cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25403/upresearchdata.25215689
title: Analyses of source water samples from three areas in South Africa for estrogenic activity and oxidative stress

description: These dataset contains concentration–effect curves and oxidative stress response results from the AREc32 reporter gene assay (table 1). Samples were analyzed in replicate through bioassays, and screening for the presence of pharmaceuticals using ultra-high performance liquid chromatography system. During data analysis, the results for each replicate were compared to ensure that the variability did not exceed a pre-determined level. The average of the intra-assay replicates was then used as a single number. The concentration–response curve for all repeats was also evaluated together. The final result was reported as the average of the two closest results.
Estradiol equivalent concentrations (ng/L) in source water from Gauteng (GP), Mpumalanga (MP), and Limpopo (LP) provinces, South Africa, using the yeast estrogen screen (YES) (Table 2). The following equation was applied to correct for turbidity: corrected value = test abs (540 nm) – [test abs (620 nm) – median blank abs (620 nm)]. The detection limit of the yeast assay was calculated as absorbance induced by the solvent control (blank) plus three times the standard deviation. Sample concentrations with absorbance values below the solvent control minus three times the standard deviation were considered cytotoxic concentrations. The estradiol equivalents (EEq) of the samples were interpolated from the estradiol standard curve and corrected with the appropriate dilution factor for each sample. This was calculated for samples with 3 or more points above the detection limit. EEq values were reported as the average ± SD of three independent repeats.
Pharmaceutical compounds were detected using the Dionex Ultimate 3000 UPLC (table 3). Compass Data Analysis 4.3 (Bruker, Germany) software package together with the tools found in the software package such as compass isotope pattern and compound crawler were used in the screening workflow. Accurate mass measurements of each peak from the extracted ion chromatograms were obtained using a sodium formate calibrant solution delivered by a Kd Scientific external pump. The function edit chromatogram was used to obtain the extracted ion chromatogram (EIC) of each compound using their molecular formula. MS/MS spectrum of each compound was then obtained using the find compound spectra function in the data analysis. The compound crawler function in the Data Analysis 4.3 software was used to confirm that the peak represents the suspect compounds in online databases of KEGG (Kyoto Encyclopedia of Genes and Genomes), CHEBI (Chemical Entities of Biological Interest), HMBD (Human Metabolome Data Base), and FOR-IDENT. Parameters used in screening were mass accuracy ≤5 ppm, isotopic fit (mSigma) less than or equal to 100, signal-to-noise ratio of 3, minimum intensity threshold of 500, and presence of a minimum of one production.
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DOI: 10.6084/m9.figshare.22811268
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.12849719.v2
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.7082147.v1
title: Additional file 8: of A metagenome-wide association study of gut microbiota in asthma in UK adults

description: Table S5. MGSs from the cohort: The relative abundance and statistical test of the MGSs. (XLS 1648 kb)
DOI: 10.6084/m9.figshare.7082546
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.7082546.v1
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.
DOI: 10.6084/m9.figshare.7082561
title: <i>Mir223</i> restrains autophagy and promotes CNS inflammation by targeting ATG16L1

description: Microglia are innate immune cells in the central nervous system (CNS), that supplies neurons with key factors for executing autophagosomal/lysosomal functions. Macroautophagy/autophagy is a cellular catabolic process that maintains cell balance in response to stress-related stimulation. Abnormal autophagy occurs with many pathologies, such as cancer, and autoimmune and neurodegenerative diseases. Hence, clarification of the mechanisms of autophagy regulation is of utmost importance. Recently, researchers presented microRNAs (miRNAs) as novel and potent modulators of autophagic activity. Here, we found that <i>Mir223</i> deficiency significantly ameliorated CNS inflammation, demyelination and the clinical symptoms of experimental autoimmune encephalomyelitis (EAE) and increased resting microglia and autophagy in brain microglial cells. In contrast, the autophagy inhibitor 3-methylademine (3-MA) aggravated the clinical symptoms of EAE in wild-type (WT) and <i>Mir223</i>-deficienct mice. Furthermore, it was confirmed that <i>Mir223</i> deficiency in mice increased the protein expression of ATG16L1 (autophagy related 16-like 1 [S. cerevisiae]) and LC3-II in bone marrow-derived macrophage cells compared with cells from WT mice. Indeed, the cellular level of <i>Atg16l1</i> was decreased in BV2 cells upon <i>Mir223</i> overexpression and increased following the introduction of antagomirs. We also showed that the 3’ UTR of <i>Atg16l1</i> contained functional <i>Mir223</i>-responsive sequences and that overexpression of ATG16L1 returned autophagy to normal levels even in the presence of <i>Mir223</i> mimics. Collectively, these data indicate that <i>Mir223</i> is a novel and important regulator of autophagy and that <i>Atg16l1</i> is a <i>Mir223</i> target in this process, which may have implications for improving our understanding of the neuroinflammatory process of EAE. <b>Abbreviations:</b> 3-MA: 3-methylademine; ACTB/β-actin: actin, beta; ATG: autophagy related; ATG16L1: autophagy related 16-like 1 (S. cerevisiae); BECN1: beclin 1, autophagy related; CNR2: cannabinoid receptor 2 (macrophage); CNS: central nervous system; CQ: chloroquine; EAE: experimental autoimmune encephalomyelitis; FOXO3: forkhead box O3; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; H&E: hematoxylin and eosin; ITGAM: integrin alpha M; LPS: lipoplysaccharide; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; miRNAs: microRNAs; MS: multiple sclerosis; PPARG: peroxisome proliferator activated receptor gamma; PTPRC: protein tyrosine phosphatase, receptor type, C; RA: rheumatoid arthritis; SQSTM1: sequestosome 1; TB: tuberculosis; TIMM23: translocase of inner mitochondrial membrane 23; TLR: toll-like receptor.
DOI: 10.6084/m9.figshare.24117213
title: Effective <i>Agrobacterium</i>-mediated genetic transformation of okra (<i>Abelmoschus esculentus</i> L.) and generation of RNAi plants resistant to <i>Begomovirus</i> infecting okra

description: Okra is an important vegetable crop of the Malvaceae family and is infected by varying numbers of viruses of the genus <i>Begomovirus</i>. Regardless of the importance of the crop, very little consideration has been given to its genetic improvement. RNA interference (RNAi), a potent biotechnological tool, is known to control <i>Begomovirus</i> in many crops. For the implementation of successful RNAi, there is a need for an efficient genetic transformation system in okra. In the present study, we developed a procedure for <i>Agrobacterium</i>-mediated tissue culture–dependent regeneration of okra plants for the application of RNAi. Eleven transgenic okra RNAi plants were regenerated by utilising hypocotyls as explants. Transformed plants were screened with hygromycin at the regeneration stage and the presence of transgenes (<i>AC1</i>, <i>AC2</i> & <i>AC4</i> codes for replication-associated protein, transcriptional activator protein and suppressor of PTGS) in putative transformed plants was confirmed by polymerase chain reaction (PCR). Wild and transgenic lines were challenged with a dimeric <i>Begomovirus</i> clone or viruliferous whiteflies and the level of resistance was estimated with quantitative real-time reverse transcriptase PCR (qRT-PCR) by utilising viral gene–specific primers. The resistant transgenic lines accumulated very low titres of viral gene products according to the qRT-PCR assays compared to the control plants. This is the first report of tissue culture–mediated RNAi-derived resistance in okra against <i>Begomovirus</i> infection.
DOI: 10.5517/ccdc.csd.cc28kvc2
title: CCDC 2102524: Experimental Crystal Structure Determination

description: Related Article: Fei-Fei Yu, Yun-Hong Du, Guo-Long Pang|2023|J.Cluster Sci.|34|1185|doi:10.1007/s10876-021-02200-7
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.7082561.v1
title: <i>Mir223</i> restrains autophagy and promotes CNS inflammation by targeting ATG16L1

description: Microglia are innate immune cells in the central nervous system (CNS), that supplies neurons with key factors for executing autophagosomal/lysosomal functions. Macroautophagy/autophagy is a cellular catabolic process that maintains cell balance in response to stress-related stimulation. Abnormal autophagy occurs with many pathologies, such as cancer, and autoimmune and neurodegenerative diseases. Hence, clarification of the mechanisms of autophagy regulation is of utmost importance. Recently, researchers presented microRNAs (miRNAs) as novel and potent modulators of autophagic activity. Here, we found that <i>Mir223</i> deficiency significantly ameliorated CNS inflammation, demyelination and the clinical symptoms of experimental autoimmune encephalomyelitis (EAE) and increased resting microglia and autophagy in brain microglial cells. In contrast, the autophagy inhibitor 3-methylademine (3-MA) aggravated the clinical symptoms of EAE in wild-type (WT) and <i>Mir223</i>-deficienct mice. Furthermore, it was confirmed that <i>Mir223</i> deficiency in mice increased the protein expression of ATG16L1 (autophagy related 16-like 1 [S. cerevisiae]) and LC3-II in bone marrow-derived macrophage cells compared with cells from WT mice. Indeed, the cellular level of <i>Atg16l1</i> was decreased in BV2 cells upon <i>Mir223</i> overexpression and increased following the introduction of antagomirs. We also showed that the 3’ UTR of <i>Atg16l1</i> contained functional <i>Mir223</i>-responsive sequences and that overexpression of ATG16L1 returned autophagy to normal levels even in the presence of <i>Mir223</i> mimics. Collectively, these data indicate that <i>Mir223</i> is a novel and important regulator of autophagy and that <i>Atg16l1</i> is a <i>Mir223</i> target in this process, which may have implications for improving our understanding of the neuroinflammatory process of EAE. <b>Abbreviations:</b> 3-MA: 3-methylademine; ACTB/β-actin: actin, beta; ATG: autophagy related; ATG16L1: autophagy related 16-like 1 (S. cerevisiae); BECN1: beclin 1, autophagy related; CNR2: cannabinoid receptor 2 (macrophage); CNS: central nervous system; CQ: chloroquine; EAE: experimental autoimmune encephalomyelitis; FOXO3: forkhead box O3; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; H&E: hematoxylin and eosin; ITGAM: integrin alpha M; LPS: lipoplysaccharide; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; miRNAs: microRNAs; MS: multiple sclerosis; PPARG: peroxisome proliferator activated receptor gamma; PTPRC: protein tyrosine phosphatase, receptor type, C; RA: rheumatoid arthritis; SQSTM1: sequestosome 1; TB: tuberculosis; TIMM23: translocase of inner mitochondrial membrane 23; TLR: toll-like receptor.
DOI: 10.6084/m9.figshare.7082276.v1
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.13373870
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.19665270
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.21762453
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: 10.25387/g3.7607060
title: Supplemental Material for Xu et al., 2019

description: Supplemental Tables S1, S2, S3; <br>Supplemental Figures S1, S2;Supplemental Files S1, S2
DOI: 10.6084/m9.figshare.12849620.v1
title: Large-dimensional Factor Analysis without Moment Constraints*

description: Large-dimensional factor model has drawn much attention in the big-data era, in order to reduce the dimensionality and extract underlying features using a few latent common factors. Conventional methods for estimating the factor model typically requires finite fourth moment of the data, which ignores the effect of heavy-tailedness and thus may result in unrobust or even inconsistent estimation of the factor space and common components. In this paper, we propose to recover the factor space by performing principal component analysis to the spatial Kendall’s tau matrix instead of the sample covariance matrix. In a second step, we estimate the factor scores by the ordinary least square (OLS) regression. Theoretically, we show that under the elliptical distribution framework the factor loadings and scores as well as the common components can be estimated consistently without any moment constraint. The convergence rates of the estimated factor loadings, scores and common components are provided. The finite sample performance of the proposed procedure is assessed through thorough simulations. An analysis of a financial data set of asset returns shows the superiority of the proposed method over the classical PCA method.