cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7082003
title: Additional file 11: of Nogo-B receptor increases the resistance to tamoxifen in estrogen receptor-positive breast cancer cells

description: NgBR (NUS1) mRNA expression data were retrieved from GSE6532 database. Kaplan–Meier analysis revealed significantly reduced relapse-free survival (RFS) (p &lt; 0.05) in patients with high NgBR expression in tumors (n = 189) as compared to patients with low NgBR expression in tumors (n = 154). (XLS 67 kb)
DOI: 10.6084/m9.figshare.7082063.v1
title: Additional file 2: of A metagenome-wide association study of gut microbiota in asthma in UK adults

description: Table S2. Factors influence the gut microbiome: Test the factors influence the gut microbiome with PERMANOVA. (XLS 7 kb)
DOI: 10.6084/m9.figshare.7082276
title: MOESM4 of Modulation of mitochondrial DNA copy number in a model of glioblastoma induces changes to DNA methylation and gene expression of the nuclear genome in tumours

description: Additional file 4. DMRs identified using MeDIP-Seq and MEDIPS package.
DOI: 10.6084/m9.figshare.21762453.v1
title: Complete trajectory extraction for moving targets in traffic scenes that considers multi-level semantic features

description: Complex traffic scenes are susceptible to the occlusion of moving targets and blurred target images, resulting in incomplete extraction of target trajectories within the field of view (FOV). To address this issue, we proposed a complete trajectory extraction algorithm for moving targets (TraEA) that considers the multi-level semantic features of traffic scenes following the FOV of single-camera surveillance videos. TraEA utilizes semantic information from the multi-level scene structure, such as image pixel features, geometric features, as well as temporal and spatial relationships between targets within each keyframe image. The semantic information helps extract and optimize the complete trajectory of a target, to assemble the target’s moving trajectory with improved integrity. An experiment with real-world traffic videos collected in Beijing, China validated the proposed algorithm and showed that TraEA improved the completeness, accuracy and robustness of target trajectory extraction. Traffic trajectories from the experiment can facilitate traffic supervision by analyzing the moving behaviors of individual targets. While the proposed TraEA algorithm is applicable to extract trajectories from videos in other domains, such as animal movements, potential privacy infringement and abusive applications warrant cautions of ethical considerations.
DOI: 10.6084/m9.figshare.24117214.v1
title: Effect of microclimate and photosynthesis on strawberry reproductive growth in a greenhouse: using cumulative leaf photosynthesis as an index to predict the time of harvest

description: We evaluate whether cumulative photosynthesis (<i>A</i><sub>n,C</sub>) could predict the time of harvest in strawberry better than light (<i>I</i><sub>C</sub>) or temperature (<i>T</i><sub>a,C</sub>) as forecast indices. We monitored the daily dynamics of flowering, fruit set, and harvest in over 2,700 fruits across the growing season in a greenhouse in Japan. Photosynthesis was calculated using a biochemical model, and <i>A</i><sub>n,C</sub> calculated by totalling the cumulative rate from flowering to harvest in each fruit. <i>I</i><sub>C</sub> and <i>T</i><sub>a,C</sub> were calculated by totalling daily cumulative light intensity and average temperature. A new index (<i>D</i>) was defined as the normalised variation of <i>A</i><sub>n,C</sub>, <i>I</i><sub>C</sub>, and <i>T</i><sub>a,C</sub>, and a statistical analysis was conducted on the means for each index. The results showed that <i>A</i><sub>n,C</sub> had the lowest <i>D</i> (0.114), suggesting that it was a better index for predicting the time of harvest. This study suggests the importance of considering the accumulation of photosynthates in individual fruit, which cannot be achieved by <i>I</i><sub>C</sub> or <i>T</i><sub>a,C</sub>, these results can be used to improve the forecasting and optimisation of yield. However, further research is required to substantiate these claims.
DOI: 10.6084/m9.figshare.7082069.v1
title: Additional file 8: of Identification and expression analysis of genes with pathogen-inducible cis-regulatory elements in the promoter regions in Oryza sativa

description: Table S7. Differentially expressed transcripts in common from the rice microarray and RNA-Seq data analyses. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.13373870.v1
title: Association Analysis and Validation of Simple Sequence Repeat Markers for Fiber Fineness in Ramie (<i>Boehmeria Nivea</i> L. Gaudich)

description: This study investigated simple sequence repeat (SSR) marker associated with fiber fineness in ramie (<i>Boehmeria nivea</i> L. Gaudich). Firstly, association analysis was carried out using 107 ramie accessions and 95 SSR markers. Three stable molecular markers related to fiber fineness were detected in multiple environments. Furthermore, we validated the three SSR markers using single marker association on a set of 286 accessions planted in another three environments. The result of polymorphisms analysis found that the average polymorphism information content (PIC) of three markers was 0.5149; average number of alleles was 3.6667; average genetic diversity was 0.6043; average Shannon-Wiener diversity index was 0.9710; and average major allele frequency (MAF) was 0.4488. We demonstrated that marker RAM39 was stably associated with fiber fineness, highlighting its utility for breeding. These findings provide a basis for genetic improvement of ramie quality traits through marker-assisted selection.
DOI: 10.6084/m9.figshare.7082036.v1
title: Additional file 11: of A metagenome-wide association study of gut microbiota in asthma in UK adults

description: Table S7. The VFG: The relative abundance and statistical test of the VFGs. (XLS 3741 kb)
DOI: 10.6084/m9.figshare.19665345
title: Translocator protein (18 kDa) regulates the microglial phenotype in Parkinson’s disease through P47

description: Numerous studies have suggested that the phenotypic transformation of microglia plays a role in the pathogenesis of Parkinson’s disease (PD). Translocator protein (TSPO) is an 18 kDa translocator membrane protein that acts as a marker of neuroinflammation and suppresses neuroinflammation; however, its underlying mechanism remains unclear. Although TSPO ligands were found to be protective in several neurodegenerative paradigms, few studies have evaluated their effects on microglial polarization, and underlying mechanisms need to be explored. In the present study, we examined the effects of TSPO and PK11195, a TSPO ligand, on lipopolysaccharide (LPS)+interferon (IFN)-γ-induced inflammatory factors and oxidative stress in microglia using enzyme-linked immunosorbent assay. The effect of TSPO and PK11195 on LPS+IFN-γ-induced microglial cell apoptosis was examined using immunofluorescence (IF), flow cytometry, and western blotting. The interaction between TSPO and P47 was investigated using IF and co-immunoprecipitation analysis. <i>In vivo</i> experiments confirmed the influence of TSPO and its ligand on motility, a-Syn, and dopaminergic neuronal damage. Our findings indicate that TSPO may regulate the microglial phenotype in PD via P47, suggesting a potential role in anti-PD therapy.
DOI: 10.6084/m9.figshare.19665345.v1
title: Translocator protein (18 kDa) regulates the microglial phenotype in Parkinson’s disease through P47

description: Numerous studies have suggested that the phenotypic transformation of microglia plays a role in the pathogenesis of Parkinson’s disease (PD). Translocator protein (TSPO) is an 18 kDa translocator membrane protein that acts as a marker of neuroinflammation and suppresses neuroinflammation; however, its underlying mechanism remains unclear. Although TSPO ligands were found to be protective in several neurodegenerative paradigms, few studies have evaluated their effects on microglial polarization, and underlying mechanisms need to be explored. In the present study, we examined the effects of TSPO and PK11195, a TSPO ligand, on lipopolysaccharide (LPS)+interferon (IFN)-γ-induced inflammatory factors and oxidative stress in microglia using enzyme-linked immunosorbent assay. The effect of TSPO and PK11195 on LPS+IFN-γ-induced microglial cell apoptosis was examined using immunofluorescence (IF), flow cytometry, and western blotting. The interaction between TSPO and P47 was investigated using IF and co-immunoprecipitation analysis. <i>In vivo</i> experiments confirmed the influence of TSPO and its ligand on motility, a-Syn, and dopaminergic neuronal damage. Our findings indicate that TSPO may regulate the microglial phenotype in PD via P47, suggesting a potential role in anti-PD therapy.
DOI: 10.6084/m9.figshare.19665467.v1
title: Euphorbia factor L3 ameliorates rheumatoid arthritis by suppressing the inflammatory response by targeting Rac family small GTPase 1

description: Euphorbia factor L3 (EFL3) is extracted from <i>Euphorbia lathyris</i> and is known for its anti-inflammatory properties. This study focused on the potential anti-inflammatory and therapeutic effects of EFL3 on rheumatoid arthritis (RA) using fibroblast-like synoviocytes (FLSs) and arthritis animal models. Functional analysis showed that EFL3 could ameliorate the inflammatory phenotype of FLSs derived from RA patients, as evidenced by the decreases in cell viability, migration, invasion and cytokine production. Luciferase activity, Western blotting and immunofluorescence assays demonstrated that EFL3 inhibited the nuclear translocation of the p65 subunit and the subsequent activation of the nuclear factor kappa-Β (NF-κB) pathway. Furthermore, the therapeutic effects of EFL3 against arthritic progression were evidenced by decreases in joint swelling, arthritis scores, inflammatory factor production, synovial hyperplasia, and bone destruction in collagen-induced arthritis (CIA) and tumor necrosis factor-α (TNF-α) transgenic (TNF-tg) mouse models. Molecular analysis identified Rac family small GTPase 1 (Rac1) as the potential target that was required for EFL3-mediated suppression of the inflammatory RA FLS phenotype. In summary, this study uncovered the therapeutic potential of EFL3 in RA, which suggests its future clinical use.
DOI: 10.6084/m9.figshare.19665467
title: Euphorbia factor L3 ameliorates rheumatoid arthritis by suppressing the inflammatory response by targeting Rac family small GTPase 1

description: Euphorbia factor L3 (EFL3) is extracted from <i>Euphorbia lathyris</i> and is known for its anti-inflammatory properties. This study focused on the potential anti-inflammatory and therapeutic effects of EFL3 on rheumatoid arthritis (RA) using fibroblast-like synoviocytes (FLSs) and arthritis animal models. Functional analysis showed that EFL3 could ameliorate the inflammatory phenotype of FLSs derived from RA patients, as evidenced by the decreases in cell viability, migration, invasion and cytokine production. Luciferase activity, Western blotting and immunofluorescence assays demonstrated that EFL3 inhibited the nuclear translocation of the p65 subunit and the subsequent activation of the nuclear factor kappa-Β (NF-κB) pathway. Furthermore, the therapeutic effects of EFL3 against arthritic progression were evidenced by decreases in joint swelling, arthritis scores, inflammatory factor production, synovial hyperplasia, and bone destruction in collagen-induced arthritis (CIA) and tumor necrosis factor-α (TNF-α) transgenic (TNF-tg) mouse models. Molecular analysis identified Rac family small GTPase 1 (Rac1) as the potential target that was required for EFL3-mediated suppression of the inflammatory RA FLS phenotype. In summary, this study uncovered the therapeutic potential of EFL3 in RA, which suggests its future clinical use.
DOI: 10.6084/m9.figshare.7082108
title: Additional file 6: of Nogo-B receptor increases the resistance to tamoxifen in estrogen receptor-positive breast cancer cells

description: NgBR (NUS1) mRNA expression data were retrieved from a gene-expression profiling dataset (225071_x from Kaplan–Meier Plot database) of 755 patients with ERα-positive breast cancer and 335 patients with ERα-positive breast cancer treated with endocrine therapy. Kaplan–Meier analysis revealed significantly reduced relapse-free survival (RFS) (p &lt; 0.05) in 373 patients with ERα positive breast cancer with high NgBR expression in tumors as compared to 382 patients with low NgBR expression in tumors. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.7082120.v1
title: Additional file 6: of A metagenome-wide association study of gut microbiota in asthma in UK adults

description: Table S4. The phylum: The relative abundance and statistical test of the phylum. (XLS 95 kb)
DOI: 10.6084/m9.figshare.7082126
title: Additional file 7: of Nogo-B receptor increases the resistance to tamoxifen in estrogen receptor-positive breast cancer cells

description: NgBR (NUS1) mRNA expression data were retrieved from a gene-expression profiling dataset (225071_x from Kaplan–Meier Plot database) of 755 patients with ERα-positive breast cancer and 335 patients with ERα-positive breast cancer treated with endocrine therapy. Kaplan–Meier analysis revealed that the RFS in patients with ERα-positive breast cancer treated with endocrine therapy is significantly decreased in 167 patients with high NgBR expression in tumors as compared to 168 patients with low NgBR expression in tumors (p &lt; 0.05). (XLSX 32 kb)
DOI: 10.6084/m9.figshare.19665270.v1
title: Angiotensin-converting enzyme 2 inhibits inflammation and apoptosis in high glucose-stimulated microvascular endothelial cell damage by regulating the JAK2/STAT3 signaling pathway

description: Mounting evidence supports that angiotensin-converting enzyme 2 (ACE2) may exert a vital function in multiple complications induced by diabetes. The aim of this research was to verify the function of ACE2 in diabetic angiopathy (DA). In our study, it was revealed that high glucose (HG) treatment impeded cell proliferation and induced cell apoptosis. Moreover, ACE2 level was reduced in HG-stimulated HMEC-1 cells. Functional assays demonstrated that ACE2 addition promoted cell viability, suppressed apoptosis, oxidative stress, ROS generation, and inflammation in HG-stimulated HMEC-1 cells. Furthermore, the activation of the JAK2/STAT3 pathway induced by HG was impeded by overexpression of ACE2. Besides, JAK2/STAT3 pathway inhibitor AG490 reversed the changes of cell viability, apoptosis, oxidative stress, and inflammation caused by ACE2 deletion in HG-treated HMEC-1 cells. In sum, our findings highlighted that ACE2 promoted the viability and restrained the oxidative stress, inflammation, and apoptosis in HG-induced microvascular endothelial cells (VECs) injury via regulating the JAK2/STAT3 pathway, suggesting ACE2 might be a potential therapeutic target for DA treatment.
DOI: 10.6084/m9.figshare.7082546.v2
title: Autophagy regulates glucose-mediated root meristem activity by modulating ROS production in <i>Arabidopsis</i>

description: Glucose produced from photosynthesis is a key nutrient signal regulating root meristem activity in plants; however, the underlying mechanisms remain poorly understood. Here, we show that, by modulating reactive oxygen species (ROS) levels, the conserved macroautophagy/autophagy degradation pathway contributes to glucose-regulated root meristem maintenance. In <i>Arabidopsis thaliana</i> roots, a short exposure to elevated glucose temporarily suppresses constitutive autophagosome formation. The autophagy-defective <i>autophagy-related gene</i> (<i>atg</i>) mutants have enhanced tolerance to glucose, established downstream of the glucose sensors, and accumulate less glucose-induced ROS in the root tips. Moreover, the enhanced root meristem activities in the <i>atg</i> mutants are associated with improved auxin gradients and auxin responses. By acting with AT4G39850/ABCD1 (ATP-binding cassette D1; Formerly PXA1/peroxisomal ABC transporter 1), autophagy plays an indispensable role in the glucose-promoted degradation of root peroxisomes, and the <i>atg</i> mutant phenotype is partially rescued by the overexpression of <i>ABCD1</i>. Together, our findings suggest that autophagy is an essential mechanism for glucose-mediated maintenance of the root meristem. <b>Abbreviation:</b> ABA: abscisic acid; ABCD1: ATP-binding cassette D1; ABO: ABA overly sensitive; AsA: ascorbic acid; ATG: autophagy related; CFP: cyan fluorescent protein; Co-IP: co-immunoprecipitation; DAB: 3’,3’-diaininobenzidine; DCFH-DA: 2’,7’-dichlorodihydrofluorescin diacetate; DR5: a synthetic auxin response element consists of tandem direct repeats of 11 bp that included the auxin-responsive TGTCTC element; DZ: differentiation zone; EZ, elongation zone; GFP, green fluorescent protein; GSH, glutathione; GUS: β-glucuronidase; HXK1: hexokinase 1; H<sub>2</sub>O<sub>2</sub>: hydrogen peroxide; IAA: indole-3-acetic acid; IBA: indole-3-butyric acid; KIN10/11: SNF1 kinase homolog 10/11; MDC: monodansylcadaverine; MS: Murashige and Skoog; MZ: meristem zone; NBT: nitroblue tetrazolium; NPA: 1-N-naphtylphthalamic acid; OxIAA: 2-oxindole-3-acetic acid; PIN: PIN-FORMED; PLT: PLETHORA; QC: quiescent center; RGS1: Regulator of G-protein signaling 1; ROS: reactive oxygen species; SCR: SCARECROW; SHR, SHORT-ROOT; SKL: Ser-Lys-Leu; SnRK1: SNF1-related kinase 1; TOR: target of rapamycin; UPB1: UPBEAT1; WOX5: WUSCHEL related homeobox 5; Y2H: yeast two-hybrid; YFP: yellow fluorescent protein
DOI: 10.6084/m9.figshare.12849719.v3
title: A Nonparametric Nonclassical Measurement Error Approach to Estimating Intergenerational Mobility Elasticities

description: This article provides a framework for estimating intergenerational mobility elasticities (IGEs) of children’s income with respect to parental income. We allow the IGEs to be heterogeneous, by leaving the relationship of parental and child incomes unspecified, while acknowledging and addressing the <i>latent</i> nature of both child and parental <i>permanent</i> incomes and the resulted life-cycle bias. Our framework enables us to test the widely imposed assumption that the intergenerational mobility function is linear. Applying our method to the Panel Studies of Income Dynamics data, we decisively reject the commonly imposed linearity assumption and find substantial heterogeneity in the IGEs across the population. We confirm an important finding that the IGEs with respect to parental income exhibit a U-shape pattern, which is occasionally highlighted in the analysis using transition matrices. Specifically, there is a considerable degree of mobility among the broadly defined middle class, but the children of both high- and low-income parents are more likely to be high- and low-income adults, respectively. This result also provides insights into the (intertemporal) Great Gatsby curve, suggesting that a higher level of inequality within one generation may lead to a higher level of social immobility in the next generation in the United States.
DOI: 10.6084/m9.figshare.22811268.v1
title: The complete chloroplast genome sequence of <i>Zannichellia palustris</i> (Potamogetonaceae)

description: <i>Zannichellia palustris</i> Linnaeus 1753 is a cosmopolitan submerged species capable of rapidly responding to environmental changes, with potential applications in the ecological treatment of heavy metal pollution in water bodies. This study aimed to characterize the complete chloroplast genome of <i>Z. palustris</i>, which has not been reported previously. The chloroplast genome of <i>Z. palustris</i> displays a quadripartite structure with a length of 155,262 base pairs (bp), comprising a large single copy (LSC) region of 85,397 bp, a small single copy (SSC) region of 18,057 bp, and a pair of inverted repeat (IR) regions of 25,904 bp. The GC content of the genome is 35.8%, with corresponding values of 33.4% for the LSC, 28.2% for the SSC, and 42.5% for the IR regions. The genome contained 130 genes, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis within the order Alismatales revealed that <i>Z. palustris</i> clusters with the clade of <i>Potamogeton perfoliatus</i>, <i>P. crispus</i> and <i>Stuckenia pectinata</i>.
DOI: 10.6084/m9.figshare.7082102.v1
title: Additional file 5: of A metagenome-wide association study of gut microbiota in asthma in UK adults

description: Table S3. The genus: The relative abundance and statistical test of the genus. (XLS 1084 kb)
DOI: 10.6084/m9.figshare.7082114.v1
title: Additional file 2: of LGR5, a novel functional glioma stem cell marker, promotes EMT by activating the Wnt/Î˛-catenin pathway and predicts poor survival of glioma patients

description: Table S2. Association of LGR5 expression with clinicopathological features in LGG group. (XLS 10 kb)
DOI: 10.6084/m9.figshare.7082459.v1
title: Role of plant respiratory burst oxidase homologs in stress responses

description: Plant respiratory burst oxidase homologs (Rbohs), which are also named nicotinamide adenine dinucleotide phosphate (NADPH) oxidases (NOXs), are the homologs of mammalian phagocyte gp91<sup>phox</sup>. As a unique among other reactive oxygen species (ROS) production mechanisms in plants, NADPH oxidases can integrate different signal transduction pathways, such as calcium, protein phosphorylation catalysed by protein kinases, nitric oxide, and lipid messengers. Coupling with genetic studies, the ability of plant NADPH oxidases to integrate different signal transduction pathways with ROS production demonstrates their involvement in many important biological processes in cells, such as morphogenesis and development, and stress responses. Here, we focus on several current studies concerning the role of plant NADPH oxidases in stress responses.