cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22639630.v1
title: Additional file 2 of Pan-cancer landscape of CENPO and its underlying mechanism in LUAD

description: Additional file 2: Figure S1. Differential expression of CENPO. (A) Gene transcript exon expression of CENPO and (B) isoform expression of CENPO in the GTEx database. (C) Single-tissue eQTL of CENPO tissue specific expression. (D) Single cell expression of CENPO. Figure S2. The diagnostic value of CENPO in pan-cancer. (A) The expression of CENPO in the Sangerbox database. (B) The ROC curves of CENPO in ACC, BLCA, BRCA, CESC, CHOL, ESCA, GBM, HNSC, KICH, UCEC, KIRP, LGG, LIHC, LUAD, LUSC, and OV. Figure S3. The prognosis value of CENPO in pan-cancer. (A) Kaplan–Meier analysis of the association between CENPO expression and overall survival (OS). (B) Kaplan–Meier analysis of the association between CENPO expression and disease-free survival (DFS). Figure S4. The association between CENPO expression and immune cell infiltration, including T-cell NK cells, CD8 + T cells, Tregs, B cells, Myeloid dendritic cells, Monocytes and Macrophage M2. Figure S5. The correlation between CENPO expression and major histocompatibility complexes (MHCs) in the TISIDB database. (A) The expression of CENPO is negatively associated with most MHCs in pan-cancer. (B) The expression of CENPO is negatively associated with most chemokine receptors in LUAD. Figure S6. (A) The mutation annotation format (MAF) summary plots of CENPO in the CENPOhigh group and CENPOlow group. (B) OS, DFS, DSS, and PFS analysis stratified by CENPO mutation status in bladder urothelial carcinoma (BLCA). Figure S7. CENPO is decreased in shRNA mediated knockdown of A549 and HCI-H1299 cells. The specificity and validity of the lentivirus-mediated shRNA knockdown of CENPO in A549 and HCI-H1299 cells was measured by RT-qPCR (A) and Western blot (B). The protein blot images are cropped.
DOI: 10.6084/m9.figshare.22639633.v1
title: Additional file 3 of Pan-cancer landscape of CENPO and its underlying mechanism in LUAD

description: Additional file 3: Table S1. The value of ROC, DFS, and OS curves of CENPO in multiple types of cancers.
DOI: 10.25549/usctheses-ouc11364467
title: The effectiveness of undivided elementary classrooms in California
DOI: 10.6084/m9.figshare.20018192
title: EPO activates PI3K-IKKα-CDK1 signaling pathway to promote the proliferation of Glial Cells under hypoxia environment

description: Abstract Erythropoietin (EPO), supports the function and survival of neurons through astrocytes and has a protective role in neonatal asphyxia brain injury; yet, its mechanism of action remains unclear. As a neuroprotective factor, EPO is also used in the treatment of various diseases, such as neurodegenerative diseases, Parkinson’s disease, traumatic brain injury, by decreasing inflammatory reaction, resisting apoptosis, and lowering oxidative stress. The aim of this study was to examine the effect and mechanism of EPO on promoting human brain glial cell proliferation under hypoxia in vitro. Under CoC12-induced hypoxia, after adding EPO, high-throughput sequencing was used to screen out meaningful up-regulated and significant differentially expressed genes PI3K, IKKα CDK1 related to proliferation, and make further verification by qPCR and western blotting. Under hypoxia, EPO promoted cell proliferation and the expression of PI3K while this effect was inhibited (along with a decrease of downstream genes IKKα and CDK1 decreased) after adding PI3K inhibitor to cell culture. EPO can promote cell proliferation and CDK1 expression, while after inhibiting CDK1 expression, the promotion of EPO on cell proliferation was eliminated. These data proved that EPO promotes the proliferation of U251 cells by activating the PI3K-IKKα-CDK1 signaling pathway under CoC12-induced hypoxia.
DOI: 10.6084/m9.figshare.22639636
title: Additional file 4 of Pan-cancer landscape of CENPO and its underlying mechanism in LUAD

description: Additional file 4: Table S2. The correlation of CENPO expression and ESTIMATEScore, ImmuneScore, and StromalScore in multiple types of cancers.
DOI: 10.6084/m9.figshare.22639642.v1
title: Additional file 6 of Pan-cancer landscape of CENPO and its underlying mechanism in LUAD

description: Additional file 6: Table S4. The correlation of CENPO expression with TMB, MSI, and MATH in multiple types of cancers.
DOI: 10.6084/m9.figshare.16864760.v1
title: Additional file 2 of TPSC: a module detection method based on topology potential and spectral clustering in weighted networks and its application in gene co-expression module discovery

description: Additional file 2: Detailed result of biological process, pathway and cytoband enrichment on each module. Only items with top 5 enrichment significance and number of overlap genes are displayed in this table.
DOI: 10.6084/m9.figshare.22639546
title: Additional file 2 of Excessive exogenous cholesterol activating intestinal LXRα-ABCA1/G5/G8 signaling pathway can not reverse atherosclerosis in ApoE−/− mice

description: Additional file 2. Lipids in feed.
DOI: 10.6084/m9.figshare.20018162.v1
title: Identification of bZIP transcription factors and their responses to brown spot in pear

description: Abstract Basic leucine zipper (bZIP) is a conserved transcription factor (TF) widely present in eukaryotes, and it plays an important role in regulating plant growth and stress responses. To better understand the white pear bZIP gene family, comprehensive bioinformatics analysis of the pear genome was performed. A total of 84 PbbZIP genes were identified, which were divided into 13 subfamilies by phylogenetic analysis. The 84 PbbZIP genes were all located in the nucleus, and 77 of those genes were unevenly distributed across the 17 chromosomes of white pear. The other 7 PbbZIP genes were located on the scaffold. Subsequent expression profile analysis showed that PbbZIP genes in exocarp were significantly upregulated or downregulated in ‘Huangguan’ pear with brown spot (BS) compared with healthy pear and in response to hormonal treatment with gibberellin A3 (GA3). These results provide helpful insights into the characteristics of PbbZIP genes and their responses to BS in ‘Huangguan’ pear.
DOI: 10.6084/m9.figshare.22639546.v1
title: Additional file 2 of Excessive exogenous cholesterol activating intestinal LXRα-ABCA1/G5/G8 signaling pathway can not reverse atherosclerosis in ApoE−/− mice

description: Additional file 2. Lipids in feed.
DOI: 10.25549/usctheses-ouc11258219
title: Microsoft Word - Anita Vidai Singh Dissertation.docx
DOI: 10.25549/usctheses-ouc11258220
title: Microsoft Word - Systematic Review of Elder Abuse Dissertation__Clean Copy_formatted.docx
DOI: 10.25549/usctheses-ouc11258226
title: MergedFile
DOI: 10.6084/m9.figshare.12153801.v1
title: Additional file 1 of Correlation between gene polymorphism in angiotensin II type 1 receptor and type 2 diabetes mellitus complicated by hypertension in a population of Inner Mongolia

description: Additional file 1. The questionnaire of diabetes with hypertension and diabetes.
DOI: 10.25549/usctheses-ouc11258231
title: Microsoft Word - MEDIEVAL AMERICA FINAL SUBMISSION.docx
DOI: 10.25549/usctheses-ouc11258237
title: Alle Thesis Revision I 2017 04 16
DOI: 10.25549/usctheses-ouc11258249
title: Microsoft Word - REAL Catherine Dissertation 04-12-17.docx
DOI: 10.25549/usctheses-ouc11258250
title: VARGAS thesis_submission
DOI: 10.25549/usctheses-ouc11258253
title: Microsoft Word - KWM thesis Complete corrected.docx
DOI: 10.6084/m9.figshare.20018123
title: Integrated analysis of gene expression and DNA methylation datasets identified key genes and a 6-gene prognostic signature for primary lung adenocarcinoma

description: Abstract Lung adenocarcinoma (LUAD) is the main subtype of non-small cell lung cancer with a poor survival prognosis. In our study, gene expression, DNA methylation, and clinicopathological data of primary LUAD were utilized to identify potential prognostic markers for LUAD, which were recruited from The Cancer Genome Atlas (TCGA) database. Univariate regression analysis showed that there were 21 methylation-associated DEGs related to overall survival (OS), including 9 down- and 12 up-regulated genes. The 12 up-regulated genes with hypomethylation may be risky genes, whereas the other 9 down-regulated genes with hypermethylation might be protective genes. By using the Step-wise multivariate Cox analysis, a methylation-associated 6-gene (consisting of CCL20, F2, GNPNAT1, NT5E, B3GALT2, and VSIG2) prognostic signature was constructed and the risk score based on this gene signature classified patients into high- or low-risk groups. Patients of the high-risk group had shorter OS than those of the low-risk group in both the training and validation cohort. Multivariate Cox analysis and the stratified analysis revealed that the risk score was an independent prognostic factor for LUAD patients. The methylation-associated gene signature may serve as a prognostic factor for LUAD patients and the represent hypermethylated or hypomethylated genes might be potential targets for LUAD therapy.
DOI: 10.25549/usctheses-ouc11258260
title: Microsoft Word - Solis Final Dissertation1.doc
DOI: 10.6084/m9.figshare.12153879
title: Additional file 1 of Construction of a high-density genetic map and mapping of growth related QTLs in the grass carp (Ctenopharyngodon idellus)

description: Additional file 1.
DOI: 10.25549/usctheses-ouc11258269
title: Microsoft Word - Dissertation Thesis Wen-Hsuan Chang.docx
DOI: 10.25549/usctheses-c40-381683
title: etd-ShinPeterS-5383-11-flomotions
DOI: 10.25549/usctheses-ouc11258278
title: Microsoft Word - timmons_dissertation_final.docx
DOI: 10.25549/usctheses-ouc11258287
title: THIRD FULL PRINT Complete Manuscript [6.1]
DOI: 10.25549/usctheses-c40-381678
title: etd-ShinPeterS-5383-06-screamingshapesferal
DOI: 10.6084/m9.figshare.20018186
title: LINC00974 sponges miR-33a to facilitate cell proliferation, invasion, and EMT of ovarian cancer through HMGB2 upregulation

description: Abstract The function and mechanism of long intergenic non-protein coding RNA 974 (LINC00974) are rarely reported in ovarian cancer (OC). The study aimed to investigate how LINC00974 affects the progression of OC. The expression levels of LINC00974, microRNA-33a (miR-33a), and high mobility group box 2 (HMGB2) mRNA were detected by qRT-PCR. The LINC00974/miR-33a/HMGB2 axis was confirmed by dual-luciferase reporter, RNA-binding protein immunoprecipitation (RIP), and biotinylated RNA pull-down assays. A series of in vitro experiments were employed to assess the effects of LINC00974/miR-33a/HMGB2 axis on the proliferation, invasion and epithelial mesenchymal transition (EMT) of OC cells. Results showed that LINC00974 and HMGB2 mRNA expression were upregulated in OC cells, while miR-33a expression was downregulated. HMGB2 was a direct target gene of miR-33a. LINC00974 act as a competing endogenous RNA (ceRNA) to directly bind with miR-33a, thereby upregulated HMGB2 expression. Notably, silencing of LINC00974 suppressed cell proliferation, invasion and EMT of OC cells, whereas miR-33a knockdown partially reversed the phenotypes of LINC00974 on OC cells. Overall, our study demonstrated that LINC00974 sponges miR-33a to promote cell proliferation, invasion, and EMT of OC through HMGB2 upregulation. LINC00974/miR-33a/HMGB2 axis may be an important signaling pathway in the progression of OC.
DOI: 10.6084/m9.figshare.20018187.v1
title: MT1G inhibits the growth and epithelial-mesenchymal transition of gastric cancer cells by regulating the PI3K/AKT signaling pathway

description: Abstract Gastric carcinoma (GC) is a malignant tumor that has high mortality and morbidity worldwide. Although many efforts have been focused on the development and progression of GC, the underlying functional regulatory mechanism of GC needs more clarification. Metallothionein 1G (MT1G) is a member of the metallothionein family (MTs), and hypermethylation of MT1G occurred in a variety of cancers, including gastric cancer. However, the functional mechanism of MT1G in GC remains unclear. Here, we demonstrated that MT1G was down-regulated in GC tissues and cells. Overexpression of MT1G inhibited cell proliferation, foci formation and cell invasion, while knockdown of MT1G increased cell proliferation, foci formation and cell invasion. In addition, MT1G overexpression inhibited cell cycle progression and MT1G deficiency exerted opposite phenotype. p-AKT was negatively regulated by MT1G. In summary, our study reveals that MT1G exerts crucial role in regulating of cell proliferation and migration of gastric cancer, providing new insights for MT1G-related pathogenesis and a basis for developing new strategies for treatment of GC.
DOI: 10.6084/m9.figshare.20018192.v1
title: EPO activates PI3K-IKKα-CDK1 signaling pathway to promote the proliferation of Glial Cells under hypoxia environment

description: Abstract Erythropoietin (EPO), supports the function and survival of neurons through astrocytes and has a protective role in neonatal asphyxia brain injury; yet, its mechanism of action remains unclear. As a neuroprotective factor, EPO is also used in the treatment of various diseases, such as neurodegenerative diseases, Parkinson’s disease, traumatic brain injury, by decreasing inflammatory reaction, resisting apoptosis, and lowering oxidative stress. The aim of this study was to examine the effect and mechanism of EPO on promoting human brain glial cell proliferation under hypoxia in vitro. Under CoC12-induced hypoxia, after adding EPO, high-throughput sequencing was used to screen out meaningful up-regulated and significant differentially expressed genes PI3K, IKKα CDK1 related to proliferation, and make further verification by qPCR and western blotting. Under hypoxia, EPO promoted cell proliferation and the expression of PI3K while this effect was inhibited (along with a decrease of downstream genes IKKα and CDK1 decreased) after adding PI3K inhibitor to cell culture. EPO can promote cell proliferation and CDK1 expression, while after inhibiting CDK1 expression, the promotion of EPO on cell proliferation was eliminated. These data proved that EPO promotes the proliferation of U251 cells by activating the PI3K-IKKα-CDK1 signaling pathway under CoC12-induced hypoxia.
DOI: 10.6084/m9.figshare.16864760
title: Additional file 2 of TPSC: a module detection method based on topology potential and spectral clustering in weighted networks and its application in gene co-expression module discovery

description: Additional file 2: Detailed result of biological process, pathway and cytoband enrichment on each module. Only items with top 5 enrichment significance and number of overlap genes are displayed in this table.
DOI: 10.6084/m9.figshare.20018205
title: Correlation between vaginal microbiota and different progression stages of cervical cancer

description: Abstract The process from high-risk human papillomavirus (HR-HPV) infection to cervical cancer is a continuous and long-term process, but the pathogenesis of the whole process is not completely clear. Here, 59 Chinese women were engaged in this study, and divided into five groups: normal healthy group, HR-HPV infections group, low-grade intraepithelial neoplasia (LSIL) group, high-SIL(HSIL) group, and cervical cancer group. With the occurrence of HR-HPV infection and the development of cervical lesions, the diversity of vaginal microbiota species was increased, and the relative abundance of Lactobacillus (L.), the dominant bacteria in maintaining vaginal microecological balance, was decreased gradually. In contrast, the abundance of Actinobacteria in the four disease groups was significantly higher than that in normal group. Furthermore L. iners may be related to the serious progression of cervical cancer. After analyzing the whole process, we found that Gardnerella(G.), Atopobium(A.) and Dialister(D.) have important effects on both persistent HR-HPV infection and the pathogenesis of cervical cancer. In addition, PICRUSt2 and KEGG results showed that the KEGG pathways enriched by the predicted genes of vaginal microbiota in cancer group included metabolic diseases, endocrine system and immune systems when compared with that in normal group. These findings may provide insights into the pathogenesis of cervical cancer, and help to improve the early detection and prevention of cervical precancerous lesions.
DOI: 10.6084/m9.figshare.22639633
title: Additional file 3 of Pan-cancer landscape of CENPO and its underlying mechanism in LUAD

description: Additional file 3: Table S1. The value of ROC, DFS, and OS curves of CENPO in multiple types of cancers.
DOI: 10.6084/m9.figshare.22639597
title: Additional file 6 of Synchronization of inspiratory burst onset along the ventral respiratory column in the neonate mouse is mediated by electrotonic coupling

description: Additional file 6: Video: Synchronized syncytial rhythmic activity overlaps with respiratory network activity The video consists of the following elements: 1. View of the preparation with VIIn outlined. 2. Differenced view of baseline activity over 3 respiratory cycles (10X, 20Hz, 18 ms exposure); regions of interest are superimposed over the final inspiratory burst. 3. Averaged differenced inspiratory activity with ROIs superimposed. 4. Differenced view of syncytial activity over 5 cycles (10X, 10Hz, 50 ms exposure); two large ROIs used to generate traces in Supplemental Fig. 2 are superimposed over the last syncytial activation wave. Available at: https://figshare.com/articles/media/SV4_2102152_2_syncytial_video_mp4/21901209
DOI: 10.6084/m9.figshare.22639636.v1
title: Additional file 4 of Pan-cancer landscape of CENPO and its underlying mechanism in LUAD

description: Additional file 4: Table S2. The correlation of CENPO expression and ESTIMATEScore, ImmuneScore, and StromalScore in multiple types of cancers.
DOI: 10.6084/m9.figshare.22639642
title: Additional file 6 of Pan-cancer landscape of CENPO and its underlying mechanism in LUAD

description: Additional file 6: Table S4. The correlation of CENPO expression with TMB, MSI, and MATH in multiple types of cancers.
DOI: 10.6084/m9.figshare.20018162
title: Identification of bZIP transcription factors and their responses to brown spot in pear

description: Abstract Basic leucine zipper (bZIP) is a conserved transcription factor (TF) widely present in eukaryotes, and it plays an important role in regulating plant growth and stress responses. To better understand the white pear bZIP gene family, comprehensive bioinformatics analysis of the pear genome was performed. A total of 84 PbbZIP genes were identified, which were divided into 13 subfamilies by phylogenetic analysis. The 84 PbbZIP genes were all located in the nucleus, and 77 of those genes were unevenly distributed across the 17 chromosomes of white pear. The other 7 PbbZIP genes were located on the scaffold. Subsequent expression profile analysis showed that PbbZIP genes in exocarp were significantly upregulated or downregulated in ‘Huangguan’ pear with brown spot (BS) compared with healthy pear and in response to hormonal treatment with gibberellin A3 (GA3). These results provide helpful insights into the characteristics of PbbZIP genes and their responses to BS in ‘Huangguan’ pear.
DOI: 10.6084/m9.figshare.14775402.v1
title: Additional file 5 of Selective delignification of poplar wood with a newly isolated white-rot basidiomycete Peniophora incarnata T-7 by submerged fermentation to enhance saccharification

description: Additional file 5: The annotation of lignocellulolytic enzyme genes in the transcriptome.
DOI: 10.6084/m9.figshare.16864790
title: Additional file 1 of Development of whole-cell catalyst system for sulfide biotreatment based on the engineered haloalkaliphilic bacterium

description: Additional file 1: Table S1. Reference sequences of different types of Sqr and FCSD used for evolutionary analysis. Table S2. Sequence data of 484 Sqrs and FCSDs used in the evolutionary tree. Table S3. Results of mass spectrometry.
DOI: 10.6084/m9.figshare.14775405
title: Additional file 6 of Selective delignification of poplar wood with a newly isolated white-rot basidiomycete Peniophora incarnata T-7 by submerged fermentation to enhance saccharification

description: Additional file 6: Differential expression analysis of P. incarnate T-7 total genes in comparison of poplar wood substrate versus glucose substrate.
DOI: 10.6084/m9.figshare.20018207
title: A novel PRRX1 loss-of-function variation contributing to familial atrial fibrillation and congenital patent ductus arteriosus

description: Abstract Atrial fibrillation (AF) represents the most common type of sustained cardiac arrhythmia in humans and confers a significantly increased risk for thromboembolic stroke, congestive heart failure and premature death. Aggregating evidence emphasizes the predominant genetic defects underpinning AF and an increasing number of deleterious variations in more than 50 genes have been involved in the pathogenesis of AF. Nevertheless, the genetic basis underlying AF remains incompletely understood. In the current research, by whole-exome sequencing and Sanger sequencing analysis in a family with autosomal-dominant AF and congenital patent ductus arteriosus (PDA), a novel heterozygous variation in the PRRX1 gene encoding a homeobox transcription factor critical for cardiovascular development, NM_022716.4:c.373G&gt;T;p.(Glu125*), was identified to be in co-segregation with AF and PDA in the whole family. The truncating variation was not detected in 306 unrelated healthy individuals employed as controls. Quantitative biological measurements with a reporter gene analysis system revealed that the Glu125*-mutant PRRX1 protein failed to transactivate its downstream target genes SHOX2 and ISL1, two genes that have been causally linked to AF. Conclusively, the present study firstly links PRRX1 loss-of-function variation to AF and PDA, suggesting that AF and PDA share a common abnormal developmental basis in a proportion of cases.
DOI: 10.6084/m9.figshare.20018207.v1
title: A novel PRRX1 loss-of-function variation contributing to familial atrial fibrillation and congenital patent ductus arteriosus

description: Abstract Atrial fibrillation (AF) represents the most common type of sustained cardiac arrhythmia in humans and confers a significantly increased risk for thromboembolic stroke, congestive heart failure and premature death. Aggregating evidence emphasizes the predominant genetic defects underpinning AF and an increasing number of deleterious variations in more than 50 genes have been involved in the pathogenesis of AF. Nevertheless, the genetic basis underlying AF remains incompletely understood. In the current research, by whole-exome sequencing and Sanger sequencing analysis in a family with autosomal-dominant AF and congenital patent ductus arteriosus (PDA), a novel heterozygous variation in the PRRX1 gene encoding a homeobox transcription factor critical for cardiovascular development, NM_022716.4:c.373G&gt;T;p.(Glu125*), was identified to be in co-segregation with AF and PDA in the whole family. The truncating variation was not detected in 306 unrelated healthy individuals employed as controls. Quantitative biological measurements with a reporter gene analysis system revealed that the Glu125*-mutant PRRX1 protein failed to transactivate its downstream target genes SHOX2 and ISL1, two genes that have been causally linked to AF. Conclusively, the present study firstly links PRRX1 loss-of-function variation to AF and PDA, suggesting that AF and PDA share a common abnormal developmental basis in a proportion of cases.
DOI: 10.6084/m9.figshare.14775405.v1
title: Additional file 6 of Selective delignification of poplar wood with a newly isolated white-rot basidiomycete Peniophora incarnata T-7 by submerged fermentation to enhance saccharification

description: Additional file 6: Differential expression analysis of P. incarnate T-7 total genes in comparison of poplar wood substrate versus glucose substrate.