cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21835489.v1
title: Systematically analyzed molecular characteristics of lung adenocarcinoma using metabolism-related genes classification

description: Abstract High heterogeneity of lung adenocarcinoma (LUAD) is a major clinical challenge. This study aims to characterize the molecular features of LUAD through classification based on metabolism-related genes. A total of 500 LUAD samples from The Cancer Genome Atlas (TCGA) and 612 from Gene Expression Omnibus (GEO) were integrated with 2,753 metabolism-related genes to determine the molecular classification. Systematic bioinformatics analysis was used to conduct correlation analysis between metabolism-related classification and molecular characteristics of LUAD. LUAD patients were divided into three molecular clusters (C1-C3). Survival analysis revealed that C1 and C2 showed good and poor prognoses, respectively. Associational analysis of classification and molecular characteristics revealed that C1 was associated with low pathological stage, metabolic pathways, high metabolic process, active immune process and checkpoint, sensitive drug response, as well as a low genetic mutation. Nevertheless, C2 was associated with high pathological stage, carcinogenic pathways, low metabolic process, inactive immune signatures, resistant drug response, and frequent genetic mutation. Eventually, a classifier with 60 metabolic genes was constructed, confirming the robustness of molecular classification on LUAD. Our findings promote the understanding of LUAD molecular characteristics, and the research data may be used for providing information be helpful for clinical diagnosis and treatment.
DOI: 10.6084/m9.figshare.12922609
title: Additional file 1 of Bioinformatics and expression analysis of histone modification genes in grapevine predict their involvement in seed development, powdery mildew resistance, and hormonal signaling

description: Additional file 1: Table S1. The primer sequences used for qRT-PCR amplification.
DOI: 10.6084/m9.figshare.12922615
title: Additional file 3 of Bioinformatics and expression analysis of histone modification genes in grapevine predict their involvement in seed development, powdery mildew resistance, and hormonal signaling

description: Additional file 3: Table S2. Synteny blocks of HM genes within grape genome.
DOI: 10.6084/m9.figshare.20787031
title: Additional file 2 of The role of LINC01419 in regulating the cell stemness in lung adenocarcinoma through recruiting EZH2 and regulating FBP1 expression

description: Additional file 2: Table S1. List of primers used for ChIP-PCR in this study.
DOI: 10.6084/m9.figshare.10302836
title: MOESM1 of Folate deficiency induced H2A ubiquitination toÂ lead to downregulated expression of genes involved in neural tube defects

description: Additional file 1: Table S1. RNA-seq assay of all gene changes.
DOI: 10.6084/m9.figshare.10302836.v1
title: MOESM1 of Folate deficiency induced H2A ubiquitination toÂ lead to downregulated expression of genes involved in neural tube defects

description: Additional file 1: Table S1. RNA-seq assay of all gene changes.
DOI: 10.25386/genetics.6108551
title: Supplemental Material for Li et al., 2018

description: <b>SUPPLEMENTAL MATERIAL</b>
DOI: 10.25386/genetics.6108551.v1
title: Supplemental Material for Li et al., 2018

description: <b>SUPPLEMENTAL MATERIAL</b>
DOI: 10.6084/m9.figshare.10302857
title: MOESM3 of Folate deficiency induced H2A ubiquitination toÂ lead to downregulated expression of genes involved in neural tube defects

description: Additional file 3: Table S2. RNA-seq assay of KEGG.
DOI: 10.6084/m9.figshare.10302857.v1
title: MOESM3 of Folate deficiency induced H2A ubiquitination toÂ lead to downregulated expression of genes involved in neural tube defects

description: Additional file 3: Table S2. RNA-seq assay of KEGG.
DOI: 10.6084/m9.figshare.20787074
title: Additional file 8 of TaPYL4, an ABA receptor gene of wheat, positively regulates plant drought adaptation through modulating the osmotic stress-associated processes

description: Additional file 8. Down-regulated differentially expressed (DE) genes underlying modulation of TaPYL4.
DOI: 10.6084/m9.figshare.20787074.v1
title: Additional file 8 of TaPYL4, an ABA receptor gene of wheat, positively regulates plant drought adaptation through modulating the osmotic stress-associated processes

description: Additional file 8. Down-regulated differentially expressed (DE) genes underlying modulation of TaPYL4.
DOI: 10.6084/m9.figshare.21837195
title: Dataset and code for bulk materials flows and GHG emission reduction potential in China.

description: These datasets include material flows and GHG emissions for circular economy stategies in China. These datasets are constructed for peer review.
DOI: 10.6084/m9.figshare.21837201
title: The virome of bladder tumors arising in people living with HIV

description: Fasta file of anellovirus fragments identified in whole genome and transcriptome sequencing of bladder tumors from patients living with HIV.
DOI: 10.6084/m9.figshare.10302866
title: MOESM4 of Folate deficiency induced H2A ubiquitination toÂ lead to downregulated expression of genes involved in neural tube defects

description: Additional file 4: Table S3. RNA- seq assay of different gene greater than 2.
DOI: 10.6084/m9.figshare.20787071
title: Additional file 7 of TaPYL4, an ABA receptor gene of wheat, positively regulates plant drought adaptation through modulating the osmotic stress-associated processes

description: Additional file 7. Up-regulated differentially expressed (DE) genes underlying modulation of TaPYL4.
DOI: 10.6084/m9.figshare.10302866.v1
title: MOESM4 of Folate deficiency induced H2A ubiquitination toÂ lead to downregulated expression of genes involved in neural tube defects

description: Additional file 4: Table S3. RNA- seq assay of different gene greater than 2.
DOI: 10.6084/m9.figshare.10302875
title: MOESM5 of Folate deficiency induced H2A ubiquitination toÂ lead to downregulated expression of genes involved in neural tube defects

description: Additional file 5: Table S4. ChIP-seq assay of peaks.loc.
DOI: 10.6084/m9.figshare.10302875.v1
title: MOESM5 of Folate deficiency induced H2A ubiquitination toÂ lead to downregulated expression of genes involved in neural tube defects

description: Additional file 5: Table S4. ChIP-seq assay of peaks.loc.
DOI: 10.6084/m9.figshare.20787071.v1
title: Additional file 7 of TaPYL4, an ABA receptor gene of wheat, positively regulates plant drought adaptation through modulating the osmotic stress-associated processes

description: Additional file 7. Up-regulated differentially expressed (DE) genes underlying modulation of TaPYL4.
DOI: 10.6084/m9.figshare.10302884
title: MOESM6 of Folate deficiency induced H2A ubiquitination toÂ lead to downregulated expression of genes involved in neural tube defects

description: Additional file 6: Table S5. ChIP-seq assay of GO.
DOI: 10.6084/m9.figshare.10302884.v1
title: MOESM6 of Folate deficiency induced H2A ubiquitination toÂ lead to downregulated expression of genes involved in neural tube defects

description: Additional file 6: Table S5. ChIP-seq assay of GO.
DOI: 10.6084/m9.figshare.10302890
title: MOESM7 of Folate deficiency induced H2A ubiquitination toÂ lead to downregulated expression of genes involved in neural tube defects

description: Additional file 7: Table S6. ChIP-seq assay of KEGG.
DOI: 10.6084/m9.figshare.10302890.v1
title: MOESM7 of Folate deficiency induced H2A ubiquitination toÂ lead to downregulated expression of genes involved in neural tube defects

description: Additional file 7: Table S6. ChIP-seq assay of KEGG.
DOI: 10.6084/m9.figshare.21311457.v1
title: Tanshinone increases Hemopexin expression in lung cells and macrophages to protect against cigarette smoke-induced COPD and enhance antiviral responses

description: Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory disease, while respiratory infections can elicit exacerbations in COPD patients to mediate increased mortality. Administration of Tanshinones (TS) derivatives has been demonstrated to protect against cigarette smoking (CS) and lipopolysaccharide (LPS)-induced COPD progression. However, the underlying molecular mechanisms and the roles of TS in mitigating the severity of viral-mediated exacerbations of COPD have not been elucidated. Here, we found that TS treatments significantly attenuated lung function decline, inflammatory responses and oxidative stress in CS and LPS-induced COPD mice. Subsequent RNA-seq analysis revealed significantly upregulated Hemopexin expression and enriched interferons (IFNs) signaling pathways in lung tissues of COPD mice upon TS treatments. Moreover, TS administration demonstrated Hemopexin-dependent beneficial roles in BEAS-2B lung cells and RAW264.7 macrophages, which was associated with the suppression of oxidative stress and ERK, NF-κB, and NLRP3 inflammasome signaling pathways-mediated inflammation. Furthermore, TS promoted IFN signaling and rescued impaired antiviral responses in CS and LPS-exposed lung cells that were infected by influenza virus. Notably, hemopexin over-expression in lung cells and macrophages recapitulated the pharmacological activities of TS. Taken together, these results indicate that TS administration is a promising and potential therapeutic strategy for treating COPD and preventing COPD exacerbations.
DOI: 10.6084/m9.figshare.10302893
title: MOESM8 of Folate deficiency induced H2A ubiquitination toÂ lead to downregulated expression of genes involved in neural tube defects

description: Additional file 8: Table S7. ChIP-qPCR and qPCR primers.
DOI: 10.6084/m9.figshare.10302893.v1
title: MOESM8 of Folate deficiency induced H2A ubiquitination toÂ lead to downregulated expression of genes involved in neural tube defects

description: Additional file 8: Table S7. ChIP-qPCR and qPCR primers.
DOI: 10.6084/m9.figshare.16590990.v1
title: Additional file 1 of ALKBH5-HOXA10 loop-mediated JAK2 m6A demethylation and cisplatin resistance in epithelial ovarian cancer

description: Additional file 1. Gene Ontology (GO) analysis of differentially expressed genes of RNA-seq.
DOI: 10.6084/m9.figshare.16590993
title: Additional file 2 of ALKBH5-HOXA10 loop-mediated JAK2 m6A demethylation and cisplatin resistance in epithelial ovarian cancer

description: Additional file 2 The differentially enriched m6A-peaks of MeRIP-seq (|log2 fold change (FC)| ≥1, p&lt;0.05).
DOI: 10.6084/m9.figshare.10302911
title: MOESM2 of circLMTK2 acts as a sponge of miR-150-5p and promotes proliferation and metastasis in gastric cancer

description: Additional file 2: Table S1. 35,350 distinct circRNA candidates.
DOI: 10.6084/m9.figshare.10302911.v1
title: MOESM2 of circLMTK2 acts as a sponge of miR-150-5p and promotes proliferation and metastasis in gastric cancer

description: Additional file 2: Table S1. 35,350 distinct circRNA candidates.
DOI: 10.6084/m9.figshare.10302920
title: MOESM3 of circLMTK2 acts as a sponge of miR-150-5p and promotes proliferation and metastasis in gastric cancer

description: Additional file 3: Table S2. 142 differentially expressed circRNAs in GC compared with those in normal tissues.
DOI: 10.6084/m9.figshare.10302920.v1
title: MOESM3 of circLMTK2 acts as a sponge of miR-150-5p and promotes proliferation and metastasis in gastric cancer

description: Additional file 3: Table S2. 142 differentially expressed circRNAs in GC compared with those in normal tissues.
DOI: 10.6084/m9.figshare.10302953
title: MOESM1 of Evolutionary balance between LRR domain loss and young NBS–LRR genes production governs disease resistance in Arachis hypogaea cv. Tifrunner

description: Additional file 1: Table S1. Information of chromosomal location and structure in Arachis hypogaea cv. Tifrunner NBS–LRRs.
DOI: 10.6084/m9.figshare.10302953.v1
title: MOESM1 of Evolutionary balance between LRR domain loss and young NBS–LRR genes production governs disease resistance in Arachis hypogaea cv. Tifrunner

description: Additional file 1: Table S1. Information of chromosomal location and structure in Arachis hypogaea cv. Tifrunner NBS–LRRs.
DOI: 10.6084/m9.figshare.10302959
title: MOESM2 of Evolutionary balance between LRR domain loss and young NBS–LRR genes production governs disease resistance in Arachis hypogaea cv. Tifrunner

description: Additional file 2: Table S2. The paralogous NBS–LRRs in Arachis duranensis, A. ipaenesis. MAFFT was used to align amino acid sequence pairs. PAL2NAL was used to convert amino acid sequences into the corresponding nucleotide sequences. PAML 4.0 was used to calculate the nonsynonymous substitution per nonsynonymous site (Ka), synonymous substitution per synonymous site (Ks), and nonsynonymous to synonymous per site substitution rates (Ka/Ks).
DOI: 10.6084/m9.figshare.10302959.v1
title: MOESM2 of Evolutionary balance between LRR domain loss and young NBS–LRR genes production governs disease resistance in Arachis hypogaea cv. Tifrunner

description: Additional file 2: Table S2. The paralogous NBS–LRRs in Arachis duranensis, A. ipaenesis. MAFFT was used to align amino acid sequence pairs. PAL2NAL was used to convert amino acid sequences into the corresponding nucleotide sequences. PAML 4.0 was used to calculate the nonsynonymous substitution per nonsynonymous site (Ka), synonymous substitution per synonymous site (Ks), and nonsynonymous to synonymous per site substitution rates (Ka/Ks).
DOI: 10.6084/m9.figshare.10302965
title: MOESM3 of Evolutionary balance between LRR domain loss and young NBS–LRR genes production governs disease resistance in Arachis hypogaea cv. Tifrunner

description: Additional file 3: Table S3. The paralogous NBS–LRRs in A. hypogaea cv. Tifrunner. MAFFT was used to align amino acid sequence pairs. PAL2NAL was used to convert amino acid sequences into the corresponding nucleotide sequences. PAML 4.0 was used to calculate the nonsynonymous substitution per nonsynonymous site (Ka), synonymous substitution per synonymous site (Ks), and nonsynonymous to synonymous per site substitution rates (Ka/Ks).
DOI: 10.6084/m9.figshare.10302965.v1
title: MOESM3 of Evolutionary balance between LRR domain loss and young NBS–LRR genes production governs disease resistance in Arachis hypogaea cv. Tifrunner

description: Additional file 3: Table S3. The paralogous NBS–LRRs in A. hypogaea cv. Tifrunner. MAFFT was used to align amino acid sequence pairs. PAL2NAL was used to convert amino acid sequences into the corresponding nucleotide sequences. PAML 4.0 was used to calculate the nonsynonymous substitution per nonsynonymous site (Ka), synonymous substitution per synonymous site (Ks), and nonsynonymous to synonymous per site substitution rates (Ka/Ks).
DOI: 10.6084/m9.figshare.10302974
title: MOESM4 of Evolutionary balance between LRR domain loss and young NBS–LRR genes production governs disease resistance in Arachis hypogaea cv. Tifrunner

description: Additional file 4: Table S4. The NBS–LRRs identified in each QTL in Arachis duranensis, A. ipaenesis, and A. hypogaea cv. Tifrunner. QTL: quantitative trait loci. a The QTLs are named from references 55 and 56. A and B indicated the chromosome in A. duranensis and A. ipaensis, respectively. b The genomic region of QTLs located on A. duranensis and A. ipaensis.
DOI: 10.6084/m9.figshare.10302974.v1
title: MOESM4 of Evolutionary balance between LRR domain loss and young NBS–LRR genes production governs disease resistance in Arachis hypogaea cv. Tifrunner

description: Additional file 4: Table S4. The NBS–LRRs identified in each QTL in Arachis duranensis, A. ipaenesis, and A. hypogaea cv. Tifrunner. QTL: quantitative trait loci. a The QTLs are named from references 55 and 56. A and B indicated the chromosome in A. duranensis and A. ipaensis, respectively. b The genomic region of QTLs located on A. duranensis and A. ipaensis.
DOI: 10.6084/m9.figshare.12924486
title: High intensity focused ultrasound treatment for diffuse uterine leiomyomatosis: a feasibility study

description: To investigate the safety and efficacy of high-intensity focused ultrasound (HIFU) treatment for diffuse uterine leiomyomatosis (DUL). Eight patients with DUL were admitted to the Department of Gynecology of Shanghai First Maternity and Infant Hospital and underwent HIFU treatment. MRI was performed before and one day after HIFU treatment for the evaluation of lesion ablation. The uterine size was measured at 3-8 months after HIFU ablation. The menstrual volume score and serum levels of hemoglobin and CA-125 were measured pre-HIFU ablation and 12-36 months post-HIFU ablation. After an average of 5.9 months of follow-up after HIFU treatment, an average uterine volume reduction of 67.6% was observed. Menstruation returned to normal in all patients, and their serum HGB and CA-125 levels also returned to normal after an average of 19.1 months of clinical follow-up. The quality of life of all patients improved significantly. HIFU treatment is safe and effective in the treatment of patients with DUL.
DOI: 10.6084/m9.figshare.22263847
title: Epidemiology of critically ill patients in intensive care units in Nepal: a retrospective observational study

description: Epidemiological data on critically ill patients is crucial for understanding resource utilisation, gaps in quality of care and for supporting surveillance of endemic or emerging diseases. We report the epidemiology of critically ill patients from 17 ICUs in Nepal using an established and standardised intensive care unit (ICU) registry. The ICU registry data is collected prospectively and includes data on case mix, severity, organ support and outcomes. We conducted a retrospective observational study with all adult (≥18 years) critically ill patients admitted to 17 ICUs in Nepal between September 2019 and September 2022. We report on case mix, treatment received, severity of illness, standardised mortality rates (SMR), discharge outcomes and ICU service activity. Descriptive statistics were used to report the findings. Ethical approval was received from Nepal Health Research Council (reference number: 4/2023P). All data contributed to the registry was de-identified prior to analysis. All findings will be made publicly available through the Mahidol-Oxford Tropical Medicine Research Unit (MORU) Tropical Health Network website (www.tropmedres.ac).<br>
DOI: 10.6084/m9.figshare.10303253
title: MOESM3 of Integrative molecular analysis of metastatic hepatocellular carcinoma

description: Additional file 3: Table S2. siRNA design.
DOI: 10.6084/m9.figshare.10303253.v1
title: MOESM3 of Integrative molecular analysis of metastatic hepatocellular carcinoma

description: Additional file 3: Table S2. siRNA design.
DOI: 10.6084/m9.figshare.10303259
title: MOESM4 of Integrative molecular analysis of metastatic hepatocellular carcinoma

description: Additional file 4: Table S3. CNV analysis.
DOI: 10.6084/m9.figshare.10303259.v1
title: MOESM4 of Integrative molecular analysis of metastatic hepatocellular carcinoma

description: Additional file 4: Table S3. CNV analysis.
DOI: 10.6084/m9.figshare.10303268
title: MOESM5 of Integrative molecular analysis of metastatic hepatocellular carcinoma

description: Additional file 5: Table S4. DNA methylation analysis.
DOI: 10.6084/m9.figshare.10303268.v1
title: MOESM5 of Integrative molecular analysis of metastatic hepatocellular carcinoma

description: Additional file 5: Table S4. DNA methylation analysis.
DOI: 10.6084/m9.figshare.10303274
title: MOESM6 of Integrative molecular analysis of metastatic hepatocellular carcinoma

description: Additional file 6: Table S5. RNA sequencing analysis.
DOI: 10.6084/m9.figshare.10303274.v1
title: MOESM6 of Integrative molecular analysis of metastatic hepatocellular carcinoma

description: Additional file 6: Table S5. RNA sequencing analysis.
DOI: 10.6084/m9.figshare.10303277
title: MOESM7 of Integrative molecular analysis of metastatic hepatocellular carcinoma

description: Additional file 7: Table S6. Integrative analysis with RNA-seq.
DOI: 10.6084/m9.figshare.10303277.v1
title: MOESM7 of Integrative molecular analysis of metastatic hepatocellular carcinoma

description: Additional file 7: Table S6. Integrative analysis with RNA-seq.
DOI: 10.6084/m9.figshare.10303280
title: MOESM8 of Integrative molecular analysis of metastatic hepatocellular carcinoma

description: Additional file 8: Table S7. IDASeq analysis.
DOI: 10.6084/m9.figshare.10303280.v1
title: MOESM8 of Integrative molecular analysis of metastatic hepatocellular carcinoma

description: Additional file 8: Table S7. IDASeq analysis.
DOI: 10.6084/m9.figshare.10303283
title: MOESM1 of Lysine pathway metabolites and the risk of type 2 diabetes and cardiovascular disease in the PREDIMED study: results from two case-cohort studies

description: Additional file 1. Additional figures and tables.
DOI: 10.6084/m9.figshare.10303283.v1
title: MOESM1 of Lysine pathway metabolites and the risk of type 2 diabetes and cardiovascular disease in the PREDIMED study: results from two case-cohort studies

description: Additional file 1. Additional figures and tables.
DOI: 10.17608/k6.auckland.12924735
title: Hadden Little penguin micro CT head

description: Part of collection that contains images obtained during scanning and dissection of the heads of little penguins (<i>Eudyptula minor</i>) from Auckland, king penguins (<i>Aptenodytes patagonicus</i>) and gentoo penguins (<i>Pygoscelis papua</i>), the latter two descended from penguins from South Georgia. It also contains a video of the eye of a little penguin from Auckland viewed under both bright (photopic) and dim (mesopic) conditions, while undergoing general anaesthesia, to show the movement of the pupil as well as renders made from these images.<br>
DOI: 10.17608/k6.auckland.12924735.v1
title: Hadden Little penguin micro CT head

description: This DOI contains a micro CT stack of the frozen head of a little penguin (<i>Eudyptula minor</i>) collected in Auckland.

<br>
DOI: 10.17608/k6.auckland.12924744
title: Hadden King penguin micro CT head

description: Part of collection that contains images obtained during scanning and dissection of the heads of little penguins (<i>Eudyptula minor</i>) from Auckland, king penguins (<i>Aptenodytes patagonicus</i>) and gentoo penguins (<i>Pygoscelis papua</i>), the latter two descended from penguins from South Georgia. It also contains a video of the eye of a little penguin from Auckland viewed under both bright (photopic) and dim (mesopic) conditions, while undergoing general anaesthesia, to show the movement of the pupil as well as renders made from these images.<br>

 <br>
DOI: 10.17608/k6.auckland.12924744.v1
title: Hadden King penguin micro CT head

description: This DOI contains a micro CT stack of the frozen head of a King penguin (<i>Aptenodytes patagonicus</i>), originally from South Georgia.

<br>

 <br>
DOI: 10.17608/k6.auckland.12924744.v2
title: Hadden King penguin micro CT head

description: This DOI contains a micro CT stack of the frozen head of a King penguin (<i>Aptenodytes patagonicus</i>), originally from South Georgia.

<br>

 <br>
DOI: 10.17608/k6.auckland.12924782
title: Hadden Gentoo penguin micro CT head

description: Part of collection that contains images obtained during scanning and dissection of the heads of little penguins (<i>Eudyptula minor</i>) from Auckland, king penguins (<i>Aptenodytes patagonicus</i>) and gentoo penguins (<i>Pygoscelis papua</i>), the latter two descended from penguins from South Georgia. It also contains a video of the eye of a little penguin from Auckland viewed under both bright (photopic) and dim (mesopic) conditions, while undergoing general anaesthesia, to show the movement of the pupil as well as renders made from these images.<br>
DOI: 10.17608/k6.auckland.12924782.v1
title: Hadden Gentoo penguin micro CT head

description: This DOI contains the micro CT stack of the frozen head of a gentoo penguin (<i>Pygoscelis papua</i>) descended from penguins collected from South Georgia.<br><br>
DOI: 10.6084/m9.figshare.19738606
title: Additional file 2 of Identification of miRNA-mRNA-TF regulatory networks in peripheral blood mononuclear cells of type 1 diabetes

description: Additional file 2.