cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5188297
title: Dong, et al-Acidification mediated by a river plume and coastal upwelling on a fringing reef at the east coast of Hainan Island, Northern South China Sea

description: This dataset mainly contains discrete sampling results of carbonate system and modeled results with respect to pH and Ω<sub>Ar</sub> variations over reefs at the east coast of Hainan Island (ECH), Northern South China Sea. Methods of analysis are contained within the material and methods section of the published article.
DOI: 10.6084/m9.figshare.5188297.v1
title: Dong, et al-Acidification mediated by a river plume and coastal upwelling on a fringing reef at the east coast of Hainan Island, Northern South China Sea

description: This dataset mainly contains discrete sampling results of carbonate system and modeled results with respect to pH and Ω<sub>Ar</sub> variations over reefs at the east coast of Hainan Island (ECH), Northern South China Sea. Methods of analysis are contained within the material and methods section of the published article.
DOI: 10.6084/m9.figshare.5189083
title: Theoretical study on the cage-like nanostructures formed by amino acids and their potential applications as drug carriers

description: The cage-like octamer, decamer and dodecamer constructed from aspartic acid monomers have been studied to explore their potential applications as drug carriers using the density functional theory. The calculation results indicate that these stable cage-like oligomers are mainly connected by the –C=O…HOOC– and –HN…HOOC– H-bonds and still keep stability and good drum-shaped topologies after the incorporation of 5-fluorouracil, paraldehyde and C<sub>24</sub>, respectively. The self-assembled cage-like oligomers may be applied to the preparation of new biological materials and the design of drug delivery systems.
DOI: 10.6084/m9.figshare.5189083.v1
title: Theoretical study on the cage-like nanostructures formed by amino acids and their potential applications as drug carriers

description: The cage-like octamer, decamer and dodecamer constructed from aspartic acid monomers have been studied to explore their potential applications as drug carriers using the density functional theory. The calculation results indicate that these stable cage-like oligomers are mainly connected by the –C=O…HOOC– and –HN…HOOC– H-bonds and still keep stability and good drum-shaped topologies after the incorporation of 5-fluorouracil, paraldehyde and C<sub>24</sub>, respectively. The self-assembled cage-like oligomers may be applied to the preparation of new biological materials and the design of drug delivery systems.
DOI: 10.6084/m9.figshare.5194990
title: Differential gene expression in banana roots in response to Fusarium wilt

description: Banana wilt disease, caused by <i>Fusarium oxysporum</i> f. sp. <i>cubense</i> tropical race 4 (Foc TR4), is a devastating disease in the banana industry. The molecular mechanism underlying the wilt resistance of AAA-type banana cultivars has not been fully characterized. Our objective was to analyse the genes differentially expressed in roots during the time of flower bud differentiation in plants grown in fields infested with Foc TR4. We compared the Foc TR4-tolerant ‘Formosana’ banana and the susceptible ‘Brazil’ banana. cDNA libraries were constructed from RNA isolated from the roots of both cultivars, and generated approximately 40 million and 35 million high-quality reads, respectively. We mapped 28 353 810 ‘Formosana’ reads and 26 917 421 ‘Brazil’ reads to the banana genome. A search of the NR (non-redundant) database resulted in the annotation of 34 408 genes. Additionally, 107 genes were differentially expressed between the two cultivars. Among the 48 differentially expressed genes with known functions, 41 were expressed more highly in ‘Formosana’ than in ‘Brazil’. These genes were divided into several categories, including specific resistance mechanism-related enzyme genes and phytoalexin synthesis-related genes. The expression levels of eight genes were validated by a quantitative real-time polymerase chain reaction. Our results indicate that ‘Formosana’ may enhance its tolerance to Foc TR4 by increasing the expression of defence-related genes (possibly constitutively). This cultivar also exhibits up-regulated expression of non-specific stress-related genes, which may enhance its overall disease tolerance. This study provides important transcript-level details potentially useful for clarifying the molecular mechanism underlying the disease resistance of Cavendish banana cultivars.
DOI: 10.17633/rd.brunel.5195731
title: Analysis of Scavenge Port Designs and Exhaust Valve Profiles on the In-cylinder Flow and Scavenging Performance in a 2-Stroke Boosted Uniflow Scavenged Direct Injection Gasoline (BUSDIG) Engine

description: The data used in the following paper is archived here:Wang, X., Ma, J., and Zhao, H., "Analysis of Scavenge Port Designs and Exhaust Valve Profiles on the In-cylinder Flow and Scavenging Performance in a 2-Stroke Boosted Uniflow Scavenged Direct Injection Gasoline (BUSDIG) Engine". International Journal of Engine Research. Accepted.<br>The descriptions for each data are listed in "captions.docx".
DOI: 10.17633/rd.brunel.5195731.v1
title: Analysis of Scavenge Port Designs and Exhaust Valve Profiles on the In-cylinder Flow and Scavenging Performance in a 2-Stroke Boosted Uniflow Scavenged Direct Injection Gasoline (BUSDIG) Engine

description: The data used in the following paper is archived here:Wang, X., Ma, J., and Zhao, H., "Analysis of Scavenge Port Designs and Exhaust Valve Profiles on the In-cylinder Flow and Scavenging Performance in a 2-Stroke Boosted Uniflow Scavenged Direct Injection Gasoline (BUSDIG) Engine". International Journal of Engine Research. Accepted.<br>The descriptions for each data are listed in "captions.docx".
DOI: 10.6084/m9.figshare.5202496
title: Design of cinnamaldehyde amino acids Schiff base compounds based on the quantitative structure activity relationship

description: Supplementary material and original data for manuscript RSOS-170516.R1 entitled "Design of cinnamaldehyde amino acids Schiff base compounds based on the quantitative structure activity relationship".
DOI: 10.6084/m9.figshare.5202496.v2
title: Design of cinnamaldehyde amino acids Schiff base compounds based on the quantitative structure activity relationship

description: Supplementary material and original data for manuscript RSOS-170516.R1 entitled "Design of cinnamaldehyde amino acids Schiff base compounds based on the quantitative structure activity relationship".
DOI: 10.6084/m9.figshare.5202496.v3
title: Design of cinnamaldehyde amino acids Schiff base compounds based on the quantitative structure activity relationship

description: Supplementary material and original data for manuscript RSOS-170516.R1 entitled "Design of cinnamaldehyde amino acids Schiff base compounds based on the quantitative structure activity relationship".
DOI: 10.6084/m9.figshare.5202496.v4
title: Design of cinnamaldehyde amino acids Schiff base compounds based on the quantitative structure activity relationship

description: Supplementary material and original data for manuscript RSOS-170516.R1 entitled "Design of cinnamaldehyde amino acids Schiff base compounds based on the quantitative structure activity relationship".
DOI: 10.6084/m9.figshare.5202499
title: A salt-bridge switch in the molecular recognition between RS receptor and RGD ligand from the ABEEM <i>σπ</i> molecular dynamics simulations

description: How the receptor and ligand recognise each other is a challenging subject in explaining the mechanism of recognition at the molecular level. As a starting point, here, a synthesised RS receptor and its RGD ligand were investigated as a proper model to simulate their recognition process in terms of ABEEM<i>σπ</i>/MM polarisable force field. It is found that a switch of forming up a salt bridge in the ligand triggers the recognition of the receptor and ligand. Through the salt-bridge switch that undergoes several cycles from on-state with parallel hydrogen bonds to off-state with bifurcated hydrogen bonds, the active site of ligand can flex easily to interact with the active site of the receptor. In addition, the water molecules form a decisive bridge connecting the active sites of the bound system. The salt-bridge switch and water-mediated movement are cooperative as the important factors for the receptor-ligand recognition. In addition, the properties, such as binding free energy, conformational flexibility and solvent accessible surface area have been calculated to provide adequate evidence for the whole recognition process. According to the simulation, a detailed mechanism was derived involving diffusion, a switch triggered cooperative water-mediated movement, and conformational folding, for the flexible recognition.
DOI: 10.6084/m9.figshare.5202499.v1
title: A salt-bridge switch in the molecular recognition between RS receptor and RGD ligand from the ABEEM <i>σπ</i> molecular dynamics simulations

description: How the receptor and ligand recognise each other is a challenging subject in explaining the mechanism of recognition at the molecular level. As a starting point, here, a synthesised RS receptor and its RGD ligand were investigated as a proper model to simulate their recognition process in terms of ABEEM<i>σπ</i>/MM polarisable force field. It is found that a switch of forming up a salt bridge in the ligand triggers the recognition of the receptor and ligand. Through the salt-bridge switch that undergoes several cycles from on-state with parallel hydrogen bonds to off-state with bifurcated hydrogen bonds, the active site of ligand can flex easily to interact with the active site of the receptor. In addition, the water molecules form a decisive bridge connecting the active sites of the bound system. The salt-bridge switch and water-mediated movement are cooperative as the important factors for the receptor-ligand recognition. In addition, the properties, such as binding free energy, conformational flexibility and solvent accessible surface area have been calculated to provide adequate evidence for the whole recognition process. According to the simulation, a detailed mechanism was derived involving diffusion, a switch triggered cooperative water-mediated movement, and conformational folding, for the flexible recognition.
DOI: 10.6084/m9.figshare.5202751
title: The entropy value for driver fatigue detection

description: This is the four entropies of twelve healthy subjects for driver fatigue detection. Due to personal privacy, the digital number represents different participants. Each .mat file included five files, namely FE, SE, AE and PE described four entropy values in the training data and the corresponding label of class, which the number 1 represents the fatigue state and 0 represents the normal state in the process of driving.
DOI: 10.6084/m9.figshare.5203651
title: Epigenetic silencing of miR-203 in Kazakh patients with esophageal squamous cell carcinoma by MassARRAY spectrometry

description: Dysregulation of miR-203 by promoter methylation is associated with the development of various cancers. We aimed to explore the underlying link between promoter methylation and miR-203 expression in Kazakh esophageal squamous cell carcinoma (ESCC). MassARRAY® System spectrometry was used to quantitatively analyze the DNA methylation of 32 CpG sites within miR-203 in 99 Kazakh ESCC and 46 normal esophageal tissues (NETs) with similar population characteristics. We conducted real-time PCR to detect miR-203 expression levels and evaluated their association with methylation. Eleven CpG units within miR-203 promoter were frequently hypermethylated in ESCC compared with NETs <i>(P &lt; 0.05)</i>. The hypermethylation of several CpG units positively correlated with age, lower esophagus, constrictive type of ESCC, and moderately differentiated ESCC. Given the involvement of human papillomavirus (HPV) in etiology of ESCC was confirmed from our previous reports, herein we found that CpG units within miR-203 in HPV16-positive ESCC are more heavily methylated. Furthermore, miR-203 expression showed a nearly 4.5-fold decrease in ESCC than NETs (0.206 ± 0.336 vs. 0.908 ± 1.424, <i>P</i> &lt; 0.001) and was significantly associated with lymph node metastasis <i>(P</i> = 0.012). The expression of miR-203 with 11 completely hypermethylated CpG units was approximately 6.5-fold lower than that with at least 1 unmethylated CpG unit <i>(P</i> &lt; 0.001) and especially the CpG_15.16 and CpG_31.32 with higher methylation levels in ESCC tissues exhibited lower expression levels of miR-203, which indicated a reverse association between miR-203 methylation and expression. Hypermethylated miR-203 is a potential biomarker and targeted delivery of miR-203 could therefore serve as a preventive or therapeutic strategy for Kazakh ESCC.
DOI: 10.6084/m9.figshare.5203651.v1
title: Epigenetic silencing of miR-203 in Kazakh patients with esophageal squamous cell carcinoma by MassARRAY spectrometry

description: Dysregulation of miR-203 by promoter methylation is associated with the development of various cancers. We aimed to explore the underlying link between promoter methylation and miR-203 expression in Kazakh esophageal squamous cell carcinoma (ESCC). MassARRAY® System spectrometry was used to quantitatively analyze the DNA methylation of 32 CpG sites within miR-203 in 99 Kazakh ESCC and 46 normal esophageal tissues (NETs) with similar population characteristics. We conducted real-time PCR to detect miR-203 expression levels and evaluated their association with methylation. Eleven CpG units within miR-203 promoter were frequently hypermethylated in ESCC compared with NETs <i>(P &lt; 0.05)</i>. The hypermethylation of several CpG units positively correlated with age, lower esophagus, constrictive type of ESCC, and moderately differentiated ESCC. Given the involvement of human papillomavirus (HPV) in etiology of ESCC was confirmed from our previous reports, herein we found that CpG units within miR-203 in HPV16-positive ESCC are more heavily methylated. Furthermore, miR-203 expression showed a nearly 4.5-fold decrease in ESCC than NETs (0.206 ± 0.336 vs. 0.908 ± 1.424, <i>P</i> &lt; 0.001) and was significantly associated with lymph node metastasis <i>(P</i> = 0.012). The expression of miR-203 with 11 completely hypermethylated CpG units was approximately 6.5-fold lower than that with at least 1 unmethylated CpG unit <i>(P</i> &lt; 0.001) and especially the CpG_15.16 and CpG_31.32 with higher methylation levels in ESCC tissues exhibited lower expression levels of miR-203, which indicated a reverse association between miR-203 methylation and expression. Hypermethylated miR-203 is a potential biomarker and targeted delivery of miR-203 could therefore serve as a preventive or therapeutic strategy for Kazakh ESCC.
DOI: 10.6084/m9.figshare.5208205
title: Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

description: Currently, genome-wide scans for positive selection signatures in commercial breed have been
investigated. However, most selection signatures were population specific. Few studies have focused
on selection footprints of indigenous breeds. Laiwu pigs are an invaluable Chinese typical
indigenous pig breed with extremely high proportion of intramuscular fat (IMF), and an excellent
model to detect footprint as the result of natural and artificial selection for fat deposition in muscle.
In this study, based on GeneSeek Genomic profiler for Porcine HD data, three complementary
methods, FST, iHS (integrated haplotype homozygosity score) and CLR (Composite Likelihood Ratio)
were implemented to detect selection signatures in the whole genome of Laiwu pigs. Totally, 193
candidate selected regions were obtained by at least two of the three methods, which covered 48.25
Mb genomic regions and corresponded to 1.72% of the genome sequence. Gene annotation of the
selected regions revealed a list of functionally important genes for feed intake and fat deposition,
reproduction, and immune response. Especially, in accordance to the phenotypic features of Laiwu
pigs, among the candidate genes, we identified several genes, <i>NPY1R</i>, <i>NPY5R</i>, <i>PIK3R1, Rab11-FIP2</i>
and <i>JAKMIP1</i>, involved in the actions of two sets of neurons, which are central regulators in
maintaining the balance between food intake and energy expenditure. Our results identified a number
of regions showing signatures of selection, as well as a list of functionally candidate genes with
potential effect on phenotypic traits, especially fat deposition in muscle. Our findings provide
insights into the mechanisms of artificial selection of fat deposition and further facilitate follow-up
functional studies.<br>
DOI: 10.6084/m9.figshare.5208766
title: Chen et al. 2017 (Fig 3f. and Supplementary Fig. 1e chromatograms)

description: This file contain Sanger sequencing data analyzed in Fig. 3f. and Supplementary Fig 1e.
DOI: 10.6084/m9.figshare.5208766.v1
title: Chen et al. 2017 (Fig 3f. and Supplementary Fig. 1e chromatograms)

description: This file contain Sanger sequencing data analyzed in Fig. 3f. and Supplementary Fig 1e.
DOI: 10.6084/m9.figshare.5211424
title: Effects of altered photoperiod on circadian clock and lipid metabolism in rats

description: Disruption of circadian clock timekeeping due to changes in the photoperiod enhances the risk of lipid metabolism disorders and metabolic syndrome. However, the effects of altered photoperiods on the circadian clock and lipid metabolism are not well understood. To explore the effects of altered photoperiods, we developed a rat model where rats were exposed to either short-day or long-day conditions. Our findings demonstrated that altered photoperiods mediated circadian clocks by partly disrupting rhythmicity and shifting phase values of clock genes. We also showed that compared to long-day conditions, rats under short-day conditions exhibited more photoperiodic changes in a variety of physiological outputs related to lipid metabolism, such as significant increases in serum triglyceride (TG), high-density lipoprotein, and leptin levels, as well as increased body weight, fat:weight ratio, and hepatic TG levels. These increments were gained possibly through upregulated expression of forkhead box O1 (<i>FoxO1</i>), which partly mediates the expression of peroxisome proliferator-activated receptorα (<i>PPARα</i>) to increase the expression of phosphoenolpyruvate carboxykinase (<i>PEPCK</i>), peroxisome proliferator-activated receptor-g coactivator-1β (<i>PGC1β</i>), and fatty acid synthase (<i>Fas</i>n). In addition, the oscillation rhythms of <i>FoxO1, PEPCK, PGC1β</i>, and <i>Fasn</i> expression levels in the livers of rats exposed to a short-day photoperiod were more robust than those exposed to a long-day photoperiod. These findings suggest that a change in photoperiod can partly disrupt the circadian rhythmcity of clock genes, impair lipid metabolism, and promote obesity.
DOI: 10.6084/m9.figshare.5211424.v1
title: Effects of altered photoperiod on circadian clock and lipid metabolism in rats

description: Disruption of circadian clock timekeeping due to changes in the photoperiod enhances the risk of lipid metabolism disorders and metabolic syndrome. However, the effects of altered photoperiods on the circadian clock and lipid metabolism are not well understood. To explore the effects of altered photoperiods, we developed a rat model where rats were exposed to either short-day or long-day conditions. Our findings demonstrated that altered photoperiods mediated circadian clocks by partly disrupting rhythmicity and shifting phase values of clock genes. We also showed that compared to long-day conditions, rats under short-day conditions exhibited more photoperiodic changes in a variety of physiological outputs related to lipid metabolism, such as significant increases in serum triglyceride (TG), high-density lipoprotein, and leptin levels, as well as increased body weight, fat:weight ratio, and hepatic TG levels. These increments were gained possibly through upregulated expression of forkhead box O1 (<i>FoxO1</i>), which partly mediates the expression of peroxisome proliferator-activated receptorα (<i>PPARα</i>) to increase the expression of phosphoenolpyruvate carboxykinase (<i>PEPCK</i>), peroxisome proliferator-activated receptor-g coactivator-1β (<i>PGC1β</i>), and fatty acid synthase (<i>Fas</i>n). In addition, the oscillation rhythms of <i>FoxO1, PEPCK, PGC1β</i>, and <i>Fasn</i> expression levels in the livers of rats exposed to a short-day photoperiod were more robust than those exposed to a long-day photoperiod. These findings suggest that a change in photoperiod can partly disrupt the circadian rhythmcity of clock genes, impair lipid metabolism, and promote obesity.
DOI: 10.6084/m9.figshare.5213194
title: Early Jurassic granitoids from deep drill holes in the East China Sea Basin: implications for the initiation of Palaeo-Pacific tectono-magmatic cycle

description: The timing of the Palaeo-Pacific Plate (PPP) subduction in East Asia, following the amalgamation of the North and South China Blocks (NCB and SCB), remains equivocal despite several investigations on the widespread subduction-related Mesozoic magmatism in this region. Here we report newly discovered granodiorites in the East China Sea Basin (ECSB) from deep boreholes (2945–2983 m), which yield SHRIMP zircon U–Pb age of 174 ± 1.1 Ma. The rock shows relatively high Sr/Y and La/Yb ratios, low contents of Ni, Cr, and MgO, and markedly negative values of <i>ε</i>Hf(<i>t</i>) (21.0 to −27.0). These geochemical and isotopic features are similar to those of the tonalite-trondhjemite-granodiorite (TTG) suites produced by the partial melting of the thickened lower continental crust. Our data, together with the ca. 190–180 Ma I-type granites reported from the eastern Zhejiang–Fujian and Taiwan areas, lead us to conclude that the continental crust in the coastal areas of South China underwent some degree of thickening during the Early Jurassic. A comparison with the coeval magmatic rocks in South Korea and Japan suggests that a large NE-trending continental arc (ca. 190–170 Ma) might have been constructed along the eastern margin of Asia at this time. Our study provides insights into the initiation of the Palaeo-Pacific tectono-magmatic cycle immediately following the consolidation of the SCB and NCB.
DOI: 10.6084/m9.figshare.5213194.v1
title: Early Jurassic granitoids from deep drill holes in the East China Sea Basin: implications for the initiation of Palaeo-Pacific tectono-magmatic cycle

description: The timing of the Palaeo-Pacific Plate (PPP) subduction in East Asia, following the amalgamation of the North and South China Blocks (NCB and SCB), remains equivocal despite several investigations on the widespread subduction-related Mesozoic magmatism in this region. Here we report newly discovered granodiorites in the East China Sea Basin (ECSB) from deep boreholes (2945–2983 m), which yield SHRIMP zircon U–Pb age of 174 ± 1.1 Ma. The rock shows relatively high Sr/Y and La/Yb ratios, low contents of Ni, Cr, and MgO, and markedly negative values of <i>ε</i>Hf(<i>t</i>) (21.0 to −27.0). These geochemical and isotopic features are similar to those of the tonalite-trondhjemite-granodiorite (TTG) suites produced by the partial melting of the thickened lower continental crust. Our data, together with the ca. 190–180 Ma I-type granites reported from the eastern Zhejiang–Fujian and Taiwan areas, lead us to conclude that the continental crust in the coastal areas of South China underwent some degree of thickening during the Early Jurassic. A comparison with the coeval magmatic rocks in South Korea and Japan suggests that a large NE-trending continental arc (ca. 190–170 Ma) might have been constructed along the eastern margin of Asia at this time. Our study provides insights into the initiation of the Palaeo-Pacific tectono-magmatic cycle immediately following the consolidation of the SCB and NCB.