cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17185699
title: Excavating novel diagnostic and prognostic long non-coding RNAs (lncRNAs) for head and neck squamous cell carcinoma: an integrated bioinformatics analysis of competing endogenous RNAs (ceRNAs) and gene co-expression networks

description: Long non-coding RNAs (lncRNAs) have been demonstrated to fine-tune gene regulations that govern a broad spectrum of oncogenic processes. Nonetheless, our understanding of the roles of lncRNAs and their interactions with miRNAs and mRNAs in HNSCC is still highly rudimentary. Here, we present a comprehensive bioinformatics analysis in which competing endogenous RNA (ceRNA) network construction and weighted gene co-expression network analysis (WGCNA) were combined to explore novel diagnostic and prognostic lncRNAs for HNSCC. Differentially expressed mRNAs (DEGs), miRNAs (DEMs) and lncRNAs (DELs) were identified based on the RNA sequencing data and clinical data retrieved from TCGA database. LncRNA-regulated ceRNA networks were constructed based on the interactive RNA pairs predicted by miRDB, miRcode and TargetScan. WGCNA was conducted to identify lncRNAs that were significantly correlated with patient overall survival (OS) and HNSCC tumor. RT-qPCR was employed to validate the expression of lncRNAs in HNSCC cell lines and patient sera. A ceRNA network consisting of 90 DEGs, 7 DEMs and 67 DELs associated with clinical traits was established. WGCNA and Kaplan-Meier survival analysis revealed that 5 DELs (MIR4435-2 HG, CASC9, LINC01980, STARD4-AS1 and MIR99AHG) were significantly correlated with OS of HNSCC patients, whereas DEL PART1 was most significantly correlated with the HNSCC tumor. The <i>in silico</i> predicted expression patterns of PART1, LINC01980 and MIR4435-2 HG were further validated in HNSCC cell lines and patient sera. Collectively, the present study provided novel insights into the lncRNA-regulated ceRNA networks in HNSCC and identified novel lncRNAs that harbor diagnostic and prognostic potentials for HNSCC. <b>Abbreviations</b> BP, biological process. CC, cellular component. ceRNA, competing endogenous RNA. DEG, differential expressions of mRNA. DEL, differentially expressed lncRNA. DEM, differentially expressed miRNA. ESCC, esophageal squamous cell carcinoma. FPKM, Fragments Per Kilobase Million. GO, Gene Ontology. GS, gene significance. HNSCC, head and neck squamous cell carcinoma. KEGG, Kyoto Encyclopedia of Genes and Genomes. LncRNA, long non-coding RNA. MCC, Maximal Clique Centrality. ME, module eigengenes. MF, molecular functions. MM, module membership. MRE, miRNA-binding site. MYO5A, Myosin-Va. PART1, prostate androgen-regulated transcript 1. RBM3, RNA‑binding motif protein 3. TCGA, The Cancer Genome Atlas. TOM, topological overlap measure. TSCC, tongue squamous cell carcinoma. WGCNA, weighted gene co-expression network analysis.
DOI: 10.34740/kaggle/dsv/7685176
title: ⏳ endoflife.date database (duckdb)
DOI: 10.6084/m9.figshare.21904375
title: R-spondin family biology and emerging linkages to cancer

description: The R-spondin protein family comprises four members (RSPO1-4), which are agonists of the canonical Wnt/β-catenin pathway. Emerging evidence revealed that RSPOs should not only be viewed as agonists of the Wnt/β-catenin pathway but also as regulators for tumor development and progression. Aberrant expression of RSPOs is related to tumorigenesis and tumor development in multiple cancers and their expression of RSPOs has also been correlated with anticancer immune cell signatures. More importantly, the role of RSPOs as potential target therapies and their implication in cancer progressions has been studied in the preclinical and clinical settings. These findings highlight the possible therapeutic value of RSPOs in cancer medicine. However, the expression pattern, effects, and mechanisms of RSPO proteins in cancer remain elusive. Investigating the many roles of RSPOs is likely to expand and improve our understanding of the oncogenic mechanisms mediated by RSPOs. Here, we reviewed the recent advances in the functions and underlying molecular mechanisms of RSPOs in tumor development, cancer microenvironment regulation, and immunity, and discussed the therapeutic potential of targeting RSPOs for cancer treatment. In addition, we also explored the biological feature and clinical relevance of RSPOs in cancer mutagenesis, transcriptional regulation, and immune correlation by bioinformatics analysis.KEY MESSAGESAberrant expressions of RSPOs are detected in various human malignancies and are always correlated with oncogenesis.Although extensive studies of RSPOs have been conducted, their precise molecular mechanism remains poorly understood.Bioinformatic analysis revealed that RSPOs may play a part in the development of the immune composition of the tumor microenvironment. Aberrant expressions of RSPOs are detected in various human malignancies and are always correlated with oncogenesis. Although extensive studies of RSPOs have been conducted, their precise molecular mechanism remains poorly understood. Bioinformatic analysis revealed that RSPOs may play a part in the development of the immune composition of the tumor microenvironment.
DOI: 10.6084/m9.figshare.17185699.v1
title: Excavating novel diagnostic and prognostic long non-coding RNAs (lncRNAs) for head and neck squamous cell carcinoma: an integrated bioinformatics analysis of competing endogenous RNAs (ceRNAs) and gene co-expression networks

description: Long non-coding RNAs (lncRNAs) have been demonstrated to fine-tune gene regulations that govern a broad spectrum of oncogenic processes. Nonetheless, our understanding of the roles of lncRNAs and their interactions with miRNAs and mRNAs in HNSCC is still highly rudimentary. Here, we present a comprehensive bioinformatics analysis in which competing endogenous RNA (ceRNA) network construction and weighted gene co-expression network analysis (WGCNA) were combined to explore novel diagnostic and prognostic lncRNAs for HNSCC. Differentially expressed mRNAs (DEGs), miRNAs (DEMs) and lncRNAs (DELs) were identified based on the RNA sequencing data and clinical data retrieved from TCGA database. LncRNA-regulated ceRNA networks were constructed based on the interactive RNA pairs predicted by miRDB, miRcode and TargetScan. WGCNA was conducted to identify lncRNAs that were significantly correlated with patient overall survival (OS) and HNSCC tumor. RT-qPCR was employed to validate the expression of lncRNAs in HNSCC cell lines and patient sera. A ceRNA network consisting of 90 DEGs, 7 DEMs and 67 DELs associated with clinical traits was established. WGCNA and Kaplan-Meier survival analysis revealed that 5 DELs (MIR4435-2 HG, CASC9, LINC01980, STARD4-AS1 and MIR99AHG) were significantly correlated with OS of HNSCC patients, whereas DEL PART1 was most significantly correlated with the HNSCC tumor. The <i>in silico</i> predicted expression patterns of PART1, LINC01980 and MIR4435-2 HG were further validated in HNSCC cell lines and patient sera. Collectively, the present study provided novel insights into the lncRNA-regulated ceRNA networks in HNSCC and identified novel lncRNAs that harbor diagnostic and prognostic potentials for HNSCC. <b>Abbreviations</b> BP, biological process. CC, cellular component. ceRNA, competing endogenous RNA. DEG, differential expressions of mRNA. DEL, differentially expressed lncRNA. DEM, differentially expressed miRNA. ESCC, esophageal squamous cell carcinoma. FPKM, Fragments Per Kilobase Million. GO, Gene Ontology. GS, gene significance. HNSCC, head and neck squamous cell carcinoma. KEGG, Kyoto Encyclopedia of Genes and Genomes. LncRNA, long non-coding RNA. MCC, Maximal Clique Centrality. ME, module eigengenes. MF, molecular functions. MM, module membership. MRE, miRNA-binding site. MYO5A, Myosin-Va. PART1, prostate androgen-regulated transcript 1. RBM3, RNA‑binding motif protein 3. TCGA, The Cancer Genome Atlas. TOM, topological overlap measure. TSCC, tongue squamous cell carcinoma. WGCNA, weighted gene co-expression network analysis.
DOI: 10.6084/m9.figshare.14564332.v1
title: Effects of intensive blood pressure control on mortality and cardiorenal function in chronic kidney disease patients

description: Blood pressure (BP) variability is highly correlated with cardiovascular and kidney outcomes in patients with chronic kidney disease (CKD). However, appropriate BP targets in patients with CKD remain uncertain. We searched PubMed, Embase, and the Cochrane Library for randomized controlled trials (RCTs) of CKD patients who underwent intensive BP management. Kappa score was used to assess inter-rater agreement. A good agreement between the authors was observed to inter-rater reliability of RCTs selection (kappa = 0.77; <i>P</i> = 0.005). Ten relevant studies involving 20 059 patients were included in the meta-analysis. Overall, intensive BP management may reduce the incidence of cardiovascular disease mortality (RR: 0.69, 95% CI: 0.53 to 0.90, <i>P</i>: 0.01), all-cause mortality (RR: 0.77, 95% CI: 0.67 to 0.88, <i>P</i> &lt; 0.01) and composite cardiovascular events (RR: 0.84 95% CI: 0.75 to 0.95, <i>P</i> &lt; 0.01) in patients with CKD. However, reducing BP has no significant effect on the incidence of doubling of serum creatinine level or 50% reduction in GFR (RR: 1.26, 95% CI: 0.66 to 2.40, <i>P</i> = 0.48), composite renal events (RR 1.07, 95% CI: 0.81 to 1.41, <i>P</i> = 0.64) or SAEs (RR: 0.97, 95% CI: 0.90 to 1.05, <i>P</i> = 0.48). In patients with CKD, enhanced BP management is associated with reduced all-cause mortality, cardiovascular mortality, and incidence of composite cardiovascular events.
DOI: 10.6084/m9.figshare.20331495.v1
title: PARP Inhibitors Rising as an Epoch-Making Strategy in First-Line Maintenance Therapy of Ovarian Cancer: A Systematic Review and Meta-Analysis

description: To illustrate the accurate location of Poly-ADP-ribose polymerase inhibitor (PARPi) as the first-line maintenance therapy in advanced ovarian cancer (AOC). Search for eligible studies and calculate clinical outcomes. PARPi as a first-line maintenance treatment significantly prolonged the BRCAmut population and the homologous recombination deficiency (HRD) positive population. PARPi as first-line maintenance therapy significantly improves the progression-free survival in AOC, especially in the BRCAmut and HRD positive populations. PARPi has been becoming the standard first-line maintenance therapy for AOC.
DOI: 10.6084/m9.figshare.20331495
title: PARP Inhibitors Rising as an Epoch-Making Strategy in First-Line Maintenance Therapy of Ovarian Cancer: A Systematic Review and Meta-Analysis

description: To illustrate the accurate location of Poly-ADP-ribose polymerase inhibitor (PARPi) as the first-line maintenance therapy in advanced ovarian cancer (AOC). Search for eligible studies and calculate clinical outcomes. PARPi as a first-line maintenance treatment significantly prolonged the BRCAmut population and the homologous recombination deficiency (HRD) positive population. PARPi as first-line maintenance therapy significantly improves the progression-free survival in AOC, especially in the BRCAmut and HRD positive populations. PARPi has been becoming the standard first-line maintenance therapy for AOC.
DOI: 10.6084/m9.figshare.14564332
title: Effects of intensive blood pressure control on mortality and cardiorenal function in chronic kidney disease patients

description: Blood pressure (BP) variability is highly correlated with cardiovascular and kidney outcomes in patients with chronic kidney disease (CKD). However, appropriate BP targets in patients with CKD remain uncertain. We searched PubMed, Embase, and the Cochrane Library for randomized controlled trials (RCTs) of CKD patients who underwent intensive BP management. Kappa score was used to assess inter-rater agreement. A good agreement between the authors was observed to inter-rater reliability of RCTs selection (kappa = 0.77; <i>P</i> = 0.005). Ten relevant studies involving 20 059 patients were included in the meta-analysis. Overall, intensive BP management may reduce the incidence of cardiovascular disease mortality (RR: 0.69, 95% CI: 0.53 to 0.90, <i>P</i>: 0.01), all-cause mortality (RR: 0.77, 95% CI: 0.67 to 0.88, <i>P</i> &lt; 0.01) and composite cardiovascular events (RR: 0.84 95% CI: 0.75 to 0.95, <i>P</i> &lt; 0.01) in patients with CKD. However, reducing BP has no significant effect on the incidence of doubling of serum creatinine level or 50% reduction in GFR (RR: 1.26, 95% CI: 0.66 to 2.40, <i>P</i> = 0.48), composite renal events (RR 1.07, 95% CI: 0.81 to 1.41, <i>P</i> = 0.64) or SAEs (RR: 0.97, 95% CI: 0.90 to 1.05, <i>P</i> = 0.48). In patients with CKD, enhanced BP management is associated with reduced all-cause mortality, cardiovascular mortality, and incidence of composite cardiovascular events.
DOI: 10.6084/m9.figshare.15087595.v1
title: Additional file 1 of Brain organoid: a 3D technology for investigating cellular composition and interactions in human neurological development and disease models in vitro

description: Additional file 1.
DOI: 10.6084/m9.figshare.15087595
title: Additional file 1 of Brain organoid: a 3D technology for investigating cellular composition and interactions in human neurological development and disease models in vitro

description: Additional file 1.
DOI: 10.6084/m9.figshare.12991508
title: The Tat system and its dependent cell division proteins are critical for virulence of extra-intestinal pathogenic <i>Escherichia coli</i>

description: The twin-arginine translocation (Tat) system is involved in a variety of important bacterial physiological processes. Conserved among bacteria and crucial for virulence, the Tat system is deemed as a promising anti-microbial drug target. However, the mechanism of how the Tat system functions in bacterial pathogenesis has not been fully understood. In this study, we showed that the Tat system was critical for the virulence of an extra-intestinal pathogenic <i>E. coli</i> (ExPEC) strain PCN033. A total of 20 Tat-related mutant strains were constructed, and competitive infection assays were performed to evaluate the relative virulence of these mutants. The results demonstrated that several Tat substrate mutants, including the Δ<i>sufI</i>, Δ<i>amiA</i>Δ<i>amiC</i> double mutant as well as each single mutant, Δ<i>yahJ</i>, Δ<i>cueO</i>, and Δ<i>napG</i>, were significantly outcompeted by the WT strain, among which the Δ<i>sufI</i> and Δ<i>amiA</i>Δ<i>amiC</i> strains showed the lowest competitive index (CI) value. Results of individual mouse infection assay, <i>in vitro</i> cell adhesion assay, whole blood bactericidal assay, and serum bactericidal assay further confirmed the virulence attenuation phenotype of the Δ<i>sufI</i> and Δ<i>amiA</i>Δ<i>amiC</i> strains. Moreover, the two mutants displayed chained morphology in the log phase resembling the Δ<i>tat</i> and were defective in stress response. Our results suggest that the Tat system and its dependent cell division proteins SufI, AmiA, and AmiC play critical roles during ExPEC pathogenesis.
DOI: 10.6084/m9.figshare.16137363
title: figshare file 1

description: The binary matrix merging 149 sectors into 49 sectors.
DOI: 10.6084/m9.figshare.16137363.v1
title: figshare file 1

description: The binary matrix merging 149 sectors into 49 sectors.
DOI: 10.6084/m9.figshare.24850647
title: Novogene - questions for new projects

description: Minimum required information to set up new projects
DOI: 10.6084/m9.figshare.24850647.v3
title: Novogene - questions for new projects

description: Minimum required information to set up new projects
DOI: 10.6084/m9.figshare.24850647.v2
title: Novogene - questions for new projects

description: Minimum required information to set up new projects
DOI: 10.6084/m9.figshare.12991508.v1
title: The Tat system and its dependent cell division proteins are critical for virulence of extra-intestinal pathogenic <i>Escherichia coli</i>

description: The twin-arginine translocation (Tat) system is involved in a variety of important bacterial physiological processes. Conserved among bacteria and crucial for virulence, the Tat system is deemed as a promising anti-microbial drug target. However, the mechanism of how the Tat system functions in bacterial pathogenesis has not been fully understood. In this study, we showed that the Tat system was critical for the virulence of an extra-intestinal pathogenic <i>E. coli</i> (ExPEC) strain PCN033. A total of 20 Tat-related mutant strains were constructed, and competitive infection assays were performed to evaluate the relative virulence of these mutants. The results demonstrated that several Tat substrate mutants, including the Δ<i>sufI</i>, Δ<i>amiA</i>Δ<i>amiC</i> double mutant as well as each single mutant, Δ<i>yahJ</i>, Δ<i>cueO</i>, and Δ<i>napG</i>, were significantly outcompeted by the WT strain, among which the Δ<i>sufI</i> and Δ<i>amiA</i>Δ<i>amiC</i> strains showed the lowest competitive index (CI) value. Results of individual mouse infection assay, <i>in vitro</i> cell adhesion assay, whole blood bactericidal assay, and serum bactericidal assay further confirmed the virulence attenuation phenotype of the Δ<i>sufI</i> and Δ<i>amiA</i>Δ<i>amiC</i> strains. Moreover, the two mutants displayed chained morphology in the log phase resembling the Δ<i>tat</i> and were defective in stress response. Our results suggest that the Tat system and its dependent cell division proteins SufI, AmiA, and AmiC play critical roles during ExPEC pathogenesis.
DOI: 10.6084/m9.figshare.13515613
title: Additional file 4 of Transcriptome profiling reveals the effects of drought tolerance in Giant Juncao

description: Additional file 4. DEGs associated with photosynthesis at different drought stress and rehydration conditions.
DOI: 10.6084/m9.figshare.13515616
title: Additional file 5 of Transcriptome profiling reveals the effects of drought tolerance in Giant Juncao

description: Additional file 5. DEGs associated with plant hormone signal transduction pathway at different drought stress and rehydration condition.
DOI: 10.6084/m9.figshare.13515607
title: Additional file 2 of Transcriptome profiling reveals the effects of drought tolerance in Giant Juncao

description: Additional file 2. GO enrichment in DEGs when FDR&lt;0.01.
DOI: 10.6084/m9.figshare.13515610
title: Additional file 3 of Transcriptome profiling reveals the effects of drought tolerance in Giant Juncao

description: Additional file 3. KEGG enrichment in DEGs at different drought stress and rehydration conditions.
DOI: 10.15468/dl.ucf3hh
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is one of (CHN.6_1, CHN.HKG, CHN.MAC)",
 "OccurrenceStatus is Present",
 "TaxonKey is Nauclea officinalis (Pierre ex Pit.) Merr. & Chun"
 ]
}

 The dataset includes 16 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039820-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-59686
title: Redemption tidings, vol. 39, nos. 1-52, 4 Jan. - 27 Dec. 1963

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.
DOI: 10.15468/dl.myzhtw
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mimulus glabratus var. externus (Skottsb.) Skottsb."
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029774-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4t496b
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "VerbatimScientificName is one of (Evylaeus corvinus (Morawitz, 1876), Evylaeus corvinus, , , , , )",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Country is Ukraine"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0091725-230530130749713/datasets/export for details.
DOI: 10.25549/pcra-c14-55720
title: Redemption tidings, vol. 36, nos. 1-52, 1 Jan. - 23 Dec. 1960

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.
DOI: 10.15468/dl.5h5kgf
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "VerbatimScientificName is one of (Alaus parreyssi (Steven, 1830), Alaus parreyssi, Calais parreysii (Steven, 1829), Calais parreyssi Steven,1830, Alaus parreyssi Stev., Alaus parreyssi Steven, )",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Country is Ukraine"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0091729-230530130749713/datasets/export for details.
DOI: 10.15468/dl.fkaebg
title: Occurrence Download

description: A dataset containing 1603 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "MediaType is Image",
 "TaxonKey is Helianthus angustifolius L.",
 "Year 1899-2024"
 ]
}

 The dataset includes 1603 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005031-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ixnhfx
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-20.14723 29.74421,16.14723 29.74421,16.14723 44.25579,-20.14723 44.25579,-20.14723 29.74421))",
 "HasCoordinate is true",
 "TaxonKey is Pinus uncinata Steud.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002185-190320150433242/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-55917
title: Redemption tidings, vol. 37, nos. 1-52, 1 Jan. - 22 Dec. 1961

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.
DOI: 10.15468/dl.2pswuc
title: Occurrence Download

description: A dataset containing 139 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is FBIP: Actinobacterial diversity associated with rooibos plants"
 ]
}

 The dataset includes 139 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0100751-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hsgp6n
title: Occurrence Download

description: A dataset containing 3425 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Venezuela (Bolivarian Republic of)",
 "OccurrenceStatus is Present",
 "TaxonKey is Nymphalidae"
 ]
}

 The dataset includes 3425 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003178-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.