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Q-BioLiP:A Comprehensive Resource for Quaternary Structure-based Protein-ligand Interactions

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Genomics, Proteomics & Bioinformatics 2024年第1期22卷 151-159页

作者： hong wei Wenkai Wang Zhenling Peng Jianyi Yang School of Mathematical Sciences Nankai UniversityTianjin 300071China MOE Frontiers Science Center for Nonlinear Expectations Research Center for Mathematics and Interdisciplinary SciencesShandong UniversityQingdao 266237China

Since its establishment in 2013,BioLiP has become one of the widely used resources for protein-ligand ***,several known issues occurred with it over the past *** example,the protein-ligand interactions are represented in the form of single chain-based tertiary structures,which may be inappropriate as many interactions involve multiple protein chains(known as quaternary structures).We sought to address these issues,resulting in Q-BioLiP,a comprehensive resource for quaternary structure-based protein-ligand *** major features of Q-BioLiP include:(1)representing protein structures in the form of quaternary structures rather than single chain-based tertiary structures;(2)pairing DNA/RNA chains properly rather than separation;(3)providing both experimental and predicted binding affinities;(4)retaining both biologically relevant and irrelevant interactions to alleviate the wrong justification of ligands’biological relevance;and(5)developing a new quaternary structure-based algorithm for the modelling of protein-ligand complex *** these new features,Q-BioLiP is expected to be a valuable resource for studying biomolecule interactions,including protein-small molecule interaction,protein-metal ion interaction,protein-peptide interaction,protein-protein interaction,protein-DNA/RNA interaction,and RNA-small molecule interaction.Q-BioLiP is freely available at https://***/Q-BioLiP/.

关键词： Protein-ligand interaction Quaternary structure Protein-ligand binding site Protein-protein interaction Binding affinity

On traceable iterated line graph and hamiltonian path index

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Applied Mathematics(A Journal of Chinese Universities) 2024年第2期39卷 239-252页

作者： NIU Zhao-hong XIONG Li-ming YANG wei-hua School of Mathematical Sciences Shanxi UniversityTaiyuan 030006China School of Mathematics and Statistics Beijing Key Laboratory on MCAACIBeijing Institute of TechnologyBeijing 100081China Department of Mathematics Taiyuan University of TechnologyTaiyuan 030024China

Xiong and Liu[21]gave a characterization of the graphs G for which the n-iterated line graph L^(n)(G)is hamiltonian,for n≥*** this paper,we study the existence of a hamiltonian path in L^(n)(G),and give a characterization of G for which L^(n)(G)has a hamiltonian *** applications,we use this characterization to give several upper bounds on the hamiltonian path index of a graph.

关键词： iterated line graph traceable hamiltonian index hamiltonian path index

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Enhancing personalized exercise recommendation with student and exercise portraits

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Journal of Electronic Science and Technology 2024年第2期22卷 91-109页

作者： wei-wei Gao Hui-Fang Ma Yan Zhao Jing Wang Quan-hong Tian College of Computer Science and Engineering Northwest Normal UniversityLanzhou730070China Computer Center of Gansu Province Lanzhou730070China

The exercise recommendation system is emerging as a promising application in online learning scenarios,providing personalized recommendations to assist students with explicit learning *** solutions generally follow a collaborative filtering paradigm,while the implicit connections between students(exercises)have been largely *** this study,we aim to propose an exercise recommendation paradigm that can reveal the latent connections between student-student(exercise-exercise).Specifically,a new framework was proposed,namely personalized exercise recommendation with student and exercise portraits(PERP).It consists of three sequential and interdependent modules:Collaborative student exercise graph(CSEG)construction,joint random walk,and recommendation list ***,CSEG is created as a unified heterogeneous graph with students’response behaviors and student(exercise)***,a joint random walk to take full advantage of the spectral properties of nearly uncoupled Markov chains is performed on CSEG,which allows for full exploration of both similar exercises that students have finished and connections between students(exercises)with similar ***,we propose to optimize the recommendation list to obtain different exercise *** analyses of two public datasets,the results demonstrated that PERP can satisfy novelty,accuracy,and diversity.

关键词： Educational data mining Exercise recommend Joint random walk Nearly uncoupled Markov chains Optimization Personalized learning

Irrational-Behavior-Proof Conditions for Stochastic Games over Event Trees

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Journal of the Operations Research Society of China 2024年第1期12卷 243-263页

作者： Lei Wang Cui Liu hong-wei Gao Chong Lin School of Automation Institute of Complexity ScienceQingdao UniversityQingdao 266071ShandongChina School of Mathematics and Statistics Institute of Applied Mathematics of ShandongQingdao UniversityQingdao 266071ShandongChina

In this paper,the irrational-behavior-proof conditions in a class of stochastic dynamic games over event trees are *** kinds of irrational-behavior-proof conditions are proposed by the imputation distribution procedure,and their relationships are *** specific properties for the general transformation of characteristic functions are developed,based on which,the irrational-behavior-proof conditions are proved to be true in a transformed cooperative game.

关键词： Dynamic cooperative game Event tree Irrational-behavior-proof condition Imputation distribution procedure Transformation of characteristic function

Low-cycle fatigue behavior of solutionized and aged WE43 magnesium alloys at room temperature

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Journal of Magnesium and Alloys 2024年第6期12卷 2284-2297页

作者： Yong Cai Jianxiong wei hong Yan Yipeng Chen Rongshi Chen School of Materials Science and Engineering University of Science and Technology of China72 Wenhua RoadShenyang 110016China Shi-changxu Innovation Center for Advanced Materials Institute of Metal ResearchChinese Academy of Sciences72 Wenhua RoadShenyang 110016China School of Materials Science and Engineering Shandong University of Science and TechnologyQingdaoShandong 266590China

The low-cycle fatigue behavior of solutionized(T4)and aged(T6)WE43 magnesium alloys was studied at room *** total strain amplitudes(△ε_(t)/2)were 0.4%,0.5%,0.6%,0.7%and 1.0%.Detailed microstructure evolution was characterized by scanning electron microscope(SEM),electron backscattered diffraction(EBSD)and transmission electron microscopy(TEM).The results showed that plastic strain amplitude decreased with the increasing cycle number in T4 alloy,which is due to the dense persistent slip bands(PSBs)and dynamic precipitates hinderingdislocation *** contrast,the plastic strain amplitude increases gradually in T6 alloy,which is attributed to the enhanced activation of pyramidal *** low-cycle fatigue life of T6 alloy with larger fatigue ductility coefficient is longer than that of T4 *** Coffin-Manson model can accurately predict the fatigue life of T4 and T6 alloys compared to Jahed-Varvani(JV)energy *** T4 alloy,the fatigue damage mechanism was dominated by basal *** T6 alloy,the enhanced pyramidal slip plays an important role to accommodate plastic deformation.

关键词： Low-cycle fatigue WE43 alloy Cyclic hardening/softening JV model Dislocation

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Phase engineering of Ni-Mn binary layered oxide cathodes for sodiumion batteries

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Journal of Energy Chemistry 2024年第4期91卷 501-511页

作者： Feifei hong Xin Zhou Xiaohong Liu Guilin Feng Heng Zhang weifeng Fan Bin Zhang Meihua Zuo Wangyan Xing ping Zhang Hua Yan wei Xiang College of Materials and Chemistry&Chemical Engineering Chengdu University of TechnologyChengdu 610059SichuanChina College of Chemical Engineering Sichuan UniversityChengdu 610065SichuanChina Research Institute for Electronic Science(RIES)and Division of Information Science and Technology Graduate School of Information Science and TechnologyHokkaido UniversityN20W10SapporoHokkaido 001-0020Japan School of Materials Science and Engineering Suzhou University of Science and TechnologySuzhou 215009JiangsuChina Yibin Libode New Materials Co. Ltd.Yibin 644200SichuanChina Engineering Research Center of the Ministry of Education for Advanced Battery Materials School of Metallurgy and EnvironmentCentral South UniversityChangsha 410083HunanChina

Nickel-manganese binary layered oxides with high working potential and low cost are potential candidates for sodium-ion batteries,but their electrochemical properties are highly related to compositional *** composite materials with various phase structures of P3,P2/P3,P2,P2/O3,and P2/P3/O3 were synthesized by manipulating the sodium content and calcination conditions,leading to the construction of a synthetic phase diagram for Na_(x)Ni_(0.25)Mn_(0.75)O_(2)(0.45≤x≤1.1).Then,we compared the electrochemical characteristics and structural evolution during the desodiation/sodiation process of P2,P2/P3,P2/03,and P2/P3/O3-Na_(x)Ni_(0.25)Mn_(0.75)O_(2).Among them,P2/P3-Na0.75Ni0.25Mn0.75O2exhibits the best rate capability of 90.9 mA h g^(-1)at 5 C,with an initial discharge capacity of 142.62 mA h g^(-1)at 0.1 C and a capacity retention rate of 78.25%after 100 cycles at 1 C in the voltage range of 2-4.3 *** observed superior sodium storage performance of P2/P3 hybrids compared to other composite phases can be attributed to the enhanced Na^(+)transfer dynamic,reduction of the Jahn-teller effect,and improved reaction reversibility induced by the synergistic effect of P2 and P3 *** systematic research and exploration of phases in Na_(x)Ni_(0.25)Mn_(0.75)O_(2)provide new sights into high-performance nickel-manganese binary layered oxide for sodium-ion batteries.

关键词： Phase engineering Ni-Mn layered oxide Cathode Sodium-ion batteries

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Overview of computation strategies on the dispersion analysis for explicit finite difference solution of acoustic wave equation

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Petroleum Science 2024年第4期21卷 2311-2328页

作者： Jian-ping Huang wei-Ting Peng Ji-Dong Yang Lu-Feng Lou School of Geosciences China University of Petroleum (East China) Pilot National Laboratory for Marine Science and Technology (Qingdao)

Finite-difference(FD) method is the most extensively employed numerical modeling technique. Nevertheless, when using the FD method to simulate the seismic wave propagation, the large spatial or temporal sampling interval can lead to dispersion errors and numerical instability. In the FD scheme, the key factor in determining both dispersion errors and stability is the selection of the FD weights. Thus,How to obtain appropriate FD weights to guarantee a stable numerical modeling process with minimum dispersion error is critical. The FD weights computation strategies can be classified into three types based on different computational ideologies, window function strategy, optimization strategy, and Taylor expansion strategy. In this paper, we provide a comprehensive overview of these three strategies by presenting their fundamental theories. We conduct a set of comparative analyses of their strengths and weaknesses through various analysis tests and numerical modelings. According to these comparisons, we provide two potential research directions of this field: Firstly, the development of a computational strategy for FD weights that enhances stability; Secondly, obtaining FD weights that exhibit a wide bandwidth while minimizing dispersion errors.

关键词： Finite-difference scheme FD coefficients Dispersion error Forward modeling Numerical simulation

MicroRNA let-7 targets BmCDK1 to regulate cell proliferation and endomitosis of silk gland in the silkworm,Bombyx mori

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Insect Science 2024年第4期31卷 1026-1040页

作者： wei Wang Linshengzhe Ji Xinyuan Jing ping Zhao Qingyou Xia Integrative Science Center of Germplasm Creation in Western China(Chongqing)Science City Biological Science Research CenterSouthwest UniversityChina Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River Ministry of Agriculture and Rural AffairsChongqingChina Engineering Laboratory of Sericultural and Functional Genome and Biotechnology Development and Reform CommissionChongqingChina

MicroRNAs play critical roles in multiple developmental processes in *** previous study showed that CRISPR/Cas9-mediated knock down of the microRNA let-7 in silkworms increased the size of larvae and silk glands,thereby improving the silk production *** this study,we elucidate the molecular mechanism underlying of let-7 regulates *** of differentially expressed genes in response to let-7 knock down revealed enrichment of pathways associated with cell proliferation and DNA ***-7 dysregulation affected the cell cycle and proliferation of the Bombyx mori cell line ***-luciferase and target site mutation assays showed that BmCDK1 is a direct target gene of let-7,with only 1 binding site on its 3′-untranslated *** interference of BmCDK1 inhibited cell proliferation,but this effect was counteracted by co-transfection with let-7 ***,let-7 knock down induced BmCDK1 expression and promoted cell proliferation in multiple tissues,and further induced endomitosis in the silk gland in *** down of BmCDK1 resulted in abnormal formation of a new epidermis,and larval development was arrested at the 2nd or 3rd molt *** together,our results demonstrated that BmCDK1 is a novel target of let-7 in cell fate determination,possessing potential for improving silk yield in silkworm.

关键词： BmCDKI CRISPR/Cas9 cell proliferation let-7 silkworm

Development and validation of a novel non-invasive test for diagnosing nonalcoholic fatty liver disease in Chinese children

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World Journal of Pediatrics 2024年第4期20卷 413-421页

作者： Zhe-Wen Qin Qian-Nan Ren hong-Xi Zhang Ya-Ru Liu Ke Huang wei Wu Guan-ping Dong Yan Ni Jun-Fen Fu Division of Endocrinology National Clinical Research Center for Child HealthNational Children’s Regional Medical CenterThe Children’s HospitalDepartment of EndocrinologyNational Clinical Research Center for Child HealthNational Children’s Regional Medical CenterThe Children’s HospitalZhejiang University School of MedicineHangzhou310052China

With the exploding prevalence of obesity,many children are at risk of developing nonalcoholic fatty liver *** anthropometric and laboratory parameters,our study aimed to develop a model to quantitatively evaluate liver fat content(LFC)in children with *** A well-characterized cohort of 181 children between 5 and 16 years of age were recruited to the study in the Endocrinology Department as the derivation *** external validation cohort comprised 77 *** assessment of liver fat content was performed using proton magnetic resonance *** and laboratory metrics were measured in all subjects.B-ultrasound examination was carried out in the external validation *** Kruskal-Wallis test,Spearman bivariate correlation analyses,univariable linear regressions and multivariable linear regression were used to build the optimal predictive *** The model was based on indicators including alanine aminotransferase,homeostasis model assessment of insulin resistance,triglycerides,waist circumference and Tanner *** adjusted R^(2)of the model was 0.589,which presented high sensitivity and specificity both in internal[sensitivity of 0.824,specificity of 0.900,area under curve(AUC)of 0.900 with a 95%confidence interval:0.783–1.000]and external validation(sensitivity of 0.918 and specificity of 0.821,AUC of 0.901 with a 95%confidence interval:0.818–0.984).Conclusions Our model based on five clinical indicators was simple,non-invasive,and inexpensive;it had high sensitivity and specificity in predicting LFC in ***,it may be useful for identifying children with obesity who are at risk for developing nonalcoholic fatty liver disease.

关键词： Biochemical markers Children Magnetic resonance spectroscopy Nonalcoholic fatty liver disease Pediatric obesity