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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 discovery.Most 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： Drug-target interactions Signed heterogeneous network Link sign prediction Graph neural networks

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Mesenchymal stem cells for repairing glaucomatous optic nerve

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International Journal of Ophthalmology(English edition) 2024年第4期17卷 748-760页

作者： Bai-Yu Hu Mei Xin ming chen Ping Yu Liu-Zhi Zeng Eye School of chengdu University of TCM Chengdu 610000Sichuan ProvinceChina Department of Ophthalmology Chengdu First People’s HospitalChengdu 610095Sichuan ProvinceChina

Glaucoma is a common and complex neurodegenerative disease characterized by progressive loss of retinal ganglion cells(RGCs)and axons.Currently,there is no effective method to address the cause of RGCs degeneration.However,studies on neuroprotective strategies for optic neuropathy have increased in recent years.Cell replacement and neuroprotection are major strategies for treating glaucoma and optic neuropathy.Regenerative medicine research into the repair of optic nerve damage using stem cells has Received considerable attention.Stem cells possess the potential for multidirectional differentiation abilities and are capable of producing RGCfriendly microenvironments through paracrine effects.This article reviews a thorough researches of recent advances and approaches in stem cell repair of optic nerve injury,raising the controversies and unresolved issues surrounding the future of stem cells.

关键词： stem cell glaucoma retinal ganglion cell optic nerve axon regeneration

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A Multi-Channel CMOS Analog Front-End Interface IC with 157.8 d B Current Detection Dynamic Range

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Chinese Journal of Electronics 2024年第2期33卷 393-402页

作者： Kunyu WANG Wenjing XU chengbin ZHANG Yanjun YANG Man-Kay LAW Li ZHOU Jie chen ming chen Institute of Microelectronics of the Chinese Academy of Science University of Chinese Academy of Sciences Zunyi Normal University Institute of Microelectronics and Dept.of ECE FST University of Macau

A high dynamic range and low-noise CMOS(complementary metal-oxide-semiconductor transistor)front-end interface integrated circuit(IC) with multi-channel detection is presented in this paper. Two different current detection channels, composed of a trans-impedance amplifier(TIA) and an integrator-differentiator TIA, are used to boost the current detection range. A capacitance-coupled instrument amplifier(CCIA) is also included to realize high precision voltage detection. A fourth-order sigma-delta modulator using a second-order loop filter and a second-order noise shaping integral quantizer is adopted to realize effective number of bits above 16 bits. The presented interface IC is implemented in 0.18-μm CMOS process with supply voltage of 3.3 V, and a proto-type electrochemical sensor platform with miniaturized sensor array is developed to verify the functionality of the interface IC. Measurement results indicate that the designed interface IC achieves 157.8 d B current detection dynamic range, and the measured input-referred current noise and voltage noise floor are 1.04 p A and 58.4 n V within 10 k Hz integration bandwidths,respectively.

关键词： Readout integrated circuit Sigma-delta modulator Complementary metal-oxide-semiconductor transistor Current detection dynamic range

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Application of machine learning in perovskite materials and devices:A review

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Journal of Energy Chemistry 2024年第7期94卷 254-272页

作者： ming chen Zhenhua Yin Zhicheng Shan Xiaokai Zheng Lei Liu Zhonghua Dai Jun Zhang Shengzhong(Frank)Liu Zhuo Xu School of Electric Power Civil Engineering and ArchitectureCollege of Physics and Electronics EngineeringState Key Laboratory of Quantum Optics and Quantum Optics DevicesShanxiUniversityTaiyuan030006ShanxiChina Key Laboratory of Applied Surface and Colloid Chemistry National Ministry of EducationShanxi Engineering Lab for Advanced Energy TechnologySchool of Materials Science and EngineeringShaanxi Normal UniversityXi'an 710119ShaanxiChina State Key Laboratory of Catalysis Dalian National Laboratory for Clean EnergyDalian Institute of Chemical PhysicsChinese Academy of SciencesDalian 116023LiaoningChina

Metal-halide hybrid perovskite materials are excellent candidates for solar cells and photoelectric devices.In recent years,machine learning(ML)techniques have developed rapidly in many fields and provided ideas for material discovery and design.ML can be applied to discover new materials quickly and effectively,with significant savings in resources and time compared with traditional experiments and density functional theory(DFT)calculations.In this review,we present the application of ML in per-ovskites and briefly review the recent works in the field of ML-assisted perovskite design.Firstly,the advantages of perovskites in solar cells and the merits of ML applied to perovskites are discussed.Secondly,the workflow of ML in perovskite design and some basic ML algorithms are introduced.Thirdly,the applications of ML in predicting various properties of perovskite materials and devices are reviewed.Finally,we propose some prospects for the future development of this field.The rapid devel-opment of ML technology will largely promote the process of materials science,and ML will become an increasingly popular method for predicting the target properties of materials and devices.

关键词： Machine learning Perovskite Materials design Bandgap engineering Stability Crystal structure

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Genome-wide association study of seedling nitrogen-use efficiency-associated traits in common wheat(Triticum aestivum L.)

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The Crop Journal 2024年第1期12卷 222-231页

作者： Huawei Shi Weichong Wang Lifeng Gao Jirong Wu chengmei Hu Huishu Yan Yugang Shi Ning Li Youzhi Ma Yongbin Zhou Zhaoshi Xu Jun chen Wensi Tang Kai chen Daizhen Sun Yuxiang Wu ming chen College of Agriculture Shanxi Agricultural UniversityJinzhong 030801ShanxiChina National Key Facility for Crop Gene Resources and Genetic Improvement Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Nitrogen(N)fertilizer application is essential for crop-plant growth and development.Identifying genetic loci associated with N-use efficiency(NUE)could increase wheat yields and reduce environmental pollution caused by overfertilization.We subjected a panel of 389 wheat accessions to N and chlorate(a nitrate analog)treatments to identify quantitative trait loci(QTL)controlling NUE-associated traits at the wheat seedling stage.Genotyping the panel with a 660K single-nucleotide polymorphism(SNP)array,we identified 397 SNPs associated with N-sensitivity index and chlorate inhibition rate.These SNPs were merged into 49 QTL,of which eight were multi-environment stable QTL and 27 were located near previously reported QTL.A set of 135 candidate genes near the 49 QTL included TaBOX(F-box family protein)and TaERF(ethylene-responsive transcription factor).A Tabox mutant was more sensitive to low-N stress than the wild-type plant.We developed two functional markers for Hap 1,the favorable allele of TaBOX.

关键词： Wheat NUE Genome-wide association study Nitrogen sensitive index Chlorate inhibition rate

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Research on Work-Life Balance of Female Employees

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Proceedings of Business and Economic Studies 2024年第1期7卷 145-149页

作者： ming chen Woosong University Daejeon 34606the Republic of Korea

Nowadays,the pace of work and life is accelerating rapidly,accompanied by significant changes in work content and family structure.Enterprises and employees are encountering various pressures and conflicts.Female employees,in particular,are experiencing increasing pressure in both social labor and family affairs,resulting in ongoing conflicts between work and life.Achieving a balance between these two domains is crucial for female employees.This article aims to analyze the influencing factors of work-life balance for female employees and to propose useful strategies to help them improve it.

关键词： Work-life balance Work-life conflict Female employees

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Efficacy and safety of anlotinib combined with the STUPP regimen in patients with newly diagnosed glioblastoma:a multicenter,single-arm,phase II trial

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Cancer Biology & Medicine 2024年第5期21卷 433-444页

作者： Shuzhen Lai Peijing Li Xiaohui Liu Guihong Liu Tieming Xie Xing Zhang Xiaoxuan Wang Jing Huang Yiqiang Tang Zhigang Liu Guoping Shen Chaoming Li Fangxiao Lu Lei Wang Fagui Jiang Caixing Sun Yuanyuan chen ming chen Department of Radiation Oncology The Second Affiliated Hospital of Soochow UniversitySuzhou 215000China Department of Radiation Oncology Yuebei People’s Hospital Affiliated to the Medical College of Shantou UniversityShaoguan 512026China Chinese Academy of SciencesHangzhou 310022China Department of Radiation Oncology The Second Clinical Medical College of Zhejiang Chinese Medical UniversityHangzhou 311403China Department of Radiation Oncology The Affiliated Hospital of Xuzhou Medical UniversityXuzhou 221004China Chinese Academy of SciencesHangzhou 310022China State Key Laboratory of Translational Medicine and Innovative Drug Development Jiangsu Simcere Diagnostics Co.LtdNanjing 210000China Department of Radiation Oncology The Affiliated Huai’an First People’s Hospital of Nanjing Medical UniversityHuai’an 223399China Department of Radiation Oncology Jiangxi Cancer Hospital of Nanchang UniversityNanchang 330029China Department of Radiotherapy Dongguan Institute of Clinical Cancer ResearchDongguan Key Laboratory of Precision Diagnosis and Treatment for TumorsAffiliated Dongguan HospitalSouthern Medical UniversityDongguan 523059China The Cancer Center The Fifth Affiliated Hospital of Sun Yat-Sen UniversityZhuhai 519000China Department of Radiation Oncology The First Affiliated Hospital of Sun Yat-Sen UniversityGuangzhou 510080China Department of Oncology Maoming People’s HospitalMaoming 525000China Department of Radiation Oncology Kecheng District People’s HospitalQuzhou 324003China Chinese Academy of SciencesHangzhou 310022China Department of Radiation Oncology State Key Laboratory of Oncology in South ChinaSun Yat-sen University Cancer CenterGuangzhou 510060China United Laboratory of Frontier Radiotherapy Technology of Sun Yat-sen University&Chinese Academy of Sciences Ion Medical Technology Co. LtdGuangzhou 510060China

Objective:Glioblastomas are highly vascularized malignant tumors.We determined the efficacy and safety of the anti-angiogenic multi-kinase inhibitor,anlotinib,for a newly diagnosed glioblastoma.Methods:This multicenter,single-arm trial(NCT04119674)enrolled 33 treatment-naïve patients with histologically proven glioblastomas between March 2019 and November 2020.Patients underwent treatment with the standard STUPP regimen[fractionated focal irradiation in daily fractions of 1.8-2 Gy given 5 d/w×6 w(total=54-60 Gy)]or radiotherapy plus continuous daily temozolomide(TMZ)(75 mg/m^(2)of body surface area/d,7 d/w from the first to the last day of radiotherapy),followed by 6 cycles of adjuvant TMZ(150-200 mg/m^(2)×5 d during each 28-d cycle)plus anlotinib(8 mg/d on d 1-14 of each 3-w cycle for 2 cycles during concomitant chemoradiotherapy,8 maximal cycles as adjuvant therapy,followed by maintenance at 8 mg/d.The primary endpoint was progression-free survival(PFS).Secondary endpoints included overall survival(OS)and adverse events(AEs).Results:Thirty-three patients received the planned treatment.The median PFS was 10.9 months(95%CI,9.9-18.7 months)and the 12-month PFS rate was 48.5%.The median OS was 17.4 months(95%CI,14.5-21.1 months)and the 12-month OS rate was 81.8%.The most common AEs included hypertriglyceridemia[58%(n=19)],hypoalbuminemia[46%(n=15)],and hypercholesterolemia[46%(n=15)]during concurrent chemoradiotherapy and leukopenia[73%(n=24)],hypertriglyceridemia[67%(n=22)],and neutropenia[52%(n=17)]during adjuvant therapy.Five patients discontinued treatment due to AEs.HEG1(HR,5.6;95%CI,1.3-23.7;P=0.021)and RP1L1 alterations(HR,11.1;95%CI,2.2-57.2;P=0.004)were associated with a significantly shorter PFS.Conclusions:Anlotinib plus the STUPP regimen has promising anti-tumor activity against glioblastoma and manageable toxicity.HEG1 and RP1L1 alterations might be novel predictive biomarkers of the response to anlotinib.

关键词： Glioblastoma anti-angiogenesis multi-kinase inhibitor anlotinib temozolomide progression-free survival

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Engineered extracellular vesicles: A new approach for targeted therapy of tumors and overcoming drug resistance

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Cancer Communications 2024年第2期44卷 205-225页

作者： chen ming-Kun chen Zi-Xian Cai Mao-Ping chen Hong chen Zhuang-Fei Zhao Shan-Chao Department of Urology The Third Affiliated Hospital of Southern Medical UniversityGuangzhouGuangdongP.R.China The Third Clinical College Southern Medical UniversityGuangzhouGuangdongP.R.China Luoyang Key Laboratory of Organic Functional Molecules College of Food and DrugLuoyang Normal UniversityLuoyangHenanP.R.China Department of Urology Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdongP.R.China

Targeted delivery of anti-tumor drugs and overcoming drug resistance in malig-nant tumor cells remain significant clinical challenges.However,there are only few effective methods to address these issues.Extracellular vesicles(EVs),actively secreted by cells,play a crucial role in intercellular information transmis-sion and cargo transportation.Recent studies have demonstrated that engineered EVs can serve as drug delivery carriers and showed promising application prospects.Nevertheless,there is an urgent need for further improvements in the isolation and purification of EVs,surface modification techniques,drug assem-bly processes,and precise recognition of tumor cells for targeted drug delivery purposes.In this review,we summarize the applications of engineered EVs in cancer treatment and overcoming drug resistance,and current challenges asso-ciated with engineered EVs are also discussed.This review aims to provide new insights and potential directions for utilizing engineered EVs as targeted delivery systems for anti-tumor drugs and overcoming drug resistance in the near future.

关键词： drug delivery drug resistance extracellular vesicles nanoparticles

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Fangji Fuling Decoction Alleviates Sepsis by Blocking MAPK14/FOXO3A Signaling Pathway

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Chinese Journal of Integrative Medicine 2024年第3期30卷 230-242页

作者： WANG Yi chen ming-qi DAI Lin-feng ZHANG Hai-dong WANG Xing Department of Critical Care Medicine Changzhou Hospital of Traditional of Chinese Medicine Affiliated to Nanjing University of Chinese MedicineChangzhouJiangsu Province213000China Department of Critical Care Medicine Jiangsu Province Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese MedicineNanjing210029China

Objective:To examine the therapeutic effect of Fangji Fuling Decoction(FFD) on sepsis through network pharmacological analysis combined with in vitro and in vivo experiments.Methods:A sepsis mouse model was constructed through intraperitoneal injection of 20 mg/kg lipopolysaccharide(LPS).RAW264.7 cells were stimulated by 250 ng/m L LPS to establish an in vitro cell model.Network pharmacology analysis identified the key molecular pathway associated with FFD in sepsis.Through ectopic expression and depletion experiments,the effect of FFD on multiple organ damage in septic mice,as well as on cell proliferation and apoptosis in relation to the mitogen-activated protein kinase 14/Forkhead Box O 3A(MAPK14/FOXO3A) signaling pathway,was analyzed.Results:FFD reduced organ damage and inflammation in LPS-induced septic mice and suppressed LPS-induced macrophage apoptosis and inflammation in vitro(P<0.05).Network pharmacology analysis showed that FFD could regulate the MAPK14/FOXO signaling pathway during sepsis.As confirmed by in vitro cell experiments,FFD inhibited the MAPK14 signaling pathway or FOXO3A expression to relieve LPS-induced macrophage apoptosis and inflammation(P<0.05).Furthermore,FFD inhibited the MAPK14/FOXO3A signaling pathway to inhibit LPS-induced macrophage apoptosis in the lung tissue of septic mice(P<0.05).Conclusion:FFD could ameliorate the LPS-induced inflammatory response in septic mice by inhibiting the MAPK14/FOXO3A signaling pathway.

关键词： sepsis Fangji Fuling Decoction mitogen-activated protein kinase 14/Forkhead Box O 3A signaling pathway inflammatory response apoptosis lung injury Chinese medicine

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On the inviscid limit of the compressible Navier-Stokes equations near Onsager's regularity in bounded domains

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Science China Mathematics 2024年第1期67卷 1-22页

作者： Robin ming chen Zhilei Liang Dehua Wang Runzhang Xu Department of Mathematics University of PittsburghPittsburghPA 15260USA School of Mathematics Southwestern University of Finance and EconomicsChengdu 611130China College of Mathematical Sciences Harbin Engineering UniversityHarbin 150001China

The viscous dissipation limit of weak solutions is considered for the Navier-Stokes equations of compressible isentropic flows confined in a bounded domain.We establish a Kato-type criterion for the validity of the inviscid limit for the weak solutions of the Navier-Stokes equations in a function space with the regularity index close to Onsager’s critical threshold.In particular,we prove that under such a regularity assumption,if the viscous energy dissipation rate vanishes in a boundary layer of thickness in the order of the viscosity,then the weak solutions of the Navier-Stokes equations converge to a weak admissible solution of the Euler equations.Our approach is based on the commutator estimates and a subtle foliation technique near the boundary of the domain.

关键词： inviscid limit Navier-Stokes equations Euler equations weak solutions bounded domain Katotype criterion Onsager’s regularity

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