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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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TransRec++:Translation-based sequential recommendation with heterogeneous feedback

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Frontiers of Computer Science 2022年第2期16卷 190-192页

作者： Zhuo-Xin ZHAN ming-Kai HE Wei-Ke pan Zhong ming National Engineering Laboratory for Big Data System Computing Technology Shenzhen UniversityShenzhen 518060China College of Computer Science and Software Engineering Shenzhen UniversityShenzhen 518060China

1 Introduction Nowadays,recommender systems are widely used because of the information overload problem on the *** are a variety of feedback in recommender systems,such as explicit feedback,implicit feedback,sequential feedback,*** them,modeling of heterogeneous sequential feedback,which contains not only different types of feedback such as examinations and purchases but also the sequential information,is an emerging and important problem receiving more and more *** sequential feedback is relatively easy to be collected in a deployed system and is also able to provide more information than the homogeneous feedback,which is thus expected to be helpful in improving the recommendation accuracy.

关键词： feedback recommendation sequential

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Hyperbranched polylysine:Synthesis,mechanism and preparation for NIR-absorbing gold nanoparticles

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Chinese Chemical Letters 2019年第7期30卷 1428-1431页

作者： Yiying Ge pan Li Yanfei Guan Chang-ming Dong School of Chemistry and Chemical Engineering Shanghai Key Laboratory of Electrical Insulation and Thermal Aging Shanghai Jiao Tong University

The ring-opening polymerization (ROP) of N-(tetrafluoroboran ammonium)-L-lysine-N-carboxyanhydride (NH3BF4-Lys NCA) was initiated by triethylamine to prepare hyperbranched polylysine (HPlys) fluoroborate with narrow polydispersity at a low temperature. Both mass spectroscopy analysis and DFT computation evidenced that the resultant cyclic dimer mainly initiated ROP as a secondary species according to normal amine mechanism. The hyperbranched polylysine in aqueous solution existed in a unimolecular state at low concentrations, but transformed into spherical micellar aggregates at a high concentration of 5 mg/mL, as characterized by dynamic laser scattering and transmission electron microscopy. By utilizing multivalent coordination interactions between hyperbranched polylysine and gold, the plasmonic gold nanoparticles (HPlys@Au NPs) were successfully prepared in aqueous solution, which elevated the solution by 23.1℃ upon 5 min of NIR laser irradiation (808 nm, 2 W/cm2).

关键词： Hyperbranched polylysine NCA ROP NIR Gold nanoparticles

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EXTRACTION OF INTERNAL TIDE FROM CURRENT

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Journal of Hydrodynamics 2001年第3期13卷 138-142页

作者： pan, Zeng-Di Han, Chun-ming Yu, Wei-Dong Key Lab. of Mar. Sci. and Numl. Mode First Inst. of Oceanography State Oceanic Administration Qingdao 266061 China

In order to extract the internal tidal current from the current data which is not measured from the sea surface to the bottom, a data processing method is developed. It is based on the fact that the internal wave currents above and below the sharp thermocline are inverse in direction. This method is a practical extension to that proposed by Shu (1985) that can be only used to quite ideal current data. The ADCP data collected on the South China Sea is then processed by this method. The internal tidal current is successfully extracted.

关键词： Data processing Thermal gradients Tides

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Migration of ammonium nitrogen in ion-absorbed rare earth soils during and post in situ mining: a column study and numerical simulation analysis

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Frontiers of Environmental Science & Engineering 2023年第8期17卷 137-151页

作者： Gaosheng Xi Xiaojiang Gao ming Zhou Xiangmei Zhai ming Chen Xingxiang Wang Xiaoying Yang Zezhen pan Zimeng Wang Department of Environmental Science and Engineering Fudan UniversityShanghai 200438China School of Resource and Environmental Engineering Jiangxi University of Science and TechnologyGanzhou 341000China CAS Key Laboratory of Soil Environment and Pollution Remediation Institute of Soil ScienceChinese Academy of SciencesNanjing 210008China National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary Shanghai 202151China Shanghai Institute of Pollution Control and Ecological Security Shanghai 200001China

Ion-absorbed rare earth mines,leached in situ,retain a large amount of ammonium nitrogen(NH4–N)that continuously releases into the surrounding ***,quantitative descriptions and predictions of the transport of NH4–N across mining area with hill slopes are not fully ***,laboratory column experiments were designed with an inclined slope(a sand box)to examine the spatial temporal transport of NH4–N in soils collected from the ionic rare earth elements(REE)mining *** HYDRUS-2D model simulation of the experimental data over time showed that soils had a strong adsorption capacity toward NH4–*** non-equilibrium model(CNEM)could well simulate the transport of NH4–N through the soil-packed *** simulation of the transport-adsorption processes at three flow rates of leaching agents revealed that low flow rate enabled a longer residence time and an increased NH4-N adsorption,but reduced the extraction efficiency for *** the subsequent rainwater washing process,the presence of slope resulted in the leaching of NH4–N on the surface of the slope,while the leaching of NH4–N deep inside the column was ***,the high-intensity rainfall significantly increased the leaching,highlighting the importance of considering the impact of extreme weather conditions during the leaching ***,our study advances the understanding of the transport of NH4–N in mining area with hills,the impact of flow rates of leaching agents and precipitation intensities,and presents as a feasible modeling method to evaluate the environmental risks of NH4–N pollution during and post REE in situ mining activities.

关键词： Ion-absorbed rare earth Ammonium nitrogen transport HYDRUS-2D Numerical simulation

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Progranulin:A promising biomarker and therapeutic target for fibrotic diseases

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Acta Pharmaceutica Sinica B 2024年第8期14卷 3312-3326页

作者： Fan Yang ming-Han Cheng Hai-Feng pan Jian Gao Pediatric Translational Medicine Institute Shanghai Children’s Medical CenterSchool of MedicineShanghai Jiao Tong UniversityShanghai 200000China Department of Ophthalmology the First Affiliated Hospital of Anhui Medical UniversityHefei 230022China Department of Epidemiology and Biostatistics School of Public HealthAnhui Medical UniversityHefei 230022China Inflammation and Immune Mediated Diseases Laboratory of Anhui Province Hefei 230022China

Progranulin(PGRN),a multifunctional growth factor-like protein expressed by a variety of cell types,serves an important function in the physiologic and pathologic processes of fibrotic diseases,including wound healing and the inflammatory *** was discovered to inhibit proinflammation effect by competing with tumor necrosis factor-alpha(TNF-a)binding to TNF ***,excessive tissue repair in the development of inflammation causes tissue *** investigations have indicated the significance of PGRN in regulating inflammatory ***,multiple studies have shown that PGRN was linked to fibrogenesis,and was considered to monitor the formation of fibrosis in multiple organs,including liver,cardiovascular,lung and *** paper is a comprehensive review summarizing our current knowledge of PGRN,from its discovery to the role in *** is followed by an in-depth look at the characteristics of PGRN,consisting of its structure,basic function and intracellular ***,we will discuss the potential of PGRN in the diagnosis and treatment of fibrosis.

关键词： Progranulin Fibrotic disease Fibrosis Inflammation Biomarker Therapeutic target PGRN/TNFR interaction Signaling pathway

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Hydroxycalciopyrochlore, A New Mineral Species from Sichuan, China

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Acta Geologica Sinica(English Edition) 2014年第3期88卷 748-753页

作者： YANG Guangming LI Guowu XIONG ming pan Baoming YAN Chenjie State Key Laboratory of Geological Processes and Mineral Resources China University of Geosciences Crystal Structure Laboratory China University of Geosciences

Hydroxycalciopyrochlore,ideally （Ca,Na,U,□）2（Nb,Ti）2O6（OH）,cubic,is a new mineral species （IMA2011-026） within the pyrochlore supergroup that was found occurring at the Maoniuping mine,Mianning County,Xichang prefecture,Sichuan Province,southwest *** mineral is found in an alkali feldspar granite rare-earth ore deposit （26-27 Ma）.Associated minerals include calcite,barite,celestine,albite,aegirine,aegirine-augite,fluorite,parasite-（Ce）,thorite,thorianite,zircon,galena,sphalerite,magnetite,and *** occur mostly as octahedra,and less often as dodecahedra and tetrahexahedra or combinations *** occur with an allotriomorphic habit with a thick triangular tabular *** generally range from 0.1 to 1 mm in *** mineral is brownishblack,greenish-black and black on fresh sections with a brown *** crystal is translucent,and has a greasy lustre on fresh *** is metamict without any observed parting or cleavage and with a conchoidal *** Vickers microhardness is 572 kg/mm2 （5-6 on the Mohs hardness scale）.The density measured by hydrostatic weighing is 5.10（3） g/*** strongest four reflections in the X-ray powder-diffraction pattern [d in（A）（Ⅰ） hkl] are：2.9657 （100） 2 2 2,1.8142 （34） 0 4 4,1.5463 （21） 2 2 6,2.5688 （18） 0 0 *** unit-cell parameters are a =10.381（4）（A）,V=1118.7（7）（A）3,Z =*** structure was solved and refined in the space group Fd3m with R =*** empirical formula is （Ca0.74Na0.5sU0.40Ce0.05Fe0.02□0.21）2.00（Nb1.15Ti0.s0Ta0.03Al0.01Mg0.01）2.00O6.02 [（OH）1.01F0.09]1.10,on the basis of 2 atoms of B pfu; the simplified formula is （Ca,Na,U,□）2（Nb,Ti）2O6（OH）.Type material is deposited in the Geological Museum of China,Beijing,People＇s Republic of China,catalogue number M11800.

关键词： Mineralogy Hydroxycalciopyrochlore pyrochlore supergroup crystal structure Sichuanprovince

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Two New Cadmium Metal-organic Frameworks Based on a Mixed-donor Ligand

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Chemical Research in Chinese Universities 2016年第4期32卷 539-544页

作者： WANG Xiaofang SONG Qingshan pan Ying QIU Shilun XUE ming State Key Laboratory of lnorganie Synthesis and Preparative Chemistry Jilin University Changehun 130012 P. R. China

The self-assembly of a prominent mixed-donor ligand, 5-[4-（1H-tetrazolyl）phen]isophthalic acid（H3TZPl）, with a Cd2＋ center generates two new metal-organic frameworks： [Cd（H2TZPI）2（H2O）2]n（JUC-163） and [Cd2（TZPI）（μ3-OH）（H2O）2]-***（JUC-164）. The two complexes demonstrate different structures for the ligand＇s different coordination modes and configurations. JUC-163 shows a 2D layer structure and further forms into a 3D supramolecular framework by noncovalent interactions（C--H…O, O--H…N and π…π interactions）, whereas JUC-164 exhibits a fascinating 3D framework for the outstanding coordination modes and configurations of the ligand, which are fit for the complex structure. And also, the factor of different cadmium salts（chloride and nitrate） which are used in synthesis progress is worth to notice for the construction of the two distinct structures. The luminescent properties of these metal-organic frameworks were also investigated.

关键词： Cadmium Mixed-donor ligand Metal-organic framework Luminescence

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WB crystals with oxidized surface as counter electrode in dye-sensitized solar cells

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Science Bulletin 2017年第2期62卷 114-118页

作者： Jian pan Chao Zhen Lianzhou Wang Gang Liu Hui-ming Cheng Shenyang National Laboratory for Materials Science Institute of Metal Research Chinese Academy of Sciences Shenyang 11O016 China ARC Centre of Excellence for Functional Nanomaterials School of Chemical Engineering and AIBN The University of Queensland QLD 4072 Australia

Tungsten boride(WB) crystals, whose surface tends to be oxidized when exposed to air, were demonstrated to have a comparable activity to platinum as counter electrode material in dye-sensitized solar cells. The synergistic effect of both catalytically active surface layer WOxand electronically conductive internal WB is considered to be responsible for the high activity of the WB crystals.

关键词： Counter electrode Tungsten boride Dye-sensitized solar cell Tungsten oxide

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An investigation on changes in glacier mass balance and hypsometry for a small mountainous glacier in the northeastern Tibetan Plateau

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Journal of Mountain Science 2017年第8期14卷 1624-1632页

作者： CAO Bo pan Bao-tian CAI ming-yong WANG Jie Key Laboratory of Western China's Environmental Systems (MOE) College of Earth and Environmental SciencesLanzhou University Satellite Environment Center of Ministy of Environmental Protection (MEP)

Mass balance is a key indicator of the sensitivity of glaciers to climate change. Field measurement is one of the most important ways to study the mass balance of glaciers. Based on observations of mass balance in the ablation zone of Shuiguan Glacier No.4, Qilian Mountains, China, combined with the balance ratio between accumulation and ablation, we established a linear relation between mass balance and altitude. The results show that the mean annual mass balance of this glacier was ~510 mm w.e. from 2010 to 2013. The uncertainty in the balance ratio value does not lead to a significant difference in the mass balance. The equilibrium-line altitude rose by 180 m from 1972 to 2013, while the accumulation–area ratio decreased from 0.68 to 0.25. These variations may be caused by changes in air temperature. Meanwhile, the glacier is at present not in a steady state, and it may continue to shrink by a further ~900 m, even without further climate warming. In the western Lenglongling Mountains, assuming that the glaciers are in a steady state and the Equilibrium-line altitudes(ELAs)remain similar, there will be only 46 glaciers left, covering a total area of 19.2 km^2, in other words, only 22.3% of the glaciers area in 1972.

关键词： Accumulation-area ratio (AAR) Equilibrium-line altitude (ELA) Glacier mass balance

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