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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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Safety and efficacy comparison of remimazolam and propofol for intravenous anesthesia during gastroenteroscopic surgery of older patients:A meta-analysis

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World Journal of Clinical Cases 2024年第7期12卷 1272-1283页

作者： Fang-Zhuo Li cheng Zhao Yi-Xun Tang ji-Tong Liu Department of Anesthesiology The First Affiliated Hospital of Hunan Normal University(Hunan Provincial People’s Hospital)Changsha 410005Hunan ProvinceChina Department of Anesthesiology Zhangjiajie People's HospitalZhangjiajie 427000Hunan ProvinceChina

BACKGROUND Remimazolam is characterized by rapid action and inactive metabolites.It is used as the general anesthetic for many clinical surgeries.In this study,we performed a meta-analysis to evaluate whether remimazolam is superior to propofol for gastroenteroscopy in older patients.AIM To compare the adverse events and efficacy of remimazolam and propofol during gastroenteroscopy in older adults.METHODS The PubMed,Web of Science,the Cochrane Library databases were queried for the relevant key words"remimazolam,""and propofol,""and gastrointestinal endoscopy or gastroscopy."The search scope was"Title and Abstract,"and the search was limited to human studies and publications in English.Seven studies wherein remimazolam and propofol were compared were included for the metaanalysis.RESULTS We selected seven randomized controlled trials involving 1445 cases for the analysis.Remimazolam reduced the hypotension(relative risk,RR=0.44,95%CI:0.29-0.66,P=0.000),respiratory depression(RR=0.46,95%CI:0.30-0.70,P=0.000),injection pain(RR=0.12,95%CI:0.05-0.25,P=0.000),bradycardia(RR=0.37,95%CI:0.24-0.58,P=0.000),and time to discharge[weighted mean difference(WMD)=-0.58,95%CI:-0.97 to-0.18,P=0.005],compared to those after propofol administration.No obvious differences were observed for postoperative nausea and vomiting(RR=1.09,95%CI:0.97-1.24,P=0.151),dizziness(RR=0.77,95%CI:0.43-1.36,P=0.361),successful sedation rate(RR=0.96,95%CI:0.93-1.00,P=0.083),or the time to become fully alert(WMD=0.00,95%CI:-1.08-1.08,P=0.998).CONCLUSION Remimazolam appears to be safer than propofol for gastroenteroscopy in older adults.However,further studies are required to confirm these findings.

关键词： Remimazolam Propofol Gastroenteroscopy Anesthesia Older adults Sedation Adverse events

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Evaluating different levels of information on the calibration of building energy simulation models

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Building Simulation 2024年第4期17卷 657-676页

作者： Siyu cheng Zeynep Duygu Tekler Hongyuan ji Wenxin Li Adrian Chong Department of the Built Environment College of Design and EngineeringNational University of Singapore4 Architecture DriveSingapore117566Singapore School of Civil Engineering and Architecture Chongqing University of Science and TechnologyChongqing401331China School of Energy and Environment Southeast UniversityNanjing210096China

A poorly calibrated model undermines confidence in the effectiveness of building energy simulation, impeding the widespread application of advanced energy conservation measures (ECMs). Striking a balance between information-gathering efforts and achieving sufficient model credibility is crucial but often obscured by ambiguities. To address this gap, we model and calibrate a test bed with different levels of information (LOI). Beginning with an initial model based on building geometry (LOI 1), we progressively introduce additional information, including nameplate information (LOI 2), envelope conductivity (LOI 3), zone infiltration rate (LOI 4), AHU fan power (LOI 5), and HVAC data (LOI 6). The models are evaluated for accuracy, consistency, and the robustness of their predictions. Our results indicate that adding more information for calibration leads to improved data fit. However, this improvement is not uniform across all observed outputs due to identifiability issues. Furthermore, for energy-saving analysis, adding more information can significantly affect the projected energy savings by up to two times. Nevertheless, for ECM ranking, models that did not meet ASHRAE 14 accuracy thresholds can yield correct retrofit decisions. These findings underscore equifinality in modeling complex building systems. Clearly, predictive accuracy is not synonymous with model credibility. Therefore, to balance efforts in information-gathering and model reliability, it is crucial to (1) determine the minimum level of information required for calibration compatible with its intended purpose and (2) calibrate models with information closely linked to all outputs of interest, particularly when simultaneous accuracy for multiple outputs is necessary.

关键词： calibration building energy simulation(BES) energy conservation measure(ECM) level of information field measurements

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Quantitative discrimination of surface adsorbed NOx species on CeO_(2) via spectrophotometry for SCR denitration investigation

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Journal of Rare Earths 2024年第6期42卷 1066-1072,I0003页

作者： Songil Sin jiawei ji Lijun cheng Zhiwen Gu Chong Tan Kwangchol Ri Changjin Tang School of Environment Nanjing Normal UniversityNanjing210023China Department of Mining Engineering Kim Chaek University of TechnologyPyongyang999093Democratic People's Republic of Korea Laboratory of Mesoscopic Chemistry of MOE School of Chemistry and Chemical EngineeringNanjing UniversityNanjing20023China Institute of Chemical Engineering Hamhung University of Chemical EngineeringHamhungDemocratic People's Republic of Korea jiangsu Province Engineering Research Center of Environmental Risk Prevention and Emergency Response Technology Nanjing210023China

CeO_(2)-based catalysts are widely investigated for selective catalytic reduction(SCR)of NO with NH3.Interaction of NO/O_(2) with CeO_(2) generally produces two surface species,i.e.,nitrates and nitrites.However,the explicit quantification of these two species is still unresolved.Herein,we reported that spectrophotometry characterization was effective in determining surface adsorbed NOx species on CeO_(2) by measuring the corresponding ions(NO_(2)-and NO_(3)^(-))dissolved in aqueous solution.Experimental results show that both nitrate(-NO_(3))and nitrite(-NO_(2))species can be quantitatively evaluated and the accuracy is verified by calibrating with NOx-TPD result.Exclusive transfer of adsorbed NOx from catalyst surface to aqueous solution is confirmed and the dissolution process can be accelerated by ultrasonic treatment.Moreover,useful information related to evolution of surface NOx species under various conditions(O_(2) treatment,different adsorption temperature and duration)and over different catalysts(Fe_(2)O_(3),MnO_(2) and MnOx—CeO_(2))are provided.The result of present study demonstrates the potential of spectrophotometry for quantitative discrimination of surface NOx species on CeO_(2) and other oxide-based materials,which is conducive to mechanism analysis of SCR reaction.

关键词： Quantitative evaluation Spectrophotometry analysis Nitrate species Nitrite species CeO_(2)catalyst NH_(3)-SCR

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A reweighted damped singular spectrum analysis method for robust seismic noise suppression

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Petroleum Science 2024年第3期21卷 1671-1682页

作者： wei-Lin Huang Yan-Xin Zhou Yang Zhou wei-jie Liu ji-Dong Li State Key Laboratory of Petroleum Resources and Engineering China University of Petroleum (Beijing) SINOPEC Petroleum Exploration and Production Research Institute SINOPEC Geophysical Research Institute

(Multichannel) Singular spectrum analysis is considered as one of the most effective methods for seismic incoherent noise suppression. It utilizes the low-rank feature of seismic signal and regards the noise suppression as a low-rank reconstruction problem. However, in some cases the seismic geophones receive some erratic disturbances and the amplitudes are dramatically larger than other receivers. The presence of this kind of noise, called erratic noise, makes singular spectrum analysis(SSA) reconstruction unstable and has undesirable effects on the final results. We robustify the low-rank reconstruction of seismic data by a reweighted damped SSA(RD-SSA) method. It incorporates the damped SSA, an improved version of SSA, into a reweighted framework. The damping operator is used to weaken the artificial disturbance introduced by the low-rank projection of both erratic and random noise. The central idea of the RD-SSA method is to iteratively approximate the observed data with the quadratic norm for the first iteration and the Tukeys bisquare norm for the rest iterations. The RD-SSA method can suppress seismic incoherent noise and keep the reconstruction process robust to the erratic disturbance. The feasibility of RD-SSA is validated via both synthetic and field data examples.

关键词： Singular spectrum analysis Damping operator Seismic erratic noise Seismic signal processing Robust low-rank reconstruction

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Cavitation research with computational fluid dynamics:From Euler-Euler to Euler-Lagrange approach

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Journal of Hydrodynamics 2024年第1期36卷 1-23页

作者： Bin ji Zi-yang Wang Huai-yu cheng Rickard E.Bensow State Key Laboratory of Water Resources Engineering and Management Wuhan UniversityWuhan430072China Department of Mechanics and Maritime Sciences Chalmers University of TechnologyGothenburgSweden

Unsteady cavitating flow often contains vapor structures with a wide range of different length scales,from micro-bubbles to large cavities,which issues a big challenge to precisely investigate its evolution mechanism by computational fluid dynamics(CFD)method.The present work reviews the development of simulation methods for cavitation,especially the emerging Euler-Lagrange approach.Additionally,the progress of the numerical investigation of hot and vital issues is discussed,including cavitation inception,cloud cavitation inner structure and its formation mechanism,cavitation erosion,and cavitation noise.It is indicated that the Euler-Lagrange method can determine cavitation inception point better.For cloud cavitation,the Euler-Lagrange method can reveal the source of microbubbles and their distribution law inside the shedding cloud.This method also has advantages and great potential in assessing cloud cavitation-induced erosion and noise.With the ever-growing demands of cavitation simulation accuracy in basic research and engineering applications,how to improve the Euler-Lagrange method’s stability and applicability is still an open problem.To further promote the application of this advanced CFD simulation technology in cavitation research,some key issues are to be solved and feasible suggestions are put forward for further work.

关键词： numerical simulation Euler-Euler method Euler-Lagrange method bubble dynamicsgy,Gothenburg,Sweden

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Calcitonin gene-related peptide inhibits neuronal apoptosis in heatstroke rats via PKA/p-CREB pathway

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Chinese Journal of Traumatology 2024年第1期27卷 18-26页

作者： jie Zhu Ya-Hong Chen jing-jing ji cheng-Xiang Lu Zhi-Feng Liu Department of Pediatric General Hospital of Southern Theater Command of PLAGuangzhou510010China Department of Medical Intensive Care Unit General Hospital of Southern Theater Command of PLAGuangzhou510010China Department of Intensive Care Unit Zhongshan Hospital Xiamen UniversityXiamenFujian province361004China

Purpose:The incidence of heatstroke(HS)is not particularly high;however,once it occurs,the consequences are serious.It is reported that calcitonin gene-related peptide(CGRP)is protective against brain injury in HS rats,but detailed molecular mechanisms need to be further investigated.In this study,we further explored whether CGRP inhibited neuronal apoptosis in HS rats via protein kinase A(PKA)/p-cAMP response element-binding protein(p-CREB)pathway.Methods:We established a HS rat model in a pre-warmed artificial climate chamber with a temperature of(35.5±0.5)℃and a relative humidity of 60%±5%.Heatstress was stopped once core body temperature reaches above 41℃.A total of 25 rats were randomly divided into 5 groups with 5 animals each:control group,HS group,HS+CGRP group,HS+CGRP antagonist(CGRP8-37)group,and HS+CGRP+PKA/p-CREB pathway blocker(H89)group.A bolus injection of CGRP was administered to each rat in HS+CGRP group,CGRP8-37(antagonist of CGRP)in HS+CGRP8-37 group,and CGRP with H89 in HS+CGRP+H89 group.Electroencephalograms were recorded and the serum concentration of S100B,neuron-specific enolase(NSE),neuron apoptosis,activated caspase-3 and CGRP expression,as well as pathological morphology of brain tissue were detected at 2 h,6 h,and 24 h after HSin vivo.The expression of PKA,p-CREB,and Bcl-2 in rat neurons were also detected at 2 h after HSin vitro.Exogenous CGRP,CGRP8-37,or H89 were used to determine whether CGRP plays a protective role in brain injury via PKA/p-CREB pathway.The unpairedt-test was used between the 2 samples,and the mean±SD was used for multiple samples.Double-tailedp<0.05 was considered statistically significant.Results:Electroencephalogram showed significant alteration ofθ(54.50±11.51vs.31.30±8.71,F=6.790,p=0.005)andαwave(16.60±3.21vs.35.40±11.28,F=4.549,p=0.020)in HS group compared to the control group 2 h after HS.The results of triphosphate gap terminal labeling(TUNEL)showed that the neuronal apoptosis of HS rats was increased in the cortex(9.67±3.16vs.1.80±1.10,F=11.002,p=0.001)and

关键词： Heatstroke Calcitonin gene-related peptide Brain injury Apoptosis

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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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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 attention.Herein,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 manner.Detailed 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 media.The 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,respectively.RuSe_(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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Single-cluster electronics using metallic clusters:Fabrications,regulations,and applications

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Nano Research 2024年第1期17卷 65-78页

作者： Caiyun wei wei Xu Shurui ji Ruiyun Huang Junyang Liu Wenqiu Su jie Bai jiale Huang Wenjing Hong State Key Laboratory of Physical Chemistry of Solid Surfaces National Engineering Research Centre of Chemicals for Electronic ManufacturingCollege of Chemistry and Chemical Engineering&Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province(IKKEM)Xiamen UniversityXiamen 361005China

Metallic clusters,ranging from 1 to 2 nm in size,have emerged as promising candidates for creating nanoelectronic devices at the single-cluster level.With the intermediate quantum properties between metals and semiconductors,these metallic clusters offer an alternative pathway to silicon-based electronics and organic molecules for miniaturized electronics with dimensions below 5 nm.Significant progress has been made in studies of single-cluster electronic devices.However,a clear guide for selecting,synthesizing,and fabricating functional single-cluster electronic devices is still required.This review article provides a comprehensive overview of single-cluster electronic devices,including the mechanisms of electron transport,the fabrication of devices,and the regulations of electron transport properties.Furthermore,we discuss the challenges and future directions for single-cluster electronic devices and their potential applications.

关键词： single-cluster junctions electronic properties electron transport metallic clusters structure regulation

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