cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12703604
title: Additional file 9 of Trem2 deficiency differentially affects phenotype and transcriptome of human APOE3 and APOE4 mice

description: Additional file 9: Supplemental-Table 3. APOE-Isoform-GO terms.
DOI: 10.6084/m9.figshare.12703604.v1
title: Additional file 9 of Trem2 deficiency differentially affects phenotype and transcriptome of human APOE3 and APOE4 mice

description: Additional file 9: Supplemental-Table 3. APOE-Isoform-GO terms.
DOI: 10.6084/m9.figshare.12703598.v1
title: Additional file 7 of Trem2 deficiency differentially affects phenotype and transcriptome of human APOE3 and APOE4 mice

description: Additional file 7: Supplemental Table 1. WGCNA.
DOI: 10.6084/m9.figshare.12703601
title: Additional file 8 of Trem2 deficiency differentially affects phenotype and transcriptome of human APOE3 and APOE4 mice

description: Additional file 8: Supplemental Table 2. Trem2-GO terms.
DOI: 10.6084/m9.figshare.12703685.v1
title: Additional file 2 of Integrated metabolomic and transcriptomic analysis of the anthocyanin regulatory networks in Salvia miltiorrhiza Bge. flowers

description: Additional file 2 Supplemental Table S2. Different flavonoid metabolites in WPSM vs. PFSM.
DOI: 10.6084/m9.figshare.12703601.v1
title: Additional file 8 of Trem2 deficiency differentially affects phenotype and transcriptome of human APOE3 and APOE4 mice

description: Additional file 8: Supplemental Table 2. Trem2-GO terms.
DOI: 10.6084/m9.figshare.12703685
title: Additional file 2 of Integrated metabolomic and transcriptomic analysis of the anthocyanin regulatory networks in Salvia miltiorrhiza Bge. flowers

description: Additional file 2 Supplemental Table S2. Different flavonoid metabolites in WPSM vs. PFSM.
DOI: 10.6084/m9.figshare.12703688
title: Additional file 3 of Integrated metabolomic and transcriptomic analysis of the anthocyanin regulatory networks in Salvia miltiorrhiza Bge. flowers

description: Additional file 3 Supplemental Table S3. Differentially expressed genes in WFSM vs. PFSM.
DOI: 10.6084/m9.figshare.12703688.v1
title: Additional file 3 of Integrated metabolomic and transcriptomic analysis of the anthocyanin regulatory networks in Salvia miltiorrhiza Bge. flowers

description: Additional file 3 Supplemental Table S3. Differentially expressed genes in WFSM vs. PFSM.
DOI: 10.6084/m9.figshare.12703691
title: Additional file 4 of Integrated metabolomic and transcriptomic analysis of the anthocyanin regulatory networks in Salvia miltiorrhiza Bge. flowers

description: Additional file 4 Supplemental Table S4. Differentially expressed genes of anthocyanin biosynthesis in WPSM vs. PFSM.
DOI: 10.6084/m9.figshare.23707075
title: Additional file 2 of Neural network-based prognostic predictive tool for gastric cardiac cancer: the worldwide retrospective study

description: Additional file 2: Supplement File 1. The Neural network-based prognostic predictive tool for GCC patients.
DOI: 10.6084/m9.figshare.13228217
title: In vitro study of the effects of DC electric fields on cell activities and gene expression in human choriocarcinoma cells

description: Physiological electric fields (EFs), as one of the environmental cues influencing both normal and tumor cells, have profound effects on tumor cell malignancy potential. The cellular responses to EFs by choriocarcinoma cells and their underlying mechanisms are unknown. In this study, the migration/motility, cell cycle progression and proliferation of choriocarcinoma cells in electric field culture showed that choriocarcinoma cells migrated cathodally in an applied EF, and EF stimulation influenced cell cycle progression through G2/M arrest and therefore induced a reduction in cellular proliferation. The transcriptome of choriocarcinoma cells subjected to EF stimulation (150 mV/mm) was analyzed using RNA sequencing (RNA-Seq), and the results were verified by reverse transcription quantitative polymerase chain reaction. A Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that ErbB and HIF-1 signaling pathways that are involved in cell migration/motility, cell cycle progression and proliferation were significantly altered in cells treated with an EF of 150 mV/mm compared with control cells, and in addition, the downstream pathways of these signaling pathways such as AKT and P42/P44 MAPK (ERK1/2) showed primary activation by Western blotting. This study’s results suggest that an applied EF is an effective cue in regulating cellular phenotypes of choriocarcinoma cells and that transcriptional analysis contributes to the understanding of the mechanism of EF-guided cell functions.
DOI: 10.6084/m9.figshare.23706967.v1
title: Additional file 2 of DNMT3A mutation promotes leukemia development through NAM-NAD metabolic reprogramming

description: Additional file 2: Table S2. The mRNA expression level of NAMPT in AML obtained from the Oncomine database.
DOI: 10.6084/m9.figshare.22665213.v1
title: A Unified Inference for Predictive Quantile Regression

description: The asymptotic behavior of quantile regression inference becomes dramatically different when it involves a persistent predictor with zero or nonzero intercept. Distinguishing various properties of a predictor is empirically challenging. In this paper, we develop a unified predictability test for quantile regression regardless of the presence of intercept and persistence of a predictor. The developed test is a novel combination of data splitting, weighted inference, and a random weighted bootstrap method. Monte Carlo simulations show that the new approach displays significantly better size and power performance than other competing methods in various scenarios, particularly when the predictive regressor contains a nonzero intercept. In an empirical application, we revisit the quantile predictability of the monthly S&P 500 returns between 1980 and 2019.
DOI: 10.6084/m9.figshare.9033830.v1
title: Hepatitis E-related adverse pregnancy outcomes and their prevention by hepatitis E vaccine in a rabbit model

description: Hepatitis E virus (HEV) can lead to high mortality during pregnancy. This study was to investigate the adverse pregnancy outcomes caused by different HEV genotypes and their prevention by HEV 239 vaccine in rabbits. Forty-two female rabbits were randomly and equally divided into 7 groups (A-G). HEV 239 vaccine and a placebo were administered to groups E (10 μg×2), F (5 μg×2) and G (1 mL of PBS×2) before copulation. After pregnancy, 1 mL of 1.5×106 copies/mL rabbit HEV3 was inoculated to groups A, E, F and G, swine HEV4/human HEV3 to groups B/C, and group D was a negative control. Anti-HEV antibody, HEV RNA, and alanine aminotransferase (ALT)/aspartate aminotransferase (AST) levels were monitored. Pregnant rabbits infected by HEV manifested HEV infection symptoms including fecal virus shedding, ALT/AST elevation, and histopathological changes, and adverse pregnancy outcomes. Immunized pregnant rabbits in groups E and F showed no HEV infection symptoms and adverse outcomes. The newborn rabbits delivered by pregnant rabbits with/without immunization showed without/with HEV infection symptoms. This study demonstrated that multiple genotypes of HEV infection can cause adverse outcomes and HEV 239 vaccine can prevent HEV-related adverse outcomes in pregnant rabbits.
DOI: 10.6084/m9.figshare.12703850
title: Additional file 1 of An integrative network-driven pipeline for systematic identification of lncRNA-associated regulatory network motifs in metastatic melanoma

description: Additional file 1: Table S1A. Predicted lncRNA-miRNA interactions; Table S1B. MiRNA-target gene interactions; Table S1C. TF-miRNA interactions; Table S1D. Predicted lncRNA-TF interactions; Table S1E. TF-TF interactions; Table S1F. Topological and non-topological parameters calculated for each node of regulatory network motif; Table S1G. Prioritized motifs for metastatic and non-metastatic melanoma phenotype; Table S1H. Predictive statistics for motif 1; Table S1I. Predictive statistics for motif 2; Table S1J. Predictive statistics for motif 3; Table S1K.P-value identified from pairwise and overall comparison of three patient subgroups; Table S2. Weighting scenarios for ranking of motifs; Table S3. Patient-derived RNAseq expression profile (pan-cancer normalized log 2) of nodes in three prioritized motifs (lncRNA/miRNA/TF); Figures S1-S17. Hybridization maps of putative miRNAs binding sites across lncRNA sequences; Figure S18. LncRNA-miRNA interaction network. Rectangular nodes designate lncRNA (peach color) and miRNA (cyan color). The network consists of 47 nodes (including 17 lncRNAs and 30 miRNAs) and 174 prioritized edges link the pairs of lncRNA and miRNAs in cluster; Figure S19. TF-miRNA interaction network. Experimentally validated target genes of miRNAs which act as TFs are represented by octagon nodes (yellow color) and miRNAs are showed by rectangular nodes (cyan color). The network is comprised of 146 nodes with 25 TFs and 121 miRNAs. The edges of the network (total 247) signify predictions of miRNA regulation by TFs. Arrow-headed lines are for activation (purple color) and bar-headed lines are for repression (green color); Data S1. Python script for retrieval of FASTA sequences from NCBI; Data S2. Pseudo code for ranking of network motifs.
DOI: 10.6084/m9.figshare.23707078
title: Additional file 3 of Neural network-based prognostic predictive tool for gastric cardiac cancer: the worldwide retrospective study

description: Additional file 3: Supplement File 2. The raw data of this study.
DOI: 10.6084/m9.figshare.23707078.v1
title: Additional file 3 of Neural network-based prognostic predictive tool for gastric cardiac cancer: the worldwide retrospective study

description: Additional file 3: Supplement File 2. The raw data of this study.
DOI: 10.6084/m9.figshare.12703830
title: Additional file 1 of Overexpression of the Transcription Factor Gene OsSTAP1 Increases Salt Tolerance in Rice

description: Additional file 1: Table S1. Cis-elements analysis of the OsSTAP1 promoter sequence. Table S2. List of the differentially expressed gene in the OsSTAP1 overexpression line compared with WT under normal growth conditions. Table S3. List of the differentially expressed gene in the OsSTAP1 overexpression line compared with WT under salt stress conditions. Table S4. The primers used in the present study. Table S5. The expression levels of 24 differentially expressed gene detected by transcriptome and qRT-PCR.
DOI: 10.6084/m9.figshare.22140915.v1
title: The Chromosome-Level Assembly of Ramie (Boehmeria Nivea L.) Genome Provides Insights into Molecular Regulation of Fiber Fineness

description: Ramie (<i>Boehmeria nivea</i> L.), belonging to Urticaceae, is principally used for fabric production. It is a well-known natural fiber material for ancient clothing. Despite its important position and application value, the understanding on genetic regulation mechanism of fiber quality is limited. Here, we generate a chromosome-scale, high-quality reference genome of ramie, in which, approximately 90.2% of the assembled sequences have been anchored to 14 pseudochromosomes. Totally 27,664 protein-coding genes are predicted which cover 268.24 Mb region of the genome. Comparative genomic analysis reveals that 2,047 and 796 gene clusters expand and contract, respectively, underlying significant genes in plant hormone signal transduction and cellulose/lignin biosynthesis pathways. An integrative analysis combining quantitative trait loci (QTL), comparative transcriptomic data, and cytological experiments unravels the molecular regulatory mechanism of ramie fiber fineness, especially the critical regulating role of ethylene. This study would lay a solid foundation for the research of molecular biology in ramie and provide valuable reference for the improvement of high-quality fiber varieties.
DOI: 10.6084/m9.figshare.12703956
title: Additional file 2 of Exogenous 2-(3,4-Dichlorophenoxy) triethylamine alleviates salinity stress in maize by enhancing photosynthetic capacity, improving water status and maintaining K+/Na+ homeostasis

description: Additional file 2. Research data.
DOI: 10.6084/m9.figshare.22140915
title: The Chromosome-Level Assembly of Ramie (Boehmeria Nivea L.) Genome Provides Insights into Molecular Regulation of Fiber Fineness

description: Ramie (<i>Boehmeria nivea</i> L.), belonging to Urticaceae, is principally used for fabric production. It is a well-known natural fiber material for ancient clothing. Despite its important position and application value, the understanding on genetic regulation mechanism of fiber quality is limited. Here, we generate a chromosome-scale, high-quality reference genome of ramie, in which, approximately 90.2% of the assembled sequences have been anchored to 14 pseudochromosomes. Totally 27,664 protein-coding genes are predicted which cover 268.24 Mb region of the genome. Comparative genomic analysis reveals that 2,047 and 796 gene clusters expand and contract, respectively, underlying significant genes in plant hormone signal transduction and cellulose/lignin biosynthesis pathways. An integrative analysis combining quantitative trait loci (QTL), comparative transcriptomic data, and cytological experiments unravels the molecular regulatory mechanism of ramie fiber fineness, especially the critical regulating role of ethylene. This study would lay a solid foundation for the research of molecular biology in ramie and provide valuable reference for the improvement of high-quality fiber varieties.
DOI: 10.6084/m9.figshare.14795150
title: Additional file 4 of Genome-wide DNA methylation analysis in Chinese Chenghua and Yorkshire pigs

description: Additional file 4: Table S4. Summary of hypomethylation genes in CHP vs. YP.
DOI: 10.6084/m9.figshare.12703850.v1
title: Additional file 1 of An integrative network-driven pipeline for systematic identification of lncRNA-associated regulatory network motifs in metastatic melanoma

description: Additional file 1: Table S1A. Predicted lncRNA-miRNA interactions; Table S1B. MiRNA-target gene interactions; Table S1C. TF-miRNA interactions; Table S1D. Predicted lncRNA-TF interactions; Table S1E. TF-TF interactions; Table S1F. Topological and non-topological parameters calculated for each node of regulatory network motif; Table S1G. Prioritized motifs for metastatic and non-metastatic melanoma phenotype; Table S1H. Predictive statistics for motif 1; Table S1I. Predictive statistics for motif 2; Table S1J. Predictive statistics for motif 3; Table S1K.P-value identified from pairwise and overall comparison of three patient subgroups; Table S2. Weighting scenarios for ranking of motifs; Table S3. Patient-derived RNAseq expression profile (pan-cancer normalized log 2) of nodes in three prioritized motifs (lncRNA/miRNA/TF); Figures S1-S17. Hybridization maps of putative miRNAs binding sites across lncRNA sequences; Figure S18. LncRNA-miRNA interaction network. Rectangular nodes designate lncRNA (peach color) and miRNA (cyan color). The network consists of 47 nodes (including 17 lncRNAs and 30 miRNAs) and 174 prioritized edges link the pairs of lncRNA and miRNAs in cluster; Figure S19. TF-miRNA interaction network. Experimentally validated target genes of miRNAs which act as TFs are represented by octagon nodes (yellow color) and miRNAs are showed by rectangular nodes (cyan color). The network is comprised of 146 nodes with 25 TFs and 121 miRNAs. The edges of the network (total 247) signify predictions of miRNA regulation by TFs. Arrow-headed lines are for activation (purple color) and bar-headed lines are for repression (green color); Data S1. Python script for retrieval of FASTA sequences from NCBI; Data S2. Pseudo code for ranking of network motifs.
DOI: 10.6084/m9.figshare.22665371.v1
title: Associations between weather conditions and osteoarthritis pain: a systematic review and meta-analysis

description: Although there is an assertion that weather conditions affect osteoarthritis (OA) pain, the results from clinical studies remain inconsistent. This meta-analysis was performed to evaluate the association between weather conditions and OA pain. Cochrane Library, Embase, PubMed, and Web of Science were searched from inception to September 30, 2022. Observational studies that explored all weather conditions associated with pain intensity were included. In the systematic review, the methodological quality of the selected studies was assessed and a best-evidence synthesis was used to make qualitative conclusions. Based on homogeneous results, Fisher’s <i>Z</i> scores derived from the effect size of temperature (T), barometric pressure (BP) or relative humidity (RH) related to OA pain were synthesized and further transformed to the correlation coefficients (summary r) in meta-analysis. A total of 14 studies were included in the best-evidence synthesis of a qualitative systematic review. There was strong evidence with 13 of 14 studies reporting consistent findings that weather factors in general, including any kind of meteorological condition, were associated with OA pain. Subsequently, 3 studies regarding BP or T, and 5 studies regarding RH with the pain of OA were included in quantitative meta-analyses. Both BP (pooled Fisher’s <i>Z</i> = 0.37, 95% CI 0.15 to 0.59; summary <i>r</i> = 0.35, 95% CI 0.15 to 0.53) and RH (pooled Fisher’s <i>Z</i> = 0.10, 95% CI 0.01 to 0.18; summary <i>r</i> = 0.086, 95% CI −0.05 to 0.22) were positively related to OA pain, while T was negatively related to OA pain (pooled Fisher’s <i>Z</i> = −0.38, 95% CI −0.60 to −0.16; summary <i>r</i> = −0.36, 95% CI −0.54 to −0.16). In this study, weather factors in general were significantly associated with OA pain. It may provide useful references for the daily health management of OA. More studies designed with the consistent meteorological condition are warranted to validate the findings.KEY MESSAGEMany people with osteoarthritis think their joint pain is affected by the weather, while the association between OA pain and weather conditions is still unclear.This is a systematic review and meta-analysis of 14 observational studies for the association between weather conditions and OA pain.Weather conditions appear to be associated with OA pain. Barometric pressure and relative humidity were positively correlated to OA pain intensity, while temperature was negatively correlated to OA pain. Many people with osteoarthritis think their joint pain is affected by the weather, while the association between OA pain and weather conditions is still unclear. This is a systematic review and meta-analysis of 14 observational studies for the association between weather conditions and OA pain. Weather conditions appear to be associated with OA pain. Barometric pressure and relative humidity were positively correlated to OA pain intensity, while temperature was negatively correlated to OA pain.
DOI: 10.6084/m9.figshare.22665371
title: Associations between weather conditions and osteoarthritis pain: a systematic review and meta-analysis

description: Although there is an assertion that weather conditions affect osteoarthritis (OA) pain, the results from clinical studies remain inconsistent. This meta-analysis was performed to evaluate the association between weather conditions and OA pain. Cochrane Library, Embase, PubMed, and Web of Science were searched from inception to September 30, 2022. Observational studies that explored all weather conditions associated with pain intensity were included. In the systematic review, the methodological quality of the selected studies was assessed and a best-evidence synthesis was used to make qualitative conclusions. Based on homogeneous results, Fisher’s <i>Z</i> scores derived from the effect size of temperature (T), barometric pressure (BP) or relative humidity (RH) related to OA pain were synthesized and further transformed to the correlation coefficients (summary r) in meta-analysis. A total of 14 studies were included in the best-evidence synthesis of a qualitative systematic review. There was strong evidence with 13 of 14 studies reporting consistent findings that weather factors in general, including any kind of meteorological condition, were associated with OA pain. Subsequently, 3 studies regarding BP or T, and 5 studies regarding RH with the pain of OA were included in quantitative meta-analyses. Both BP (pooled Fisher’s <i>Z</i> = 0.37, 95% CI 0.15 to 0.59; summary <i>r</i> = 0.35, 95% CI 0.15 to 0.53) and RH (pooled Fisher’s <i>Z</i> = 0.10, 95% CI 0.01 to 0.18; summary <i>r</i> = 0.086, 95% CI −0.05 to 0.22) were positively related to OA pain, while T was negatively related to OA pain (pooled Fisher’s <i>Z</i> = −0.38, 95% CI −0.60 to −0.16; summary <i>r</i> = −0.36, 95% CI −0.54 to −0.16). In this study, weather factors in general were significantly associated with OA pain. It may provide useful references for the daily health management of OA. More studies designed with the consistent meteorological condition are warranted to validate the findings.KEY MESSAGEMany people with osteoarthritis think their joint pain is affected by the weather, while the association between OA pain and weather conditions is still unclear.This is a systematic review and meta-analysis of 14 observational studies for the association between weather conditions and OA pain.Weather conditions appear to be associated with OA pain. Barometric pressure and relative humidity were positively correlated to OA pain intensity, while temperature was negatively correlated to OA pain. Many people with osteoarthritis think their joint pain is affected by the weather, while the association between OA pain and weather conditions is still unclear. This is a systematic review and meta-analysis of 14 observational studies for the association between weather conditions and OA pain. Weather conditions appear to be associated with OA pain. Barometric pressure and relative humidity were positively correlated to OA pain intensity, while temperature was negatively correlated to OA pain.