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Continuous and Discrete Similarity Coefficient for Identifying Essential Proteins Using Gene Expression Data

Big Data Mining and Analytics 2023年第2期6卷 185-200页

作者： jiancheng zhong Zuohang Qu Ying zhong Chao Tang Yi Pan College of Information Science and Engineering Hunan Normal UniversityChangsha 410081China Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of Sciences ShenzhenGuangzhou 518055China

Essential proteins play a vital role in biological processes,and the combination of gene expression profiles with Protein-Protein Interaction(PPI)networks can improve the identification of essential ***,gene expression data are prone to significant fluctuations due to noise interference in topological *** this work,we discretized gene expression data and used the discrete similarities of the gene expression spectrum to eliminate noise *** then proposed the Pearson Jaccard coefficient(PJC)that consisted of continuous and discrete similarities in the gene expression *** the graph theory as the basis,we fused the newly proposed similarity coefficient with the existing network topology prediction algorithm at each protein node to recognize essential *** strategy exhibited a high recognition rate and good *** validated the new similarity coefficient PJC on PPI datasets of Krogan,Gavin,and DIP of yeast species and evaluated the results by receiver operating characteristic analysis,jackknife analysis,top analysis,and accuracy *** with that of node-based network topology centrality and fusion biological information centrality methods,the new similarity coefficient PJC showed a significantly improved prediction performance for essential proteins in DC,IC,Eigenvector centrality,subgraph centrality,betweenness centrality,closeness centrality,NC,PeC,and *** also compared the PJC coefficient with other methods using the NF-PIN algorithm,which predicts proteins by constructing active PPI networks through dynamic gene *** experimental results proved that our newly proposed similarity coefficient PJC has superior advantages in predicting essential proteins.

关键词： Protein-Protein Interaction(PPI)network continuous and discrete similarity coefficient essential proteins

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A Feature Selection Method for Prediction Essential Protein

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Tsinghua Science and Technology 2015年第5期20卷 491-499页

作者： jiancheng zhong Jianxin Wang Wei Peng Zhen Zhang Min Li the School of Information Science and Engineering Central South University the College of Polytechnic Hunan Normal University the Computer Center Kunming University of Science and Technology

Essential proteins are vital to the survival of a cell. There are various features related to the essentiality of proteins, such as biological and topological features. Many computational methods have been developed to identify essential proteins by using these features. However, it is still a big challenge to design an effective method that is able to select suitable features and integrate them to predict essential proteins. In this work, we first collect 26 features, and use SVM-RFE to select some of them to create a feature space for predicting essential proteins, and then remove the features that share the biological meaning with other features in the feature space according to their Pearson Correlation Coefficients（PCC）. The experiments are carried out on S. cerevisiae data. Six features are determined as the best subset of features. To assess the prediction performance of our method, we further compare it with some machine learning methods, such as SVM, Naive Bayes, Bayes Network, and NBTree when inputting the different number of features. The results show that those methods using the 6 features outperform that using other features, which confirms the effectiveness of our feature selection method for essential protein prediction.

关键词： essential protein feature selection Protein-Protein Interaction(PPI) machine learning centrality algorithm

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基于动态网络切分的关键蛋白质预测方法

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计算机研究与发展 2022年第7期59卷 1569-1588页

作者：钟坚成方卓瞿佐航钟颖彭玮潘毅湖南师范大学信息科学与工程学院长沙410081 昆明理工大学信息工程与自动化学院昆明650500 中国科学院深圳理工大学计算机与控制工程学院广东深圳518055

关键蛋白质作为蛋白质中的关键物质,不仅对研究细胞生长调控有着重要意义,也为更深层次的疾病研究奠定理论基础.目前,针对关键蛋白质的识别方法大多为应用基因表达信息和蛋白质相互作用网络,提出识别关键蛋白质的静态和动态网络方法,但... 详细信息

关键蛋白质作为蛋白质中的关键物质,不仅对研究细胞生长调控有着重要意义,也为更深层次的疾病研究奠定理论基础.目前,针对关键蛋白质的识别方法大多为应用基因表达信息和蛋白质相互作用网络,提出识别关键蛋白质的静态和动态网络方法,但这些方法未考虑基因表达调控的周期性规律,无法准确地刻画受基因周期调控的蛋白质网络.为此,在基因表达动态性的基础上引入了基因周期性表达的概念,提出了一种动态网络切分方法.该方法通过构建基因“活性”表达矩阵,利用切分后的“活性”表达矩阵作用于蛋白质相互作用网络,从而形成蛋白质周期子网络,最终综合各周期子网络来衡量蛋白质结点在网络中的重要性.实验结果表明,该方法在酵母、大肠杆菌和人类膀胱数据中可以有效地提高关键蛋白质预测率.

关键词：关键蛋白质蛋白质相互作用网络动态网络周期子网络动态基因表达

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浅述深基坑工程的特点及其支护技术

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资源环境与工程 2012年第1期26卷 33-35,39页

作者：钟建成武汉市公路勘察设计院湖北武汉430015

深基坑工程的支护技术能够有效地控制基坑开挖过程中的围护结构变形位移,防止引起基坑外地面沉降,保证施工工期和安全。分析深基坑工程的特点,介绍各种深基坑工程的支护技术,并列出了深基坑支护应用中的注意事项和预防措施。

关键词：深基坑工程特点支护技术

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人防地下室渗漏的修补措施探讨

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资源环境与工程 2011年第6期25卷 607-609页

作者：钟建成武汉市公路勘察设计院湖北武汉430015

随着中国高层建筑的增加,人防地下室的施工建筑越来越多,而渗漏是人防地下室工程的主要工程质量问题。结合人防地下室的渗漏修补实际工程问题,介绍了地下室渗漏补救的两种措施———聚合物防水灰浆堵漏和压力灌浆堵漏措施。结果表明上... 详细信息

随着中国高层建筑的增加,人防地下室的施工建筑越来越多,而渗漏是人防地下室工程的主要工程质量问题。结合人防地下室的渗漏修补实际工程问题,介绍了地下室渗漏补救的两种措施———聚合物防水灰浆堵漏和压力灌浆堵漏措施。结果表明上述两种渗漏补救措施能够很好地解决人防地下室的渗漏问题,为解决其它地下室渗漏问题提供了参考。

关键词：人防地下室渗漏修补堵漏

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铈-邻苯二酚衍生物配合物的氧化显色反应及其机理

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中国稀土学报 1997年第3期15卷 252-256页

作者：邓建成钟超凡童珏湘潭大学应用化学系

对邻苯二酚、邻苯二酚３，５二磺酸钠、连苯三酚、３，４二羟基苯甲酸及３，４，５三羟基苯甲酸等系列邻苯二酚衍生物和Ｃｅ３＋生成紫红色配合物的反应进行了研究，结果表明，该显色反应是因Ｃｅ３＋配合物被氧化成了Ｃｅ４＋... 详细信息

对邻苯二酚、邻苯二酚３，５二磺酸钠、连苯三酚、３，４二羟基苯甲酸及３，４，５三羟基苯甲酸等系列邻苯二酚衍生物和Ｃｅ３＋生成紫红色配合物的反应进行了研究，结果表明，该显色反应是因Ｃｅ３＋配合物被氧化成了Ｃｅ４＋配合物；提出了Ｃｅ３＋与这类试剂氧化显色反应的机理并对其进行了验证实验。

关键词：铈邻苯二酚衍生物氧化显色反应络合物

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Analysis of terrestrial water storage changes in the Shaan-Gan-Ning Region using GPS and GRACE/GFO

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Geodesy and Geodynamics 2022年第2期13卷 179-188页

作者： Xianpao Li Bo zhong jiancheng Li Renli Liu School of Geodesy and Geomatics Wuhan UniversityWuhan430079China Key Laboratory of Geospace Environment and Geodesy Ministry of EducationWuhan UniversityWuhan430079China School of Water Resources and Hydropower Engineering Wuhan UniversityWuhan430072China

Both the Global Positioning System(GPS)and Gravity Recovery and Climate Experiment(GRACE)/GRACE Follow-On(GFO)provide effective tools to infer surface mass *** this paper,we combined GPS,GRACE/GFO spherical harmonic(SH)solutions and GRACE/GFO mascon solutions to analyze the total surface mass changes and terrestrial water storage(TWS)changes in the Shaan-Gan-Ning Region(SGNR)over the period from December 2010 to February *** improve the reliability of GPS inversion results,an improved regularization Laplace matrix and monthly optimal regularization parameter estimation strategy were employed to solve the ill-posed *** results show that the improved Laplace matrix can suppress the edge effects better than that of the traditional Laplace matrix,and the corre-lation coefficient and standard deviation(STD)between the original signal and inversion results from the traditional and improved Laplace matrix are 0.84 and 0.88,and 17.49 mm and 15.16 mm,*** spatial distributions of annual amplitudes and time series changes for total surface mass changes derived from GPS agree well with GRACE/GFO SH solutions and mascon solutions,and the correlation coefficients of total surface mass change time series between GPS and GRACE/GFO SH solutions,GPS and GRACE/GFO mascon solutions are 0.80 and ***,the obvious differences still exist in local *** addition,the seasonal characteristics,increasing and decreasing rate of TWS change time series derived from GPS,GRACE/GFO SH and mascon solutions agree well with the Global Land Data Assimilation System(GLDAS)hydrological model in the studied area,and generally consistent with the precipitation ***,TWS changes derived from GPS and GRACE mascon solutions in the SGNR are more reliable than those of GRACE SH solutions over the period from January 2016 to June 2017(the final operation phase of the GRACE mission).

关键词： Terrestrial water storage Shaan-Gan-Ning Region GPS vertical displacements GRACE/GFO Improved Laplace matrix

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Cobalamin-dependent radical S-adenosyl-L-methionine protein functions with a partner to successively methylate tricyclic indole alkaloid for chuangxinmycin maturation and derivatization

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Science China Chemistry 2025年第1期 308-316页

作者： Sili Wang jiancheng Huang Yanan Du Wei Huang Yufeng Xue Xiaokun Xu Guannan zhong Yuanyuan Shi Bin Hong Xiaoying Bian Wen Liu State Key Laboratory of Chemical Biology Shanghai Institute of Organic Chemistry University of Chinese Academy of SciencesChinese Academy of Sciences State Key Laboratory of Microbial Technology Shandong University National Health Commission (NHC) Key Laboratory of Biotechnology for Microbial Drugs Institute of Medicinal BiotechnologyChinese Academy of Medical Science & Peking Union Medical College

Cobalamin(Cbl)-dependent radical S-adenosyl-L-methionine(SAM) proteins constitute the largest collection of the radical SAM superfamily that has hundreds of thousands of individual members. Many of these proteins are involved in the biosynthesis of pharmaceutically important natural products to catalyze chemically demanding reactions. In the biosynthetic pathway of chuangxinmycin(CXM), a unique indole alkaloid antibiotic with potent anti-infective activity, functionalization of the characteristic thiopyrano[4,3,2-cd]indole scaffold by regio-and stereoselective C3-methylation is believed to rely on a Cbl-dependent radical process, which, however, remained to be reconstituted biochemically. We here report the dissection of this enzymatic process, which requires the incorporation of Cxm8, a Cbl-dependent radical SAM protein, with Cxm9, a DUF5825family protein that shares no homology to any proteins of known functions. Cxm8 and Cxm9 function together by forming an unexpected heterodimeric complex that selectively catalyzes C3-methylation of the tricyclic indole-S-hetero ring system in a successive manner, achieving CXM and a recently identified, C3-dimethylated congener. Detailed biochemical characterization,isotope labeling, structural simulation and bioinformatics analysis rationalized the catalysis of the Cxm8/Cxm9 complex and particularly the necessity of the DUF5825 protein for C3-methylase activity. This is the first example that a Cbl-dependent protein acts with a partner to exhibit radical SAM activity.

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Multi boron-doping effects in hard carbon toward enhanced sodium ion storage

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Journal of Energy Chemistry 2025年第1期100卷 730-738页

作者： Peng Zheng Wang Zhou Ying Mo Biao Zheng Miaomiao Han Qin zhong Wenwen Yang Peng Gao Lezhi Yang Jilei Liu College of Materials Science and Engineering Hunan Joint International Laboratory of Advanced Materials and Technology for Clean Energy Hunan Province Key Laboratory for Advanced Carbon Materials and Applied Technology Hunan University Greater Bay Area Institute for Innovation Hunan University Changsha Research Institute of Mining & Metallurgy Co. LTD.

Hard carbon （HC） has been considered as promising anode material for sodium-ion batteries （SIBs）.The optimization of hard carbon’s microstructure and solid electrolyte interface （SEI） property are demonstrated effective in enhancing the Na+storage capability,however,a one-step regulation strategy to achieve simultaneous multi-scale structures optimization is highly ***,we have systematically investigated the effects of boron doping on hard carbon’s microstructure and interface chemistry.A variety of structure characterizations show that appropriate amount of boron doping can increase the size of closed pores via rearrangement of carbon layers with improved graphitization degree,which provides more Na+storage ***-situ Fourier transform infrared spectroscopy/electrochemical impedance spectroscopy （FTIR/EIS） and X-ray photoelectron spectroscopy （XPS） analysis demonstrate the presence of more BC3and less B–C–O structures that result in enhanced ion diffusion kinetics and the formation of inorganic rich and robust SEI,which leads to facilitated charge transfer and excellent rate *** a result,the hard carbon anode with optimized boron doping content exhibits enhanced rate and cycling *** general,this work unravels the critical role of boron doping in optimizing the pore structure,interface chemistry and diffusion kinetics of hard carbon,which enables rational design of sodium-ion battery anode with enhanced Na+storage performance.

关键词： X ray photoelectron spectroscopy

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Dynamic Regulation of Hydrogen Bonding Networks and Solvation Structures for Synergistic Solar‑Thermal Desalination of Seawater and Catalytic Degradation of Organic Pollutants

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Nano-Micro Letters 2025年第2期17卷 548-565页

作者： Ming‑Yuan Yu Jing Wu Guang Yin Fan‑Zhen Jiao zhong‑Zhen Yu Jin Qu Beijing Key Laboratory of Advanced Functional Polymer Composites Beijing University of Chemical TechnologyBeijing 100029People’s Republic of China State Key Laboratory of Organic‑Inorganic Composites College of Materials Science and EngineeringBeijing University of Chemical TechnologyBeijing 100029People’s Republic of China

Although solar steam generation strategy is efficient in desalinating seawater,it is still challenging to achieve continuous solar-thermal desalination of seawater and catalytic degradation of organic ***,dynamic regulations of hydrogen bonding networks and solvation structures are realized by designing an asymmetric bilayer membrane consisting of a bacterial cellulose/carbon nanotube/Co_(2)(OH)_(2)CO_(3)nanorod top layer and a bacterial cellulose/Co_(2)(OH)_(2)CO_(3)nanorod(BCH)bottom ***,the hydrogen bonding networks inside the membrane can be tuned by the rich surface–OH groups of the bacterial cellulose and Co_(2)(OH)_(2)CO_(3)as well as the ions and radicals in situ generated during the catalysis ***,both SO_(4)^(2−)and HSO_(5)−can regulate the solvation structure of Na^(+)and be adsorbed more preferentially on the evaporation surface than Cl^(−),thus hindering the de-solvation of the solvated Na^(+)and subsequent nucleation/growth of ***,the heat generated by the solar-thermal energy conversion can accelerate the reaction kinetics and enhance the catalytic degradation *** work provides a flow-bed water purification system with an asymmetric solar-thermal and catalytic membrane for synergistic solar thermal desalination of seawater/brine and catalytic degradation of organic pollutants.

关键词： Solar steam generation Seawater desalination Catalytic degradation Bacterial cellulose Cobalt hydroxycarbonate nanorods

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