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

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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

Thermal stability of permafrost under U-shaped crushed rock embankment of the Qinghai-Tibet Railway

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Advances in Climate Change Research 2024年第1期15卷 158-169页

作者： Kun-ming XU Guan-Li jiANG ji chen Qing-Bai WU State Key Laboratory of Frozen Soil Engineering Northwest Institute of Eco-Environment and ResourcesChinese Academy of SciencesLanzhou 730000China University of Chinese Academy of Sciences Beijing 100049China Beiluhe Observation Station of Frozen Soil Environment and Engineering Northwest Institute of Eco-Environment and ResourcesChinese Academy of SciencesLanzhou730000China

The U-shaped crushed rock embankment(UCRE),of which widely utilized in the permafrost regions along the Qinghai-Tibet Railway,has the capability to rapidly reduce the ground temperature of the underlying ***,there remains uncertainty regarding the adaptation of UCRE to climate change and its long-term cooling *** study focuses on nine UCRE monitoring sites along the Qinghai-Tibet Railway to analyze the dynamic variations of the ground temperature underlying permafrost from 2006 to *** efficiency of UCRE in stabilizing permafrost temperature in different permafrost zones is evaluated by considering the permafrost table,ground temperature,and MAGT,as well as the temperature difference between the top and bottom of the crushed rock layer and the ground temperature variation index(GTVI).The results show that UCRE is suitable for application in extremely unstable warm permafrost regions where the MAGT is higher than-0.5℃.Moreover,UCRE effectively diminishes the disparity in permafrost thermal stability between the sunny and shaded shoulders of the *** short-term and long-term effect of cooling permafrost is experiencing a change related with permafrost ***,in stable cold permafrost regions with MAGT lower than-1.5℃,the long-term cooling effect of UCRE on permafrost seems to gradually di-minishes,but UCRE continues to fulfill the role of stabilizing the underlying permafrost thermal state over the *** results show that UCRE can quickly restore and stabilize the thermal state of permafrost in the early stages of construction,and adapt to the influence of future climate *** findings provide important guidance for understanding the variations of permafrost thermal stability beneath the embankment in permafrost regions,as well as for improving the embankment stability and operational safety of the Qinghai-Tibet Railway.

关键词： Qinghai-Tibet Railway U-shaped crushed rock embankment Climate change Permafrost zone Ground temperature variation index Long-term coolingrole

Surface reconstruction of heterostructures in alkaline medium towards enhanced electrocatalytic hydrogen evolution

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Rare Metals 2024年第6期43卷 2636-2647页

作者： ming-Yang Yang ji Yuan Xue-Lian Fu jing-jing chen jing Hu Zhou-Guang Lu chen Liu Guangdong Research Center for Interfacial Engineering of Functional Materials Shenzhen Key Laboratory of Polymer Science and TechnologyShenzhen Key Laboratory of Energy Electrocatalytic MaterialsCollege of Materials Science and EngineeringShenzhen UniversityShenzhen 518060China Shenzhen Key Laboratory of Interfacial Science and Engineering of Materials Department of Materials Science and EngineeringSouthern University of Science and TechnologyShenzhen 518055China

Constructing heterostructures has proved to be a successful strategy to fabricate electrocatalysts with high efficiency for water ***,the structure evolution in alkaline hydrogen evolution reaction lacks investigation and the specific active center remains ***,we take the well-designed Ni_(3)S_(2)@VO_(2) heterostructures as a model to investigate the electrocatalytic activity and the surface reconstruction process of heterostructure catalysts in alkaline *** Ni_(3)S_(2)@VO_(2) heterostructures,with Ni_(3)S_(2) nanorods as the core and VO_(2) nanoflakes as the shell,coupled with the high conductive Ni_(3)S_(2),the hydrophilic VO_(2) and modulated electronic structures at the interfaces,exhibited prominent activity and superior stability at various current ***,the ex-situ characterizations confirmed that the surface reconstruction from Ni_(3)S_(2)@VO_(2) into Ni_(3)S_(2)@amorphous-Ni(OH)_(2) in alkaline media could optimize the water dissociation barrier and exposed large active area,thereby contributing to improved electrocatalytic *** study not only introduces novel high-performance electrocatalysts for hydrogen evolution reaction(HER),but also provides a new avenue for re-examining hetero-structural catalysts in alkaline solutions.

关键词： Heterostructures Ni_(3)S_(2)@VO_(2) Surface reconstruction Water dissociation Alkaline hydrogen evolution

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Differences in Variations of Long-Lived and Short-Lived Summer Heat Waves during 1981-2020 over Eastern China and Their Corresponding Large-Scale Circulation Anomalies

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Journal of Meteorological Research 2024年第3期38卷 414-436页

作者： Liqun ji Haishan chen Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters/Key Laboratory of Meteorological Disaster Ministry of EducationNanjing University of Information Science&TechnologyNanjing210044China School of Atmospheric Sciences Nanjing University of Information Science&TechnologyNanjing210044China

Using daily maximum temperature(Tmax)data from 516 observation stations in eastern China from 1981 to 2020,this study employed a relative threshold method to define short-and long-lived heat waves(HWs)by considering regional climate differences to investigate the spatial characteristics and evolution of large-scale circulation during summer *** results demonstrated spatial disparities in the frequency distribution of HWs of different durations and differences in the magnitude of duration and intensity between short-and long-lived *** orthogonal function analysis revealed three dominant spatial modes for both short-and long-lived *** first mode showed that short-lived HWs occur prominently in both northern and southern regions,whereas long-lived HWs mainly occur in the northern *** second mode was characterized by a meridional dipole pattern in both *** third mode exhibited a quadrupole pattern for short-lived HWs and a tripole pattern for long-lived *** in the center locations of anomalies in the 500-hPa geopotential height and 850-hPa wind fields significantly influenced the temperature and precipitation anomaly distribution of typical HWs by affecting the warm column in the lower troposphere,cloud distribution,and moisture ***,the atmospheric circulation evolution processes of typical HWs associated with the different modes of long-and short-lived HWs were linked to distinct teleconnection *** the three modes of long-lived(short-lived)HWs,there was stronger(weaker)wave flux activity with multiple(single)propagation *** westward Atlantic wave train activity at 300 hPa triggered the synergistic action of meridional and zonal wave fluxes,favoring the strengthening and maintenance of positive anomalies in geopotential height of 500 *** may have contributed to the formation of long-lived *** findings provide valuable insights to enhance our understanding and prediction of summer

关键词： short-lived heat waves(HWs) long-lived HWs empirical orthogonal function(EOF)modes large-scale atmospheric circulation

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Better use of experience from other reservoirs for accurate production forecasting by learn-to-learn method

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Petroleum Science 2024年第1期21卷 716-728页

作者： Hao-chen Wang Kai Zhang Nancy chen Wen-Sheng Zhou chen Liu ji-Fu Wang Li-ming Zhang Zhi-Gang Yu Shi-Ti Cui Mei-Chun Yang China University of Petroleum(East China) 66 Changjiang West RoadQingdao West Coast New AreaQingdao266580ShandongChina University of Calgary 2500 University Dr NWCalgaryT2N 1N4AlbertaCanada Qingdao University of Technology Qingdao266071ShandongChina State Key Laboratory of Offshore Oil Exploitation Beijing100028China CNOOC Research Institute Ltd. Beijing100028China CNPC Tarim Oilfield Branch Company Korla841000XinjiangChina National Engineering Laboratory for Exploration and Development of Low-Permeability Oil and Gas Fields Xi'an710000ShaanxiChina Sinopec Matrix Co. LTDQingdao266000ShandongChina

To assess whether a development strategy will be profitable enough,production forecasting is a crucial and difficult step in the *** development history of other reservoirs in the same class tends to be studied to make predictions ***,the permeability field,well patterns,and development regime must all be similar for two reservoirs to be considered in the same *** results in very few available experiences from other reservoirs even though there is a lot of historical information on numerous reservoirs because it is difficult to find such similar *** paper proposes a learn-to-learn method,which can better utilize a vast amount of historical data from various ***,the proposed method first learns how to learn samples before directly learning rules in ***,by utilizing gradients from networks with independent parameters and copied structure in each class of reservoirs,the proposed network obtains the optimal shared initial parameters which are regarded as transferable information across different *** on that,the network is able to predict future production indices for the target reservoir by only training with very limited samples collected from reservoirs in the same *** cases further demonstrate its superiority in accuracy to other widely-used network methods.

关键词： Production forecasting Multiple patterns Few-shot learning Transfer learning

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Advances in the study of gastric organoids as disease models

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World Journal of Gastrointestinal Oncology 2024年第5期16卷 1725-1736页

作者： Yi-Yang Liu De-Kun Wu ji-Bing chen You-ming Tang Feng jiang Graduate School Guangxi University of Chinese MedicineNanning 530011Guangxi Zhuang Autonomous RegionChina Teaching Experiment and Training Center Guangxi University of Chinese MedicineNanning 530011Guangxi Zhuang Autonomous RegionChina Central Laboratory Ruikang Hospital Affiliated to Guangxi University of Traditional Chinese MedicineNanning 530011Guangxi Zhuang Autonomous RegionChina Department of Digestive Disease Ruikang Hospital Affiliated to Guangxi University of Traditional Chinese MedicineNanning 530011Guangxi Zhuang Autonomous RegionChina AIDS Research Center Ruikang Hospital Affiliated to Guangxi University of Traditional Chinese MedicineNanning 530011Guangxi Zhuang Autonomous RegionChina

Gastric organoids are models created in the laboratory using stem cells and sophisticated three-dimensional cell culture *** models have shown great promise in providing valuable insights into gastric physiology and advanced disease *** review comprehensively summarizes and analyzes the research advances in culture methods and techniques for adult stem cells and induced pluripotent stem cell-derived organoids,and patient-derived *** potential value of gastric organoids in studying the pathogenesis of stomach-related diseases and facilitating drug screening is initially *** construction of gastric organoids involves several key steps,including cell extraction and culture,three-dimensional structure formation,and functional *** the structure and function of the human stomach by disease modeling with gastric organoids provides a platform to study the mechanism of gastric cancer induction by Helicobacter *** addition,in drug screening and development,gastric organoids can be used as a key tool to evaluate drug efficacy and toxicity in preclinical *** can also be used for precision medicine according to the specific conditions of patients with gastric cancer,to assess drug resistance,and to predict the possibility of adverse ***,despite the impressive progress in the field of gastric organoids,there are still many unknowns that need to be addressed,especially in the field of regenerative ***,the reproducibility and consistency of organoid cultures are major challenges that must be *** challenges have had a significant impact on the development of gastric ***,as technology continues to advance,we can foresee more comprehensive research in the construction of gastric *** research will provide better solutions for the treatment of stomach-related diseases and personalized medicine.

关键词： Organoids Stomach neoplasms Helicobacter pylori Drug evaluation Preclinical Precision

In-situ powder mixing for laser-based directed energy deposition of functionally graded materials

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Advances in Manufacturing 2024年第1期12卷 150-166页

作者： ji-Peng chen Shou-Chun Xie He Huang School of Mechanical and Electronic Engineering Nanjing Forestry UniversityNanjing210037People’s Republic of China Nanjing Huirui Photoelectric Technology Co. LtdNanjing211121People’s Republic of China

The mixing of powders is a highly relevant field under additive manufacturing,however,it has attracted limited interest to *** in-situ mixing of various powders remains a significant *** paper proposes a new method utilizing a static mixer for the in-situ mixing of multiple powders through the laser-based directed energy deposition(DED)of functionally graded ***,a powder-mixing experimental platform was established;WC and 316L powders were selected for the mixing ***,scanning electron microscopy,energy dispersive spectroscopy,and image processing were used to visually evaluate the homogeneity and proportion of the in-situ mixed ***,powder-mixing simulations were conducted to determine the powder-mixing *** the simulations,a powder carrier gas flow field and particle mixing were ***,a WC/316L metal matrix composite sample was produced using laser-based DED to verify the application potential of the static *** was found that the static mixer could adjust the powder ratio online,and a response time of 1–2 s should be considered when adjusting the ratio of the mixed powder.A feasible approach for in-situ powder mixing for laser-based DED was demonstrated and investigated,creating the basis for functionally graded materials.

关键词： Laser Deposition Static mixer Powder mixing Functionally graded materials

Polyoxometalates for continuous power generation by atmospheric humidity

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Nano Research 2024年第3期17卷 1875-1885页

作者： Tuo ji Weilin chen Zhenhui Kang Liming Zhang Key Laboratory of Polyoxometalate and Reticular Material Chemistry of Ministry of Education Northeast Normal UniversityChangchun 130024China Institute of Functional Nano&Soft Materials(FUNSOM) Jiangsu Key Laboratory for Carbon-Based Functional Materials&Devices DepartmentSoochow UniversitySuzhou 215123China Macao Institute of Materials Science and Engineering Macao University of Science and TechnologyTaipaMacao 999078China Institute of Functional State Key Laboratory of Luminescence and Applications Changchun Institute of OpticsFine Mechanics and PhysicsChinese Academy of SciencesChangchun 130033China

Atmospheric humidity is a sustainable low-value energy widely existing in natural environment,which is a promising candidate to solve the noncontinuous and low efficiency of low-value energy power *** the mono-substituted Dawson-type polyoxometalates are constructed to be highly dispersed organic ammonium-polyoxoanion clusters and are assembled into thin films power generators with micropores,working in atmospheric *** optimal polyoxometalates generator with the thickness of 7.2μm and the area of 0.36 cm^(2) produces a voltage of 0.68 V and a current density of 19.5μA·cm^(-2) under simulated natural environment,and works continuously and stably under almost all-natural environments(humidity 10%–90%).The highly dispersed polyoxometalate nanoclusters can form microporous in polyoxometalate films to effectively absorb atmospheric humidity and spontaneously form distribution gradient of water,which is the structural basis of power *** continuous power generation may be maintained by the effective adsorption and utilization of H_(2)O,the huge electrostatic field of organic ammonium-polyoxoanion clusters,and the reasonably designed polyoxometalates containing inorganic small ions with high *** is the first humidity generator designed with polyoxometalates,which may provide a new research direction for polyoxometalates in sustainable utilization of low-value energy.

关键词： atmospheric humidity continuous power generations nanomaterials polyoxoanions polyoxometalates

Transitional Revenue Scheme for High-cost Generator Unit in Guangdong Electricity Market Based on Government Authorized Contracts

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CSEE Journal of Power and Energy Systems 2024年第1期10卷 208-221页

作者： jisong Zhu Baike chen Tianyao ji Zhaoxia jing School of Electric Power Engineering South China University of TechnologyGuangzhou 510640China

High-cost generator units are at a cost disadvantage in electricity spot *** study focuses on revenue mechanisms of gas-fired units affected by power market reform in Guangdong province,*** the first time,we compare impacts on market indicators of five settlement mechanisms:feed-in tariff(FiT),location marginal price(LMP),contract for difference(CFD),direct subsidy(DS),and estimated revenue method(ERM).In particular,we design key parameters,including authorized CFD and ERM of two kinds of government authorized contracts based on traditional dispatching patterns to avoid significant profit fluctuations brought by market *** also analyze impact of factors such as climbing performance,seasonal load,and subsidy amount on the overall market and its *** of a case study show to directly subsidize gasfired units will lead higher-cost units to generate more electricity,with a resulting loss of social *** of market prices and provision of unreasonable incentives are fatal disadvantages of this subsidy *** government and policymakers should consider financial means to adjust benefits to reduce production costs and increase social ***,by case analysis,the ERM shows its stable performance in revenue of high-cost units,while we find that authorized CFD is not applicable for gas-fired units whose output is unstable as a marginal unit ***,we suggest government agencies adopt ERM to sign contracts with gas-fired units,to attain a balance between fairness and efficiency.

关键词： Guangdong electricity market high-cost generator unit settlement mechanism subsidy