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Collaborative Matrix Factorization with Soft Regularization for Drug-Target Interaction Prediction

Journal of Computer Science & Technology 2021年第2期36卷 310-322页

作者： Li-Gang Gao Meng-yun yang Jian-Xin Wang School of Computer Science and Engineering Central South UniversityChangsha 410083China Hunan Provincial Key Laboratory of Bioinformatics Central South UniversityChangsha 410083China School of Science Shaoyang UniversityShaoyang 422000China

Identifying the potential drug-target interactions(DTI)is critical in drug *** drug-target interaction prediction methods based on collaborative filtering have demonstrated attractive prediction ***,many corresponding models cannot accurately express the relationship between similarity features and DTI *** order to rationally represent the correlation,we propose a novel matrix factorization method,so-called collaborative matrix factorization with soft regularization(SRCMF).SRCMF improves the prediction performance by combining the drug and the target similarity information with matrix *** contrast to general collaborative matrix factorization,the fundamental idea of SRCMF is to make the similarity features and the potential features of DTI approximate,not ***,SRCMF obtains low-rank feature representations of drug similarity and target similarity,and then uses a soft regularization term to constrain the approximation between drug(target)similarity features and drug(target)potential features of *** comprehensively evaluate the prediction performance of SRCMF,we conduct cross-validation experiments under three different *** terms of the area under the precision-recall curve(AUPR),SRCMF achieves better prediction results than six state-of-the-art ***,under different noise levels of similarity data,the prediction performance of SRCMF is much better than that of collaborative matrix *** conclusion,SRCMF is robust leading to performance improvement in drug-target interaction prediction.

关键词： drug-target interaction collaborative matrix factorization soft regularization noisy data

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NUMERICAL SIMULATION OF UNSTEADY FLOW FOR VISCO- ELASTIC FLUID IN AN ECCENTRIC ANNULUS WITH INNER ROD RECIPROCATION

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Journal of Hydrodynamics 2008年第2期20卷 261-266页

作者： HE Feng-yun yang Shu-ren Department of Petroleum Engineering Daqing Petroleum Institute Daqing 163318 China

The equation governing the unsteady flow of viscoelastic fluids in an eccentric annulus was derived by using the common conversion Maxwell fluid constitutive equation and then discretized by the control volume method. The velocity distribution of flow field was computed by using the ADI method. The influences of the pressure gradient, eccentricity, stroke length, and stroke frequency on the velocity and flow capacity in the flow field was analyzed. The foundation for further research of the eccentric wear problem of the pumping rod in polymer-flood well was laid.

关键词： polymer-flood well viscoelastic fluid eccentric annulus unsteady flow eccentric wear

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Synergetic N-doped carbon with MoPd alloy for robust oxygen reduction reaction

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Nano Research 2023年第7期16卷 8996-9002页

作者： Chaojie Cen Wenjing Tang Tonghui Zhao yun Song yun yang Quanlong Xu Wei Chen Zhejiang Key Laboratory of Carbon Materials College of Chemistry and Materials EngineeringWenzhou UniversityWenzhou 325035China

Synergistic catalysis opens up a new venue to improve the comprehensive application of the ***,a composite catalyst(Mo-Pd@N-C)consisting of the N-doped carbon derived from pyrolysis of spherical polypyrrole and MoPd nanoparticles(NPs)was constructed to emphasize the strong metal-support interaction for robust oxygen reduction reaction(ORR).The enhanced anchoring between the MoPd NPs and the substrate,and the N-species formed on the carbon matrix make the Mo-Pd@N-C deliver excellent performance with a half-wave potential of 0.945 V(*** hydrogen electrode(RHE))for ORR,superior than that of commercial Pt/C(0.86 V).More importantly,it shows a negligible half-wave potential decline(<5 mV)and only~20%of mass activity(MA)attenuation after 30,000 cycles stability test,obviously better than those of Pt/C(~70%of MA attenuation and~30 mV of half-wave potential decline after only 15,000 cycles).This work highlights a novel synergistic method to prolong the life and improve the commercial prospects of the catalysts.

关键词： synergistic catalysis oxygen reduction reaction N-doped carbon MoPd alloy stability

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Study on HOBEM Based on Analytical Panel Integrals Related to Translating-Pulsating Source for Hydrodynamic Responses of Vessels Sailing in Waves

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China Ocean Engineering 2022年第3期36卷 348-362页

作者： yang yun-tao ZHU Ren-chuan LI Yu-long School of Naval Architecture and Civil Engineering Jiangsu University of Science and TechnologyZhangjiagang 215600China State Key Laboratory of Ocean Engineering Collaborative Innovation Center for Advanced Ship and Deep-Sea ExplorationSchool of Naval ArchitectureOcean and Civil EngineeringShanghai Jiao Tong UniversityShanghai 200240China Technology Centre for Offshore and Marine Singapore(TCOMS)Singapore

A higher-order boundary element method(HOBEM)incorporated with analytical panel integrals related to translat-ing-pulsating source Green’s function is proposed for the hydrodynamic response prediction of ships advancing in *** this method,the 9-node bi-quadratic curvilinear elements employed to discretize the mixed-source/dipole boundary integral equation are mapped into the parametric plane through a coordinate *** in order to ease the numerical instability problem,a novel analytical quadrature is derived to calculate the influence coefficients by changing the integral order and using integration by *** singularity caused by infinite discontinuity is analyzed and eliminated by adopting some mathematical *** the calculations of panel integrals of Green’s function and its x-derivative,the analytical integral method is proved to be always accurate even for field points approaching the free surface,where numerical quadrature is impossible to give reasonable *** on this,a higher-order seakeeping program is developed and applied in the motion response prediction of two different types of ships(i.e.,a wall-sided ship Wigley III and a non-wall-sided ship S175).By comparing the computed results with the corresponding experimental data and numerical solutions of the translating-pulsating and higher-order Green’s function methods based on traditional Gauss quadrature,it is found that the HOBEM based on analytical quadrature is of better accuracy and *** the non-wall-sided ship,only the present method can produce reasonable pre-diction of motion responses,while obvious oscillatory phenomenon is observed in the results of the other two numerical methods based on Gauss quadrature.

关键词： HOBEM translating-pulsating Green’s function analytical quadrature seakeeping forward speed

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Subacute toxicity of exogenous manganese on rat hippocampal neurons Examination by MRI and optical microscopy

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Neural Regeneration Research 2008年第5期3卷 550-553页

作者： Xiaoli Xu yun Xiang Min yang School of Medicine ＆ Life Science Jianghan University Wuhan 430056 Hubei Province China

BACKGROUND： Manganism may cause learning and memory impairment by influencing the normal function of the hippocampus, however, this effect requires further examination. OBJECTIVE： To investigate the effects of manganism on the rat hippocampus using immunohistochemistry and MRI examination. DESIGN, TIME AND SETTING： A randomized controlled study, performed in the School of Medicine and Life Science, Jianghan University and the State Key Laboratory of Atomic ＆ Molecular Physics and Spectroscopy, Chinese Academy of Science, from July to September 2005. MATERIALS： Fourteen healthy SD rats aged two months were selected for this study. MnCl2 4H2O （BHD, UK）（batch number： 9791325）; glial fibrillary acidic protein （GFAP） staining kit （Beijing Zhongshan Biotechnology）; Biospec 4.7T/30 animal MRI formatter （Bruker, Germany）. METHODS： Fourteen rats were randomly divided into a control group （n =7） and a manganism group （n = 7）. Rats in the manganism group received intraperitoneal injection of MnCl2 · 4H2O （50 mg/kg）, once a day, for four successive days. Rats in the control group were injected according to the manganism regimen, but using saline instead of manganese solution. MAIN OUTCOME MEASURES： Twenty-four hours after the last injection, rats were examined using MRI. Immunohistochemically stained GFAP and hematoxylin-eosin stained hippocampal sections were observed under optical microscopy. RESULTS： Fourteen rats were included in the final analysis. After manganese treatment, T1 weighted image and inversion recovery MR1 demonstrated that the signal intensity was significantly enhanced in hippocampus, compared to controls. Neuronal necrosis was not observed in the hippocampus after HE staining. As compared to the control group, GFAP expression was markedly enhanced in the hippocampus of the manganism group. CONCLUSION： Within the rat brain, manganese preferentially localizes to the hippocampus and can induce astroctye activation.

关键词： manganism hippocampus rats MRI glial fibrillary acidic protein

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Synthesis of 6,8-dichloroquinolones utilizing new method and evaluation of their antibacterial activities

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Chinese Chemical Letters 2007年第12期18卷 1479-1482页

作者： yun Xu yang Hui Yuan Guo Department of Chemistry University of Science and Technology Beijing 100083 China Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences Peking Union Medical College Beijing 100050 China

Several 6,8-dichloroquinolone analogues were synthesized from the key intermediate compound of 2,3,4,5-tetrachlorobenzene carbonyl chloride, which was obtained from the starting material of tetrachlorophthalic anhydride. Their in vitro antibacterial activities were evaluated. As a result of this study, compounds 21e and 21d were twofold more potent than ciprofloxacin （CPFX） and norfloxacin （NFLX） against Staphylococcus aureus-9, and with the same potent as CPFX and NFLX while against Escherichia coli-2, but were less potent than references in against Pseudomonas aeruginosa-17.

关键词： Quinolones Synthesis Antibacterial 6,8-Dichloroquinolone

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Novel synthesis of a strained para-cyclophane derivative

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Chinese Chemical Letters 2007年第4期18卷 397-399页

作者： Zhi Hao Shi yun yang Wei Institute of Chemical Engineering Nanjing University of Science and Technology Nanjing 210094 China

A [P. Rajakumar, A.M.A. Rasheed, Tetrahedron 61（22）（2005） 5351] para-cyclophane derivative was synthesized via intramolecular esterification of a dipeptide surrogate containing asparagine to form tetrahydropyrimi... 详细信息

关键词： Asparagine Cyclization Para-cyclophane

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Rotor orientation direction controls geometric curvature and chirality for assemblies of motor amphiphiles in water

Aggregate

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Aggregate 2023年第2期4卷 237-246页

作者： yun-Han yang yang Qin yang Zhang Ling Zhang PCFM Lab and GDHPRC Lab School of ChemistrySun Yat-Sen UniversityGuangzhouChina

Control over geometric curvature and chirality of assemblies in pure aqueous media is key to the design of responsive materials and molecular *** we show how aggregate geometric curvature and chirality of motor amphiphiles could be switched from bicontinuous calabashes to nanoribbons or from vesicles to nanoribbons by modulating rotor orientation direction with dual light/heat stimuli to influence spontaneous curvature in *** photoisomerization and thermal helix inversion processes of molecular motors have been studied at the molecular level,and the transformation of supramolecular assemblies has been investigated at the microscopic *** morphological evolution of the calabash-shaped assembly can be kinetically captured,suggesting that the bicontinuous calabash-shaped structures are different from the bowl-shaped aggregates based on solvent-driven assembly upon the addition of non-solvent or *** investigation of dual optical/thermal control of rotor orientation can provide a new strategy for tuning the geometric curvature and chirality of nanoassemblies at the nanoscale,arriving ultimately the clusteroluminescence through-space electronic communication at responsive supramolecular nanosystems.

关键词： aqueous media chiral control curvature control dynamic assemblies molecular motor rotor orientation direction

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Improvement, Comparison, and Application of Field Measurement Methods for Grassland Vegetation Fractional Coverage

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Journal of Integrative Plant Biology 2005年第9期47卷 1074-1083页

作者： Xiao-Bing LI yun-Hao CHEN Hua yang yun-Xia ZHANG College of Resources Sciences and Technology Key Laboratory of Environmental Change and Natural Disaster of the Ministry of Education Beijing Normal University Beijing 100875 China

As one of the important vegetation parameters, vegetation fractional coverage （VFC） is more difficult to measure accurately among a good many parameters of plant communities. The temperate typical steppe in the north of China was chosen for investigation in the present study and a digital camera was used to measure herb community coverage in the field, adopting methods of ocular estimation, gridding measurement, visual interpretation, supervised classification, and information extraction of color spatial transformation to calculate the VFC of images captured by the digital camera. In addition VFC calculated by various methods was analyzed and compared VFC, enabling us to propose an effective method for measuring VFC using a digital camera. The results of the present study indicate that：（i） as two common useful and effective methods of measuring VFC with a digital camera, not only does the error of estimated values of visual estimation and supervised classification vary considerably, but the degree of automatization is very low and depends, to a great extent, on the manipulator; （ii） although the method of visual interpretation may assure the precision of the calculated VFC and enable the precision of results obtained using other methods to be determined, as far as large quantities of data are concerned, this method has the disadvantages of wasting time and energy, and the applications of this method are limited; （iii） the precision and stability of VFC calculated using the grid and node method are superior to those of visual estimation and supervised classification and inferior to those of visual interpretation, but, as for visual interpretation and supervised classification, gridding measurements are difficult to apply in practice because they are not time efficient; and （iv） in terms of the precision of calculation of the VFC, an information-extracting model based on an intensity, hue, saturation （IHS） color space-multi-component series segmentation strategy is s

关键词： color space transformation digital camera field measurement grassland vegetationfractional coverage.

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Control Strategies of Asymmetric Strip Shape in Six-High Cold Rolling Mill

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Journal of Iron and Steel Research International 2011年第9期18卷 27-32页

作者： ZHANG yun yang Quan WANG Xiao-chen Engineering Research Institute University of Science and Technology Beijing Beijing 100083 China

It is a complicated problem for cold-rolled strip to improve asymmetric strip shape in strip production. A roll system and strip coupled model of six-high cold rolling mill was established with finite element method to estimate the effect of intermediate roll shifting, tilting, symmetric and asymmetric bending technologies on strip profile. To reduce asymmetric defects of strip shape as much as possible, some control strategies were proposed, including tilting and asymmetric bending of intermediate roll and work roll. The combinations of these three control strategies can effectively eliminate asymmetric strip shape defects. Finally, the closed-loop control model of asymmetric flat- ness at the last stand was given, and the flatness control system with the function of asymmetric strip shape control was also designed for cold tandem mill.

关键词： cold rolling monitoring characteristics asymmetric strip shape control strategy

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