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Drug-Target Interactions Prediction Based on Signed Heterogeneous Graph Neural Networks

Chinese Journal of Electronics 2024年第1期33卷 231-244页

作者： Ming CHEN Yajian jiANG Xiujuan LEI Yi PAN Chunyan ji wei jiANG College of Information Science and Engineering Hunan Normal University School of Computer Science Shaanxi Normal University Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of Sciences Computer Science Department BNU-HKBU United International College

Drug-target interactions(DTIs) prediction plays an important role in the process of drug *** computational methods treat it as a binary prediction problem, determining whether there are connections between drugs and targets while ignoring relational types information. Considering the positive or negative effects of DTIs will facilitate the study on comprehensive mechanisms of multiple drugs on a common target, in this work, we model DTIs on signed heterogeneous networks, through categorizing interaction patterns of DTIs and additionally extracting interactions within drug pairs and target protein pairs. We propose signed heterogeneous graph neural networks(SHGNNs), further put forward an end-to-end framework for signed DTIs prediction, called SHGNN-DTI,which not only adapts to signed bipartite networks, but also could naturally incorporate auxiliary information from drug-drug interactions(DDIs) and protein-protein interactions(PPIs). For the framework, we solve the message passing and aggregation problem on signed DTI networks, and consider different training modes on the whole networks consisting of DTIs, DDIs and PPIs. Experiments are conducted on two datasets extracted from Drug Bank and related databases, under different settings of initial inputs, embedding dimensions and training modes. The prediction results show excellent performance in terms of metric indicators, and the feasibility is further verified by the case study with two drugs on breast cancer.

关键词： Drugs Training Proteins Measurement Message passing Prediction methods Graph neural networks

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Characterization of rock thermophysical properties and factors affecting thermal conductivity−A case study of Datong Basin,China

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Journal of Groundwater Science and Engineering 2024年第1期12卷 4-15页

作者： Meng-lei ji Shuai-chao wei wei Zhang Feng Liu Yu-zhong Liao Ruo-xi Yuan Xiao-xue Yan Long Li Institute of Hydrogeology and Environmental Geology Chinese Academy of Geological SciencesShijiazhuang 050061China Technology Innovation Center of Geothermal&Hot Dry Rock Exploration and Development Ministry of Natural ResourcesShijiazhuang 050061China China University of Geosciences(Beijing) Beijing 100083China

Rock thermal physical properties play a crucial role in understanding deep thermal conditions,modeling the thermal structure of the lithosphere,and discovering the evolutionary history of sedimentary *** advancements in geothermal exploration,particularly the identification of high-temperature geothermal resources in Datong Basin,Shanxi,China,have opened new *** study aims to characterize the thermal properties of rocks and explore factors influencing thermal conductivity in basins hosting high-temperature geothermal resources.A total of 70 groups of rock samples were collected from outcrops in and around Datong Basin,Shanxi *** property tests were carried out to analyze the rock properties,and the influencing factors of thermal conductivity were studied through experiments at different temperature and water-filled *** results indicate that the thermal conductivity of rocks in Datong,Shanxi Province,typically ranges from 0.690 W/(m·K)to 6.460 W/(m·K),the thermal diffusion coefficient ranges from 0.441 mm^(2)/s to 2.023 mm^(2)/s,and the specific heat capacity of the rocks ranges from 0.569 KJ/(kg·℃)to 1.117 KJ/(kg·°C).Experimental results reveal the impact of temperature and water saturation on the thermal conductivity of the *** thermal conductivity decreases with increasing temperature and rises with high water saturation.A temperature correction formula for the thermal conductivity of different lithologies in the area is proposed through linear *** findings from this study provide essential parameters for the assessment and prediction,development,and utilization of geothermal resources in the region and other basins with typical high-temperature geothermal resource.

关键词： Datong Basin Rock thermal conductivity Thermal diffusivity Specific heat capacity Influencing factors

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A highly reduced Mo_(74) polyoxometalate featuring high proton conductivity accessed by building block strategy

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Science China Chemistry 2024年第3期67卷 862-868页

作者： Shi-Yi Liu Xue-Xin Li wei-chao Chen Kui-Zhan Shao Xin-Long Wang chao Qin Zhong-Min Su Key Laboratory of Polyoxometalate and Reticular Material Chemistry of Ministry of Education Department of ChemistryNortheast Normal UniversityChangchun 130024China State Key Laboratory of Supramolecular Structure and Materials Institute of Theoretical ChemistryCollege of ChemistryJilin UniversityChangchun 130021China

Highly reduced polyoxometalates(POMs) are predicted to be used as rather high energy density materials;however,it still suffers from the limited cluster species and reduction *** we demonstrate that it is possible to employ the building block strategy to generate a highly reduced polyoxomolybdate(C_(2)H_(8)N)_(14)(NH_(4))_(4)H_(14)[Mo_(48)-ⅤMo_(26)ⅥO_(202)(OH)_(12)(SO_(4))_(6)]·46H_(2)O(Mo_(74)).The fundamental Mo-based{Mo_x}(x=4,5,and 6) building blocks,which are templated by tetra-coordinated anions{MoO_(4)}or{SO_(4)},not only lay foundation for the formation of Mo_(74) featuring an unprecedented reduction ratio of 65%,but also give rise to SBBs-mediated(secondary building blocks) supramolecular dense packing interactions among the isolated Mo_(74) clusters that are favorable for proton ***,high proton conductivity(2.04×10^(-2)S cm^(-1)) had been realized at 50℃ and 90% relative humidity,revealing one of the well-known POMs-based crystalline proton conducting *** result highlights that this building block approach possesses great potential in producing highly reduced POM systems that can achieve controllable reduced ratio and desirable properties.

关键词： polyoxometalate building block molybdenum highly reduced state proton conduction

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Infrared microspectroscopy beamline BL06B at SSRF

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Nuclear Science and Techniques 2024年第1期35卷 10-17页

作者： Te ji Hua-Chun Zhu wei-wei Peng jie Wang Hong-wei Zhao Ai-Guo Li Min Chen Shanghai Synchrotron Radiation Facility Shanghai Advanced Research InstituteChinese Academy of SciencesShanghai 201210China

The infrared microspectroscopy beamline(BL06B) is a phase Ⅱ beamline project at the Shanghai Synchrotron Radiation Facility(SSRF). The construction and optical alignment of BL06B were completed by the end of 2020. By 2021, it became accessible to users. The synchrotron radiation infrared(SRIR) source included edge radiation(ER) and bending magnet radiation(BMR). The extracted angles in the horizontal and vertical directions were 40 and 20 mrad, respectively. The photon flux, spectral resolution, and focused spot size were measured at the BL06B endstation, and the experimental results were consistent with theoretical calculations. SRIR light has a small divergence angle, high brightness, and a wide wavelength range. As a source of IR microscopy, it can easily focus on a diffraction-limited spatial resolution with a high signal-to-noise ratio(SNR). The BL06B endstation can be applied in a wide range of research fields, including materials, chemistry, biology, geophysics, and pharmacology.

关键词： Synchrotron radiation Infrared beamline Infrared microspectroscopy

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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

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Chalcogen-dependent catalytic properties of RuX2 (X = S/Se/Te) nanoparticles decorated carbon nanofibers for hydrogen evolution in acidic and alkaline media

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Nano Research 2024年第4期17卷 2528-2537页

作者： Chengkai He Yue wei jia Xu Yujie wei Tao Wang Rongfei Liu Lvlv ji Zhun Liu Sheng Wang School of Materials Science and Engineering Zhejiang Sci-Tech UniversityHangzhou 310018China Department of Physics Shaoxing UniversityShaoxing 312000China Zhejiang Kangjiesi New Material Technology Co. LTDZhuji 311800China

Transition metal dichalcogenides(TMDs),with the general formula MX_(2)(M=Mo/W/Fe/Co/Ni,etc.;X=S/Se/Te),have attracted extensive research interests for hydrogen evolution reaction(HER).Compared with numerous studies on noble-metal-free TMDs,the chalcogen-dependent HER catalytic properties of noble-metal-based TMDs are lack of sufficient research ***,a facile electrospinning-assisted synthetic strategy is proposed to synthesize ruthenium dichalcogenides(RuX_(2),X=S/Se/Te)nanoparticles decorated carbon nanofibers(CNFs).Benefiting from the identical nanofibrous morphology and exposed crystal planes of RuX_(2)(111),the catalytic activities of RuX_(2)@CNFs samples were investigated and compared in a fair and direct *** electrochemical measurements coupled with density functional theory calculations were carried out to probe their intrinsic HER catalytic activities,resulting in the catalytic activity order of RuS_(2)@CNFs>RuSe_(2)@CNFs>RuTe_(2)@CNFs in acidic media and that of RuS_(2)@CNFs>RuTe_(2)@CNFs>RuSe_(2)@CNFs in alkaline *** superior catalytic performance of RuS_(2)@CNFs mainly stems from the relative lower HER energy barriers and thereby the higher intrinsic catalytic activity of RuS_(2)(111),leading to ultralow overpotentials of 44 and 9 mV at 10 mA·cm^(-2) in acidic and alkaline media,***_(2)(111)is endowed with the more optimized Gibbs free energy of hydrogen adsorption(ΔGH*)than RuTe_(2)(111),but RuTe_(2)(111)shows enhanced catalytic property for H_(2)O dissociation and OH-desorption than RuSe_(2)(111),therefore,resulting in the altered catalytic activity sequences for RuSe_(2) and RuTe_(2) in acidic and alkaline media.

关键词： hydrogen evolution reaction transition metal dichalcogenides carbon nanofibers electrocatalysis catalytic activity

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Optimization of spatial layouts for underground facilities to achieve carbon neutrality in cities:A multi-agent system model

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Underground Space 2024年第6期19卷 251-278页

作者： Lingxiang wei Dongjun Guo Junyuan ji Zhilong Chen Huapeng Hu Xiaoli Peng Research Center for Underground Space Army Engineering University of PLANanjing 210007China School of Materials Science and Engineering Yancheng Institute of TechnologyYancheng 224051China

Subways,underground logistics systems and underground parking,as the primary facilities types of underground,contribute significantly to the achievement of carbon–neutral cities by moving surface transportation to underground,thereby releasing surface space for the creation of more urban blue-green space for carbon ***,in-depth studies on carbon neutrality strategies as well as reliable layout optimization solutions of these three types of underground facilities are *** study proposes a spatial layout optimization strategy for carbon neutrality using underground hydrogen storage and geothermal energy for these three types of underground facilities employing a multi-agent system ***,three spatial layout relationships,competition,coordination,and followership,between five underground facilities that contribute to emission reduction were ***,the implementation steps for optimizing the spatial layout of underground facilities were determined by defining the behavioral guidelines for spatial environment,underground facility,and synergistic ***,using the Tianfu New District in Chengdu City,China,as a case study,layouts of underground facilities under three different underground space development scenarios were simulated to verify the *** findings of this study address the gap in the research on underground spatial facilities and their layout optimization in response to emission *** study provided a significant reference for the study of underground space and underground resources at the planning level to aid in achieving carbon–neutral cities.

关键词： Urban underground space(UUS) Carbon-neutral city Multi-agent system model Underground facility Spatial layouts

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Wellbore-heat-transfer-model-based optimization and control for cooling downhole drilling fluid

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Petroleum Science 2024年第3期21卷 1955-1968页

作者： chao Wang He Liu Guo-wei Yu Chen Yu Xian-Ming Liu Peng Huang Yangtze University Jingzhou434023HubeiChina State Key Laboratory of Petroleum Resources and Engineering China University of Petroleum(Beijing)Beijing2249China CNPC Bohai Drilling Engineering Co. LtdTianjin300280China Exploration Development and Construction Engineering Division of PetroChina jidong Oilfield Company Tangshan63200HebeiChin Henan University of Urban Construction Pingdingshan467036HenanChina

To address the two critical issues of evaluating the necessity of implementing cooling techniques and achieving real-time temperature control of drilling fluids underground in the current drilling fluid cooling technology,we first established a temperature and pressure coupled downhole heat transfer model,which can be used in both water-based and oil-based drilling ***,fourteen factors,which could affect wellbore temperature,were *** on the standard deviation of the downhole temperature corresponding to each influencing factor,the influence of each factor was *** influencing factors that can be used to guide the drilling fluid's cooling technology were drilling fluid thermal conductivity,drilling fluid heat capacity,drilling fluid density,drill strings rotation speed,pump rate,viscosity,ROP,and injection *** nondominated sorting genetic algorithm was used to optimize these six parameters,but the optimization process took 182 *** these eight parameters'influence rules with the nondominated sorting genetic algorithm can reduce the optimization time to 108 ***,the downhole temperature has been demonstrated to increase with the inlet temperature increasing linearly under quasi-steady *** this law and PID,the downhole temperature can be controlled,which can reduce the energy for cooling the surface drilling fluid and can ensure the downhole temperature reaches the set value as soon as possible.

关键词： Drilling Cooling Influencing factors Analysis Optimization Control

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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

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One-Pot Stereoselective Synthesis of Different Fused Multicyclic Iminosugars Based on the Iminium-lon Intermediate

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Chinese Journal of Chemistry 2024年第2期42卷 142-150页

作者： Song Xie jilai Wu Likai Zhou chao wei Xiaoliu Li Hua Chen Key Laboratoryof Chemical Biology of Hebei Province College of Chemistry and Material ScienceHebei UniversityBaodingHebei 071002China College of Chemistry and Chemical Engineering Xingtai UniversityXingtaiHebei 054001China

Different novel fused multicyclic iminosugars were synthesized from D-ribose tosylate,aniline and vinyl ethyl ether by one-pot three-component stereoselective[4+2]reaction at different *** iminium-ion is the key intermediate for the *** a result,several complex fused iminosugars 3a were obtained by aza-Diels-Alder mechanism at 60℃,while a series of aza-C-glycosides 5a were prepared by Mannich reaction at room temperature accompanied by another tetrahydroquinoline-fused iminosugars 4a(tricyclic derivatives)through aza-Diels-Alder *** strategy will help to construct structurally diverse and bioactive iminosugar analogues.

关键词： Fused multicyclic iminosugar Aza-Diels-Alder cycloaddition Mannich reaction Tetrahydroquinoline Multicomponent reactions Enantioselectivity Cyclization

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