1,360 results on '"Yang, Chen"'
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2. Accurate Mapping and Evaluation of Small Impact Craters within the Lunar Landing Area.
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Yang, Chen, Wang, Xinglong, Zhao, Dandong, Guan, Renchu, and Zhao, Haishi
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LUNAR craters , *IMPACT craters , *LUNAR surface , *GEOLOGICAL research - Abstract
Impact craters, as the most distinct lunar structural unit and geological structure, are marked on the Moon's surface. For over a decade, researchers have focused on identifying and exploring large- to medium-sized impact craters on the surface of the Moon (craters with a diameter greater than 1 km). Small impact craters have obvious statistical significance owing to their magnitude in numbers. The identification and analysis of small craters provide indispensable clues for the study of lunar geological evolution. However, such craters only remain in specific images and regions. At present, there is no comprehensive record of small impact craters in the existing lunar impact crater databases. The small impact craters on the surface of the Moon are enormous and vary in size by orders of magnitude, exhibiting small target characteristics in space. The present study focuses on the identification and spatial analysis of small impact craters on the surface of the Moon. A feature amplification strategy-based identification model was established for small impact crater detection, achieving accurate recognition of the small impact craters on the surface of the Moon (with a recall rate of 86.97% and a false-positive rate as low as 0.54% ± 0.16%). In total, 228,897, 142,872, and 42,008 new small lunar impact craters (with diameters as low as 4.5 m) were identified in the ten lunar landing areas of returned samples from the Apollo, Luna, and Chang'e-5 missions. In addition, the spatial distribution characteristics of small impact craters during different geological periods in the landing area are provided. Data on the newly identified small impact craters will provide an important basis for revealing the lunar impact fluxes and young lunar surface dating in lunar geological evolution research. [ABSTRACT FROM AUTHOR]
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- 2024
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3. The roles of nuclear orphan receptor NR2F6 in anti-viral innate immunity.
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Yang, Chen, Wang, Chen-Yu, Long, Qiao-Yun, Cao, Zhuo, Wei, Ming-Liang, Tang, Shan-Bo, Lin, Xiang, Mu, Zi-Qi, Xiao, Yong, Chen, Ming-Kai, Wu, Min, and Li, Lian-Yun
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DNA virus diseases , *NATURAL immunity , *NUCLEAR receptors (Biochemistry) , *TRANSCRIPTION factors , *GENETIC transcription regulation , *DNA replication - Abstract
Proper transcription regulation by key transcription factors, such as IRF3, is critical for anti-viral defense. Dynamics of enhancer activity play important roles in many biological processes, and epigenomic analysis is used to determine the involved enhancers and transcription factors. To determine new transcription factors in anti-DNA-virus response, we have performed H3K27ac ChIP-Seq and identified three transcription factors, NR2F6, MEF2D and MAFF, in promoting HSV-1 replication. NR2F6 promotes HSV-1 replication and gene expression in vitro and in vivo, but not dependent on cGAS/STING pathway. NR2F6 binds to the promoter of MAP3K5 and activates AP-1/c-Jun pathway, which is critical for DNA virus replication. On the other hand, NR2F6 is transcriptionally repressed by c-Jun and forms a negative feedback loop. Meanwhile, cGAS/STING innate immunity signaling represses NR2F6 through STAT3. Taken together, we have identified new transcription factors and revealed the underlying mechanisms involved in the network between DNA viruses and host cells. Author summary: DNA virus infection, such as KSHV and HSV-1, affects a large population of human beings and difficult to be cleared from human bodies. The change of enhancer activity on chromatin reflects the cellular response upon viral infections, and Epigenomic profiling of active enhancers has been found to be a powerful tool to identify key transcription factors in biological processes. Here, we have performed H3K27ac ChIP-Seq to determine new transcription factors in anti-DNA-virus response, and identified three transcription factors, NR2F6, MEF2D and MAFF, in promoting HSV-1 replication. Further studies show that NR2F6 promotes HSV-1 replication and gene expression in vitro and in vivo, but not dependent on cGAS/STING pathway. NR2F6 is critical for AP-1/c-Jun pathway activation through direct targeting the promoter of MAP3K5, which is critical for DNA virus replication. On the other hand, host cell controls the expression of NR2F6 via c-Jun, which forms a negative feedback loop in anti-DNA-virus response. Meanwhile, cGAS/STING innate immunity signaling pathway represses NR2F6 expression through STAT3. Taken together, we have identified new transcription factors and revealed the underlying mechanisms involved in the interaction between DNA viruses and host cells. [ABSTRACT FROM AUTHOR]
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- 2024
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4. Nanofibrous Porous Organic Polymers and Their Derivatives: From Synthesis to Applications.
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Yang, Chen, Wang, Kexiang, Lyu, Wei, Liu, He, Li, Jiaqiang, Wang, Yue, Jiang, Ruyu, Yuan, Jiayin, and Liao, Yaozu
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POROUS polymers , *GAS absorption & adsorption , *CARBON nanofibers , *HETEROGENEOUS catalysis , *WATER purification , *ENERGY storage , *NANOFIBERS - Abstract
Engineering porous organic polymers (POPs) into 1D morphology holds significant promise for diverse applications due to their exceptional processability and increased surface contact for enhanced interactions with guest molecules. This article reviews the latest developments in nanofibrous POPs and their derivatives, encompassing porous organic polymer nanofibers, their composites, and POPs‐derived carbon nanofibers. The review delves into the design and fabrication strategies, elucidates the formation mechanisms, explores their functional attributes, and highlights promising applications. The first section systematically outlines two primary fabrication approaches of nanofibrous POPs, i.e., direct bulk synthesis and electrospinning technology. Both routes are discussed and compared in terms of template utilization and post‐treatments. Next, performance of nanofibrous POPs and their derivatives are reviewed for applications including water treatment, water/oil separation, gas adsorption, energy storage, heterogeneous catalysis, microwave absorption, and biomedical systems. Finally, highlighting existent challenges and offering future prospects of nanofibrous POPs and their derivatives are concluded. [ABSTRACT FROM AUTHOR]
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- 2024
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5. Noninvasive spinal stimulation improves walking in chronic stroke survivors: a proof-of-concept case series.
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Moon, Yaejin, Yang, Chen, Veit, Nicole C., McKenzie, Kelly A., Kim, Jay, Aalla, Shreya, Yingling, Lindsey, Buchler, Kristine, Hunt, Jasmine, Jenz, Sophia, Shin, Sung Yul, Kishta, Ameen, Edgerton, V. Reggie, Gerasimenko, Yury P., Roth, Elliot J., Lieber, Richard L., and Jayaraman, Arun
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SPINAL cord , *STROKE patients , *WALKING speed , *PROOF of concept , *FITNESS walking , *STROKE , *ANKLE - Abstract
Background: After stroke, restoring safe, independent, and efficient walking is a top rehabilitation priority. However, in nearly 70% of stroke survivors asymmetrical walking patterns and reduced walking speed persist. This case series study aims to investigate the effectiveness of transcutaneous spinal cord stimulation (tSCS) in enhancing walking ability of persons with chronic stroke. Methods: Eight participants with hemiparesis after a single, chronic stroke were enrolled. Each participant was assigned to either the Stim group (N = 4, gait training + tSCS) or Control group (N = 4, gait training alone). Each participant in the Stim group was matched to a participant in the Control group based on age, time since stroke, and self-selected gait speed. For the Stim group, tSCS was delivered during gait training via electrodes placed on the skin between the spinous processes of C5–C6, T11–T12, and L1–L2. Both groups received 24 sessions of gait training over 8 weeks with a physical therapist providing verbal cueing for improved gait symmetry. Gait speed (measured from 10 m walk test), endurance (measured from 6 min walk test), spatiotemporal gait symmetries (step length and swing time), as well as the neurophysiological outcomes (muscle synergy, resting motor thresholds via spinal motor evoked responses) were collected without tSCS at baseline, completion, and 3 month follow-up. Results: All four Stim participants sustained spatiotemporal symmetry improvements at the 3 month follow-up (step length: 17.7%, swing time: 10.1%) compared to the Control group (step length: 1.1%, swing time 3.6%). Additionally, 3 of 4 Stim participants showed increased number of muscle synergies and/or lowered resting motor thresholds compared to the Control group. Conclusions: This study provides promising preliminary evidence that using tSCS as a therapeutic catalyst to gait training may increase the efficacy of gait rehabilitation in individuals with chronic stroke. Trial registration NCT03714282 (clinicaltrials.gov), registration date: 2018-10-18. [ABSTRACT FROM AUTHOR]
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- 2024
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6. Management of companies' green competitiveness: Coordination degree between core determinants.
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Yang Chen, Wenqun Gao, Chygryn, Olena, Lyulyov, Oleksii, and Pimonenko, Tetyana
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ECONOMIC sectors , *COMPETITIVE advantage in business , *MECHANICAL engineering , *STATISTICAL correlation , *AGRICULTURAL industries , *BUSINESS enterprises - Abstract
Companies' green competitive advantages result from the high coordination of economic, ecological, social and corporate subsystems. Thus, it is important to investigate the influence and coupling coordination degree (CCD) of the relevant components of green competitiveness. This paper justifies the relationship between green competitiveness and the coupling degree of its components. It hypothesizes that the increasing integrated index of companies' green competitiveness was determined by levels of coordination and communication between its components. The study applies the CCD model and correlation analysis to test the hypothesis. The objects of analysis were enterprises represented by three economic sectors: agro-industrial, mechanical engineering and food. The findings show that the highest coupling coordination degree among all components is represented by the companies with the highest green competitive index. These companies are characterized by the dominance of corporate components, which can increase the general level of green competitive advantages in various combinations with other determinants. [ABSTRACT FROM AUTHOR]
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- 2024
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7. Power calculation for detecting interaction effect in cross-sectional stepped-wedge cluster randomized trials: an important tool for disparity research.
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Yang, Chen, Berkalieva, Asem, Mazumdar, Madhu, and Kwon, Deukwoo
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CLUSTER randomized controlled trials , *TREATMENT effect heterogeneity , *MEDICAL care , *GENERALIZED estimating equations , *STATISTICAL power analysis - Abstract
Background: The stepped-wedge cluster randomized trial (SW-CRT) design has become popular in healthcare research. It is an appealing alternative to traditional cluster randomized trials (CRTs) since the burden of logistical issues and ethical problems can be reduced. Several approaches for sample size determination for the overall treatment effect in the SW-CRT have been proposed. However, in certain situations we are interested in examining the heterogeneity in treatment effect (HTE) between groups instead. This is equivalent to testing the interaction effect. An important example includes the aim to reduce racial disparities through healthcare delivery interventions, where the focus is the interaction between the intervention and race. Sample size determination and power calculation for detecting an interaction effect between the intervention status variable and a key covariate in the SW-CRT study has not been proposed yet for binary outcomes. Methods: We utilize the generalized estimating equation (GEE) method for detecting the heterogeneity in treatment effect (HTE). The variance of the estimated interaction effect is approximated based on the GEE method for the marginal models. The power is calculated based on the two-sided Wald test. The Kauermann and Carroll (KC) and the Mancl and DeRouen (MD) methods along with GEE (GEE-KC and GEE-MD) are considered as bias-correction methods. Results: Among three approaches, GEE has the largest simulated power and GEE-MD has the smallest simulated power. Given cluster size of 120, GEE has over 80% statistical power. When we have a balanced binary covariate (50%), simulated power increases compared to an unbalanced binary covariate (30%). With intermediate effect size of HTE, only cluster sizes of 100 and 120 have more than 80% power using GEE for both correlation structures. With large effect size of HTE, when cluster size is at least 60, all three approaches have more than 80% power. When we compare an increase in cluster size and increase in the number of clusters based on simulated power, the latter has a slight gain in power. When the cluster size changes from 20 to 40 with 20 clusters, power increases from 53.1% to 82.1% for GEE; 50.6% to 79.7% for GEE-KC; and 48.1% to 77.1% for GEE-MD. When the number of clusters changes from 20 to 40 with cluster size of 20, power increases from 53.1% to 82.1% for GEE; 50.6% to 81% for GEE-KC; and 48.1% to 79.8% for GEE-MD. Conclusions: We propose three approaches for cluster size determination given the number of clusters for detecting the interaction effect in SW-CRT. GEE and GEE-KC have reasonable operating characteristics for both intermediate and large effect size of HTE. [ABSTRACT FROM AUTHOR]
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- 2024
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8. Analysis of flavonoid metabolism of compounds in succulent fruits and leaves of three different colors of Rosaceae.
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Yang, Chen, Sun, Nan, Qin, Xin, Liu, Yangbo, Sui, Mengyi, Zhang, Yawen, Hu, Yanli, Mao, Yunfei, and Shen, Xiang
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FLAVONOIDS , *ROSACEAE , *ORNAMENTAL plants , *ANTHOCYANINS , *FLAVONOID glycosides , *CHALCONES , *PEACH , *LOQUAT - Abstract
Red flesh apple (Malus pumila var. medzwetzkyana Dieck), purple leaf plum (Prunus cerasifera Ehrhar f), and purple leaf peach (Prunus persica 'Atropurpurea') are significant ornamental plants within the Rosaceae family. The coloration of their fruits and leaves is crucial in their appearance and nutritional quality. However, qualitative and quantitative studies on flavonoids in the succulent fruits and leaves of multicolored Rosaceae plants are lacking. To unveil the diversity and variety-specificity of flavonoids in these three varieties, we conducted a comparative analysis of flavonoid metabolic components using ultra-high-performance liquid phase mass spectrometry (UPLC-MS/MS). The results revealed the detection of 311 metabolites, including 47 flavonoids, 105 flavonols, 16 chalcones, 37 dihydroflavonoids, 8 dihydroflavonols, 30 anthocyanins, 14 flavonoid carbon glycosides, 23 flavanols, 8 isoflavones, 11 tannins, and 12 proanthocyanidins. Notably, although the purple plum and peach leaves exhibited distinct anthocyanin compounds, paeoniflorin and corythrin glycosides were common but displayed varying glycosylation levels. While the green purple leaf peach fruit (PEF) and red flesh apple leaf (AL) possessed the lowest anthocyanin content, they exhibited the highest total flavonoid content. Conversely, the red flesh apple fruit (AF) displayed the highest anthocyanin content and a diverse range of anthocyanin glycosylation modifications, indicating that anthocyanins predominantly influenced the fruit's color. Purple PLF, PLL, and PEL showcased varying concentrations of anthocyanins, suggesting that their colors result from the co-color interaction between specific types of anthocyanins and secondary metabolites, such as flavonols, flavonoids, and dihydroflavonoids. This study provides novel insights into the variations in tissue metabolites among Rosaceae plants with distinct fruit and leaf colors. [ABSTRACT FROM AUTHOR]
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- 2024
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9. The radiative association of PO/PH+ and the photodissociation of PH+.
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Yang Chen, Xiaohe Lin, Lidan Xiao, Zijian Li, Songbin Zhang, Yongjun Cheng, Yong Wu, Bing Yan, and Pantaleone, Stefano
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PHOTODISSOCIATION , *LOCAL thermodynamic equilibrium , *PLANETARY atmospheres , *DIPOLE moments , *INTERSTELLAR medium - Abstract
The potential energy curves (PECs) and transition dipole moments (TDMs) of PH+ and PO are computed with the multireference configuration interaction method, and the cross-sections for the radiative association (RA) of PH+ and PO, which is the most efficient way to form the ground states, are presented via the quantum mechanical (QM) theory and computed using ab initio molecular data. The thermal rate coefficients are also expressed and fitted with the standard formula k(T) = A(T/300)αe-β/T in the range of 10 K-15,000 K. Meanwhile, the photodissociation, that is the inverse process of RA for PH+, is also studied, including eight photodissociation channels for the computation of state-resolved cross-sections. Careful comparisons with the Leiden Observatory database are made. Considering the cross-sections mentioned above, the local thermodynamic equilibrium cross-sections at the temperatures of 0, 500, 1,000, and 2,000 K are also shown. We expect the results to be helpful for studies of phosphorus chemistry in the interstellar medium and planetary atmospheres. [ABSTRACT FROM AUTHOR]
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- 2024
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10. Anoikis related genes may be novel markers associated with prognosis for ovarian cancer.
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Yang, Chen, Zhu, LuChao, and Lin, Qin
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ANOIKIS , *OVARIAN cancer , *DISEASE risk factors , *CANCER prognosis , *NONNEGATIVE matrices , *SURVIVAL analysis (Biometry) , *LOG-rank test - Abstract
The aim of this study was to determine the prognostic significance of anoikis related genes (ARGs) in ovarian cancer (OC) and to develop a prognostic signature based on ARG expression. We analyzed cohorts of OC patients and used nonnegative matrix factorization (NMF) for clustering. Single-sample gene-set enrichment analysis (ssGSEA) was employed to quantify immune infiltration. Survival analyses were performed using the Kaplan–Meier method, and differences in survival were determined using the log-rank test. The extent of anoikis modification was quantified using a risk score generated from ARG expression. The analysis of single-cell sequencing data was performed by the Tumor Immune Single Cell Hub (TISCH). Our analyses revealed two distinct patterns of anoikis modification. The risk score was used to evaluate the anoikis modification patterns in individual tumors. Three hub-genes were screened using the LASSO (Least Absolute Shrinkage and Selection Operator) method and patients were classified into different risk groups based on their individual score and the median score. The low-risk subtype was characterized by decreased expression of hub-genes and better overall survival. The risk score, along with patient age and gender, were considered to identify the prognostic signature, which was visualized using a nomogram. Our findings suggest that ARGs may play a novel role in the prognosis of OC. Based on ARG expression, we have developed a prognostic signature for OC that can aid in patient stratification and treatment decision-making. Further studies are needed to validate these results and to explore the underlying mechanisms. [ABSTRACT FROM AUTHOR]
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- 2024
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11. Selection of Landsat-8 Operational Land Imager (OLI) Optimal Band Combinations for Mapping Alteration Zones.
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Yang, Chen, Jia, Hekun, Dong, Lifang, Zhao, Haishi, and Zhao, Minghao
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OPTIMIZATION algorithms , *MINES & mineral resources , *PRINCIPAL components analysis , *PROSPECTING , *OXIDE minerals - Abstract
In typical alteration extraction methods, e.g., band math and principal component analysis (PCA), the bands or band combinations unitized to extract altered minerals are usually selected based on empirical models or previous rules. This results in significant differences in the alteration of mineral mapping even in the same area, thus greatly increasing the uncertainty of mineral resource prediction. In this paper, an intelligent alteration extraction approach was proposed in which an optimization algorithm, i.e., a genetic algorithm (GA), was introduced into the PCA; this approach is termed GA-PCA and is used for selecting the optimized band combinations of mineralized alterations. The proposed GA-PCA was employed to map iron oxides and hydroxyl minerals using the most commonly adopted multispectral data, i.e., Landsat-8 OLI data, at the Lalingzaohuo polymetallic deposits, China. The results showed that the spectral characteristics of GA-PCA-selected OLI band combinations in the research area were beneficial for enhancing alteration information and were more capable of suppressing the interference of vegetation information. The mapping alteration zones using the GA-PCA approach had a higher agreement with known ore spots, i.e., 25% and 33.3% in ferrous-bearing and hydroxyl-bearing deposits, compared to the classical PCA. Furthermore, two predicted targets (not shown in the classical PCA results) were precisely obtained via analyzing the GA-PCA alteration maps combined with the ore-forming geological conditions of the mine and its tectonic characteristics. This indicated that the intelligent selection of mineral alteration band combinations increased the reliability of remote sensing-based mineral exploration. [ABSTRACT FROM AUTHOR]
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- 2024
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12. Mapping Cones on Mars in High-Resolution Planetary Images with Deep Learning-Based Instance Segmentation.
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Yang, Chen, Zhang, Nan, Guan, Renchu, and Zhao, Haishi
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DEEP learning , *ARTIFICIAL neural networks , *CONES , *MARS (Planet) - Abstract
Cones are among the significant and controversial landforms on Mars. Martian cones exhibit various morphological characteristics owing to their complex origin, and their precise origin remains an active research topic. A limited number of cones have been manually mapped from high-resolution images in local areas, and existing detection methods are only applicable to a single type of cone that has a similar morphology and spatial distribution, leading to the vast majority remaining unidentified. In this paper, a novel cone identification approach is proposed that is specially designed for adequately recognizing cones from different regions in high-resolution planetary images. First, due to the lack of a publicly available cone database for reference, we annotated 3681 cones according to the literature on manual interpretation and the cone information provided by the Lunar and Planetary Laboratory (IRL) in HiRISE images. Then, the cone identification problem was converted into an instance segmentation task, i.e., a cone identification approach was designed based on deep neural networks. The Feature Pyramid Network-equipped Mask R-CNN was utilized as the detection and segmentation model. Extensive experiments were conducted for fine recognition of Martian cones with HiRISE. The results show that the proposed approach achieves high performance; it especially efficiently detects multiple types of cones while generating accurate segmentation to describe the geometry contour of cones. Finally, a Martian cone dataset with deep learning-based instance segmentation (DL-MCD) was built, containing 3861 cones for exploring geological processes on the surface of Mars. [ABSTRACT FROM AUTHOR]
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- 2024
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13. An auxiliary strategy of partial least squares regression in pharmacokinetic/pharmacodynamic studies: A case of application of guhong injection in myocardial ischemia/reperfusion rats.
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Hai-yang Chen, Chang Li, Chong-yu Shao, Yu-jia Wu, Hai-tong Wan, and Yu He
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CHINESE medicine , *BIOLOGICAL models , *TROPONIN , *VERAPAMIL , *RUTIN , *MYOCARDIAL reperfusion complications , *MYOCARDIAL ischemia , *LIQUID chromatography-mass spectrometry , *RESEARCH funding , *HERBAL medicine , *ENZYME-linked immunosorbent assay , *HYDROXYBUTYRATE dehydrogenase , *CARBOXYLIC acids , *INJECTIONS , *RATS , *CREATINE kinase , *FLAVONOLS , *ANIMAL experimentation , *MASS spectrometry , *DATA analysis software , *REGRESSION analysis , *PHARMACOKINETICS - Abstract
Guhong injection (GHI) has been applied in the therapy of cardio-cerebrovascular disease in clinic, but there is no report about the pharmacokinetic/pharmacodynamic (PK/PD) research on GHI treating myocardial ischemia/reperfusion (MI/R) injury in rats. In this study, eight compounds of GHI in plasma, including N-acetyl-L-glutamine (NAG), chlorogenic acid (CGA), hydroxysafflor yellow A (HSYA), p-coumaric acid ( pCA), rutin, hyperoside, kaempferol-3-Orutinoside, and kaempferol-3-O-glucoside, were quantified by LC-MS/MS. We discovered that the values of t1/2b, k12, V2, and CL2 were larger than those of t1/2a, k21, V1, and CL1 for all compounds. The levels of four biomarkers, creatine kinase-MB (CK-MB), cardiac troponin I (cTn I), ischemia-modified albumin (IMA), and alpha-hydroxybutyrate dehydrogenase (a-HBDH) in plasma were determined by ELISA. The elevated level of these biomarkers induced by MI/R was declined to different degrees via administrating GHI and verapamil hydrochloride (positive control). The weighted regression coefficients of NAG, HSYA, CGA, and pCA in PLSR equations generated from The Unscrambler X software (version 11) were mostly minus, suggesting these four ingredients were positively correlated to the diminution of the level of four biomarkers. Emax and ED50, two parameters in PK/PD equations that were obtained by adopting Drug and Statistics software (version 3.2.6), were almost enlarged with the rise of GHI dosage. Obviously, all analytes were dominantly distributed and eliminated in the peripheral compartment with features of rapid distribution and slow elimination. With the enhancement of GHI dosage, the ingredients only filled in the central compartment if the peripheral compartment was replete. Meanwhile, high-dose of GHI generated the optimum intrinsic activity, but the af- finity of compounds with receptors was the worst, which may be caused by the saturation of receptors. Among the eight analytes, NAG, HSYA, CGA, and pCA exhibited superior cardioprotection, which probably served as the pharmacodynamic substance basis of GHI in treating MI/R injury. [ABSTRACT FROM AUTHOR]
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- 2024
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14. Ionizable copolymer functionalized magnetic nanocomposite as an adsorbent for boosting the extraction selectivity of aristolochic acids.
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Qi-Yue Xie, Yang Chen, Chang-Jun Li, Jia-Bin Zhang, Xiu-Jun Cao, and Jun Lu
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POLYMERS , *NANOSTRUCTURES , *ADSORPTION (Chemistry) , *CHINESE medicine , *HIGH performance liquid chromatography , *PROTEINS , *CATIONS , *RESEARCH funding , *ACRYLAMIDE , *MAGNETICS , *NANOTECHNOLOGY , *SURFACE active agents , *STATIC electricity - Abstract
Aristolochic acid nephropathy (AAN) has drawn increasing public attention. Organic anion transporters (OATs) are considered to be responsible for mediating nephrotoxicity of aristolochic acids (AAs), as AAs are typical OAT1 substrates that exhibit anionic properties and contain one hydrophobic domain. Inspired by the OAT1 three-dimensional structure or substrate/protein interactions involved in transport, we designed a magnetic polymeric hybrid, mimicking the effect of basic and aromatic residues of OAT1, for efficient enriching aristolochic acid I (AA I) and aristolochic acid II (AA II) in Traditional Chinese patent medicines (TCPM). N, N-dimethylaminopropyl acrylamide (DMAPAm) was used as a cationic monomer and copolymerized with divinylbenzene (DVB) onto the surface of monodisperse magnetic nanoparticles (denoted as MNs@SiO2T-DvbDam). The magnetic polymer hybrid demonstrated high selectivity and capacity for AAs, which was mainly attributed to (1) electrostatic interactions from the cationic or basic moiety of DMAPAm and (2) the hydrophobic and p-p stacking interactions from the aromatic ring of DVB. Additionally, the surface of the hybrid exhibited amphiphilic property according to the ionization of DMAPAm, thus improving the compatibility of the adsorbent with the aqueous sample matrix. This strategy was proven to be robust in the analysis of real drug samples, which was characterized by a good linearity, high recovery and satisfactory reusability. This work confirmed that the proposed tool could be a promising candidate for enhancing the extraction selectivity of AAs in Traditional Chinese medicines (TCM). [ABSTRACT FROM AUTHOR]
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- 2024
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15. MVNMDA: A Multi-View Network Combing Semantic and Global Features for Predicting miRNA–Disease Association.
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Yang, Chen, Wang, Zhen, Zhang, Shanwen, Li, Xiaoqian, Wang, Xuqi, Liu, Jiashan, Li, Ruixiang, and Zeng, Sihao
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DEEP learning , *MEDICAL screening , *VIRTUAL networks , *MICRORNA , *FORECASTING , *THERAPEUTICS - Abstract
A growing body of experimental evidence suggests that microRNAs (miRNAs) are closely associated with specific human diseases and play critical roles in their development and progression. Therefore, identifying miRNA related to specific diseases is of great significance for disease screening and treatment. In the early stages, the identification of associations between miRNAs and diseases demanded laborious and time-consuming biological experiments that often carried a substantial risk of failure. With the exponential growth in the number of potential miRNA-disease association combinations, traditional biological experimental methods face difficulties in processing massive amounts of data. Hence, developing more efficient computational methods to predict possible miRNA-disease associations and prioritize them is particularly necessary. In recent years, numerous deep learning-based computational methods have been developed and have demonstrated excellent performance. However, most of these methods rely on external databases or tools to compute various auxiliary information. Unfortunately, these external databases or tools often cover only a limited portion of miRNAs and diseases, resulting in many miRNAs and diseases being unable to match with these computational methods. Therefore, there are certain limitations associated with the practical application of these methods. To overcome the above limitations, this study proposes a multi-view computational model called MVNMDA, which predicts potential miRNA-disease associations by integrating features of miRNA and diseases from local views, global views, and semantic views. Specifically, MVNMDA utilizes known association information to construct node initial features. Then, multiple networks are constructed based on known association to extract low-dimensional feature embedding of all nodes. Finally, a cascaded attention classifier is proposed to fuse features from coarse to fine, suppressing noise within the features and making precise predictions. To validate the effectiveness of the proposed method, extensive experiments were conducted on the HMDD v2.0 and HMDD v3.2 datasets. The experimental results demonstrate that MVNMDA achieves better performance compared to other computational methods. Additionally, the case study results further demonstrate the reliable predictive performance of MVNMDA. [ABSTRACT FROM AUTHOR]
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- 2024
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16. The application of podocyte antigen PLA2R and anti-PLA2R antibody in the diagnosis and treatment of membranous nephropathy.
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Yang Chen, Ying Xu, Siyu Chen, Yedong Yu, Xueling Zhu, and Jianghua Chen
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RECEIVER operating characteristic curves , *PHOSPHOLIPASE A2 - Abstract
Background: The application of podocyte antigen M-type phospholipase A2 receptor (PLA2R, GAg) and serum anti-PLA2R antibody (SAb) in predicting the prognosis of membrane nephropathy (MN) was controversial. Method: 328 biopsy-proven MN patients were divided into three phenotypes, 182 MN patients with GAg+/SAb+, 118 MN patients with GAg+/SAb-, and 28 MN patients with GAg-/SAb-. The baseline clinicopathological characteristics, therapy response, and prognosis were compared among the three groups. Cox regression analysis was performed to assess predictors of remission. Anti-PLA2R antibody was analyzed by receiver operating characteristic curve to find the optimal titer for MN diagnosis. Result: Lower eGFR (p = 0.009), higher UPCR (p < 0.001), and lower serum albumin (p < 0.001) were observed in GAg+/SAb+ MN patients, compared to GAg+/SAb-MN patients. More GAg+/SAb+ MN patients received cyclophosphamide (CTX) combined with glucocorticoids and calcineurin inhibitors (CNI) based therapy than the other two groups (p = 0.015 and p = 0.023, respectively). No significant difference was observed among the three groups in terms of complete remission, relapse, and developing ESRD. SAb+ status was an independent predictor for no remission (hazard ratio 1.378, 95% confidence interval 1.023 to 1.855; p = 0.035). The optimal cutoff value for anti-PLA2R antibody to predict MN was 2.055 RU/mL (sensibility 0.802, specificity 0.970). Conclusion: GAg+/SAb+ MN patients were related to more severe clinical manifestations and more requisition of immunosuppressive treatment. Positive anti-PLA2R antibody was an independent predictor for no remission. An anti-PLA2R antibody above 2.055 RU/mL can be a suggestive indicator of MN diagnosis in patients with proteinuria. [ABSTRACT FROM AUTHOR]
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- 2023
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17. Origin of carbonate minerals and impacts on reservoir quality of the Wufeng and Longmaxi Shale, Sichuan Basin.
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Yang Chen, Jian-Hua Zhao, Qin-Hong Hu, Ke-Yu Liu, Wei Wu, Chao Luo, Sheng-Hui Zhao, and Yu-Ying Zhang
- Abstract
The Ordovician-Silurian Wufeng and Longmaxi Shale in the Sichuan Basin were studied to understand the genesis and diagenetic evolution of carbonate minerals and their effects on reservoir quality. The results of geochemical and petrological analyses show that calcite grains have a negative Ce anomaly indicating they formed in the oxidizing environment of seawater. The high carbonate mineral contents in the margin of basin indicate that calcite grains and cores of dolomite grains appear largely to be of detrital origin. The rhombic rims of dolomite grains and dolomite concretions with the δ13C of –15.46‰ and the enrichment of middle rare earth elements were formed during the sulfate-driven anaerobic oxidation of methane. The calcite in radiolarian were related to the microbial sulfate reduction for the abundant anhedral pyrites and δ13C value of –11.34‰. Calcite veins precipitated in the deep burial stage with homogenization temperature of the inclusions ranging from 146.70 °C to 182.90 °C. The pores in shale are mainly organic matter pores with pore size mainly in the range of 1–20 nm in diameter. Carbonate minerals influence the development of pores through offering storage space for organic matter. When calcite contents ranging from 10% to 20%, calcite grains and cement as rigid framework can preserve primary pores. Subsequently, the thermal cracking of liquid petroleum in primary pores will form organic matter pores. The radiolarian were mostly partially filled with calcite, which combining with microcrystalline quartz preserved a high storage capacity. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
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18. Time-dependent mechanical behavior of tough hydrogels under multiaxial stretching.
- Author
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Yong Liu, Yang Chen, Mengze Lu, Chuanxia Jiang, Zhiwei Fan, and Taolin Sun
- Subjects
- *
METHACRYLIC acid , *STRAIN rate , *STRAINS & stresses (Mechanics) , *HYDROGEN as fuel , *ENERGY dissipation , *ACRYLAMIDE , *STRETCHING of materials , *COPOLYMERIZATION - Abstract
Understanding the time-dependent mechanical behavior of tough and viscoelastic hydrogels under complex external loading is crucial. In this study, we utilized tough and viscoelastic hydrogels synthesized through the copolymerization of methacrylic acid and methacrylamide as a model system to investigate their mechanical behavior under multiaxial stretching across a wide range of strain rates. Three stretching modes examined were uniaxial, pure shear, and equal biaxial stretching. Our findings show that under equal biaxial stretching, the hydrogels exhibit higher mechanical properties and energy dissipation compared to uniaxial and pure shear stretching, owing to the greater contribution of hydrogen bonds to energy dissipation in the former stretching mode. Additionally, employing the time-elongation separability method during the stretching process, we observed that the relaxation of dynamic hydrogen bonds in the hydrogels only depends on stretching time, independent of the elongation ratio and stretching modes. We anticipate that this study will yield valuable contributions to the design of durable load-bearing soft materials, particularly in dealing with complex deformation and strain rate responses. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
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19. A Novel Signature Based on Anoikis Associated with BCR-Free Survival for Prostate Cancer.
- Author
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Yang, Chen, Yu, Tian, and Lin, Qin
- Subjects
- *
ANOIKIS , *PROSTATE cancer , *NOMOGRAPHY (Mathematics) , *DISEASE risk factors , *MATRIX decomposition , *PROSTATE-specific antigen , *LUTEINIZING hormone releasing hormone - Abstract
This study aimed to elucidate the role of anoikis in the progression of prostate cancer (PCa) and to develop a prognostic signature based on anoikis-related genes (ARGs). To achieve this, PCa cases were subjected to nonnegative matrix factorization (NMF) analysis, which allowed for the identification of distinct patterns of anoikis modification. Additionally, immune infiltration was evaluated using single-sample gene-set enrichment analysis (ssGSEA). Survival analysis was performed using the Kaplan-Meier method, and a risk score was generated based on the expression levels of ARGs to quantitatively assess the modification of anoikis in PCa. Using the Least Absolute Shrinkage and Selection Operator (LASSO) method, four hub-genes were identified, and patients were classified into different risk groups based on their individual scores. Importantly, the low-risk subtype was characterized by a significantly improved biochemical recurrence-free survival, underscoring the clinical relevance of the ARG-based prognostic signature. To further improve the prognostic accuracy of the signature, patient age, pathological T stage, Gleason score, and prostate-specific antigen level were incorporated into the analysis, yielding a comprehensive prognostic signature. The clinical relevance of this signature was illustrated through a nomogram, providing a visual representation of the prognostic implications of the ARG-based signature. Taken together, these findings highlight the potential of ARGs in predicting the clinical outcomes of PCa patients and provide a novel and clinically relevant prognostic signature based on the modification of anoikis in PCa. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
20. Storyline attribution of human influence on a record-breaking spatially compounding flood-heat event.
- Author
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Jun Wang, Yang Chen, Tett, Simon F. B., Stone, Dáithí, Ji Nie, Jinming Feng, Zhongwei Yan, Panmao Zhai, and Quansheng Ge
- Subjects
- *
WEATHER forecasting , *FLOOD warning systems , *SPACETIME , *EXPERIMENTAL design , *SEASONS , *RAINFALL - Abstract
Attribution of compound events informs preparedness for emerging hazards with disproportionate impacts. However, the task remains challenging because space-time interactions among extremes and uncertain dynamic changes are not satisfactorily addressed in the well-established attribution framework. For attributing the 2020 record-breaking spatially compounding flood-heat event in China, we conduct a storyline attribution analysis by designing simulation experiments via a weather forecast model, quantifying component-based attributable changes, and comparing with historical flow analogs. We quantify that given the large-scale circulation, anthropogenic influence to date has exacerbated the extreme Mei-yu rainfall in the mid-lower reaches of the Yangtze River during June-July 2020 by ~6.5% and warmed the co-occurring seasonal extreme heat in South China by ~1°C. Our projections show a further intensification of the compound event by the end of this century, with moderate emissions making the rainfall totals ~14% larger and the season ~2.1°C warmer in South China than the 2020 status. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
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21. Cognitive Radar Waveform Design Method under the Joint Constraints of Transmit Energy and Spectrum Bandwidth.
- Author
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Yang, Chen, Yang, Wei, Qiu, Xiangfeng, Zhang, Wenpeng, Lu, Zhejun, and Jiang, Weidong
- Subjects
- *
RADAR , *BANDWIDTHS , *MIMO radar , *CLOSED loop systems , *SYSTEMS design , *FREQUENCY spectra , *COGNITIVE radio - Abstract
The water-filling (WF) algorithm is a widely used design strategy in the radar waveform design field to maximize the signal-to-interference-plus-noise ratio (SINR). To address the problem of the poor resolution performance of the waveform caused by the inability to effectively control the bandwidth, a novel waveform-related optimization model is established in this paper. Specifically, a corrected SINR expression is first derived to construct the objective function in our optimization model. Then, equivalent bandwidth and energy constraints are imposed on the waveform to formulate the waveform-related non-convex optimization model. Next, the optimal frequency spectrum is obtained using the Karush–Kuhn–Tucker condition of our non-convex model. Finally, the transmit waveform in the time domain is synthesized under the constant modulus constraint. Different experiments based on simulated and real-measured data are constructed to demonstrate the superior performance of the designed waveform on the SINR and equivalent bandwidth compared to the linear frequency modulated signal and waveform designed by the WF algorithm. In addition, to further evaluate the effectiveness of the proposed algorithm in the application of cognitive radar (CR), a closed-loop radar system design strategy is introduced based on our waveform design method. The experiments under real-measured data confirm the advantages of CR compared to the traditional open-loop radar structure. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
22. The competition dynamics of approach and avoidance motivations following interpersonal transgression.
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Bo Shen, Yang Chen, Zhewen He, Weijian Li, Hongbo Yu, and Xiaolin Zhou
- Subjects
- *
MICE (Computers) , *VICTIM compensation , *MOTIVATION (Psychology) , *MULTIPLE criteria decision making , *SOCIAL interaction - Abstract
Two behavioral motivations coexist in transgressors following an interpersonal transgression--approaching and compensating the victim and avoiding the victim. Little is known about how these motivations arise, compete, and drive transgressors' decisions. The present study adopted a social interaction task to manipulate participants' (i.e., the transgressor) responsibility for another's (i.e., the victim) monetary loss and measure the participants' tradeoff between compensating the victim and avoiding face-to-face interactions with the victim. Following each transgression, participants used a computer mouse to choose between two options differing in the amount of compensation to the victim and the probability of face-to-face contact with the victim. Results showed that as participants' responsibility increased, 1) the decision weights on contact avoidance relative to compensation increased, and 2) the onset of the contact-avoidance attribute was expedited and that of the compensation attribute was delayed. These results demonstrate how competing social motivations following transgression evolve and determine social decision-making and shed light on how social-affective state modulates the dynamics of decision-making in general. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
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23. Sign-changing solutions for the Schrödinger-Poisson system with concave-convex nonlinearities in $ \mathbb{R}^{3} $.
- Author
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Yang, Chen and Tang, Chun-Lei
- Abstract
In this paper, we consider the following Schrödinger-Poisson system { − Δ u + V (x) u + ϕ u = | u | p − 2 u + λ K (x) | u | q − 2 u i n R 3 , − Δ ϕ = u 2 i n R 3. Under the weakly coercive assumption on V and an appropriate condition on K , we investigate the cases when the nonlinearities are of concave-convex type, that is, 1 < q < 2 and 4 < p < 6 . By constructing a nonempty closed subset of the sign-changing Nehari manifold, we establish the existence of least energy sign-changing solutions provided that λ ∈ (− ∞ , λ ∗) , where λ ∗ > 0 is a constant. In this paper, we consider the following Schrödinger-Poisson system Under the weakly coercive assumption on and an appropriate condition on , we investigate the cases when the nonlinearities are of concave-convex type, that is, and . By constructing a nonempty closed subset of the sign-changing Nehari manifold, we establish the existence of least energy sign-changing solutions provided that , where is a constant. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
24. An advanced buyback contract and information asymmetry.
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Alwan, Layth C., Yang, Chen, and Fang, Weiguo
- Subjects
- *
INFORMATION asymmetry , *WHOLESALE prices , *CONTRACTS , *SUPPLY chains , *AGGRESSION (Psychology) - Abstract
This paper proposes a novel advanced buyback (ABB) contract to coordinate a supply chain that consists of one supplier and one retailer. The contract stipulates when a buyback contract is executed and the amount of buyback. We model the interaction of supply chain participants as a Stackelberg game and incorporate the participants' reservation profits into the game to examine the effectiveness of the ABB contract with complete information. We demonstrate that the ABB contract can conveniently coordinate the supply chain, flexibly allocate profit, and facilitate avoidance of the aggressive overordering behavior of the retailer. This model is extended to the situation of information asymmetry, where the retailer holds private information about the cost of sales in discrete or continuous states. The optimal strategies of the supply chain and the participants are derived. Information asymmetry can damage the supplier but be beneficial to the retailer. The condition under which the supply chain achieves coordination is clarified. A numerical simulation is performed to verify and extend the results of the theoretical analysis. We show that the ABB contract always outperforms the ordinary wholesale price and buyback contracts with complete information. Supply chain coordination is more likely to be achieved if the demand variability is lower when weighing whether to share private information. Our findings can explain why retailers always have an incentive to inflate their cost of sales. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
25. Thermodynamics Analysis of a Novel Compressed Air Energy Storage System Combined with Solid Oxide Fuel Cell–Micro Gas Turbine and Using Low-Grade Waste Heat as Heat Source.
- Author
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Yang, Chen, Sun, Li, and Chen, Hao
- Subjects
- *
COMPRESSED air energy storage , *SOLID oxide fuel cells , *WASTE heat , *GAS turbines , *ENERGY storage , *THERMODYNAMICS , *GAS as fuel , *HYBRID systems - Abstract
As the next generation of advanced adiabatic compressed air energy storage systems is being developed, designing a novel integrated system is essential for its successful adaptation in the various grid load demands. This study proposes a novel design framework for a hybrid energy system comprising a CAES system, gas turbine, and high-temperature solid oxide fuel cells, aiming for power generation and energy storage solutions. The overall model of the hybrid power generation system was constructed in Aspen PlusTM, and the mass balance, energy balance, and thermodynamic properties of the thermal system were simulated and analyzed. The results demonstrate that the hybrid system utilizes the functional complementarity of CAES and solid oxide fuel cells (SOFCs), resulting in the cascade utilization of energy, a flexible operation mode, and increased efficiency. The overall round-trip efficiency of the system is 63%, and the overall exergy efficiency is 67%, with a design net power output of 12.5 MW. Additionally, thermodynamic analysis shows that it is advisable to operate the system under lower ambient temperatures of 25 °C, higher compressor and turbine isentropic efficiencies of 0.9, a higher fuel utilization of 0.62, and optimal SOFC/MGT split air flow rates of 1.1 kg/s. The results of this article provide guidance for designing innovative hybrid systems and system optimization. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
26. Experimental Study on Flame Response Characteristics of a Non-Premixed Swirl Model Combustor.
- Author
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Yang, Chen, Liu, Yong, Zhang, Xiang, Li, Hao, Ge, Xinkun, Jin, Feng, and Liu, Chongyang
- Subjects
- *
FLAME , *HEAT release rates , *COMBUSTION chambers , *SOUND pressure , *TRANSFER functions , *GAS turbines , *COMBUSTION - Abstract
Non-premixed swirl combustion has been widely used in pieces of industrial combustion equipment such as industrial boilers, furnaces, and certain specific gas turbine combustors. In recent years, the combustion instability of non-premixed swirl flames has begun receiving attention, yet there is still a lack of related research in academia. Therefore, in this study, we conducted experimental research on a swirl stabilized gas flame model combustor and studied the heat release response characteristics of the swirl combustor through the flame transfer function. Firstly, the flame transfer function (FTF) was measured under different inlet velocities and equivalence ratios, and the experimental results showed that the FTF gain curve of the non-premixed swirl flame exhibited a significant "bimodal" shape, with the gain peaks located around 230 Hz and 330 Hz, respectively. Secondly, two oscillation modes of the flame near the two gain peaks were identified (the acoustic induced vortex mode Mv and the thermoacoustic oscillation mode Ma), which have not been reported in previous studies on swirl non-premixed flames. In addition, we comprehensively analyzed the flame pulsation characteristics under the two oscillation modes. Finally, the coupling degrees between velocity fluctuations, fuel pressure fluctuations, and heat release fluctuations were analyzed using the Rayleigh Index (RI), and it was found that in the acoustic-induced vortex mode, a complete feedback loop was not formed between the combustor and the fuel pipeline, which was the main reason for the significant difference in the pressure fluctuation amplitude near 230 Hz and 330 Hz. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
27. Advanced Techniques Using In Vivo Electroporation to Study the Molecular Mechanisms of Cerebral Development Disorders.
- Author
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Yang, Chen, Shitamukai, Atsunori, Yang, Shucai, and Kawaguchi, Ayano
- Subjects
- *
ELECTROPORATION , *ANIMAL disease models , *GENETIC regulation , *GENOME editing , *NUCLEIC acids - Abstract
The mammalian cerebral cortex undergoes a strictly regulated developmental process. Detailed in situ visualizations, imaging of these dynamic processes, and in vivo functional gene studies significantly enhance our understanding of brain development and related disorders. This review introduces basic techniques and recent advancements in in vivo electroporation for investigating the molecular mechanisms underlying cerebral diseases. In utero electroporation (IUE) is extensively used to visualize and modify these processes, including the forced expression of pathological mutants in human diseases; thus, this method can be used to establish animal disease models. The advent of advanced techniques, such as genome editing, including de novo knockout, knock-in, epigenetic editing, and spatiotemporal gene regulation, has further expanded our list of investigative tools. These tools include the iON expression switch for the precise control of timing and copy numbers of exogenous genes and TEMPO for investigating the temporal effects of genes. We also introduce the iGONAD method, an improved genome editing via oviductal nucleic acid delivery approach, as a novel genome-editing technique that has accelerated brain development exploration. These advanced in vivo electroporation methods are expected to provide valuable insights into pathological conditions associated with human brain disorders. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
28. Precise Detection, Control and Synthesis of Chiral Compounds at Single-Molecule Resolution.
- Author
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Yang, Chen, Hu, Weilin, and Guo, Xuefeng
- Subjects
- *
SYMMETRY breaking , *MOLECULAR orientation , *CHIRALITY , *SPIN polarization , *CHEMISTS - Abstract
Highlights: Single-molecule electrical detection, especially the single-molecule junction setup, enables the precise detection and spatial operability of anchored molecules. The transition among asymmetric characteristics (i.e., molecular chirality, photonic polarization and electronic spin) is proposed as a universal methodology to realize the detection, control and synthesis of chirality. Exploring the origin of symmetry breaking contributes to the development of a general reliable strategy for asymmetric synthesis. Chirality, as the symmetric breaking of molecules, plays an essential role in physical, chemical and especially biological processes, which highlights the accurate distinction among heterochiralities as well as the precise preparation for homochirality. To this end, the well-designed structure-specific recognizer and catalysis reactor are necessitated, respectively. However, each kind of target molecules requires a custom-made chiral partner and the dynamic disorder of spatial-orientation distribution of molecules at the ensemble level leads to an inefficient protocol. In this perspective article, we developed a universal strategy capable of realizing the chirality detection and control by the external symmetry breaking based on the alignment of the molecular frame to external stimuli. Specifically, in combination with the discussion about the relationship among the chirality (molecule), spin (electron) and polarization (photon), i.e., the three natural symmetry breaking, single-molecule junctions were proposed to achieve a single-molecule/event-resolved detection and synthesis. The fixation of the molecular orientation and the CMOS-compatibility provide an efficient interface to achieve the external input of symmetry breaking. This perspective is believed to offer more efficient applications in accurate chirality detection and precise asymmetric synthesis via the close collaboration of chemists, physicists, materials scientists, and engineers. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
29. ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization.
- Author
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Yang, Chen, Mai, Jiahao, Cao, Xuan, Burberry, Aaron, Cominelli, Fabio, and Zhang, Liangliang
- Subjects
- *
FUNCTIONAL analysis , *DATA visualization , *GUT microbiome , *HUMAN microbiota , *BIOMES , *MICROBIAL communities , *MICROBIAL diversity - Abstract
Summary Microbiome research is now moving beyond the compositional analysis of microbial taxa in a sample. Increasing evidence from large human microbiome studies suggests that functional consequences of changes in the intestinal microbiome may provide more power for studying their impact on inflammation and immune responses. Although 16S rRNA analysis is one of the most popular and a cost-effective method to profile the microbial compositions, marker-gene sequencing cannot provide direct information about the functional genes that are present in the genomes of community members. Bioinformatic tools have been developed to predict microbiome function with 16S rRNA gene data. Among them, PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) has become one of the most popular functional profile prediction tools, which generates community-wide pathway abundances. However, no state-of-art inference tools are available to test the differences in pathway abundances between comparison groups. We have developed ggpicrust2, an R package, for analyzing functional profiles derived from 16S rRNA sequencing. This powerful tool enables researchers to conduct extensive differential abundance analyses and generate visually appealing visualizations that effectively highlight functional signals. With ggpicrust2, users can obtain publishable results and gain deeper insights into the functional composition of their microbial communities. Availability and implementation The package is open-source under the MIT and file license and is available at CRAN and https://github.com/cafferychen777/ggpicrust2. Its shiny web is available at https://a95dps-caffery-chen.shinyapps.io/ggpicrust2_shiny/. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
30. Fluctuotaxis: Nanoscale directional motion away from regions of fluctuation.
- Author
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Yang Chen, Fangyan Zhu, Jiantao Leng, Tianquan Ying, Jin-Wu Jiang, Quan Zhou, Tienchong Chang, Wanlin Guo, and Huajian Gao
- Subjects
- *
MOLECULAR dynamics , *NANOMOTORS - Abstract
Regulating the motion of nanoscale objects on a solid surface is vital for a broad range of technologies such as nanotechnology, biotechnology, and mechanotechnology. In spite of impressive advances achieved in the field, there is still a lack of a robust mechanism which can operate under a wide range of situations and in a controllable manner. Here, we report a mechanism capable of controllably driving directed motion of any nanoobjects (e.g., nanoparticles, biomolecules, etc.) in both solid and liquid forms. We show via molecular dynamics simulations that a nanoobject would move preferentially away from the fluctuating region of an underlying substrate, a phenomenon termed fluctuotaxis--for which the driving force originates from the difference in atomic fluctuations of the substrate behind and ahead of the object. In particular, we find that the driving force can depend quadratically on both the amplitude and frequency of the substrate and can thus be tuned flexibly. The proposed driving mechanism provides a robust and controllable way for nanoscale mass delivery and has potential in various applications including nanomotors, molecular machines, etc. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
31. Spatio-temporal variation of annual precipitation in China and its response to ENSO.
- Author
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Yang Chen, Long Ma, Tingxi Liu, Xing Huang, and Guohua Sun
- Subjects
- *
SPATIO-temporal variation , *TWENTY-first century ,EL Nino ,LA Nina - Abstract
The results showed that the precipitation in the study area was mainly in a downward trend before the mid-1930s, and then turned upward. In the 1950s, the precipitation generally showed a distribution of rising in the west and falling in the east, and this trend continued until the early 21st century. By 2007, except for the central part of the Continental Basin, the overall trend was mainly upward. In this study, 65 El Niño Southern Oscillation (ENSO) events were identified, including 24 El Niño events and 41 La Niña events. The precipitation was generally less when ENSO occurred. However, there were differences in the type and intensity of the event. For example, El Niño had a greater impact on precipitation than La Niña did, and extremely strong or strong El Niño/La Niña events had a more significant impact than moderate, weak, or extremely weak ones. The correlation between precipitation and El Niño or La Niña events had some similarities and differences. For example, precipitation was mainly negatively correlated with El Niño and La Niña at the same time, and both correlations were proportional to intensity, but the correlation between precipitation and El Niño was significantly stronger than that of La Niña. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
32. Proliferative capacity in relation to metamifop resistance in Echinochloa glabrescens: A case study.
- Author
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Yang Chen, Chang Liu, Feng Zhu, Tongjun Gao, and Guoqi Chen
- Subjects
- *
ECHINOCHLOA , *RICE , *BIOMASS production , *WEEDS , *SEED industry , *SEED treatment , *SEEDLINGS - Abstract
Knowing the proliferative capacity of herbicide-resistant weeds is the basis for the integrated management. We collected seeds of two Echinochloa glabrescens Munro ex Hook. f. populations (TS and WH) from rice (Oryza sativa L.) fields in eastern China (F0 populations), and those from individuals surviving the initial metamifop treatment (F1 lines) were tested for their responses to metamifop, and common garden experiments were conducted to compare their productivities. We found that TS was highly resistant to metamifop, and WH was susceptible. After treated with metamifop at the label dose (120 g ai ha-1), averagely 56% and 16% of TS and WH F1 lines contained surviving seedlings, and averagely 24% and 1% F1 seedlings survived among total seedlings of the same population, respectively. After treated with metamifop at a dose of 0, 60, 120 or 240 g ai ha-1, surviving F0 plants escaped from higher doses reproduced higher proportions of metamifop-resistant F1 progenies in both populations. At 120 d after sowing (DAS), TS individuals surviving 2 x label dose of metamifop showed nonsignificant difference in plant heights, biomass and seed production, compared with relative control treatment; while WH plants surviving the label dose of metamifop decreased seed production by 25%-39%. One WH and TS plant individual surviving metamifop treatment at the label dose may generate 10-21 and 490-701 progenies resistant to the label dose of metamifop, respectively. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
33. Phylogeny and Biogeography of Morus (Moraceae).
- Author
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Yang, Chen-Xuan, Liu, Shui-Yin, Zerega, Nyree J. C., Stull, Gregory W., Gardner, Elliot M., Tian, Qin, Gu, Wei, Lu, Qing, Folk, Ryan A., Kates, Heather R., Guralnick, Robert P., Soltis, Douglas E., Soltis, Pamela S., Wang, Yue-Hua, and Yi, Ting-Shuang
- Subjects
- *
BIOGEOGRAPHY , *PHYLOGENY , *MORACEAE , *EOCENE-Oligocene boundary , *TIME perception , *MASS extinctions , *PHYLOGEOGRAPHY - Abstract
The mulberry genus, Morus L. (Moraceae), has long been taxonomically difficult, and its species circumscription has only been defined recently. This genus comprises ca. 16 species distributed across Asia and the Americas, yet its biogeographic history remains poorly understood. In this study, we reconstructed the phylogeny and explored the biogeographic history of Morus using a combination of newly generated and previously published Hyb-Seq data. Our nuclear phylogeny recovered three well-supported geographic clades of Morus and showed that M. notabilis (China) is sister to the American clade plus the Asian clade. Multiple reticulation events among species of Morus and extensive incomplete lineage sorting (ILS) likely explain the difficulties in inferring phylogenetic relationships within the genus. Divergence time estimation indicated that Morus originated at the Eocene–Oligocene boundary, and current lineages started to diverge during the early Miocene, there is ambiguity surrounding the ancestral area with the two most likely regions being Sino-Himalaya or the Americas. Biogeographic inference and the fossil record suggest that Morus might have experienced extensive local extinction events during the Tertiary. Morus has expanded its distributional range through two dispersals from the Sino-Himalayan and Sino-Japanese regions to Southeast Asia. In summary, our new phylogenetic scheme and the biogeographic history presented here provide an essential foundation for understanding species relationships and the evolutionary history of Morus. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
34. Fads2b Plays a Dominant Role in ∆6/∆5 Desaturation Activities Compared with Fads2a in Common Carp (Cyprinus carpio).
- Author
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Zhao, Ran, Yang, Chen-Ru, Wang, Ya-Xin, Xu, Zi-Ming, Li, Shang-Qi, Li, Jin-Cheng, Sun, Xiao-Qing, Wang, Hong-Wei, Wang, Qi, Zhang, Yan, and Li, Jiong-Tang
- Subjects
- *
CARP , *OMEGA-3 fatty acids , *FATTY acid desaturase , *UNSATURATED fatty acids , *OMEGA-6 fatty acids , *BINDING sites - Abstract
Highly unsaturated fatty acids (HUFAs) are essential for mammalian health, development and growth. However, most mammals, including humans, are incapable of synthesizing n-6 and n-3 HUFAs. Fish can convert C18 unsaturated fatty acids into n-6 and n-3 HUFAs via fatty acid desaturase (Fads), in which Fads2 is a key enzyme in HUFA biosynthesis. The allo-tetraploid common carp theoretically encode two duplicated fads2 genes. The expression patterns and desaturase functions of these two homologous genes are still unknown. In this study, the full length of the fads2a and fads2b were identified in common carp (Cyprinus carpio). Expression analyses indicate that both genes were mainly expressed in the liver and the expression of fads2b is higher than fads2a at different developmental stages in carp embryos. Heterogenous expression and 3D docking analyses suggested that Fads2b demonstrated stronger ∆6 and ∆5 desaturase activities than Fads2a. The core promotor regions of fads2a and fads2b were characterized and found to have different potential transcriptional binding sites. These results revealed the same desaturase functions, but different activities of two homologues of fasd2 genes in common carp. The data showed that fads2b played a more important role in HUFA synthesis through both expression and functional analyses. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
35. Design of Flexible FeCoSiB/ZnO Thin-Film Multiferroic Module for Low-Frequency Energy Harvesting.
- Author
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Guo, Yan, Yang, Chen, and Huang, Bin
- Subjects
- *
ENERGY harvesting , *MULTIFERROIC materials , *POWER resources , *ZINC oxide , *POLYETHYLENE terephthalate , *ZINC oxide films , *POLYIMIDES - Abstract
Multiphase magnetoelectric (ME) composites deposited on flexible substrates have been widely studied, which can respond to ambient mechanical, magnetic, and electric field excitations. This paper reports an investigation of flexible FeCoSiB/ZnO thin-film generators for low-frequency energy harvesting based on three substrates. Both hard substrate Si and flexible substrates (Polyethylene terephthalate (PET) and Polyimide (PI)) are adopted to make a comparison of energy conversion efficiency. For the single ME laminate, a PET-based flexible ME generator presents the best ME coupling performance with an average coupling voltage output of ~0.643 mV and power output of ~41.3 nW under the alternating magnetic field of 40 Oe and 20 Hz. The corresponding ME coupling coefficient reaches the value of 321.5 mV/(cm·Oe) for this micrometer scale harvester. Flexible ME modules with double cantilevered ME generators are further designed and fabricated. When two PET-based generators are connected in series, the average voltage output and power are ~0.067 mV and ~0.447 nW, respectively. Although the energy harvested by ME thin-film generators is much smaller than bulk multiferroic materials, it proves the feasibility of using flexible FeCoSiB/ZnO generators for harvesting ambient magnetic energy and supplying sustainable electronic devices in the future. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
36. Ontogenetic color change in the tail of blue‐tailed skinks (Plestodion elegans).
- Author
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Yang, Chen, Chen, Siheng, and Wang, Jie
- Subjects
- *
COLOR space , *SKINKS , *ANIMAL life cycles , *COLORIMETRY , *ANIMAL coloration - Abstract
Ontogenetic color change in animals is an interesting evolution‐related phenomenon that has been studied by evolutionary biologists for decades. However, obtaining quantitative and continuous color measurements throughout the life cycle of animals is a challenge. To understand the rhythm of change in tail color and sexual dichromatism, we used a spectrometer to measure the tail color of blue‐tailed skink (Plestiodon elegans) from birth to sexual maturity. Lab color space was selected due to its simplicity, fastness, and accuracy and depends on the visual sense of the observer for measuring the tail color of skinks. A strong relationship was observed between color indexes (values of L*, a*, b*) and growth time of skink. The luminance of tail color decreased from juveniles to adults in both sexes. Moreover, we observed differences in color rhythms between the sexes, which may be influenced by different behavioral strategies used by them. This study provides continuous measurements of change in tail color in skinks from juveniles to adults and offers insights into their sex‐based differences. While this study does not provide direct evidence to explain the potential factors that drive dichromatism between the sexes of lizards, our finding could serve as a reference for future studies exploring possible mechanisms of ontogenetic color change in reptiles. [ABSTRACT FROM AUTHOR]
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- 2023
- Full Text
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37. Synthesis and Properties of the Novel High-Performance Hydroxyl-Terminated Liquid Fluoroelastomer.
- Author
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Li, Donghan, Yang, Chen, Li, Ping, Yu, Lu, Zhao, Shufa, Li, Long, Kang, Hailan, Yang, Feng, and Fang, Qinghong
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ALUMINUM hydride , *CHEMICAL stability , *MOLAR mass , *DIFLUOROETHYLENE , *FLUOROPOLYMERS , *DOUBLE bonds , *THERMOPLASTIC elastomers - Abstract
Functional liquid fluoroelastomers are in high demand in new energy fields. And these materials have potential applications in high-performance sealing materials and as electrode materials. In this study, a novel high-performance hydroxyl-terminated liquid fluoroelastomer (t-HTLF) with a high fluorine content, temperature resistance, and curing efficiency was synthesised from a terpolymer of vinylidene fluoride (VDF), tetrafluoroethylene (TFE), and hexafluoropylene (HFP). A carboxyl-terminated liquid fluoroelastomer (t-CTLF) with controllable molar mass and end-group content was first prepared from a poly(VDF-ter-TFE-ter-HFP) terpolymer using a unique oxidative degradation method. Subsequently, an efficient "one-step" reduction of the carboxyl groups (COOH) in t-CTLF into hydroxyl groups (OH) was achieved via the functional-group conversion method using lithium aluminium hydride (LiAlH4) as the reductant. Thus, t-HTLF with a controllable molar mass and end-group content and highly active end groups was synthesised. Owing to the efficient curing reaction between OH and isocyanate groups (NCO), the cured t-HTLF exhibits good surface properties, thermal properties, and chemical stability. The thermal decomposition temperature (Td) of the cured t-HTLF reaches 334 °C, and it exhibits hydrophobicity. The oxidative degradation, reduction, and curing reaction mechanisms were also determined. The effects of solvent dosage, reaction temperature, reaction time, and ratio of the reductant to the COOH content on the carboxyl conversion were also systematically investigated. An efficient reduction system comprising LiAlH4 can not only achieve an efficient conversion of the COOH groups in t-CTLF to OH groups but also the in situ hydrogenation and addition reactions of residual double bonds (C=C) groups in the chain, such that the thermal stability and terminal activity of the product are improved while maintaining a high fluorine content. [ABSTRACT FROM AUTHOR]
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- 2023
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38. TRIM21 ameliorates hepatic glucose and lipid metabolic disorders in type 2 diabetes mellitus by ubiquitination of PEPCK1 and FASN.
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Zhang, Kaini, Yang, Chen, Zhou, Xin, Liang, Jin, Guo, Jianjin, Li, Min, Zhang, Yi, Shao, Shulin, Sun, Peng, Li, Kai, Huang, Jingjing, Chen, Fang, Liang, Xiubin, and Su, Dongming
- Abstract
Hepatic glucose and lipid metabolism disorders promote the development and progression of type 2 diabetes mellitus (T2DM), yet the underlying mechanisms are not fully understood. Here, we identify tripartite motif-containing protein 21 (TRIM21), a class IV TRIM family member, as a pivotal regulator of hepatic metabolism in T2DM for the first time. Bioinformatic analysis suggests that TRIM21 expression is significantly reduced in T2DM patients. Intriguingly, in a mouse model of obese diabetes, TRIM21 expression is predominantly reduced in the liver rather than in other metabolic organs. It is further demonstrated that hepatic overexpression of TRIM21 significantly ameliorates glucose intolerance, insulin resistance, hepatic steatosis, and dyslipidemia in obese diabetic mice. In contrast, the knockdown of TRIM21 promotes glucose intolerance, insulin resistance, and triglyceride accumulation. Mechanistically, both phosphoenolpyruvate carboxykinase 1 (PEPCK1) and fatty acid synthase (FASN) are the hepatic targets of TRIM21. We revealed that TRIM21 promotes the degradation of PEPCK1 and FASN through a direct protein–protein interaction mediated K48-linked ubiquitination. Notably, overexpression of PEPCK1 and FASN essentially abolished the beneficial effects achieved by TRIM21 overexpression in obese diabetic mice. Overall, our data demonstrate that TRIM21 is a novel regulator of hepatic metabolic disorder, and suggest TRIM21 as a promising therapeutic target for T2DM. [ABSTRACT FROM AUTHOR]
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- 2023
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39. Multi-decadal trends and variability in burned area from the 5th version of the Global Fire Emissions Database (GFED5).
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Yang Chen, Hall, Joanne, van Wees, Dave, Andela, Niels, Hantson, Stijn, Giglio, Louis, van der Werf, Guido R., Morton, Douglas C., and Randerson, James T.
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CARBON cycle , *MODIS (Spectroradiometer) , *FIRE management , *DATABASES , *WILDFIRE prevention - Abstract
Long-term records of burned area are needed to understand wildfire dynamics, assess fire impacts on ecosystems and air quality, and improve fire forecasts. Here we fuse multiple streams of remote sensing data to create a 24-year (1997–2020) dataset of monthly burned area as a component of the 5th version of the Global Fire Emissions Database (GFED5). During 2001–2020, we use the Moderate Resolution Imaging Spectroradiometer (MODIS) MCD64A1 burned area product and correct for the errors of commission and omission. Adjustment factors are estimated based on region, land cover, and tree cover fraction, using spatiotemporally aligned burned area from Landsat or Sentinel-2. Burned area in cropland, peatland, and deforestation regions is estimated from MODIS active fire detections. Along Track Scanning Radiometer (ATSR) and Visible and Infrared Scanner (VIRS) active fire data are used to extend the time series back to 1997. Global annual burned area is estimated to be 774 ± 63 Mha yr−1 during 2001–2020 or 5.9 ± 0.5 % of ice-free land. Burned area declined by 1.21 ± 0.66 % yr−1, a cumulative decrease of 24.2 ± 13.2 % over 20 years. The global reduction is primarily driven by decreases in fire within savannas, grasslands, and croplands. Forest, peat, and deforestation fires did not exhibit long-term trends. GFED5 global burned area is 93 % higher than MCD64A1, 61 % higher than GFED4s, and in closer agreement with burned area products from higher-resolution satellite sensors. These data may reduce discrepancies between fire emission estimates from top-down and bottom-up approaches, and improve understanding of global fire impacts on the carbon cycle and climate system. [ABSTRACT FROM AUTHOR]
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- 2023
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40. A New Experimental Method for the Nonlinear Modal Parameter Identification of a Pressurized Water Reactor Fuel Assembly.
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Yang, Chen, Guo, Yan, Hu, Xiao, and Zhang, Yanhong
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PRESSURIZED water reactors , *NUCLEAR fuels , *PARAMETER identification , *FREE vibration , *STATIC friction , *DYNAMIC models - Abstract
Establishing a dynamic model that accurately describes a realistic pressurized water reactor (PWR) fuel assembly is crucial to precisely evaluate the mechanical properties of the fuel assembly in seismic or loss of coolant accidents (LOCAs). The pluck test combined with the logarithmic decrement method has been widely applied in previous studies to extract fundamental modal parameters to calibrate dynamic models. However, most previous investigations focused on the first cycle of free vibration, which is strongly affected by stiction, baseline shift, drop conditions, and high-order mode interference, leading to inaccurate results. Moreover, these traditional methods cannot be used to extract high-order modal parameters. In this work, a novel experimental method for identifying the nonlinear modal parameters of a PWR fuel assembly is proposed. First, two algorithms are adopted to decompose the free vibration. Second, the local linearized modal parameters are extracted by a single-degree-of-freedom fitting method with a sliding window. Finally, these local linearized modal parameters are summed to obtain the nonlinear relationships between the modal parameters and amplitude. The new method makes more effective use of experimental data, obtains more accurate modal parameters than the logarithmic decrement method, and is capable of extracting high-order modal parameters. In the end, the test results are fitted by a fractional polynomial, which is of great value for numerical simulations. [ABSTRACT FROM AUTHOR]
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- 2023
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41. Implications of CRNDE in prognosis, tumor immunity, and therapeutic sensitivity in low grade glioma patients.
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Yang, Chen, Jiang, Yingchuan, Hu, Fan, Li, Qiuping, and Qi, Biao
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GLIOMAS , *IMMUNE checkpoint proteins , *PROGNOSIS , *IMMUNITY , *COLON tumors , *BRAIN tumors - Abstract
Background: Colorectal tumor differentially expressed (CRNDE) is specifically expressed in human brains and is the most highly expressed lncRNA in gliomas. Nevertheless, its implications in low grade glioma (LGG) are still indistinct. This study presented systematic analyses of CRNDE in LGG biology. Methods: We retrospectively retrieved TCGA, CGGC and GSE16011 LGG cohorts. Survival analysis was conducted for evaluating the prognostic significance of CRNDE in LGG. A CRNDE-based nomogram was established, and its predictive performance was verified. Signaling pathways underlying CRNDE were analyzed through ssGSEA and GSEA approaches. The abundance of immune cells and activity of cancer-immunity cycle were estimated with ssGSEA approach. Immune checkpoints, HLAs, chemokines, and immunotherapeutic response indicators (TIDE, and TMB) was quantified. U251 and SW1088 cells were transfected with specific shRNAs of CRNDE, and flow cytometry (apoptosis) and western blot (β-catenin and Wnt5a) assays were conducted. Results: Up-regulated CRNDE was found in LGG, and was linked to unfavorable clinical outcomes. The CRNDE-based nomogram enabled to accurately predict patients' prognosis. High CRNDE expression was linked to more genomic variations, activity of tumorigenic pathways, tumor immunity (increase in infiltration of immune cells, expression of immune checkpoints, HLAs and chemokines, and cancer-immunity cycle), and therapeutic sensitivity. CRNDE knockdown mitigated malignant phenotypes of LGG cells. Conclusions: Our study determined CRNDE as a novel predictor for patient prognosis, tumor immunity and therapeutic response in LGG. Assessment of CRNDE expression is a promising approach for predicting the therapeutic benefits of LGG patients. [ABSTRACT FROM AUTHOR]
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- 2023
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42. EPRS1 correlates with malignant progression in hepatocellular carcinoma.
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Yang, Chen, Yang, Xiaofeng, Liu, Chenghao, Hou, Jun, Chen, Xueling, Wang, Lianghai, and Wu, Xiangwei
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DISEASE progression , *TRANSFER RNA , *CARCINOGENESIS , *IMMUNOHISTOCHEMISTRY , *GENE expression , *PROTEOMICS , *ENZYMES , *RESEARCH funding , *CELL lines , *BIOLOGICAL assay , *HEPATOCELLULAR carcinoma - Abstract
Background: Glutamyl-prolyl-tRNA synthetase 1 (EPRS1) is an aminoacyl-tRNA synthase involved in the pathology of cancer and other diseases. In this study, we investigated the carcinogenic function, potential mechanism, and clinical significance of EPRS1 in human hepatocellular carcinoma (HCC). Methods: The expression, clinical significance, and prognostic value of EPRS1 in HCC were assessed using the TCGA and GEO databases. The function of EPRS1 in HCC cells was detected by CCK-8, Transwell, and hepatosphere formation assays. Immunohistochemistry was used to explore the difference in EPRS1 levels in HCC tissues and peri-cancerous tissues. The mechanism of EPRS1 was studied using a proteomics method. Finally, cBioportal and MEXEPRSS were used to analyze the variations involved in the differential expression of EPRS1. Results: EPRS1 was frequently upregulated at the mRNA and protein levels in liver cancer. Increased EPRS1 correlated with shortened patient survival. EPRS1 could promote cancer cell proliferation, characteristics of cell stemness, and mobility. Mechanistically, EPRS1 played a carcinogenic role by upregulating several downstream proline-rich proteins, primarily LAMC1 and CCNB1. In addition, copy number variation could contribute to the high expression of EPRS1 in liver cancer. Conclusion: Together, our data imply that enhanced EPRS1 contributes to the development of HCC by increasing the expression of oncogenes in the tumor microenvironment. EPRS1 may be a successful treatment target. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
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43. Microbial dysbiosis and the host airway epithelial response: insights into HIV-associated COPD using multi'omics profiling.
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Jude, Marcia Smiti, Yang, Chen Xi, Filho, Fernando Studart Leitao, Hernandez Cordero, Ana I., Yang, Julia, Shaipanich, Tawimas, Li, Xuan, Lin, David, MacIsaac, Julie, Kobor, Michael S., Sinha, Sunita, Nislow, Corey, Singh, Amrit, Lam, Wan, Lam, Stephen, Guillemi, Silvia, Harris, Marianne, Montaner, Julio, Ng, Raymond T., and Carlsten, Christopher
- Subjects
- *
CHRONIC obstructive pulmonary disease , *SMOKING , *DYSBIOSIS - Abstract
Background: People living with HIV (PLWH) are at increased risk of developing Chronic Obstructive Pulmonary Disease (COPD) independent of cigarette smoking. We hypothesized that dysbiosis in PLWH is associated with epigenetic and transcriptomic disruptions in the airway epithelium. Methods: Airway epithelial brushings were collected from 18 COPD + HIV + , 16 COPD − HIV + , 22 COPD + HIV − and 20 COPD – HIV − subjects. The microbiome, methylome, and transcriptome were profiled using 16S sequencing, Illumina Infinium Methylation EPIC chip, and RNA sequencing, respectively. Multi 'omic integration was performed using Data Integration Analysis for Biomarker discovery using Latent cOmponents. A correlation > 0.7 was used to identify key interactions between the 'omes. Results: The COPD + HIV −, COPD −HIV + , and COPD + HIV + groups had reduced Shannon Diversity (p = 0.004, p = 0.023, and p = 5.5e−06, respectively) compared to individuals with neither COPD nor HIV, with the COPD + HIV + group demonstrating the most reduced diversity. Microbial communities were significantly different between the four groups (p = 0.001). Multi 'omic integration identified correlations between Bacteroidetes Prevotella, genes FUZ, FASTKD3, and ACVR1B, and epigenetic features CpG-FUZ and CpG-PHLDB3. Conclusion: PLWH with COPD manifest decreased diversity and altered microbial communities in their airway epithelial microbiome. The reduction in Prevotella in this group was linked with epigenetic and transcriptomic disruptions in host genes including FUZ, FASTKD3, and ACVR1B. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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- View/download PDF
44. Quantitative Analysis of Deformity in Digital Model of Congenital Radioulnar Synostosis.
- Author
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Yang, Chen, Liu, Lu, Wei, Qipei, Bai, Fan, and Chen, Shanlin
- Subjects
- *
JOINTS (Anatomy) , *PEARSON correlation (Statistics) , *QUANTITATIVE research , *CLUBFOOT , *HUMAN abnormalities , *REGRESSION analysis - Abstract
Objective: The deformity of congenital radioulnar synostosis is quite complicated and difficult. This study aims to find out the related factors of the "forearm rotation angle" (FR) which relate to the severity of congenital radioulnar synostosis (CRUS), and try to quantify the internal relations of each deformity and help to understand the reconstruction method in surgery treatment of this disease. Methods: This study is case series research. We established 48 digital three‐dimensional forearm bone models of 48 patients with congenital radioulnar synostosis classified as Cleary and Omer type 3. All the patients were treated at our institution from January 2010 to June 2016. In total, 10 independent deformities (the rotation angle of forearm; the internal rotation, radial, and dorsal angulation of radius and ulna; the relative length of osseous fusion at PRUJ; the relative dislocation distance of distal radioulnar joint; the relative area of proximal radial epiphysis) involved in the CRUS complex deformity were measured. Pearson correlation analysis for each deformity which was mentioned above was performed, and multivariate linear regression analysis was also performed with FR as the dependent variable and the other deformities as the influential factors. Results: The "dorsal angle of radius" (DAR, 21.69° ± 21.55°) had the strongest correlation with the FR (79.72° ± 40.39°), the Pearson correlation coefficient was 0.601 (p < 0.01), the internal rotation angle of the radius (IRAR, 82.69° ± 54.98°) had a moderate correlation with FR, the Pearson correlation coefficient was 0.552 (p < 0.01). A forearm deformity equation was established: FR = 35.896 + 0.271 DAR + 0.989 IRAR. Conclusion: The dorsal angulation deformity of radius may be the most important deformity that effects the severity of CRUS and should be correct in the first place during reconstruction operation. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
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45. EphA3 deficiency in the hypothalamus promotes high-fat diet-induced obesity in mice.
- Author
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Jubiao Zhang, Yang Chen, Lihong Yan, Xin Zhang, Xiaoyan Zheng, Junxia Qi, Fen Yang, and Juxue Li
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HYPOTHALAMUS , *PROTEIN-tyrosine kinases , *OBESITY , *HIGH-fat diet , *GENOME editing - Abstract
Erythropoietin-producing hepatocellular carcinoma A3 (EphA3) is a member of the largest subfamily of tyrosine kinase receptors-Eph receptors. Previous studies have shown that EphA3 is associated with tissue development. Recently, we have found that the expression of EphA3 is elevated in the hypothalamus of mice with diet-induced obesity (DIO). However, the role of EphA3 in hypothalamic-controlled energy metabolism remains unclear. In the current study, we demonstrated that the deletion of EphA3 in the hypothalamus by CRISPR/Cas9-mediated gene editing promotes obesity in male mice with high-fat diet feeding rather than those with normal chow diet feeding. Moreover, the deletion of hypothalamic EphA3 promotes high-fat DIO by increasing food intake and reducing energy expenditure. Knockdown of EphA3 leads to smaller intracellular vesicles in GT1-7 cells. The current study reveals that hypothalamic EphA3 plays important roles in promoting DIO. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
46. Accelerating the Lagrangian Particle Tracking in Hydrologic Modeling to Continental‐Scale.
- Author
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Yang, Chen, Ponder, Carl, Wang, Bei, Tran, Hoang, Zhang, Jun, Swilley, Jackson, Condon, Laura, and Maxwell, Reed
- Subjects
- *
HYDROLOGIC models , *EARTH system science , *EFFECT of human beings on climate change , *HYDROLOGIC cycle , *COMMUNITIES , *ECOHYDROLOGY - Abstract
Unprecedented climate change and anthropogenic activities have induced increasing ecohydrological problems, motivating the development of large‐scale hydrologic modeling for solutions. Water age/quality is as important as water quantity for understanding the terrestrial water cycle. However, scientific progress in tracking water parcels at large‐scale with high spatiotemporal resolutions is far behind that in simulating water balance/quantity owing to the lack of powerful modeling tools. EcoSLIM is a particle tracking model working with ParFlow‐CLM that couples integrated surface‐subsurface hydrology with land surface processes. Here, we demonstrate a parallel framework on distributed, multi‐Graphics Processing Unit platforms with Compute Unified Device Architecture‐Aware Message Passing Interface for accelerating EcoSLIM to continental‐scale. In tests from catchment‐, to regional‐, and then to continental‐scale using 25‐million to 1.6‐billion particles, EcoSLIM shows significant speedup and excellent parallel performance. The parallel framework is portable to atmospheric and oceanic particle tracking models, where the parallelization is inadequate, and a standard parallel framework is also absent. The parallelized EcoSLIM is a promising tool to accelerate our understanding of the terrestrial water cycle and the upscaling of subsurface hydrology to Earth System Models. Plain Language Summary: Studies of water ages at multiple spatiotemporal scales are urgent to better understand the connections between different hydrologic compartments. Climate change and anthropogenic activities make this requirement more pressing. Lagrangian particle tracking is a powerful tool to simulate water ages. However, it is computationally demanding, which hampers its wide application. In this study, we provide a Lagrangian particle tracking model, EcoSLIM, with a novel parallel framework that enables it to handle large‐scale water age simulations with high spatiotemporal resolutions. We combined the efforts of engineers and scientists from multiple disciplines on this work which cannot be achieved by the knowledge of an individual discipline. To the best of our knowledge, such a modeling tool is absent in communities of hydrology and Earth Surface Processes. In tests from catchment‐, to regional‐, and then to continental‐scale using 25‐million to 1.6‐billion particles, EcoSLIM shows significant speedup and excellent parallel performance. Although we take EcoSLIM as an example here, the parallel framework is portable to other particle tracking models in Earth System Science, such as those in atmospheric and oceanic disciplines. The parallelized EcoSLIM is a promising tool to hydrologic community and Earth System Model developers for scientific exploration. Key Points: Numerical models for large‐scale water age/quality simulations are absent in communities of hydrology and Earth Surface ProcessesA parallel framework for accelerating Lagrangian particle tracking to continental‐scale on distributed, multi‐Graphics Processing Unit platforms is establishedThe parallelized particle tracking model, EcoSLIM, is a promising tool to accelerate our understanding of the terrestrial water cycle [ABSTRACT FROM AUTHOR]
- Published
- 2023
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47. HISTONE DEACETYLASE 15 and MOS4-associated complex subunits 3A/3B coregulate intron retention of ABA-responsive genes.
- Author
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Yi-Tsung Tu, Chia-Yang Chen, Yi-Sui Huang, Chung-Han Chang, Ming-Ren Yen, Jo-Wei Allison Hsieh, Pao-Yang Chen, and Keqiang Wu
- Abstract
Histone deacetylases (HDAs) play an important role in transcriptional regulation of multiple biological processes. In this study, we investigated the function of HDA15 in abscisic acid (ABA) responses. We used immunopurification coupled with mass spectrometry-based proteomics to identify proteins interacting with HDA15 in Arabidopsis (Arabidopsis thaliana). HDA15 interacted with the core subunits of the MOS4-associated complex (MAC), MAC3A and MAC3B, with interaction between HDA15 and MAC3B enhanced by ABA. hda15 and mac3a/mac3b mutants were ABA-insensitive during seed germination and hyposensitive to salinity. RNA sequencing analysis demonstrated that HDA15 and MAC3A/MAC3B coregulate ABA-responsive intron retention (IR). Furthermore, HDA15 reduced the histone acetylation level of genomic regions near ABA-responsive IR sites and the association of MAC3B with ABA-responsive pre-mRNA was dependent on HDA15. Our results indicate that HDA15 is involved in ABA responses by interacting with MAC3A/MAC3B to mediate splicing of introns. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
48. Suprapatellar vs infrapatellar approaches for intramedullary nailing of distal tibial fractures: a systematic review and meta-analysis.
- Author
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Yang, Chen-Yuan, Tay, Soon-Tzeh, and Kuo, Liang-Tseng
- Subjects
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INTRAMEDULLARY fracture fixation , *TIBIAL fractures , *ODDS ratio , *CONFIDENCE intervals - Abstract
Background: This review was conducted to compare the efficacy of suprapatellar (SP) and infrapatellar (IP) approaches for treating distal tibial fractures with intramedullary nailing. Method: This systematic review included studies comparing the outcomes of patients receiving nailing for distal tibial fractures using the SP and IP approaches. We searched the Cochrane CENTRAL, MEDLINE and Embase databases for relevant studies till 18th Sep. 2022. We used the Newcastle Ottawa Scale to assess study quality and a random-effects meta-analysis to synthesize the outcomes. We used the mean difference (MD) or standardized mean difference (SMD) with the 95% confidence interval (CI) for continuous data and the odds ratio (OR) with the 95% CI for dichotomous data. Results: Four studies with 586 patients (302 in the SP group and 284 in the IP group) were included in this systematic review. The SP group may have had little or no difference in pain and slightly better knee function (MD 3.90 points, 95% CI 0.83 to 5.36) and better ankle function (MD: 8.25 points, 95% CI 3.35 to 13.15) than the IP group 12 months after surgery. Furthermore, compared to the IP group, the SP group had a lower risk of malalignment (OR: 0.22, 95% CI 0.06 to 0.75; number needed to treat (NNT): 6), a lower risk for open reduction (OR: 0.58, 95% CI 0.35 to 0.97; NNT: 16) and a shorter surgical time (MD: − 15.14 min, 95% CI − 21.28 to − 9.00). Conclusions: With more advantages, the suprapatellar approach may be the preferred nailing technique over the infrapatellar approach when treating distal tibial fractures. Level of evidence: Level III, systematic review of non-randomized studies. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
49. Three new species of the Clubiona corticalis group (Araneae, Clubionidae) from China.
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Panlong Wu, Yang Chen, and Feng Zhang
- Subjects
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SPIDERS , *JUMPING spiders , *SPECIES , *SPECIES diversity - Abstract
Three new species of the Clubiona corticalis group in China are described: Clubiona bidactylina sp. nov., C. camela sp. nov., and C. subhuiming sp. nov. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
50. CHINA’S DIGITAL ECONOMY DEVELOPMENT: INCENTIVES AND CHALLENGES.
- Author
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Yang CHEN, Shaorui XU, LYULYOV, Oleksii, and PIMONENKO, Tetyana
- Subjects
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HIGH technology industries , *REAL economy , *ECONOMIC development , *INFORMATION & communication technologies ,ECONOMIC conditions in China - Abstract
The development of the digital economy has become a new way to respond to the epidemic impact effectively. With the innovative breakthrough of information and communication technology, the digital and real economies are deeply integrated. The digital economy has become an important driving force for the transformation of economic momentum and development. Panel data from 31 provinces in China from 2010 to 2019 were selected for analysis. In the first stage, the study constructed the evaluation index system of digital economy development. Then, the quality development index of the digital economy is calculated by using the entropy method. Finally, the main factors of digital economy development are analysed by spatial measurement. The research results prove that: (1) the development of China’s digital economy in 2010–2019 has gradually increased; (2) the development of the digital economy has a positive correlation between regions and has a spatial spillover effect; (3) the level of economic development, urbanisation, government support, industrial structure, and the level of opening will promote the development of the digital economy. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
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