cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11590545.v1
title: HuR stabilizes <i>HTT</i> mRNA via interacting with its exon 11 in a mutant HTT-dependent manner

description: Huntington’s Disease (HD) is a monogenetic neurodegenerative disorder mainly caused by the cytotoxicity of the mutant HTT protein (mHTT) encoded by the mutant <i>HTT</i> gene. Lowering <i>HTT</i> mRNA has been extensively studied as a potential therapeutic strategy, but how its level is regulated endogenously has been unclear. Here we report that the RNA-binding protein (RBP) HuR interacts with and stabilizes <i>HTT</i> mRNA in an mHTT-dependent manner. In HD cells but not wild-type cells, siRNA knockdown or CRISPR-induced heterozygous knockout of HuR decreased <i>HTT</i> mRNA stability. HuR interacted with <i>HTT</i> mRNA at a conserved site in exon 11 rather than the 3ʹ-UTR region of the mRNA. Interestingly, this interaction was dependent on the presence of mHTT, likely <i>via</i> the activation of MAPK11, which enhanced cytosolic localization of the HuR protein. Thus, mHTT, MAPK11 and HuR may form a positive feedback loop that stabilizes <i>HTT</i> mRNA and enhances mHTT accumulation, which may contribute to HD progression. Our data reveal a novel regulatory mechanism of <i>HTT</i> mRNA <i>via</i> non-canonical binding of HuR.
DOI: 10.6084/m9.figshare.22599173.v1
title: Additional file 7 of FZD1/KLF10-hsa-miR-4762-5p/miR-224-3p-circular RNAs axis as prognostic biomarkers and therapeutic targets for glioblastoma: a comprehensive report

description: Additional file 7. The statistical characteristics of DEcircRNAs in this study.
DOI: 10.6084/m9.figshare.12637822.v1
title: Additional file 6 of Genome-wide studies reveal the essential and opposite roles of ARID1A in controlling human cardiogenesis and neurogenesis from pluripotent stem cells

description: Additional file 6: Table S4. Oligonucleotides.
DOI: 10.6084/m9.figshare.12637822
title: Additional file 6 of Genome-wide studies reveal the essential and opposite roles of ARID1A in controlling human cardiogenesis and neurogenesis from pluripotent stem cells

description: Additional file 6: Table S4. Oligonucleotides.
DOI: 10.6084/m9.figshare.16829863
title: Additional file 5 of Cys-SH based quantitative redox proteomics of salt induced response in sugar beet monosomic addition line M14

description: Additional file 5: Table S3. List of 42 differential redox proteins from BvM14 leaves between control and NaCl treatment using LC-MS/MS.
DOI: 10.6084/m9.figshare.12637813.v1
title: Additional file 3 of Genome-wide studies reveal the essential and opposite roles of ARID1A in controlling human cardiogenesis and neurogenesis from pluripotent stem cells

description: Additional file 3: contractile activity videos of differentiated (day 10) WT and ARID1A KO hESCs.
DOI: 10.6084/m9.figshare.1629357
title: Fatty acid degradation plays an essential role in proliferation of mouse female primordial germ cells via the p53-dependent cell cycle regulation

description: Primordial germ cells (PGCs) are embryonic founders of germ cells that ultimately differentiate into oocytes and spermatogonia. Embryonic proliferation of PGCs starting from E11.5 ensures the presence of germ cells in adulthood, especially in female mammals whose total number of oocytes declines after this initial proliferation period. To better understand mechanisms underlying PGC proliferation in female mice, we constructed a proteome profile of female mouse gonads at E11.5. Subsequent KEGG pathway analysis of the 3,662 proteins profiled showed significant enrichment of pathways involved in fatty acid degradation. Further, the number of PGCs found in <i>in vitro</i> cultured fetal gonads significantly decreased with application of etomoxir, an inhibitor of the key rate-limiting enzyme of fatty acid degradation carnitine acyltransferase I (CPT1). Decrease in PGCs was further determined to be the result of reduced proliferation rather than apoptosis. The inhibition of fatty acid degradation by etomoxir has the potential to activate the Ca<sup>2+</sup>/CamKII/5′-adenosine monophosphate-activated protein kinase (AMPK) pathway; while as an upstream activator, activated AMPK can function as activator of p53 to induce cell cycle arrest. Thus, we detected the expressional level of AMPK, phosphorylated AMPK (P-AMPK), phosphorylated p53 (P-p53) and cyclin-dependent kinase inhibitor 1 (p21) by Western blots, the results showed increased expression of them after treatment with etomoxir, suggested the activation of p53 pathway was the reason for reduced proliferation of PGCs. Finally, the involvement of p53-dependent G1 cell cycle arrest in defective proliferation of PGCs was verified by rescue experiments. Our results demonstrate that fatty acid degradation plays an important role in proliferation of female PGCs via the p53-dependent cell cycle regulation.
DOI: 10.6084/m9.figshare.14736573
title: Polystyrene nanoplastics exposure caused defective neural tube morphogenesis through caveolae-mediated endocytosis and faulty apoptosis

description: Growing evidence demonstrated that bioaccumulation of polystyrene nanoplastics (PS-NPs) in various organisms including human beings caused destructive effects on health. Nanoplastics may adversely affect fetal development potentially since they can pass through the placental barrier. However, very little has been known about the embryonic toxicity of polystyrene nanoplastics, especially in embryonic neurulation, the early developmental stage of the fetus, as well as the corresponding mechanisms. In this study, we first observed that 60- or 900-nm PS-NPs (especially 60-nm PS-NPs) could cross mouse placentas and affect developing mice fetuses. To avoid the indirect adverse effects derived from the restricted placenta, we employed early chick embryos as a developmental model to evaluate direct adverse effects of PS-NPs on embryo/fetal development, revealing suppressive effects on embryo development and an increased frequency of congenital abnormalities (especially in the nervous system), including neural tube defects. Thus, we focused on the potential negative effects of PS-NPs on neurulation, the earliest stage of nervous system development. Using caveolin-1 immunofluorescent staining of SH-SY5Y cells exposed to PS-NPs-GFP, we demonstrated that PS-NPs were internalized by SH-SY5Y cells via caveolae-mediated endocytosis. Transmission electron microscopy; LC3B immunofluorescent staining; and Atg7, Atg5, p62 and LC3B western blot results revealed that autophagy was activated in SH-SY5Y cells exposed to PS-NPs. However, PS-NPs were not degraded by the autophagic-lysosomal system given the lack of LAMP1 changes and minimal PS-NPs-GFP and LAMP1 colocalization. Furthermore, the cytoplasmic accumulation of PS-NPs caused faulty apoptotic cell death in SH-SY5Y cells and the developing neural tube as revealed by c-caspase3 immunofluorescent staining. Thus, defective neural tube morphogenesis, as demonstrated by neural tube defects, occurred during embryogenesis in the context of PS-NP exposure.
DOI: 10.6084/m9.figshare.11473929
title: MOESM2 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals

description: Additional file 2 Reference genes and transcripts (structure, expression) of the 4 species. Archive content:• bos_taurus.gtf• bos_taurus.refgn.tpm.tsv• capra_hircus.gtf• capra_hircus.refgn.tpm.tsv• gallus_gallus.gtf• gallus_gallus.refgn.tpm.tsv• sus_scrofa.gtf•sus_scrofa.refgn.tpm.tsv
DOI: 10.6084/m9.figshare.11473929.v2
title: MOESM2 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals

description: Additional file 2 Reference genes and transcripts (structure, expression) of the 4 species. Archive content:• bos_taurus.gtf• bos_taurus.refgn.tpm.tsv• capra_hircus.gtf• capra_hircus.refgn.tpm.tsv• gallus_gallus.gtf• gallus_gallus.refgn.tpm.tsv• sus_scrofa.gtf•sus_scrofa.refgn.tpm.tsv
DOI: 10.6084/m9.figshare.11473929.v1
title: MOESM2 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals

description: Additional file 2 Reference genes and transcripts (structure, expression) of the 4 species. Archive content: • bos_taurus.gtf • bos_taurus.refgn.tpm.tsv • capra_hircus.gtf • capra_hircus.refgn.tpm.tsv • gallus_gallus.gtf • gallus_gallus.refgn.tpm.tsv • sus_scrofa.gtf •sus_scrofa.refgn.tpm.tsv
DOI: 10.6084/m9.figshare.11473932
title: MOESM3 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals

description: Additional file 3 Orthologs between the 4 livestock species. We used Biomart to retrieve the 1 to 1 orthology relationships between chicken, pig and cattle and added goat via gene name. The human gene id is given for reference.
DOI: 10.6084/m9.figshare.12637813
title: Additional file 3 of Genome-wide studies reveal the essential and opposite roles of ARID1A in controlling human cardiogenesis and neurogenesis from pluripotent stem cells

description: Additional file 3: contractile activity videos of differentiated (day 10) WT and ARID1A KO hESCs.
DOI: 10.6084/m9.figshare.11473932.v2
title: MOESM3 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals

description: Additional file 3 Orthologs between the 4 livestock species. We used Biomart to retrieve the 1 to 1 orthology relationships between chicken, pig and cattle and added goat via gene name. The human gene id is given for reference.
DOI: 10.6084/m9.figshare.11473932.v1
title: MOESM3 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals

description: Additional file 3 Orthologs between the 4 livestock species. We used Biomart to retrieve the 1 to 1 orthology relationships between chicken, pig and cattle and added goat via gene name. The human gene id is given for reference.
DOI: 10.6084/m9.figshare.12637819
title: Additional file 5 of Genome-wide studies reveal the essential and opposite roles of ARID1A in controlling human cardiogenesis and neurogenesis from pluripotent stem cells

description: Additional file 5: Table S3. ARID1A ChIP-seq paired genes.
DOI: 10.6084/m9.figshare.11590884
title: Single-nucleus RNA sequencing reveals transcriptional changes of hippocampal neurons in APP23 mouse model of Alzheimer’s disease

description: Alzheimer’s disease (AD) is a progressive neurodegenerative disorder that mostly strikes the elderly. However, the exact molecular and cellular pathogenesis of AD, especially the dynamic changes of neurons during disease progression, remains poorly understood. Here we used single-nucleus RNA sequencing (snRNA-seq) to access the transcriptional changes of hippocampal neurons in APP23 mouse model of AD. We performed snRNA-seq using a modified Smart-seq2 technique on 3,280 neuronal nuclei from the hippocampus of young and aged APP23 and control mice and identified four distinct subpopulations. Comparative transcriptional analysis showed multiple changes in different subtypes of hippocampal neurons of APP23 mice in comparison to control mice, as well as the transcriptional changes in these neurons during disease progression. Our findings revealed multiple neuronal subtype-specific transcriptional changes that may lead to targets for future studies of AD. Single-nucleus RNA-seq for identifying the transcriptional changes in hippocampal neurons of an Alzheimer’s disease mouse model.
DOI: 10.6084/m9.figshare.11590884.v1
title: Single-nucleus RNA sequencing reveals transcriptional changes of hippocampal neurons in APP23 mouse model of Alzheimer’s disease

description: Alzheimer’s disease (AD) is a progressive neurodegenerative disorder that mostly strikes the elderly. However, the exact molecular and cellular pathogenesis of AD, especially the dynamic changes of neurons during disease progression, remains poorly understood. Here we used single-nucleus RNA sequencing (snRNA-seq) to access the transcriptional changes of hippocampal neurons in APP23 mouse model of AD. We performed snRNA-seq using a modified Smart-seq2 technique on 3,280 neuronal nuclei from the hippocampus of young and aged APP23 and control mice and identified four distinct subpopulations. Comparative transcriptional analysis showed multiple changes in different subtypes of hippocampal neurons of APP23 mice in comparison to control mice, as well as the transcriptional changes in these neurons during disease progression. Our findings revealed multiple neuronal subtype-specific transcriptional changes that may lead to targets for future studies of AD. Single-nucleus RNA-seq for identifying the transcriptional changes in hippocampal neurons of an Alzheimer’s disease mouse model.
DOI: 10.6084/m9.figshare.20499855
title: Additional file 8 of Integrative analysis of transcriptome and metabolome reveals flavonoid biosynthesis regulation in Rhododendron pulchrum petals

description: Additional file 8: Table S4. Enrichment of TOP20 pathways in R.pulchrum Sweet based on KEGG analysis.
DOI: 10.6084/m9.figshare.20499858
title: Additional file 9 of Integrative analysis of transcriptome and metabolome reveals flavonoid biosynthesis regulation in Rhododendron pulchrum petals

description: Additional file 9: Table S5. Association analysis of DEGs and DEMs in R.pulchrum Sweet.
DOI: 10.6084/m9.figshare.16305543
title: Additional file 8 of Transcriptome profiling provides insights into the molecular mechanisms of maize kernel and silk development

description: Additional file 8: Table S6. Genes involved in the development of self-pollinated and unpollinated kernels and silks.
DOI: 10.6084/m9.figshare.16305543.v1
title: Additional file 8 of Transcriptome profiling provides insights into the molecular mechanisms of maize kernel and silk development

description: Additional file 8: Table S6. Genes involved in the development of self-pollinated and unpollinated kernels and silks.
DOI: 10.21227/xxbt-qk75
title: Supplement

description: An experimental study was conducted on a high-voltage glass-type disc (LD-160) to investigate the effect of string arrangements on pollution and icing flashover characteristics. Two Artificial Neural Network (ANN) applications were developed to simulate and calculate the flashover voltage based on the experimental results. The test results showed that the inverted T-type arrangement can improve the pollution flashover voltage and increase the icing flashover voltage of insulator strings compared to the traditional arrangement of the I-string. The simulation results indicate the efficiency of the ANN applications in obtaining the optimal arrangement of the inverted T-string with good accuracy and small error rates.
DOI: 10.6084/m9.figshare.12637819.v1
title: Additional file 5 of Genome-wide studies reveal the essential and opposite roles of ARID1A in controlling human cardiogenesis and neurogenesis from pluripotent stem cells

description: Additional file 5: Table S3. ARID1A ChIP-seq paired genes.
DOI: 10.6084/m9.figshare.22599290
title: Additional file 4 of Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim

description: Additional file 4. F-vs-M DESs and predicted targets.
DOI: 10.6084/m9.figshare.22599293
title: Additional file 5 of Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim

description: Additional file 5. F-vs-M positive and negative miRNAs.
DOI: 10.6084/m9.figshare.22599293.v1
title: Additional file 5 of Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim

description: Additional file 5. F-vs-M positive and negative miRNAs.
DOI: 10.6084/m9.figshare.19977862.v1
title: Experimental study of peripheral-blood pro-surfactant protein B for screening non-small cell lung cancer

description: Abstract Purpose: To evaluate the possibility of using peripheral-blood presurfactant protein B (Pro-SFTPB) for screening non-small cell lung cancer (NSCLC). Methods: A total of 873 healthy volunteers and 165 lung cancer patients hospitalized in the Fifth People’s Hospital of Dalian were tested Pro-SFTPB once every half year from January 2014 to September 2015. The healthy volunteers were also conducted spiral computed tomography (CT) examination once every year. The data were then com-pared and statistically analyzed. Results: The positive expression rate of Pro-SFTPB in NSCLC was significantly higher than that in healthy volunteers, and significantly higher in lung adenocarcinoma than in squamous cell carcinoma; additionally, the expression rate was increased with the in-crease of smoking index, and the intergroup differences showed statistical signifi-cance (p≤0.05). The positive rate of newly diagnosed lung cancer was 29.55%, higher than healthy volunteers (22.34%), but there was no significant difference (p&gt;0.05). Conclusion: Pro-SFTPB is over expressed in non-small cell lung cancer, especially in lung adeno-carcinoma, but it can’t be used as a clinical screening tool for lung cancer.
DOI: 10.6084/m9.figshare.19977862
title: Experimental study of peripheral-blood pro-surfactant protein B for screening non-small cell lung cancer

description: Abstract Purpose: To evaluate the possibility of using peripheral-blood presurfactant protein B (Pro-SFTPB) for screening non-small cell lung cancer (NSCLC). Methods: A total of 873 healthy volunteers and 165 lung cancer patients hospitalized in the Fifth People’s Hospital of Dalian were tested Pro-SFTPB once every half year from January 2014 to September 2015. The healthy volunteers were also conducted spiral computed tomography (CT) examination once every year. The data were then com-pared and statistically analyzed. Results: The positive expression rate of Pro-SFTPB in NSCLC was significantly higher than that in healthy volunteers, and significantly higher in lung adenocarcinoma than in squamous cell carcinoma; additionally, the expression rate was increased with the in-crease of smoking index, and the intergroup differences showed statistical signifi-cance (p≤0.05). The positive rate of newly diagnosed lung cancer was 29.55%, higher than healthy volunteers (22.34%), but there was no significant difference (p&gt;0.05). Conclusion: Pro-SFTPB is over expressed in non-small cell lung cancer, especially in lung adeno-carcinoma, but it can’t be used as a clinical screening tool for lung cancer.
DOI: 10.25402/epi.16832182.v1
title: Supplementary table 2. Methylation comparison database vs this study

description: Supplementary table 2. Methylation comparison database vs
 this study
DOI: 10.25402/epi.16832188
title: Supplementary Table 3. The differential expression profile for PD patients by RNAseq

description: Supplementary Table 3. The differential expression
 profile for PD patients by RNAseq
DOI: 10.25402/epi.16832188.v1
title: Supplementary Table 3. The differential expression profile for PD patients by RNAseq

description: Supplementary Table 3. The differential expression
 profile for PD patients by RNAseq
DOI: 10.6084/m9.figshare.5822157.v1
title: iTRAQ-based proteomics analysis of autophagy-mediated immune responses against the vascular fungal pathogen <i>Verticillium dahliae</i> in <i>Arabidopsis</i>

description: The mechanisms underlying the functional link between autophagy and plant innate immunity remain largely unknown. In this study, we investigated the autophagy-mediated plant defense responses against <i>Verticillium dahliae</i> (<i>V. dahliae</i>) infection by comparative proteomics and cellular analyses. An assessment of the autophagy activity and disease development showed that autophagic processes were tightly related to the tolerance of <i>Arabidopsis</i> plant to Verticillium wilt. An isobaric tags for relative and absolute quantification (iTRAQ)-based proteomics analysis was performed, and we identified a total of 780 differentially accumulated proteins (DAPs) between wild-type and mutant <i>atg10-1 Arabidopsis</i> plants upon <i>V. dahliae</i> infection, of which, 193 ATG8-family-interacting proteins were identified <i>in silico</i> and their associations with autophagy were verified for several selected proteins. Three important aspects of autophagy-mediated defense against <i>V. dahliae</i> infection were revealed: 1) autophagy is required for the activation of upstream defense responses; 2) autophagy-mediated mitochondrial degradation (mitophagy) occurs and is an important player in the defense process; and 3) autophagy promotes the transdifferentiation of perivascular cells and the formation of xylem hyperplasia, which are crucial for protection against this vascular disease. Together, our results provide several novel insights for understanding the functional association between autophagy and plant immune responses.
DOI: 10.25402/epi.16832182
title: Supplementary table 2. Methylation comparison database vs this study

description: Supplementary table 2. Methylation comparison database vs
 this study
DOI: 10.6084/m9.figshare.12637864
title: Additional file 6 of Identification of candidate genes for milk production traits by RNA sequencing on bovine liver at different lactation stages

description: Additional file 6. List of significant GO terms assignment for DEGs in bovine liver between early lactation and dry period/peak of lactation and dry period/peak of lactation and early lactation.
DOI: 10.6084/m9.figshare.13686571
title: Identification of key residues involved in the neuraminidase antigenic variation of H9N2 influenza virus

description: Influenza A H9N2 virus causes economic loss to the poultry industry and has likely contributed to the genesis of H5N1 and H7N9 viruses. The neuraminidase (NA) of H9N2 virus, like haemagglutinin, is under antibody selective pressure and may undergo antigenic change; however, its antigenic structure remains to be elucidated. In this study, we used monoclonal antibodies (mAbs) to probe the H9N2 viral NA residues that are key for antibody binding/inhibition. These mAbs fell into three groups based on their binding/inhibition of the NA of H9N2 viruses isolated during 1999–2019: group I only bounded the NA of the early 2000 H9N2 viruses but possessed no neutralizing ability, group II bounded and inhibited the NA of H9N2 viruses isolated before 2012, and group III reacted with most or all tested H9N2 viruses. We showed that NA residue 356 is key for the recognition by group I mAbs, residues 344, 368, 369, and 400 are key for the binding/inhibition of NA by group II antibodies, whereas residues 248, 253, and the 125/296 combination are key for neutralizing antibodies in group III. Our findings highlighted NA antigenic change of the circulating H9N2 viruses, and provided data for a more complete picture of the antigenic structure of H9N2 viral NA.
DOI: 10.6084/m9.figshare.13686571.v1
title: Identification of key residues involved in the neuraminidase antigenic variation of H9N2 influenza virus

description: Influenza A H9N2 virus causes economic loss to the poultry industry and has likely contributed to the genesis of H5N1 and H7N9 viruses. The neuraminidase (NA) of H9N2 virus, like haemagglutinin, is under antibody selective pressure and may undergo antigenic change; however, its antigenic structure remains to be elucidated. In this study, we used monoclonal antibodies (mAbs) to probe the H9N2 viral NA residues that are key for antibody binding/inhibition. These mAbs fell into three groups based on their binding/inhibition of the NA of H9N2 viruses isolated during 1999–2019: group I only bounded the NA of the early 2000 H9N2 viruses but possessed no neutralizing ability, group II bounded and inhibited the NA of H9N2 viruses isolated before 2012, and group III reacted with most or all tested H9N2 viruses. We showed that NA residue 356 is key for the recognition by group I mAbs, residues 344, 368, 369, and 400 are key for the binding/inhibition of NA by group II antibodies, whereas residues 248, 253, and the 125/296 combination are key for neutralizing antibodies in group III. Our findings highlighted NA antigenic change of the circulating H9N2 viruses, and provided data for a more complete picture of the antigenic structure of H9N2 viral NA.