelin 1; mRNA: messenger RNA; MTOR: mechanistic target of rapamycin; NES: normalized enrichment score; OCR: oxygen consumption rate; PBS: phosphate buffered saline; PCK1: phosphoenolpyruvate carboxykinase 1, cytosolic; PCR: polymerase chain reaction; PFA: paraformaldehyde; RANBP9: RAN binding protein 9; RING: really interesting new gene; RMND5: required for meiotic nuclear division5 homolog; RPS6: ribosomal protein S6; RPTOR: regulatory associated protein of MTOR, complex 1; SE: short exposure; SEM: standard error of the mean; SQSTM1/p62: sequestosome 1; TSC2: tuberous sclerosis complex 2; TUBA4A: tubulin; TUBE: tandem ubiquitin binding entities; Ub: ubiquitin; UPS: ubiquitin proteasome system; WDR26: WD repeat domain 26; WT: wild type.
DOI: 10.6084/m9.figshare.21275750.v1
title: Additional file 4 of Identification and validation of a fatty acid metabolism-related lncRNA signature as a predictor for prognosis and immunotherapy in patients with liver cancer

description: Additional file4: Supplementary excel 4. The mutation profiles in the TCGA LIHC cohort.
DOI: 10.6084/m9.figshare.8168672.v1
title: Tectonic affinity of the Khanka Massif in the easternmost Central Asian Orogenic Belt: evidence from detrital zircon geochronology of Permian sedimentary rocks

description: The tectonic affiliation of the Khanka Massif, in the easternmost section of the Central Asian Orogenic Belt (CAOB), is still a matter of debate. Here, we provide new constraints on the provenance and timing of deposition of Permian strata in the western margin of the Khanka Massif. The results, which include U–Pb dating of detrital zircon grains using laser ablation–inductively coupled plasma–mass spectrometry (LA-ICP-MS), provide evidence regarding the tectonic position of the Khanka Massif and its role in the late Palaeozoic evolution of the eastern CAOB. Detrital zircon grains from a sublitharenite (Pingyangzhen Formation), a litharenite (Liangzichuan Formation), and a metamorphic siltstone (Qinglongcun Group) yielded multiple age populations ranging from Neoproterozoic (~914 Ma) to Permian (~272 Ma). Combined with age constraints from overlying/late-stage igneous rocks and other magmatism of the Khanka Massif, we conclude that the dated strata were deposited during the early–middle Permian and were sourced from the Khanka Massif. A comparison between the detrital zircon age populations and the history of magmatic activity in the neighbouring areas suggests that the Khanka Massif was tectonically linked to the Songnen–Zhangguangcai Range Massif. Based on tectonic discrimination diagrams, we conclude that the western margin of the Khanka Massif was positioned in a convergent-boundary basin during the early–middle Permian. Strike-slip faulting along the Dunhua–Mishan Fault, in response to ridge subduction of the Paleo-Asian Ocean Plate, resulted in a north-eastward movement of the Khanka Massif. The occurrence of Precambrian detrital zircon grains (with ages of 1900–1700 and 900–700 Ma) implies the presence of an ancient basement within the Khanka Massif.
DOI: 10.6084/m9.figshare.7120127
title: Additional file 2: of Muscle-specific regulation of right ventricular transcriptional responses to chronic hypoxia-induced hypertrophy by the muscle ring finger-1 (MuRF1) ubiquitin ligase in mice

description: Table S2. Differentially expressed genes in MuRF1 Tgâ +â mice challenged with hypoxia (XLSX 22 kb)
DOI: 10.6084/m9.figshare.7120118
title: Additional file 1: of Muscle-specific regulation of right ventricular transcriptional responses to chronic hypoxia-induced hypertrophy by the muscle ring finger-1 (MuRF1) ubiquitin ligase in mice

description: Table S1. Differentially expressed genes in MuRF1â /â mice challenged with hypoxia (XLSX 59 kb)
DOI: 10.6084/m9.figshare.12885866.v1
title: Additional file 1 of Salmonella enterica serovar Typhimurium inhibits the innate immune response and promotes apoptosis in a ribosomal/TRP53-dependent manner in swine neutrophils

description: Additional file 1. Sequencing matrix, the information on total number of reads, sequencing depth, coverage, processed data, and etc.
DOI: 10.6084/m9.figshare.20227109.v1
title: Additional file 1 of Genomic analysis of Listeria monocytogenes from US food processing environments reveals a high prevalence of QAC efflux genes but limited evidence of their contribution to environmental persistence

description: Additional file 1. Listeria Isolate Dataset. A list of isolates used in the analysis within this paper and their associated metadata. The SRR codes for each isolate are given which can be used to download the sequencing reads from NCBI.
DOI: 10.6084/m9.figshare.25232255
title: Supplementary Material for: Body focused repetitive behaviors in patients with FOXP1 syndrome: an international cross-sectional survey-based study

description: Introduction: FOXP1 syndrome is a rare neurodevelopmental disorder due to forkhead box protein 1 (FOXP1) gene mutations and is associated with intellectual disability, dysmorphic features, and autism spectrum disorder. We aimed to assess body focused repetitive behavior (BFRB) prevalence in this patient population using a cross-sectional survey-based study.

Methods: A validated survey assessing for BFRBs was administered to parents attending the International FOXP1 Foundation conference 6/21/2023 and was sent to a FOXP1 syndrome listserv. 

Results: Excoriation disorder, onychophagia, onychotillomania, and trichotillomania were reported by 58.6%, 38.6%, 29.7%, and 10.0% of subjects, with 63.4%, 59.3%, 54.5%, and 14.3% having moderate to severe disease, respectively. Overall, 28.6%, 30.0%, and 10.0% had one, two, and three BFRBs, respectively. 

Conclusion: Prevalence of BFRBs is high amongst FOXP1 syndrome patients, affecting quality of life for patients and their families, and causing significant sequelae.
DOI: 10.6084/m9.figshare.25232255.v1
title: Supplementary Material for: Body focused repetitive behaviors in patients with FOXP1 syndrome: an international cross-sectional survey-based study

description: Introduction: FOXP1 syndrome is a rare neurodevelopmental disorder due to forkhead box protein 1 (FOXP1) gene mutations and is associated with intellectual disability, dysmorphic features, and autism spectrum disorder. We aimed to assess body focused repetitive behavior (BFRB) prevalence in this patient population using a cross-sectional survey-based study.

Methods: A validated survey assessing for BFRBs was administered to parents attending the International FOXP1 Foundation conference 6/21/2023 and was sent to a FOXP1 syndrome listserv. 

Results: Excoriation disorder, onychophagia, onychotillomania, and trichotillomania were reported by 58.6%, 38.6%, 29.7%, and 10.0% of subjects, with 63.4%, 59.3%, 54.5%, and 14.3% having moderate to severe disease, respectively. Overall, 28.6%, 30.0%, and 10.0% had one, two, and three BFRBs, respectively. 

Conclusion: Prevalence of BFRBs is high amongst FOXP1 syndrome patients, affecting quality of life for patients and their families, and causing significant sequelae.
DOI: 10.6084/m9.figshare.7121867.v1
title: Additional file 5 of Discovering large conserved functional components in global network alignment by graph matching

description: The results produced by HubAlign. Each pathway pair has four sheets to describe alignment results. The former two sheets represent retrieving results of two species by APID dataserver [38] respectively. The third sheet is direct alignment results of HubAlign. The forth sheet is the final conserved interactions of the pathway pair. (XLS 59 kb)