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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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Comparative analysis of DNA-SIP and magnetic-nanoparticle mediated isolation (MMI) on unraveling dimethoate degraders

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Frontiers of Environmental Science & Engineering 2024年第1期18卷 59-69页

作者： Luning Lian Yi Xing Dayi Zhang Longfei jiang Mengke Song Bo jiang School of Energy and Environmental Engineering University of Science&Technology BeijingBeijing 100083China Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants University of Science&Technology BeijingBeijing 100083China National Environmental and Energy Science and Technology International Cooperation Base University of Science&Technology BeijingBeijing 100083China College of New Energy and Environment Jilin UniversityChangchun 130021China Guangzhou Institute of Geochemistry Chinese Academy of SciencesGuangzhou 510640China College of Natural Resources and Environment South China Agricultural UniversityGuangzhou 510642China National Engineering Laboratory for Site Remediation Technologies Beijing 100015China

Microorganisms are crucial in the bioremediation of organophosphorus pesticides. However, most functional microorganisms (> 99%) are yet to be cultivated. This study applied two cultivation-independent approaches, DNA-SIP and magnetic-nanoparticle mediated isolation (MMI), to identify the functional microorganisms in degrading dimethoate in agricultural soils. MMI identified five dimethoate degraders: Pseudomonas, Bacillus, Ramlibacter, Arthrobacter, and Rhodococcus, whereas DNA-SIP identified three dimethoate degraders: Ramlibacter, Arthrobacter, and Rhodococcus. Also, MMI showed higher resolution than DNA-SIP in identifying functional microorganisms. Two organic phosphohydrolase (OPH) genes: ophC2 and ophB, were involved in dimethoate metabolism, as revealed by DNA-SIP and MMI. The degradation products of dimethoate include omethoate, O,O,S-trimethyl thiophosphorothioate, N-methyl-2-sulfanylacetamide, O,O-diethyl S-hydrogen phosphorodithioate, O,O,O-trimethyl thiophosphate, O,O,S-trimethyl thiophosphorodithioate, and O,O,O-trimethyl phosphoric. This study emphasizes the feasibility of using SIP and MMI to explore the functional dimethoate degraders, expanding our knowledge of microbial resources with cultivation-independent approaches.

关键词： Stable isotope probing(SIP) Magnetic-nanoparticle mediated isolation(MMI) Dimethoate Biodegradation Cultivation-independent approach

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Operational requirements analysis method based on question answering of WEKG

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Journal of Systems Engineering and Electronics 2024年第2期35卷 386-395页

作者： ZHANG Zhiwei DOU Yajie XU Xiangqian MA Yufeng jiang jiang TAN Yuejin College of Systems Engineering National University of Defense TechnologyChangsha 410073China

The weapon and equipment operational requirement analysis(WEORA) is a necessary condition to win a future war,among which the acquisition of knowledge about weapons and equipment is a great challenge. The main challenge is that the existing weapons and equipment data fails to carry out structured knowledge representation, and knowledge navigation based on natural language cannot efficiently support the WEORA. To solve above problem, this research proposes a method based on question answering(QA) of weapons and equipment knowledge graph(WEKG) to construct and navigate the knowledge related to weapons and equipment in the WEORA. This method firstly constructs the WEKG, and builds a neutral network-based QA system over the WEKG by means of semantic parsing for knowledge navigation. Finally, the method is evaluated and a chatbot on the QA system is developed for the WEORA. Our proposed method has good performance in the accuracy and efficiency of searching target knowledge, and can well assist the WEORA.

关键词： operational requirement analysis weapons and equipment knowledge graph(WEKG) question answering(QA) neutral network

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Three-channel CMOS transimpedance amplifier for LiDAR sensor receiver

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Journal of Systems Engineering and Electronics 2024年第1期35卷 74-80页

作者： LIU Ruqing ZHU Jingguo jiang Yan LI Feng jiang Chenghao MENG Zhe Photoelectric R&D Center Academy of Opto-ElectronicsChinese Academy of SciencesBeijing 100094China

For time-of-flight(TOF)light detection and ranging(LiDAR),a three-channel high-performance transimpedance amplifier(TIA)with high immunity to input load capacitance is presented.A regulated cascade(RGC)as the input stage is at the core of the complementary metal oxide semiconductor(CMOS)circuit chip,giving it more immunity to input photodiode detectors.A simple smart output interface acting as a feedback structure,which is rarely found in other designs,reduces the chip size and power consumption *** circuit is designed using a 0.5μm CMOS process technology to achieve low *** device delivers a 33.87 dB?transimpedance gain at 350 *** a higher input load capacitance,it shows a-3 dB bandwidth of 461 MHz,indicating a better detector tolerance at the front end of the *** a 3.3 V supply voltage,the device consumes 5.2 mW,and the total chip area with three channels is 402.8×597.0μm2(including the test pads).

关键词： transimpedance amplifier(TIA) three-channel regulated cascade(RGC) light detection and ranging(LiDAR)

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Gut microbial interactions based on network construction and bacterial pairwise cultivation

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Science China(Life Sciences) 2024年第8期67卷 1751-1762页

作者： Min-Zhi jiang Chang Liu Chang Xu He jiang Yulin Wang Shuang-jiang Liu State Key Laboratory of Microbial Technology Shandong UniversityQingdao 266000China State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center(EMRC)Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Association networks are widely applied for the prediction of bacterial interactions in studies of human gut ***,the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated *** this study,we addressed this challenge by integrating in vitro time series network(TSN)associations and cocultivation of TSN taxon *** samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 *** cells were harvested for DNA extraction and metagenomic sequencing.A total of 198 metagenome-assembled genomes(MAGs)were *** dynamics of bacteria growing on the YCFA agar were used to infer microbial association *** experimentally validate the interactions of taxon pairs in networks,we selected 24 and 19 bacterial strains from this study and from the previously established human gut microbial biobank,respectively,for pairwise *** co-culture experiments revealed that most of the interactions between taxa in networks were identified as neutralism(51.67%),followed by commensalism(21.67%),amensalism(18.33%),competition(5%)and exploitation(3.33%).Genome-centric analysis further revealed that the commensal gut bacteria(helpers and beneficiaries)might interact with each other via the exchanges of amino acids with high biosynthetic costs,short-chain fatty acids,and/or *** also validated 12 beneficiaries by adding 16 additives into the basic YCFA medium and found that the growth of 66.7%of these strains was significantly *** approach provides new insights into the gut microbiome complexity and microbial interactions in association *** work highlights that the positive relationships in gut microbial communities tend to be overestimated,and that amino acids,short-chain fatty acids,and vitamins are contributed to the positive relationships.

关键词： human gut microbiome gut microbial pairwise interaction co-culture association network microbial community

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Hybrid Block Diagonalization Precoding for Multi-User Weighted Sum-Rate Maximization

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China Communications 2024年第8期21卷 127-141页

作者： Su Xiaofeng jiang Yi Key Laboratory for Information Science of Electromagnetic Waves(MoE) Department of Communication Science and EngineeringFudan UniversityShanghai 200433China

This paper studies large-scale multi-input multi-output(MIMO)orthogonal frequency division multiplexing(OFDM)communications in a broadband frequency-selective channel,where a massive MIMO base station(BS)communicates with multiple users equipped with *** develop a hybrid precoding design to maximize the weighted sum-rate(WSR)of the users by optimizing the digital and the analog precoders *** the digital part,we employ block-diagonalization to eliminate inter-user interference and apply water-filling power allocation to maximize the *** the analog part,the optimization of the PSN is formulated as an unconstrained problem,which can be efficiently solved by a gradient descent *** results show that the proposed block-diagonal hybrid precoding algorithm can outperform the existing works.

关键词： block-diagonal gradient descent hybrid precoding iterative optimization MIMO-OFDM multi-user water-filling power allocation weighted sum-rate maximization

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CONVERGENCE OF MODIFIED TRUNCATED EULER-MARUYAMA METHOD FOR STOCHASTIC DIFFERENTIAL EQUATIONS WITH HOLDER DIFFUSION COEFFICIENTS

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Journal of Computational Mathematics 2024年第4期42卷 1109-1123页

作者： Guangqiang Lan Yu jiang College of Mathematics and Physics Beijing University of Chemical TechnologyBeijing 100029China

Convergence of modified truncated Euler-Maruyama(MTEM)method for stochastic differential equations(SDEs)with(1/2+α)-Holder continuous diffusion coefficients are investigated in this *** prove that the MTEM method for... 详细信息

关键词： Stochastic differential equations Modified truncated Euler-Maruyama method Strong convergence One-sided Lipschitz Holder continuous

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Sounding the alarm:Functionally referential signaling in Azure-winged Magpie

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Avian Research 2024年第1期15卷 35-41页

作者： Xingyi jiang Yanyun Zhang Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering College of Life SciencesBeijing Normal UniversityBeijing 100875China

Functionally referential signals are a complex form of communication that conveys information about the external *** signals have been found in a range of mammal and bird species and have helped us understand the complexities of animal *** are well known for their extraordinary cognitive abilities,but relatively little attention has been paid to their vocal ***,we investigated the functionally referential signals of a cooperatively breeding corvid species,Azure-winged Magpie(Cyanopica cyanus).Through field observations,we suggest that Azure-winged Magpie uses referential alarm calls to distinguish two types of threats:’rasp’ calls for terrestrial threats and ’chatter’ calls for aerial threats.A playback experiment revealed that Azure-winged Magpies responded to the two call types with qualitatively different *** sought cover by flying into the bushes in response to the ’chatter’ calls,and flew to or stayed at higher positions in response to ’rasp’ calls,displaying a shorter response time to ’chatter’ *** differences in acoustic structure were found between the two types of *** the extensive cognitive abilities of corvids and the fact that referential signals were once thought to be unique to primates,these findings are important for expanding our understanding of social communication and language evolution.

关键词： Alarm call Animal communication Azure-winged Magpie Referential signal

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General formalism for dirty extreme-mass-ratio inspirals

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Science China(Physics,Mechanics & Astronomy) 2024年第7期67卷 22-29页

作者： Ye jiang Wen-Biao Han Shanghai Astronomical Observatory Chinese Academy of SciencesShanghai 200030China School of Astronomy and Space Science University of Chinese Academy of SciencesBeijing 100049China School of Fundamental Physics and Mathematical Sciences Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou 310024China Shanghai Frontiers Science Center for Gravitational Wave Detection Shanghai 200240China

Detecting the environment around the supermassive black holes and tests of general relativity are important applications of extreme-mass-ratio inspirals(EMRIs).There is still a challenge to efficiently describe various“dirty”impacts on the inspirals,such as dark matter,gas,dipole radiation,and electromagnetic *** this study,we find the inherent linearity of the asymptotic solution of the inhomogeneous Teukolsky *** the basis of this property,we completely decouple the factors of the perturber and the background spacetime in the energy fluxes and *** the new decoupling form,the waveforms of EMRIs with non-geodesic motion in Kerr spacetime can be conveniently *** will help to resolve the environment(including gas,field,dark matter,electromagnetic interaction)around supermassive black holes and test general relativity.

关键词： gravitational wave Teukolsky equation extreme-mass-ratio inspirals

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Assembly of peptide nanostructures with controllable sizes

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Nano Research 2024年第1期17卷 151-161页

作者： Dan Cheng Fan Jia Yun-Bao jiang Vincent P.Conticello Tao jiang The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation Department of ChemistryCollege of Chemistry and Chemical EngineeringXiamen UniversityXiamen 361005China Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province(IKKEM) Xiamen 361005China Department of Chemistry Emory UniversityAtlanta 30033USA

Controlled peptide assembly offers significant promise to develop synthetic supramolecular nanostructures to display material and biological properties that mimic protein assemblies in *** the progress in forming peptide nanostructures of various morphology,there exists a distinct gap between natural and synthetic assembly systems in terms of size *** nanostructures with a narrow size distribution that can be tuned over a wide range of length-scales is essential for applications that require precise spacing between *** approach provides the opportunity to correlate materials and biological properties of interest with assembly *** this review,we discuss representative endeavors over the past two decades for design of size-controllable peptide nanostructures using tunable building *** mechanisms for size control,e.g.,molecular frustration,template-directed peptide assembly,and multi-component peptide co-assembly,will also be *** also demonstrate the applicable scopes of these strategies and suggest potential future avenues for scientific advances in this field.

关键词： peptide assembly controllable size template multi-component

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