cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11799108.v1
title: Cholesterol derivatives induce dephosphorylation of the histone deacetylases Rpd3/HDAC1 to upregulate autophagy

description: Histone deacetylases (HDACs) are important for global gene expression and contribute to numerous physiological events. Deacetylase Rpd3 in yeast and its conserved homolog HDAC1 in mammals oppositely regulate autophagy; however, how Rpd3/HDAC1 is regulated to mediate autophagy remains unclear. Here, we showed autophagy occurrence in silkworm (<i>Bombyx mori</i>) required BmRpd3, wherein steroid hormone 20-hydroxyecdysone (20E) signaling regulated its protein level and nuclear localization negatively. Inhibition of MTOR led to dephosphorylation and nuclear-cytoplasmic translocation of BmRpd3/HsHDAC1. Besides, cholesterol, 20E, and 27-hydroxycholesterol could all induce massive dephosphorylation and cytoplasmic localization of BmRpd3/HsHDAC1, and thus autophagy by affecting MTORC1 activity. In addition, three phosphorylation sites (Ser392, Ser421, and Ser423) identified in BmRpd3 were conserved in HsHDAC1. Single or triple phosphorylation-site mutation attenuated the phosphorylation levels of BmRpd3/HsHDAC1, leading to their cytoplasmic localization and autophagy activation. In general, cholesterol derivatives, especially hydroxylated cholesterol, caused dephosphorylation and nucleo-cytoplasmic shuttling of BmRpd3/HsHDAC1 through inhibition of MTOR signaling to facilitate autophagy in <i>B. mori</i> and mammals. These findings improve our understandings of BmRpd3/HsHDAC1-mediated autophagy induced by cholesterol derivatives and shed light on their potential as a therapeutic target for neurodegenerative diseases and autophagy-related studies.
DOI: 10.17028/rd.lboro.22284925
title: Supplementary information for Selective ablation of primary and paracrine senescent cells by targeting iron dyshomeostasis

description: Supplementary files for article Selective ablation of primary and paracrine senescent cells by targeting iron dyshomeostasis
<br>
Senescent cells can spread the senescent phenotype to other cells by secreting senescence-associated secretory phenotype factors. The resulting paracrine senescent cells make a significant contribution to the burden of senescent cell accumulation with age. Previous efforts made to characterize paracrine senescence are unreliable due to analyses being based on mixed populations of senescent and non-senescent cells. Here, we use dipeptidyl peptidase-4 (DPP4) as a surface maker to isolate senescent cells from mixed populations. Using this technique, we enrich the percentage of paracrine senescence from 40% to 85%. We then use this enriched culture to characterize DPP4+ primary and paracrine senescent cells. We observe ferroptosis dysregulation and ferrous iron accumulation as a common phenomenon in both primary and paracrine senescent cells. Finally, we identify ferroptosis induction and ferrous iron-activatable prodrug as a broad-spectrum senolytic approach to ablate multiple types of primary and paracrine senescent cells.
DOI: 10.17028/rd.lboro.22284925.v1
title: Supplementary information for Selective ablation of primary and paracrine senescent cells by targeting iron dyshomeostasis

description: Supplementary files for article Selective ablation of primary and paracrine senescent cells by targeting iron dyshomeostasis
<br>
Senescent cells can spread the senescent phenotype to other cells by secreting senescence-associated secretory phenotype factors. The resulting paracrine senescent cells make a significant contribution to the burden of senescent cell accumulation with age. Previous efforts made to characterize paracrine senescence are unreliable due to analyses being based on mixed populations of senescent and non-senescent cells. Here, we use dipeptidyl peptidase-4 (DPP4) as a surface maker to isolate senescent cells from mixed populations. Using this technique, we enrich the percentage of paracrine senescence from 40% to 85%. We then use this enriched culture to characterize DPP4+ primary and paracrine senescent cells. We observe ferroptosis dysregulation and ferrous iron accumulation as a common phenomenon in both primary and paracrine senescent cells. Finally, we identify ferroptosis induction and ferrous iron-activatable prodrug as a broad-spectrum senolytic approach to ablate multiple types of primary and paracrine senescent cells.
DOI: 10.25387/g3.11799171
title: Supplemental Material for Chen et al., 2020

description: Genotpye and phenotype data of the IL population.xlsxandBiometrical parameters of QTLs affecting fiber quality traits by single-marker analysis.doc<br>
DOI: 10.25387/g3.11799171.v1
title: Supplemental Material for Chen et al., 2020

description: Genotpye and phenotype data of the IL population.xlsxandBiometrical parameters of QTLs affecting fiber quality traits by single-marker analysis.doc<br>
DOI: 10.6084/m9.figshare.14944856
title: Additional file 2 of Development of a liquid biopsy based purely quantitative digital droplet PCR assay for detection of MLH1 promoter methylation in colorectal cancer patients

description: Additional file 2.
DOI: 10.6084/m9.figshare.14944856.v1
title: Additional file 2 of Development of a liquid biopsy based purely quantitative digital droplet PCR assay for detection of MLH1 promoter methylation in colorectal cancer patients

description: Additional file 2.
DOI: 10.6084/m9.figshare.8129168
title: Additional file 1: of Characterization of phytohormone and transcriptome reprogramming profiles during maize early kernel development

description: Table S1. Fold changes of the expression of auxin-, kernel development- and defense- related genes and certain transcription factor (TF) encoding genes during ILa and ILb early kernel development. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.8129168.v1
title: Additional file 1: of Characterization of phytohormone and transcriptome reprogramming profiles during maize early kernel development

description: Table S1. Fold changes of the expression of auxin-, kernel development- and defense- related genes and certain transcription factor (TF) encoding genes during ILa and ILb early kernel development. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.14944850
title: Additional file 1 of Development of a liquid biopsy based purely quantitative digital droplet PCR assay for detection of MLH1 promoter methylation in colorectal cancer patients

description: Additional file 1.
DOI: 10.6084/m9.figshare.14944850.v1
title: Additional file 1 of Development of a liquid biopsy based purely quantitative digital droplet PCR assay for detection of MLH1 promoter methylation in colorectal cancer patients

description: Additional file 1.
DOI: 10.6084/m9.figshare.8129183
title: Additional file 2: of Transcriptional regulation of Lonicera japonica Thunb. during flower development as revealed by comprehensive analysis of transcription factors

description: Table S1. GO enrichment results of each cluster. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.8129183.v1
title: Additional file 2: of Transcriptional regulation of Lonicera japonica Thunb. during flower development as revealed by comprehensive analysis of transcription factors

description: Table S1. GO enrichment results of each cluster. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.8129189
title: Additional file 3: of Transcriptional regulation of Lonicera japonica Thunb. during flower development as revealed by comprehensive analysis of transcription factors

description: Table S2. GO annotation involved in flavonoid synthesis in each cluster. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8129189.v1
title: Additional file 3: of Transcriptional regulation of Lonicera japonica Thunb. during flower development as revealed by comprehensive analysis of transcription factors

description: Table S2. GO annotation involved in flavonoid synthesis in each cluster. (XLSX 15 kb)
DOI: 10.25403/upresearchdata.25222493
title: Evidence of dispensational tenets before 1800

description: The research sought evidence where dispensational ideas and tenets existed in the church history before John Darby who lived in the 1800's. This research was used as a basis to conduct interviews among the Dutch Reformed ministers in Pretoria in order to formulate a model that laymen or pastors could use in other parts of South Africa to promote dialogue, interaction and discussion with their local Dutch Reformed Church minister(s). 23 participants were interviewed. Coding codes were used to analyse the data by highlighting in diffrent colours or shades and thats how themes emerged.
DOI: 10.25403/upresearchdata.25222493.v1
title: Evidence of dispensational tenets before 1800

description: The research sought evidence where dispensational ideas and tenets existed in the church history before John Darby who lived in the 1800's. This research was used as a basis to conduct interviews among the Dutch Reformed ministers in Pretoria in order to formulate a model that laymen or pastors could use in other parts of South Africa to promote dialogue, interaction and discussion with their local Dutch Reformed Church minister(s). 23 participants were interviewed. Coding codes were used to analyse the data by highlighting in diffrent colours or shades and thats how themes emerged.
DOI: 10.6084/m9.figshare.21760683
title: Analysis of microplastics released from plastic take-out food containers based on thermal properties and morphology study

description: Plastic take-out food containers may release microplastics (MPs) into food and pose a potential risk to food safety and human health. Here, after being subjected to hot water treatment, MPs released from three types of plastic food containers (polypropylene, PP; polyethylene, PE; expanded polystyrene, EPS) were identified by micro-Raman spectroscopy. The results showed that the size of released MPs ranged from 0.8–38 μm and over 96% MPs were smaller than 10 μm. Various MPs concentrations were found from the three types of containers, that is, 1.90 × 10<sup>4</sup>, 1.01 × 10<sup>5</sup>, and 2.82 × 10<sup>6</sup> particles/L on average from PP, PE, and EPS, respectively. Moreover, based on thermal and morphology analysis, we discovered that both relaxations of the polymer chains in the rubbery state and defects caused by processing techniques might contribute to the release of MPs. Thus, such release can be reduced by increasing the thermal stability of the materials and mitigating the defects generated during production.
DOI: 10.6084/m9.figshare.21760683.v1
title: Analysis of microplastics released from plastic take-out food containers based on thermal properties and morphology study

description: Plastic take-out food containers may release microplastics (MPs) into food and pose a potential risk to food safety and human health. Here, after being subjected to hot water treatment, MPs released from three types of plastic food containers (polypropylene, PP; polyethylene, PE; expanded polystyrene, EPS) were identified by micro-Raman spectroscopy. The results showed that the size of released MPs ranged from 0.8–38 μm and over 96% MPs were smaller than 10 μm. Various MPs concentrations were found from the three types of containers, that is, 1.90 × 10<sup>4</sup>, 1.01 × 10<sup>5</sup>, and 2.82 × 10<sup>6</sup> particles/L on average from PP, PE, and EPS, respectively. Moreover, based on thermal and morphology analysis, we discovered that both relaxations of the polymer chains in the rubbery state and defects caused by processing techniques might contribute to the release of MPs. Thus, such release can be reduced by increasing the thermal stability of the materials and mitigating the defects generated during production.
DOI: 10.6084/m9.figshare.8129252
title: Additional file 3: of Time series analysis of human brucellosis in mainland China by using Elman and Jordan recurrent neural networks

description: R script to perform the Elman and Jordan neural network models with leave-one-out-cross-validation method. (TXT 2 kb)
DOI: 10.6084/m9.figshare.8129234
title: Additional file 1: of Time series analysis of human brucellosis in mainland China by using Elman and Jordan recurrent neural networks

description: Monthly cases of human brucellosis in Mainland China from 2004 to 2017. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8129234.v1
title: Additional file 1: of Time series analysis of human brucellosis in mainland China by using Elman and Jordan recurrent neural networks

description: Monthly cases of human brucellosis in Mainland China from 2004 to 2017. (XLSX 13 kb)
DOI: 10.57702/y89qq7yc
title: Example CAD Visualizations

description: Example usage of CAD visualization in 2D and 3D using CKAN Views.
DOI: 10.6084/m9.figshare.8129243
title: Additional file 2: of Time series analysis of human brucellosis in mainland China by using Elman and Jordan recurrent neural networks

description: R script of the function that can fit a range of likely candidate ARIMA models automatically. (TXT 1 kb)
DOI: 10.6084/m9.figshare.22809362
title: Custom R Scripts

description: File “Custom R Scripts” contained customed code used for data generation, processing and validation.
DOI: 10.6084/m9.figshare.22809362.v1
title: Custom R Scripts

description: File “Custom R Scripts” contained customed code used for data generation, processing and validation.
DOI: 10.6084/m9.figshare.12847948
title: Effects of α-linolenic acid intake on blood lipid profiles：a systematic review and meta-analysis of randomized controlled trials

description: To investigate the effect of ALA intake on blood lipid profiles, including triglycerides (TG), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), very-low-density lipoprotein (VLDL-C) and ratio of TC to HDL-C. We systematically searched randomized controlled trials of ALA intervention on PubMed, Embase, Cochrane library and related references up to March 2018. The final values were calculated as weighted mean difference (WMD) by using a random effects model. Subgroup analysis and meta-regression were used to explore the source of heterogeneity. Generalized least square was performed for dose–response analysis. Forty-seven studies with 1305 individuals in the ALA arm and 1325 individuals in the control arm were identified. Compared with control group, dietary intake of ALA significantly reduced the concentrations of TG (WMD −0.101 mmol/L; 95% CI: −0.158 to −0.044 mmol/L; <i>P =</i> 0.001), TC (WMD −0.140 mmol/L; 95% CI: −0.224 to −0.056 mmol/L; <i>P =</i> 0.001), LDL-C (WMD −0.131 mmol/L; 95% CI: −0.191 to −0.071 mmol/L; <i>P &lt;</i> 0.001), VLDL-C (WMD −0.121 mmol/L; 95% CI: −0.170 to −0.073 mmol/L; <i>P &lt;</i> 0.001), TC/HDL-C ratio (WMD −0.165 mmol/L; 95% CI: −0.317 to −0.013 mmol/L; <i>P =</i> 0.033) and LDL-C/HDL-C ratio (WMD −0.158 mmol/L; 95% CI: −0.291 to −0.025 mmol/L; <i>P =</i> 0.02). There is no effect of ALA intake on HDL-C (WMD 0.008 mmol/L; 95% CI: −0.018 to 0.034 mmol/L; <i>P =</i> 0.541). Dose–response analysis indicated that 1 g per day increment of ALA was associated with a 0.0016 mmol/L, 0.0071 mmol/L, 0.0015 and 0.0061 mmol/L reduction in TG (95% CI: −0.0029 to −0.0002 mmol/L), TC (95% CI: −0.0085 to −0.0058 mmol/L), HDL-C (95% CI: −0.0020 to −0.0011 mmol/L) and LDL-C (95% CI: −0.0073 to −0.0049 mmol/L) levels, respectively. The effects of ALA intake on TG, TC and LDL-C concentrations were more obvious among Asian participants, and also more obvious on patients with hyperlipidemia or hyperglycemia compared to healthy individuals. Dietary ALA intervention improves blood lipid profiles by decreasing levels of TG, TC, LDL and VLDL-C. Our findings add to the evidence that increasing ALA intake could potentially prevent risk of cardiovascular diseases.
DOI: 10.17032/shu-0000000177
title:  Food Choice and Adolescence

description: The research took a focussed ethnographical approach using Photovoice methods to understand the drivers of food choice in adolescents. 
Data from the study includes interview and PhotoVoice transcripts and photographs of food environment.
DOI: 10.25381/cput.23766105
title: Crop yields, secondary metabolites and anti-fungal activities of extracts of <i>Helichrysum cymosum </i>and <i>Helichrysum odoratissimum </i>cultivated in aquaponics

description:  The growing demand for herbal remedies has resulted in the significant over-harvesting of wild plants, exacerbating the problem of species extinction. This study evaluates two cultivation approaches that could be explored to cultivate medicinal plants.  This study compared the antifungal activities, secondary metabolite contents, and crop yields of <em>Helichrysum cymosum </em>and <em>Helichrysum odoratissimum</em> extracts cultivated in aquaponic and hydroponic systems to assess the prospects of using both systems in the sustainable cultivation of medicinal plants.  The different cultivation methods (soil, aquaponics and hydroponics) were compared. Data on plant growth, antifungal activity, antioxidant activity, secondary metabolites and volatile compounds were collected and are presented. 
The Faculty of Applied Sciences Ethics Committee granted ethics approval for this study (Reference number: 212011286/06/2020)
DOI: 10.25381/cput.23766105.v3
title: Crop yields, secondary metabolites and anti-fungal activities of extracts of <i>Helichrysum cymosum </i>and <i>Helichrysum odoratissimum </i>cultivated in aquaponics

description:  The growing demand for herbal remedies has resulted in the significant over-harvesting of wild plants, exacerbating the problem of species extinction. This study evaluates two cultivation approaches that could be explored to cultivate medicinal plants.  This study compared the antifungal activities, secondary metabolite contents, and crop yields of <em>Helichrysum cymosum </em>and <em>Helichrysum odoratissimum</em> extracts cultivated in aquaponic and hydroponic systems to assess the prospects of using both systems in the sustainable cultivation of medicinal plants.  The different cultivation methods (soil, aquaponics and hydroponics) were compared. Data on plant growth, antifungal activity, antioxidant activity, secondary metabolites and volatile compounds were collected and are presented. 
The Faculty of Applied Sciences Ethics Committee granted ethics approval for this study (Reference number: 212011286/06/2020)
DOI: 10.25381/cput.23766105.v2
title: <b>Crop yields, secondary metabolites and anti-fungal activities of extracts of </b><b><i>Helichrysum cymosum </i></b><b> and </b><b><i>Helichrysum odoratissimum </i></b><b> cultivated in aquaponics</b>

description:  The growing demand for herbal remedies has resulted in the significant over-harvesting of wild plants, exacerbating the problem of species extinction. This study evaluates two cultivation approaches that could be explored to cultivate medicinal plants.  This study compared the antifungal activities, secondary metabolite contents, and crop yields of <em>Helichrysum cymosum </em>and <em>Helichrysum odoratissimum</em> extracts cultivated in aquaponic and hydroponic systems to assess the prospects of using both systems in the sustainable cultivation of medicinal plants.  The different cultivation methods (soil, aquaponics and hydroponics) were compared. Data on plant growth, antifungal activity, antioxidant activity, secondary metabolites and volatile compounds were collected and are presented. 
The Faculty of Applied Sciences Ethics Committee granted ethics approval for this study (Reference number: 212011286/06/2020)
DOI: 10.6084/m9.figshare.12847972
title: The effect of maternal seafood consumption on perinatal outcomes: a systematic review and dose-response meta-analysis

description: Observational studies have suggested inconsistent results between maternal seafood consumption and the risk of adverse birth outcomes. We aimed to explore the possible dose-response relationship between seafood consumption during pregnancy and perinatal outcomes. A systematic search was performed with the use of PubMed, Web of Science, Embase and Cochrane Library from inception to October 27, 2019. Random-effects model was used to estimate pooled odds ratios (ORs) and 95% confidence intervals (CIs). Dose-response meta-analysis was carried out by using generalized least-squares regression and restricted cubic splines. Twenty-one studies with a total of 571641 participants were included in the analyses. A 45 g/day increment in seafood consumption was associated with a reduced risk of low birth weight (LBW) (OR: 0.65, 95% CI: 0.47 to 0.90) and small for gestational age (SGA) (OR: 0.84, 95% CI: 0.71 to 0.98). Additionally, there was a non-linear dose-response relationship between maternal seafood consumption and the risk of preterm birth (PTB), with no further benefit observed when intake above 45 g/day. The results for subtypes of seafood showed a modest J-shaped association between fatty fish and PTB, and the lowest risk was observed with the consumption of 30 g/day. In conclusion, higher total seafood consumption during pregnancy was associated with a lower risk of adverse birth outcomes, but the consumption of fatty fish should not exceed 30 grams per day. These findings could provide substantial evidence for dietary recommendations regarding seafood intake for pregnant women. This review was registered in PROSPERO (CRD42020152912).
DOI: 10.6084/m9.figshare.12847978
title: Selenium status in the body and cardiovascular disease: a systematic review and meta-analysis

description: <b>Background:</b> Both experimental and observational studies have provided conflicting evidence on the associations of selenium with incidence and mortality of cardiovascular disease (CVD). The aim of this study was to evaluate the association between selenium status in the body and incidence and mortality of CVD by performing a systematic review and meta-analysis of observational studies and randomized controlled trials. <b>Methods:</b> A systematic search for articles in MEDLINE (Ovid), Embase, Web of Science (Thomson Reuters) and Cochrane library (Wiley) was conducted. Thirteen of the 1811 articles obtained from the databases met our inclusion criteria and were considered in the final analysis. The effect sizes were presented as weighted relative risk (RR) and 95% confidence intervals (CIs) using random-effects model. To detect dose-response relationships, we used meta-regression. <b>Results:</b> Overall, there was a reduced risk of CVD incidence (RR = 0.66; 95% CI: 0.40–1.09) and mortality (RR = 0.69; 95% CI: 0.57–0.84) in physiologically high selenium status compared to low selenium status in the body. There was a 15% (RR = 0.85, 95% CI: 0.76–0.94) decreased risk of CVD incidence per 10 µg increment in blood selenium concentration. In addition, a statistically significantly nonlinear dose-response relationship was found between CVD mortality and increased blood selenium concentration with the lowest risk at the 30–35 µg increment in blood selenium. <b>Conclusions:</b> Physiologically high selenium levels in the body are associated with decreased risk for CVD incidence and mortality, however, people should be cautious about the potential harmful effects from excessive intake of selenium.
DOI: 10.6084/m9.figshare.8129252.v1
title: Additional file 3: of Time series analysis of human brucellosis in mainland China by using Elman and Jordan recurrent neural networks

description: R script to perform the Elman and Jordan neural network models with leave-one-out-cross-validation method. (TXT 2 kb)
DOI: 10.6084/m9.figshare.8129243.v1
title: Additional file 2: of Time series analysis of human brucellosis in mainland China by using Elman and Jordan recurrent neural networks

description: R script of the function that can fit a range of likely candidate ARIMA models automatically. (TXT 1 kb)
DOI: 10.6084/m9.figshare.14944915
title: Additional file 2 of Elevated retrotransposon activity and genomic instability in primed pluripotent stem cells

description: Additional file 2: Table S1. Differential gene transcriptome at passage 5.
DOI: 10.6084/m9.figshare.14944921.v1
title: Additional file 3 of Elevated retrotransposon activity and genomic instability in primed pluripotent stem cells

description: Additional file 3: Table S2. Differential gene transcriptome at passage 15.