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Transcriptome sequencing and metabolome analysis reveal the mechanism of Shuanghua Baihe Tablet in the treatment of oral mucositis

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Chinese Journal of Natural Medicines 2021年第12期19卷 930-943页

作者： geng qi-shun LIU Rui-Juan SHEN Zhi-Bo WEI qian ZHENG Yuan-Yuan JIA Lan-qi WANG Long-Hao LI Li-Feng LI Jun XUE Wen-Hua Department of Pharmacy the First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052China Engineering Laboratory for Digital Telemedicine Service The first Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052China

Oral mucositis(OM) caused by cancer therapy is the most common adverse reaction in the radiotherapy of head and neck tumors. In severe cases, it can lead to the interruption of treatment, which affects the control of the disease and the quality of *** Baihe Tablet(SBT) is a traditional Chinese medicine(TCM) formula, which is administerd to treat OM in China. It has been clinically effective for more than 30 years, but the underlying mechanism is not completely understood. With the development of multiple omics, it is possible to explore the mechanism of Chinese herbal compound prescriptions. Based on transcriptomics and metabolomics, we explored the underlying mechanism of SBT in the treatment of OM. An OM model of rats was established by 5-FU induction, and SBT was orally administered at dosages of 0.75 and 3 g·kg;·d;. In order to search for SBT targets and related metabolites, the dysregulated genes and metabolites were detected by transcriptomics and metabolomics. Immune related indicators such as interleukin-17(IL-17) and tumor necrosis factor-α(TNF-α) were detected by ELISA. Treg cell disorders was analyzed by flow cytometry. Our results showed that SBT significantly alleviated the symptoms of OM rats and the inflammatory infiltration of ulcer *** SBT administration, inflammatory related metabolic pathways including linoleic acid metabolism, valine, leucine and isoleucine biosynthesis were significantly altered. Furthermore, the production of proinflammatory factors like IL-17 and TNF-α, were also dramatically reduced after SBT administration. Besides, the infiltration degree of Treg cells in the spleen of OM modeling rats was significantly improved by SBT administration, thus maintaining the immune balance of the body. The current study demonstrates that SBT regulates inoleic acid metabolism, glycerophospholipid metabolism and amino acid metabolism, and inhibits IL-17/TNF signal transduction to restore Treg and Th17 cell homeostasis in OM

关键词： Oral mucositis Shuanghua Baihe tablet Transcriptomics Metabolomics IL-17/TNF signal pathway

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基于数据库挖掘和分子生物学探讨白藜芦醇治疗肺腺癌的作用机制

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中国实验方剂学杂志 2021年第14期27卷 199-207页

作者：耿其顺李依静沈志博郑园园李砺锋薛文华赵杰郑州大学第一附属医院郑州450052

目的:结合生物信息学与分子生物学探讨白藜芦治疗肺腺癌的作用机制。方法:从DrugBank获取白藜芦醇作用靶点信息,运用STRING数据库构建蛋白质-蛋白质相互作用(PPI)网络。在TCGA数据库中分析靶标基因在肿瘤及正常组织中表达量,预示其在肿... 详细信息

目的:结合生物信息学与分子生物学探讨白藜芦治疗肺腺癌的作用机制。方法:从DrugBank获取白藜芦醇作用靶点信息,运用STRING数据库构建蛋白质-蛋白质相互作用(PPI)网络。在TCGA数据库中分析靶标基因在肿瘤及正常组织中表达量,预示其在肿瘤发生发展中的影响。然后,运用随机森林和单因素COX回归的分析方法对靶标基因进行筛选。结合生物信息学结果,使用分子生物学探究白藜芦醇治疗肺腺癌的作用机制。结果:基于白藜芦醇作用靶点的PPI网络,筛选出10个Hub基因,其中溶质载体家族2成员1(SLC2A1),花生四烯酸5-脂氧合酶(ALOX5),过氧化物酶体增殖物激活受体γ(PPARG)和花生四烯酸15-脂氧合酶(ALOX15)在肿瘤和正常组织中表达量具有显著差异。然后,随机森林和单因素COX回归分析结果表明SLC2A1对肺腺癌的生存和预后意义重大。KM-plotter生存分析结果显示SLC2A1表达量与肺癌患者的总体生存率(OS),初次进展(FP),进展后生存率(PPS)均紧密相关。分子生物学实验也进一步证明白藜芦醇能够通过降低SLC2A1表达,抑制肺腺癌细胞的增殖和迁移。免疫组化评分显示SLC2A1在肿瘤和正常组织中蛋白表达量具有显著差异。结论:白藜芦醇通过降低SLC2A1表达,抑制肺腺癌细胞的增殖和迁移,在肺腺癌的临床治疗中具有深远意义。

关键词：白藜芦醇肺腺癌生物信息学作用机制分子生物学

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基于网络药理学研究龙葵抗肺癌的生物作用机制

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中国临床药理学杂志 2020年第11期36卷 1588-1591页

作者：耿其顺朱子家王文斌沈志博李砺锋薛文华赵杰郑州大学第一附属医院药学部河南郑州450052

目的研究龙葵治疗肺癌的药理机制。方法以药代动力学参数(口服生物利用度≥30%,药物相似性≥0.18)作为筛选标准,从中药成分检索数据库中筛选出龙葵的主要活性成分,并预测活性成分相关作用靶点。用Genecards数据库查询已知的肺癌治疗靶点... 详细信息

目的研究龙葵治疗肺癌的药理机制。方法以药代动力学参数(口服生物利用度≥30%,药物相似性≥0.18)作为筛选标准,从中药成分检索数据库中筛选出龙葵的主要活性成分,并预测活性成分相关作用靶点。用Genecards数据库查询已知的肺癌治疗靶点,通过Calculate and draw custom Venn diagrams构建药物靶点与肺癌靶点韦恩图并获得两者共同靶点,用String数据库绘制共同靶点的蛋白相互作用网络图;再用Cytoscape软件构建龙葵的成分-靶点-疾病网络模型,用WebGestalt和David分别进行基因本体论和京都基因与基因组百科全书功能富集分析。结果共筛选出龙葵活性成分7个,相关靶点51个。根据蛋白质相互作用(PPI)网络图,可知共有51个节点,146条关系。富集分析显示龙葵可以通过多个通路对肺癌产生治疗作用。结论龙葵可通过作用于多个靶点,并参与调控多个网络通路发挥治疗肺癌的作用。

关键词：龙葵肺癌网络药理学作用机制物质基础

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Numerical simulation of landscape evolution and mountain uplift history constrain——A case study from the youthful stage mountains around the central Hexi Corridor,NE Tibetan Plateau

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Science China Earth Sciences 2021年第3期64卷 412-424页

作者： Baotian PAN shun CAI Haopeng geng Key Laboratory of Western China’s Environmental Systems(Ministry of Education) College of Earth and Environmental SciencesLanzhou UniversityLanzhou730000China

Landscape evolution models(LEMs)are essential tools for analyzing tectonic-climate interactions and reproducing landform-shaping *** this study we used a LEM to simulate the evolution of the mountains from the central Hexi Corridor in the northeastern Tibetan Plateau,where the climate is arid and the surface processes are relatively ***,there are pronounced differences in the topography between the mountains around the central Hexi *** East Jintanan Shan,West Jintanan Shan and Heli Shan are located in the northern part of the corridor;and the Yumu Shan in the southern ***,several representative areas were selected from these mountains to analyze the topographic characteristics,including the uniform valley spacing,local relief,and the outlet ***,a LEM for these areas was constructed using the Landlab platform,and the landscape evolution was *** uniform valley spacing and other topographic characteristics as the criteria,we compared the realistic and simulated terrain for different model ***,based on the similarity of the simulated and realistic terrain,we estimated the timing of the initial uplift and the uplift rate of the four mountain *** results are consistent with previous geological and geomorphological records from these youthful stage mountains that have not yet reached a steady *** findings demonstrate that LEMs combined with topographic characteristics are a reliable means of constraining the timing of the initial uplift and the uplift rate of the youthful stage *** approach can potentially be applied to other youthful stage mountains and it may become a valuable tool in tectonic geomorphology research.

关键词： Hexi Corridor Landscape evolution models Youthful stage mountains Topographic characteristics Uniform valley spacing

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Microstructures of Ti–Ni–Fe wire after severe cold-drawing and annealing

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Rare Metals 2013年第6期32卷 550-554页

作者： Hui-Fang geng Fu-shun Liu School of Material Science and Engineering Beijing University of Aeronautics and Astronatics

The microstructures and mechanical properties of Ti–47 at%Ni–3 at%Fe shape memory alloy wire under the condition of severe cold-drawing at room temperature and different postdeformation annealing processes were intensively investigated using transmission electron microscope(TEM),X-ray diffraction(XRD),Vickers microhardness tester and electron tensile *** is indicated that the structure of the alloy evolves into a predominant amorphous structure with a trace of nanocrystalline B2 phase after the cold-drawing of 76%areal *** annealing process exerted significant influence on the microstructure and mechanical *** occurs when the cold-drawn wire was annealed at 300℃ for 30 *** ultimate tensile strength and ductility as well as the superelasticity of the wire are improved significantly by cold-drawing plus postdeformation annealing.

关键词： Ti–Ni–Fe wire Severe plastic deformation Cold-drawing Annealing Amorphous structure

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Topological origin of global attractors in gene regulatory networks

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Science China(Physics,Mechanics & Astronomy) 2015年第2期58卷 101-108页

作者： ZHANG YunJun OUYANG qi geng Zhi Faculty of Foundation Education Peking University Health Science Center Center for Theoretical Biology School of Physics Peking University School of Mathematical Sciences Peking University

Fixed-point attractors with global stability manifest themselves in a number of gene regulatory networks. This property indicates the stability of regulatory networks against small state perturbations and is closely related to other complex dynamics. In this paper, we aim to reveal the core modules in regulatory networks that determine their global attractors and the relationship between these core modules and other motifs. This work has been done via three steps. Firstly, inspired by the signal transmission in the regulation process, we extract the model of chain-like network from regulation networks. We propose a module of "ideal transmission chain(ITC)", which is proved sufficient and necessary(under certain condition) to form a global fixed-point in the context of chain-like network. Secondly, by examining two well-studied regulatory networks(i.e., the cell-cycle regulatory networks of Budding yeast and Fission yeast), we identify the ideal modules in true regulation networks and demonstrate that the modules have a superior contribution to network stability(quantified by the relative size of the biggest attraction basin). Thirdly, in these two regulation networks, we find that the double negative feedback loops, which are the key motifs of forming bistability in regulation, are connected to these core modules with high network stability. These results have shed new light on the connection between the topological feature and the dynamic property of regulatory networks.

关键词： Boolean model bistability network module robustness

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Predicting coastal morphological changes with empirical orthogonal function method

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Water Science and Engineering 2016年第1期9卷 14-20页

作者： fernando alvarez shun-qi pan Hydro-environmental Research Centre School of Engineering Cardiff University Cardiff CF24 3AA UK

In order to improve the accuracy of prediction when using the empirical orthogonal function （EOF） method, this paper describes a novel approach for two-dimensional （2D） EOF analysis based on extrapolating both the spatial and temporal EOF components for long-term prediction of coastal morphological changes. The approach was investigated with data obtained from a process-based numerical model, COAST2D, which was applied to an idealized study site with a group of shore-parallel breakwaters. The progressive behavior of the spatial and temporal EOF components, related to bathymetric changes over a training period, was demonstrated, and EOF components were extrapolated with combined linear and exponential functions for long-term prediction. The extrapolated EOF components were then used to reconstruct bathymetric changes. The comparison of the reconstructed bathymetric changes with the modeled results from the COAST2D model illustrates that the presented approach can be effective for long-term prediction of coastal morphological changes, and extrapolating both the spatial and temporal EOF components yields better results than extrapolating only the temporal EOF component.

关键词： EOF method Coastal morphological change Long-term prediction Process-based numerical model Shore-parallel breakwater

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Aero-engine fault diagnosis applying new fast support vector algorithm

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航空动力学报 2012年第7期27卷 1604-1612页

作者： XU qi-hua geng Shuai SHI Jun College of Electronic Engineering Huaihai Institute of Technology Lianyungang Jiangsu 222005 China No. 365 Institute Northwestern Polytechnical University Xi'an 710072 China

A new fast learning algorithm was presented to solve the large-scale support vector machine ( SVM ) training problem of aero-engine fault *** relative boundary vectors ( RBVs ) instead of all the original training samples were used for the training of the binary SVM fault *** pruning strategy decreased the number of final training sample significantly and can keep classification accuracy almost *** , the training time was shortened to 1 / 20compared with basic SVM *** , owing to the reduction of support vector number , the classification time was also *** sample aliasing existed , the aliasing sample points which were not of the same class were eliminated before the relative boundary vectors were *** , the samples near the relative boundary vectors were selected for SVM training in order to prevent the loss of some key sample points resulted from *** can improve classification accuracy effectively.A simulation example to classify 5classes of combination fault of aero-engine gas path components was finished and the total fault classification accuracy reached 96.1%.Simulation results show that this fast learning algorithm is effective , reliable and easy to be implemented for engineering application.

关键词： aero-engine support vector machines fault diagnosis large-scale training set relative boundary vector sample pruning

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A VMD Based Improved De-noising of Onboard BTM Receiving Signal

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Chinese Journal of Electronics 2020年第1期29卷 66-72页

作者： geng qi WEN Yinghong LIU Shanghe ZHANG Dan Institute of Electromagnetic Compatibilit Beijing Jiaotong University National Key Laboratory of Electromagnetic Environment Effects Shijiazhuang Campus Army Engineering University

As a key equipment of the high-speed Electric multiple unit(EMU), the Balise transmission module(BTM) is tend to be affected by electromagnetic disturbances. However, the existing filter can not well eliminate electromagnetic disturbances. In order to improve the Signal to noise ratio(SNR) of BTM uplink signal, Variational mode decomposition(VMD) method is introduced into de-noising the uplink signal polluted by disturbance. The proposed de-noising method decomposes the noise-polluted signal into several narrow band subsignals. And then, the de-noised BTM transmitting signal is reconstructed by the sub-signals of the same frequency as the BTM carrier. To improve the accuracy of the VMD based signal decomposition, the Normalized short time fourier transform-Wigner ville distribution(NSTFTWVD) method are applied to determine the decomposition mode number of the target signal. The proposed method is used to deal with both simulation signal and measured BTM uplink signal. Results demonstrated good improvement in SNR by 20 dB and 12.63 dB, respectively.

关键词： Electromagnetic disturbance Balise transmission module(BTM) Variational mode decomposition(VMD) De-noising

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N-soliton solutions for the nonlocal two-wave interaction system via the Riemann–Hilbert method

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Chinese Physics B 2018年第12期27卷 157-163页

作者： Si-qi Xu Xian-Guo geng School of Mathematics and Statistics Zhengzhou UniversityZhengzhou 450001China College of Civil Engineering Xinyang Normal UniversityXinyang 464000China

In this paper, a nonlocal two-wave interaction system from the Manakov hierarchy is investigated via the Riemann–Hilbert approach. Based on the spectral analysis of the Lax pair, a Riemann–Hilbert problem for the nonlocal two-wave interaction system is constructed. By discussing the solutions of this Riemann–Hilbert problem in both the regular and nonregular cases, we explicitly present the N-soliton solution formula of the nonlocal two-wave interaction system. Moreover,the dynamical behaviour of the single-soliton solution is shown graphically.

关键词： nonlocal two-wave interaction system Riemann–Hilbert problem N-soliton solutions

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