cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12435845.v1
title: Forecasting deaths of road traffic injuries in China using an artificial neural network

description: <b>Objectives:</b> This study was conducted to estimate road traffic deaths and to forecast short-term road traffic deaths in China using the Elman recurrent neural network (ERNN) model. <b>Methods:</b> An ERNN model was developed using reported police data of road traffic deaths in China from 2000 to 2017. Different numbers of neurons of the hidden layer were tested and different combinations of subgroup datasets have been used to develop the optimal ERNN model after normalization. The mean absolute error (MAE), the root mean square error (RMSE), and the mean absolute percentage error (MAPE) were measures of the deviation between predicted and observed values. Predicted road traffic deaths from the ERNN model and the seasonal autoregressive integrated moving average (SARIMA) model were compared using the MAPE. <b>Results:</b> By comparing the MAE, RMSE and MAPE of different numbers of hidden neurons and different ERNN models, the ERNN model provided the best result when the input neurons were set to 3 and hidden neurons were set to 10. The best validated neural model (3:10:1) was further applied to make predictions for the latest 12 months of deaths (MAPE = 4.83). The best SARIMA (0, 1, 1) (0, 1, 1)<sub>12</sub> model was selected from various candidate models (MAPE = 5.04). The fitted road traffic deaths using the two selected models matched closely with the observed deaths from 2000 to 2016. The ERNN models performed better than the SARIMA model in terms of prediction of 2017 deaths. <b>Conclusions:</b> Our results suggest that the ERNN model could be utilized to model and forecast the short-term trends accurately and to evaluate the impact of traffic safety programs when applied to historical road traffic deaths data. Forecasting traffic crash deaths will provide useful information to measure burden of road traffic injuries in China.
DOI: 10.6084/m9.figshare.19776071
title: NEDD9 Mediates the FAK/Src Signaling Pathway to Promote the Adhesion of Human Trabecular Meshwork Cells after Dexamethasone Treatment

description: The differential gene expression of neural precursor cell expressed developmentally downregulated 9 (NEDD9) in human trabecular meshwork (HTM) cells after dexamethasone (Dex) treatment was confirmed through gene expression profiling. However, the regulatory mechanism of NEDD9 expression in HTM cells remains unknown. In this study, we investigated NEDD9 expression in HTM cells and gained a better understanding of glucocorticoid-induced glaucoma (GIG) pathophysiology. The Gene Expression Omnibus database and GEO2R tool were used to identify differentially expressed genes in the GSE37474 and GSE124114 datasets, and NEDD9 gene expression was found to be upregulated. Human corneoscleral segments and HTM cells were treated with 100 nM Dex or an equal volume of ethanol (0.01%) for 7 days. NEDD9 expression in TM tissues was evaluated by immunohistochemistry, and NEED9 expression in HTM cells was confirmed by RT-qPCR and western blotting. HTM cell adhesive behaviors were assessed with a cell adhesion detection kit. NEDD9 expression was knocked down with short hairpin RNA in HTM cells, and FAK/Src signaling pathway activation was found to be regulated by NEDD9. After 7 days of HTM cell Dex treatment, NEDD9 expression was upregulated to be approximately twice that of control. FAK, Src, phospho-FAK, and phospho-Src expression in Dex-treated HTM cells was markedly increased. Downregulation of NEDD9 expression reduced HTM cell adhesion to the surface of culture wells and simultaneously led to a reduction in FAK, Src, phospho-FAK and phospho-Src expression. NEDD9 expression is upregulated in HTM cells after Dex treatment and promotes HTM cell adhesion. These findings underscore the contribution of NEDD9 overexpression to altered HTM cell adhesion during glucocorticoid therapy and may play a key role in GIG pathological progression. Considering the similarity between GIG and primary open-angle glaucoma (POAG), our findings suggest that targeting NEDD9 may be a new therapeutic strategy for POAG patients.
DOI: 10.6084/m9.figshare.19776071.v1
title: NEDD9 Mediates the FAK/Src Signaling Pathway to Promote the Adhesion of Human Trabecular Meshwork Cells after Dexamethasone Treatment

description: The differential gene expression of neural precursor cell expressed developmentally downregulated 9 (NEDD9) in human trabecular meshwork (HTM) cells after dexamethasone (Dex) treatment was confirmed through gene expression profiling. However, the regulatory mechanism of NEDD9 expression in HTM cells remains unknown. In this study, we investigated NEDD9 expression in HTM cells and gained a better understanding of glucocorticoid-induced glaucoma (GIG) pathophysiology. The Gene Expression Omnibus database and GEO2R tool were used to identify differentially expressed genes in the GSE37474 and GSE124114 datasets, and NEDD9 gene expression was found to be upregulated. Human corneoscleral segments and HTM cells were treated with 100 nM Dex or an equal volume of ethanol (0.01%) for 7 days. NEDD9 expression in TM tissues was evaluated by immunohistochemistry, and NEED9 expression in HTM cells was confirmed by RT-qPCR and western blotting. HTM cell adhesive behaviors were assessed with a cell adhesion detection kit. NEDD9 expression was knocked down with short hairpin RNA in HTM cells, and FAK/Src signaling pathway activation was found to be regulated by NEDD9. After 7 days of HTM cell Dex treatment, NEDD9 expression was upregulated to be approximately twice that of control. FAK, Src, phospho-FAK, and phospho-Src expression in Dex-treated HTM cells was markedly increased. Downregulation of NEDD9 expression reduced HTM cell adhesion to the surface of culture wells and simultaneously led to a reduction in FAK, Src, phospho-FAK and phospho-Src expression. NEDD9 expression is upregulated in HTM cells after Dex treatment and promotes HTM cell adhesion. These findings underscore the contribution of NEDD9 overexpression to altered HTM cell adhesion during glucocorticoid therapy and may play a key role in GIG pathological progression. Considering the similarity between GIG and primary open-angle glaucoma (POAG), our findings suggest that targeting NEDD9 may be a new therapeutic strategy for POAG patients.
DOI: 10.6084/m9.figshare.12960008
title: Gene co-expression and alternative splicing analysis of key metabolic tissues to unravel the regulatory signatures of fatty acid composition in cattle

description: Increasing the healthy/unhealthy fatty acid (FA) ratio in meat is one of the urgent tasks required to address consumer concerns. However, the regulatory mechanisms ultimately resulting in FA profiles vary among animals and remain largely unknown. In this study, using ~1.2 Tb high-quality RNA-Seq-based transcriptomic data of 188 samples from four key metabolic tissues (rumen, liver, muscle, and backfat) together with the contents of 49 FAs in backfat, the molecular regulatory mechanisms of these tissues contributing to FA formation in cattle were explored. Using this large dataset, the alternative splicing (AS) events, one of the transcriptional regulatory mechanisms in four tissues were identified. The highly conserved and absent AS events were detected in rumen tissue, which may contribute to its functional differences compared with the other three tissues. In addition, the healthy/unhealthy FA ratio related AS events, differential expressed (DE) genes, co-expressed genes, and their functions in four tissues were analysed. Eight key genes were identified from the integrated analysis of DE, co-expressed, and AS genes between animals with high and low healthy/unhealthy FA ratios. This study provides an applicable pipeline for AS events based on comprehensive RNA-Seq analysis and improves our understanding of the regulatory mechanism of FAs in beef cattle.
DOI: 10.6084/m9.figshare.22914680
title: Additional file 2 of Targeting NRF2 uncovered an intrinsic susceptibility of acute myeloid leukemia cells to ferroptosis

description: Supplementary Material 2. The KEGG enrichment of 349 NRF2-Chip intersection genes.
DOI: 10.6084/m9.figshare.19776010
title: Tanshinone IIA down-regulates -transforming growth factor beta 1 to relieve renal tubular epithelial cell inflammation and pyroptosis caused by high glucose

description: Diabetic nephropathy (DN) is a microvascular disease caused by diabetes. Tanshinone IIA has been indicated to ameliorate streptozotocin-induced DN. This study explores the effect of tanshinone IIA on high glucose-induced renal tubular epithelial cell pyroptosis and inflammation. High glucose-stimulated HK-2 cells were used as the <i>in-vitro</i> model of DN and were treated with tanshinone IIA at concentrations of 1, 5, 10 μM for 24 h with the same doses of tolbutamide as the control. After tanshinone IIA treatment, HK-2 cells were transfected with pcDNA-transforming growth factor beta 1 (TGFB1) or sh-TGFB1 for 48 h. RT-qPCR was used to detect the mRNA levels of TNF-α, IL-6, IL-1β, and IL-18. Cell apoptosis and pyroptosis were detected by flow cytometry and cell immunofluorescence. Bioinformatics screening predicted that tanshinone IIA might be an effective component of <i>Salvia miltiorrhiza</i> Bunge (Labiatae) for the treatment of DN. Tanshinone IIA exerted a protective effect in the <i>in-vitro</i> model of DN by suppressing inflammation and pyroptosis via the TGFB1-dependent pathway. Tanshinone IIA inhibited high glucose-induced renal tubular epithelial cell inflammation and cell death through pyroptosis by regulating TGFB1, indicating the therapeutic potential of tanshinone IIA for DN treatment.
DOI: 10.6084/m9.figshare.19776010.v1
title: Tanshinone IIA down-regulates -transforming growth factor beta 1 to relieve renal tubular epithelial cell inflammation and pyroptosis caused by high glucose

description: Diabetic nephropathy (DN) is a microvascular disease caused by diabetes. Tanshinone IIA has been indicated to ameliorate streptozotocin-induced DN. This study explores the effect of tanshinone IIA on high glucose-induced renal tubular epithelial cell pyroptosis and inflammation. High glucose-stimulated HK-2 cells were used as the <i>in-vitro</i> model of DN and were treated with tanshinone IIA at concentrations of 1, 5, 10 μM for 24 h with the same doses of tolbutamide as the control. After tanshinone IIA treatment, HK-2 cells were transfected with pcDNA-transforming growth factor beta 1 (TGFB1) or sh-TGFB1 for 48 h. RT-qPCR was used to detect the mRNA levels of TNF-α, IL-6, IL-1β, and IL-18. Cell apoptosis and pyroptosis were detected by flow cytometry and cell immunofluorescence. Bioinformatics screening predicted that tanshinone IIA might be an effective component of <i>Salvia miltiorrhiza</i> Bunge (Labiatae) for the treatment of DN. Tanshinone IIA exerted a protective effect in the <i>in-vitro</i> model of DN by suppressing inflammation and pyroptosis via the TGFB1-dependent pathway. Tanshinone IIA inhibited high glucose-induced renal tubular epithelial cell inflammation and cell death through pyroptosis by regulating TGFB1, indicating the therapeutic potential of tanshinone IIA for DN treatment.
DOI: 10.6084/m9.figshare.22914680.v1
title: Additional file 2 of Targeting NRF2 uncovered an intrinsic susceptibility of acute myeloid leukemia cells to ferroptosis

description: Supplementary Material 2. The KEGG enrichment of 349 NRF2-Chip intersection genes.
DOI: 10.6084/m9.figshare.7717496.v1
title: Additional file 4: of Epigenetic findings in periodontitis in UK twins: a cross-sectional study

description: Table S4. Covariate data and methylation beta values at cg21245277 in blood (CSV 91 kb)
DOI: 10.6084/m9.figshare.7717505.v1
title: Additional file 7: of Epigenetic findings in periodontitis in UK twins: a cross-sectional study

description: Table S7. Covariate data, tooth mobility, and methylation beta values at 247 CpG sites in blood. (CSV 1486 kb)
DOI: 10.6084/m9.figshare.7717502
title: Additional file 6: of Epigenetic findings in periodontitis in UK twins: a cross-sectional study

description: Table S6. Covariate data, gingival bleeding, and methylation beta values at 247 CpG-sites in blood. (CSV 1595 kb)
DOI: 10.6084/m9.figshare.7717481.v1
title: Additional file 1: of Epigenetic findings in periodontitis in UK twins: a cross-sectional study

description: Table S1. Linear regression model describing summary statistics for the association between blood methylation at cg21245277 and gingival bleeding. (CSV 5 kb)
DOI: 10.6084/m9.figshare.7717487
title: Additional file 2: of Epigenetic findings in periodontitis in UK twins: a cross-sectional study

description: Table S2. Linear regression model describing summary statistics for the association between blood methylation at cg08157914 and tooth mobility. (CSV 5 kb)
DOI: 10.6084/m9.figshare.7717490
title: Additional file 3: of Epigenetic findings in periodontitis in UK twins: a cross-sectional study

description: Table S3. Linear regression model describing summary statistics for the association between blood methylation at cg11051055 and tooth mobility. (CSV 5 kb)
DOI: 10.6084/m9.figshare.7717508
title: Additional file 8: of Epigenetic findings in periodontitis in UK twins: a cross-sectional study

description: Table S8. Covariate data, tooth mobility, gingival bleeding, and methylation beta values at 248 CpG sites in buccal tissue for all subjects. (CSV 152 kb)
DOI: 10.6084/m9.figshare.8241878.v2
title: Variant maps for bat echolocation call identification algorithms

description: Automated ultrasonic recordings are widely used in basic and applied research to detect the presence of bats. Often, algorithms for the automated identification of species are based on a pre-processing of acoustic information that involves the generation of spectrograms. Even though this approach is technically advanced, recent surveys highlight substantially high failure rates to identify species correctly, which urges for improved processes. Here, we tested an entirely new method, in particular, the transformation of ultrasonic recordings into variant maps. To compare this method with a spectrogram-based method, we used a database consisting of 160 echolocation calls from eight European bat species, including species of the genus <i>Myotis</i> that are inherently difficult to separate based on echolocation calls. For non-<i>Myotis</i> species, both methods led to a 100% correct identification rate, while for <i>Myotis</i> species the use of variant maps led to a lower identification rate of 85.3% compared to 91.1% that was achieved with a spectrogram-based method. However, a combination of both methods could lead to an identification rate of 94.1% for <i>Myotis</i> species. This result suggests combining our approach with spectrogram-based techniques to improve the automated identification of species based on acoustic information.
DOI: 10.6084/m9.figshare.7193378.v1
title: Additional file 10: of Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

description: Up-regulated and down-regulated glutathione S-transferase in ‘Yayu889’ and ‘Zhenghong532’ at 89, 91, and 93 days post planting, respectively. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7717499.v1
title: Additional file 5: of Epigenetic findings in periodontitis in UK twins: a cross-sectional study

description: Table S5. Covariate data and methylation beta values at 58 tooth mobility significant CpG sites in blood. (CSV 410 kb)
DOI: 10.6084/m9.figshare.7717481
title: Additional file 1: of Epigenetic findings in periodontitis in UK twins: a cross-sectional study

description: Table S1. Linear regression model describing summary statistics for the association between blood methylation at cg21245277 and gingival bleeding. (CSV 5 kb)
DOI: 10.6084/m9.figshare.6744233.v1
title: Raw data ( 1H NMR specra) obtained from polar metabolite extraction of Peganum harmala L. from NMR-based metabolomic profiling of <i>Peganum harmala</i> L. reveals dynamic variations between different growth stages

description: variable bins were normalized to the whole spectral area and 20 samples data were listed in this file.
DOI: 10.6084/m9.figshare.14525999.v1
title: Additional file 6 of Genome-wide analysis of ATP-binding cassette transporter provides insight to genes related to bioactive metabolite transportation in Salvia miltiorrhiza

description: Additional file 6: Table S4. Primers used in this study
DOI: 10.6084/m9.figshare.14525999
title: Additional file 6 of Genome-wide analysis of ATP-binding cassette transporter provides insight to genes related to bioactive metabolite transportation in Salvia miltiorrhiza

description: Additional file 6: Table S4. Primers used in this study
DOI: 10.6084/m9.figshare.22914683.v1
title: Additional file 3 of Targeting NRF2 uncovered an intrinsic susceptibility of acute myeloid leukemia cells to ferroptosis

description: Supplementary Material 3. The information of 70 candidate genes.
DOI: 10.6084/m9.figshare.7717496
title: Additional file 4: of Epigenetic findings in periodontitis in UK twins: a cross-sectional study

description: Table S4. Covariate data and methylation beta values at cg21245277 in blood (CSV 91 kb)
DOI: 10.6084/m9.figshare.12960432.v1
title: Additional file 1 of Stereotactic body radiotherapy versus conventional/moderate fractionated radiation therapy with androgen deprivation therapy for unfavorable risk prostate cancer

description: Additional file 1 Supplemental Figure. Utilization of standard or moderately hypofractionated radiation (EBRT) versus ultrahypofractionated radiation (SBRT) in men with unfavorable intermediate (a) and high (b) risk prostate cancer receiving androgen deprivation therapy.
DOI: 10.6084/m9.figshare.7717499
title: Additional file 5: of Epigenetic findings in periodontitis in UK twins: a cross-sectional study

description: Table S5. Covariate data and methylation beta values at 58 tooth mobility significant CpG sites in blood. (CSV 410 kb)
DOI: 10.6084/m9.figshare.7717490.v1
title: Additional file 3: of Epigenetic findings in periodontitis in UK twins: a cross-sectional study

description: Table S3. Linear regression model describing summary statistics for the association between blood methylation at cg11051055 and tooth mobility. (CSV 5 kb)
DOI: 10.6084/m9.figshare.7717508.v1
title: Additional file 8: of Epigenetic findings in periodontitis in UK twins: a cross-sectional study

description: Table S8. Covariate data, tooth mobility, gingival bleeding, and methylation beta values at 248 CpG sites in buccal tissue for all subjects. (CSV 152 kb)
DOI: 10.20393/142676fb-d7c8-45ac-b482-24b825ed73d1
title: Vegetation cover and environmental data from baseline quadrat survey of the Nephin Forest, Co. Mayo, Ireland (2022)

description: Vegetation communities of the Nephin Forest were assessed through an 8x8m quadrat survey as part of a Cullen PhD project. Each plant species present in a quadrat and its % cover of the quadrat was recorded. Environmental variables were measured either directly in the field or through GIS software. The data are contained in three datasets, one for percentage cover of vegetation (VegDataOnly_Long), one for continuous environmental variables (EnviroCont_Long) and one environmental categorical variables (EnviroCharacter_Long ). The categorical variables are derived from published desciptive metrics including Fossit's (2000) habitat classification (FossHab, Habitat_Original, FossLv2), Teagasc Soils and Subsoils classifation (Fealy et al., 2009) (Soil, Subsoil), Geological Survey Ireland's Bedrock Geology data (GSI, 2021) (Geology) and the Von Post Scale of Humification (von_Post, Moisture). Topography describes the topographical position of the quadrat and is recorded as either Flat, Lower-slope, Mid-slope, Upper-slope or Summit. Aspect describes the orientation of the quadrat and is recorded as either Flat, East, West, North or South. Peat_depth_cat is a categorical description of the continous variable Peat_depth and is recorded as either 1(0-50cm), 2(50-100cm), 3(100-150cm), 4(150-200cm), 5(200-250cm), 6(250-300cm), 7(300-350cm), 8(350-400cm), or 9 (400+cm). Forest_Type describes the age and/or growth class of forest habitat types and is recorded as either Pre-thicket (0-10 years old), Thicket (10-20 years old), Mid-rotation (20-30 years old), Mature (30+ years old), Thinned (Mature plantations which have undergone thinning), Clearfelled (Recently felled forest), Stunted (Poorly grown plantation forest) or Unforested (Non-forest type habitat).
DOI: 10.6084/m9.figshare.6744233
title: Raw data ( 1H NMR specra) obtained from polar metabolite extraction of Peganum harmala L. from NMR-based metabolomic profiling of <i>Peganum harmala</i> L. reveals dynamic variations between different growth stages

description: variable bins were normalized to the whole spectral area and 20 samples data were listed in this file.
DOI: 10.6084/m9.figshare.22914686.v1
title: Additional file 4 of Targeting NRF2 uncovered an intrinsic susceptibility of acute myeloid leukemia cells to ferroptosis

description: Supplementary Material 4. The top 20 KEGG enrichments of the 70 candidate genes.
DOI: 10.6084/m9.figshare.7717487.v1
title: Additional file 2: of Epigenetic findings in periodontitis in UK twins: a cross-sectional study

description: Table S2. Linear regression model describing summary statistics for the association between blood methylation at cg08157914 and tooth mobility. (CSV 5 kb)
DOI: 10.6084/m9.figshare.7193378
title: Additional file 10: of Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

description: Up-regulated and down-regulated glutathione S-transferase in ‘Yayu889’ and ‘Zhenghong532’ at 89, 91, and 93 days post planting, respectively. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7193495
title: Additional file 6: of Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

description: Up-regulated and down-regulated PR genes in ‘Yayu889’ and ‘Zhenghong532’ at 89, 91, and 93 days post planting, respectively. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7193510
title: Additional file 8: of Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

description: Up-regulated and down-regulated MAP kinases in ‘Yayu889’ and ‘Zhenghong532’ at 89, 91, and 93 days post planting, respectively. (XLSX 14 kb)