cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21161929.v1
title: Identification of super-enhancer-associated transcription factors regulating glucose metabolism in poorly differentiated thyroid carcinoma

description: Abstract This study aimed to uncover transcription factors that regulate super-enhancers involved in glucose metabolism reprogramming in poorly differentiated thyroid carcinoma (PDTC). TCA cycle and pyruvate metabolism were significantly enriched in PDTC. Differentially expressed genes in PDTC vs. normal control tissues were located in key steps in TCA cycle and pyruvate metabolism. A total of 23 upregulated genes localized in TCA cycle and pyruvate metabolism were identified as super-enhancer-controlled genes. Transcription factor analysis of these 23 super-enhancer-controlled genes related to glucose metabolism was performed, and 20 transcription factors were obtained, of which KLF12, ZNF281 and RELA had a significant prognostic impact. Regulatory network of KLF12, ZNF281 and RELA controlled the expression of these four prognostic target genes (LDHA, ACLY, ME2 and IDH2). In vitro validation showed that silencing of KLF12, ZNF281 and RELA suppressed proliferation, glucose uptake, lactate production and ATP level, but increased ADP/ATP ratio in PDTC cells. In conclusion, KLF12, ZNF281 and RELA were identified as the key transcription factors that regulate super-enhancer-controlled genes related to glucose metabolism in PDTC. Our findings contribute to a deeper understanding of the regulatory mechanisms associated with glucose metabolism in PDTC, and advance the theoretical development of PDTC-targeted therapies.
DOI: 10.6084/m9.figshare.21161967
title: MiR-137-mediated negative relationship between LGR4 and RANKL modulated osteogenic differentiation of human adipose-derived mesenchymal stem cells

description: ABSTRACT MicroRNA-137 (miR-137) has recently emerged as an osteogenic regulator in several cell lines. This study aimed to identify the function of miR-137 on the crosstalk between leucine rich repeat containing G protein-coupled receptor 4 (LGR4) and receptor activator of nuclear factor-κB ligand (RANKL), thus unveiling the critical role of LGR4-RANKL interplay in the osteogenic differentiation of human adipose-derived mesenchymal stem cells (hASCs). By examining the osteogenic capacity and possible downstream genes expression with miR-137 overexpression/knockdown, we found that miR-137 downregulated LGR4 while upregulating RANKL. According to the results of dual-luciferase reporter assay, LGR4 was validated as a direct target of miR-137. Surprisingly, a negative relationship between LGR4 and RANKL was confirmed by the knockdown of these two genes. Furthermore, RANKL inhibitor could alleviate or reverse the inhibitory effects on osteogenesis generated by LGR4 knockdown. Collectively, this study indicated that miR-137-induced a negative crosstalk between LGR4 and RANKL that could contribute to the osteogenic regulation of hASCs and provide more systematic and in-depth understanding of epigenetic modulation by miR-137.
DOI: 10.6084/m9.figshare.21161967.v1
title: MiR-137-mediated negative relationship between LGR4 and RANKL modulated osteogenic differentiation of human adipose-derived mesenchymal stem cells

description: ABSTRACT MicroRNA-137 (miR-137) has recently emerged as an osteogenic regulator in several cell lines. This study aimed to identify the function of miR-137 on the crosstalk between leucine rich repeat containing G protein-coupled receptor 4 (LGR4) and receptor activator of nuclear factor-κB ligand (RANKL), thus unveiling the critical role of LGR4-RANKL interplay in the osteogenic differentiation of human adipose-derived mesenchymal stem cells (hASCs). By examining the osteogenic capacity and possible downstream genes expression with miR-137 overexpression/knockdown, we found that miR-137 downregulated LGR4 while upregulating RANKL. According to the results of dual-luciferase reporter assay, LGR4 was validated as a direct target of miR-137. Surprisingly, a negative relationship between LGR4 and RANKL was confirmed by the knockdown of these two genes. Furthermore, RANKL inhibitor could alleviate or reverse the inhibitory effects on osteogenesis generated by LGR4 knockdown. Collectively, this study indicated that miR-137-induced a negative crosstalk between LGR4 and RANKL that could contribute to the osteogenic regulation of hASCs and provide more systematic and in-depth understanding of epigenetic modulation by miR-137.
DOI: 10.6084/m9.figshare.19589034
title: Additional file 7 of Effects of salinity acclimation on histological characteristics and miRNA expression profiles of scales in juvenile rainbow trout (Oncorhynchus mykiss)

description: Additional file 7: Table S7. Detailed information for the differentially enriched KEGG pathways.
DOI: 10.6084/m9.figshare.19589034.v1
title: Additional file 7 of Effects of salinity acclimation on histological characteristics and miRNA expression profiles of scales in juvenile rainbow trout (Oncorhynchus mykiss)

description: Additional file 7: Table S7. Detailed information for the differentially enriched KEGG pathways.
DOI: 10.6084/m9.figshare.19581798
title: Additional file 3 of Gut microbiome signatures linked to HIV-1 reservoir size and viremia control

description: Additional file 2: Dataset S1. Longitudinal microbial composition (relative abundance) in viremic controllers and non-controllers analyzed by MetaPhlAn2.0. Dataset S2. Raw bacterial protein counts at baseline in viremic controllers and non-controllers analysed using Scaffold Q+ software v4.9.0. Dataset S3. Raw gene counts at baseline in viremic controllers and non-controllers estimated using RSEM v1.3.0. Dataset S4. Soluble factors (normalized protein expression units) from the Olink inflammation panel at baseline in viremic controllers and non-controllers. Dataset S5. List of transcripts significantly correlated with the Bacteroidales:Clostridiales ratio adjusted for multiple comparisons (spearman’s rho and corresponding q-value&lt;0.05 are reported). Dataset S6. Spearman’s correlation (rho=0.5) between viral reservoir (CA HIV-1 RNA and HIV-1 DNA), bacterial species (Bacteroidales and Clostrdiales), transcripts correlated with the ratio Bacteroidales / Clostridiales and differentially abundant microbial proteins (p&lt;0.025). Dataset S7. Benjamini–Hochberg multiple hypothesis correction for unadjusted p-values ≤ 0.05 (metagenomics and metaproteomics datasets).
DOI: 10.6084/m9.figshare.19581801.v1
title: Additional file 4 of Gut microbiome signatures linked to HIV-1 reservoir size and viremia control

description: Additional file 3: Table S1. List of differentially expressed genes between controllers and non-controllers at baseline (adjusted p-value &lt;0.1and log2 FoldChange = 0). Table S2. Detailed information of differentially expressed genes (DEGs) between controllers and non-controllers at baseline (adjusted p-value &lt;0.1 and log2 FoldChange = 0). Table S3. GO terms from enrichment analysis (biological process) based on upregulated genes in viremic controllers (n. transcripts =15). Table S4. Enriched GO biological process terms of host transcripts significantly correlated with the ratio Bacteroidales/Clostridiales. Table S5. Enriched GO biological process terms of transcripts (n=453) significantly correlated with the ratio Bacteroidales/Clostridiales and viral reservoir (CA HIV-1 RNA and HIV-1 DNA). Table S6. Summary of shotgun metagenomics sequencing yield from longitudinally-collected fecal samples. Statistics of reads mapped to integrated gene catalog (IGC) are also shown.
DOI: 10.6084/m9.figshare.16960234
title: Additional file 1 of Characterization of phytohormone and transcriptome profiles during protocorm-like bodies development of Paphiopedilum

description: Additional file 1: Supplemental Table S1. Overview of de novo assembly. Supplemental Table S2. Annotated genes related to IAA metabolism and signaling. Supplemental Table S3. DEGs involved in jasmonic acid, brassinosteroid, ethylene, zeatin, salicylic acid and abscisic acid metabolism and signaling transduction. Supplemental Table S4. Annotated genes related to somatic embryogenesis. Supplemental Table S5. DEGs involved in photosynthesis. Supplemental Table S6. Primers used in the reference genes selection.
DOI: 10.6084/m9.figshare.9641120
title: Additional file 2: of Cytogenetic and genomic organization analyses of chloroplast DNA invasions in the nuclear genome of Asparagus officinalis L. provides signatures of evolutionary complexity and informativity in sex chromosome evolution

description: Table S2. The primers used for amplification of chloroplast DNA fragments of A. officinalis. (XLSX 278 kb)
DOI: 10.6084/m9.figshare.9641120.v1
title: Additional file 2: of Cytogenetic and genomic organization analyses of chloroplast DNA invasions in the nuclear genome of Asparagus officinalis L. provides signatures of evolutionary complexity and informativity in sex chromosome evolution

description: Table S2. The primers used for amplification of chloroplast DNA fragments of A. officinalis. (XLSX 278 kb)
DOI: 10.6084/m9.figshare.8068262
title: A novel noise-adapted two-layer ensemble model for credit scoring based on backflow learning

description: 在该实验中，研究了来自UCI机器学习库的三个信用数据集，即澳大利亚，日本和波兰的信用数据集。这些数据集非常受欢迎，并被数据挖掘分析师广泛研究。

澳大利亚信用数据集包含690个样本，其中307个为阳性，383个为阴性。除类标签之外的输入空间的维度为14，其中六个属性是连续的，八个是分类的。已经修改了分类属性的标签，以方便将来的计算。例如，仅包含三个不同类的分类属性的标签被修改为“1”，“2”和“3”。

日本信用数据集包含690个样本，输入空间的维数为15.日本和澳大利亚数据集都相似，因为它们表现出相同的正负比和输入空间的相似维度。日语信用数据集中的分类属性标签尚未修改。

波兰信用数据集包含7027个样本，输入空间的维数为65.波兰信用数据集选自波兰制造公司的2007年财务报表，以预测2012年这些公司的破产状况。分类属性的标签波兰的信用数据集尚未修改。<br>
DOI: 10.6084/m9.figshare.9641147
title: Additional file 1: of CRABP2 regulates invasion and metastasis of breast cancer through hippo pathway dependent on ER status

description: Figure S1. a Knockdown of ER in ER+ breast cancer cells down-regulate the protein expression of CRABP2. b Overexpression of ER in ER+ breast cancer cells up-regulate the protein expression of CRABP2. c-f We have constructed stable knockdown and overexpressed CRABP2 cells.Figure S2. a-c Knockdown of CRABP2 promotesÂ metastasis and invasion of ER+ breast cancer cells in vitro. d Ectopic expression of CRABP2 in MCF7 cells can suppress EMT and activateÂ Hippo pathway.Figure S3. a-c Overexpression of CRABP2 promotes metastasis and invasion of ER- breast cancer cells in vitro.Figure S4. a-b Knockdown of Lats1 in ER+ breast cancer cells could not modify the mRNA and protein expression of CRABP2. c The mRNA expression of CTGF, CYR61 was increased in CRABP2 deficient cells. d-f The regulation of CRABP2 on metastasis, and invasion depends on Lats1 in ER+ mammary cancer cells. Figure S5. a-b Knockdown of Lats1 in ER- breast cancer cells could not modify the mRNA and protein expression of CRABP2. c The mRNA expression of CTGF, CYR61 was increased in CRABP2 overexpressed cells. d-f The regulation of CRABP2 on the metastasis, and invasion depends on Lats1 in ER- mammary cancer cells. Figure S6. a-b There was no obvious change in the mRNA expression level of Lats1 when knocking down CRABP2 in ER+ and ER- mammary cancer cells. c Knockdown of CRABP2 in MCF7 cells could not modify the protein expression of CRABP1. d Knockdown of CRABP2 in MDA-MB-468 cells could not regulate the Hippo pathway.
DOI: 10.6084/m9.figshare.9641147.v1
title: Additional file 1: of CRABP2 regulates invasion and metastasis of breast cancer through hippo pathway dependent on ER status

description: Figure S1. a Knockdown of ER in ER+ breast cancer cells down-regulate the protein expression of CRABP2. b Overexpression of ER in ER+ breast cancer cells up-regulate the protein expression of CRABP2. c-f We have constructed stable knockdown and overexpressed CRABP2 cells.Figure S2. a-c Knockdown of CRABP2 promotesÂ metastasis and invasion of ER+ breast cancer cells in vitro. d Ectopic expression of CRABP2 in MCF7 cells can suppress EMT and activateÂ Hippo pathway.Figure S3. a-c Overexpression of CRABP2 promotes metastasis and invasion of ER- breast cancer cells in vitro.Figure S4. a-b Knockdown of Lats1 in ER+ breast cancer cells could not modify the mRNA and protein expression of CRABP2. c The mRNA expression of CTGF, CYR61 was increased in CRABP2 deficient cells. d-f The regulation of CRABP2 on metastasis, and invasion depends on Lats1 in ER+ mammary cancer cells. Figure S5. a-b Knockdown of Lats1 in ER- breast cancer cells could not modify the mRNA and protein expression of CRABP2. c The mRNA expression of CTGF, CYR61 was increased in CRABP2 overexpressed cells. d-f The regulation of CRABP2 on the metastasis, and invasion depends on Lats1 in ER- mammary cancer cells. Figure S6. a-b There was no obvious change in the mRNA expression level of Lats1 when knocking down CRABP2 in ER+ and ER- mammary cancer cells. c Knockdown of CRABP2 in MCF7 cells could not modify the protein expression of CRABP1. d Knockdown of CRABP2 in MDA-MB-468 cells could not regulate the Hippo pathway.
DOI: 10.6084/m9.figshare.9641153
title: Additional file 2: of CRABP2 regulates invasion and metastasis of breast cancer through hippo pathway dependent on ER status

description: Table S1. Clinicopathological associations of CRABP2 in human breast cancers. Table S2. The sequences of primer set for real-time PCR assays. Table S3. The sequences of shRNA and siRNA used in this study. (ZIP 247 kb)
DOI: 10.6084/m9.figshare.9641153.v1
title: Additional file 2: of CRABP2 regulates invasion and metastasis of breast cancer through hippo pathway dependent on ER status

description: Table S1. Clinicopathological associations of CRABP2 in human breast cancers. Table S2. The sequences of primer set for real-time PCR assays. Table S3. The sequences of shRNA and siRNA used in this study. (ZIP 247 kb)
DOI: 10.6084/m9.figshare.9641162
title: Additional file 1: of Choroidal structural changes correlate with severity of diabetic retinopathy in diabetes mellitus

description: Demographic and clinical data in this study. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.9641162.v1
title: Additional file 1: of Choroidal structural changes correlate with severity of diabetic retinopathy in diabetes mellitus

description: Demographic and clinical data in this study. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.9641168
title: Additional file 2: of Choroidal structural changes correlate with severity of diabetic retinopathy in diabetes mellitus

description: OCT data in this study. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.9641168.v1
title: Additional file 2: of Choroidal structural changes correlate with severity of diabetic retinopathy in diabetes mellitus

description: OCT data in this study. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.23796995
title: The Presence of Lung Cancer Affects SARS-CoV-2 Vaccine Uptake and Attitude in Chinese Patients: A Clinical Cross-Sectional Investigation

description: With the SARS-CoV-2 mutations evolving and prompt of SARS-CoV-2 vaccines, no information is available on SARS-CoV-2 vaccination status in Chinese patients with lung cancer. An electronic questionnaire including sociodemographic characteristics, vaccine status, side effect post-vaccination, and attitude towards a fourth dose of vaccine was conducted within 1018 Chinese patients with lung cancer from October 18th, 2022, to November 25th, 2022. Among 1018 patients, a total of 75 (13.7%) patients reported acceptable systemic adverse events in those had received the SARS-CoV-2 vaccine (549, 54%), the most common of which was fever (39, 7%). Factors including females (OR, 1.512; 95% CI, 1.076–2.124), residents in the municipality (OR, 2.048; 95% CI, 1.238–3.389), undergoing therapy (OR, 2.897; 95% CI, 1.348–6.226), disagree to vaccines is safe for patients with lung cancer (OR, 3.816; 95% CI, 2.198–6.626) contributed to hesitancy. Among 373 patients had received three doses, half respondents (206, 55.2%) were hesitant to receive a fourth dose due to the safety concern and efficacy towards the variants. In conclusion, low vaccine uptake rates in patients with lung cancer could be improved by increasing confidence in vaccine safety, particularly for those with negative beliefs. Appropriate guidance and individualized vaccination plans that meet the healthcare needs of patients with lung cancer were needed during the constantly evolving pandemic.
DOI: 10.6084/m9.figshare.23796995.v1
title: The Presence of Lung Cancer Affects SARS-CoV-2 Vaccine Uptake and Attitude in Chinese Patients: A Clinical Cross-Sectional Investigation

description: With the SARS-CoV-2 mutations evolving and prompt of SARS-CoV-2 vaccines, no information is available on SARS-CoV-2 vaccination status in Chinese patients with lung cancer. An electronic questionnaire including sociodemographic characteristics, vaccine status, side effect post-vaccination, and attitude towards a fourth dose of vaccine was conducted within 1018 Chinese patients with lung cancer from October 18th, 2022, to November 25th, 2022. Among 1018 patients, a total of 75 (13.7%) patients reported acceptable systemic adverse events in those had received the SARS-CoV-2 vaccine (549, 54%), the most common of which was fever (39, 7%). Factors including females (OR, 1.512; 95% CI, 1.076–2.124), residents in the municipality (OR, 2.048; 95% CI, 1.238–3.389), undergoing therapy (OR, 2.897; 95% CI, 1.348–6.226), disagree to vaccines is safe for patients with lung cancer (OR, 3.816; 95% CI, 2.198–6.626) contributed to hesitancy. Among 373 patients had received three doses, half respondents (206, 55.2%) were hesitant to receive a fourth dose due to the safety concern and efficacy towards the variants. In conclusion, low vaccine uptake rates in patients with lung cancer could be improved by increasing confidence in vaccine safety, particularly for those with negative beliefs. Appropriate guidance and individualized vaccination plans that meet the healthcare needs of patients with lung cancer were needed during the constantly evolving pandemic.
DOI: 10.6084/m9.figshare.9641249
title: Additional file 2: of Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations

description: Table S1. Mapping summary of all the epigenome, RNA-seq, and DNA methylation data sets. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.9641249.v1
title: Additional file 2: of Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations

description: Table S1. Mapping summary of all the epigenome, RNA-seq, and DNA methylation data sets. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.9641252
title: Additional file 3: of Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations

description: Table S2. Motif enrichment analysis for 13 chromatin states (excluding repressed polycomb and quiescent states). (XLSX 730 kb)
DOI: 10.6084/m9.figshare.9641252.v1
title: Additional file 3: of Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations

description: Table S2. Motif enrichment analysis for 13 chromatin states (excluding repressed polycomb and quiescent states). (XLSX 730 kb)
DOI: 10.6084/m9.figshare.9641258
title: Additional file 4: of Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations

description: Table S3. Summary of upregulated differentially expressed genes (DEGs) detected in rumen epithelial primary cells (REPC) before and after (24â h) butyrate treatment. (XLSX 131 kb)
DOI: 10.6084/m9.figshare.9641258.v1
title: Additional file 4: of Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations

description: Table S3. Summary of upregulated differentially expressed genes (DEGs) detected in rumen epithelial primary cells (REPC) before and after (24â h) butyrate treatment. (XLSX 131 kb)
DOI: 10.6084/m9.figshare.9641261
title: Additional file 5: of Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations

description: Table S4. Summary of downregulated differentially expressed genes (DEGs) detected in rumen epithelial primary cells (REPC) before and after (24â h) butyrate treatment. (XLSX 70 kb)
DOI: 10.6084/m9.figshare.9641261.v1
title: Additional file 5: of Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations

description: Table S4. Summary of downregulated differentially expressed genes (DEGs) detected in rumen epithelial primary cells (REPC) before and after (24â h) butyrate treatment. (XLSX 70 kb)
DOI: 10.6084/m9.figshare.9641264
title: Additional file 6: of Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations

description: Table S5. Enrichment analysis of differentially expressed genes (DEGs) for tissue-specific genes across 91 tissues/cell types in cattle. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.9641264.v1
title: Additional file 6: of Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations

description: Table S5. Enrichment analysis of differentially expressed genes (DEGs) for tissue-specific genes across 91 tissues/cell types in cattle. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.9641267
title: Additional file 7: of Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations

description: Table S6. Significantly differentially methylated regions in rumen epithelial primary cells (REPC) before and after (24â h) butyrate treatment. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.9641267.v1
title: Additional file 7: of Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations

description: Table S6. Significantly differentially methylated regions in rumen epithelial primary cells (REPC) before and after (24â h) butyrate treatment. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.9641294
title: Additional file 3: of Genome-wide identification of AGO18b-bound miRNAs and phasiRNAs in maize by cRIP-seq

description: Table S5. List of primer sequences used in the study. (XLS 30 kb)
DOI: 10.6084/m9.figshare.9641318
title: MOESM1 of Characterization and mechanism of the effects of Mgâ Fe layered double hydroxide nanoparticles on a marine bacterium: new insights from genomic and transcriptional analyses

description: Additional file 1. The method of synthesis of Mg-Fe-LDH NPs, preparation of Aodex/Mg-Fe-LDH, and adsorbent characterization. Figure S1. Characterization of the adsorption of Aodex by Mg-Fe-LDH NPs. Table S1. Genome annotation of Arthrobacter oxidans KQ11. Table S2. for summary of raw and filtered reads; and Illumina transcriptome reads mapped to the A. oxidans KQ11 genes. Table S3. for transcriptome annotation of A. oxidans KQ11 response to Mg-Fe-LDH NPs. Table S4. for significantly differential expressed genes of A. oxidans KQ11 with the Mg-Fe-LDH NPS treatment. Table S5. for the Shine-Dalgarno sequences of A. oxidans KQ11 with the Mg-Fe-LDH NPs treatment. Table S6. for sRNA of the new transcripts in the A. oxidans KQ11 intergenic region with Mg-Fe-LDH NPs treatment were annotated by NR.