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DeepSecE:A Deep-Learning-Based Framework for Multiclass Prediction of Secreted Proteins in Gram-Negative Bacteria

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Research 2024年第3期2023卷 243-257页

作者： yumeng zhang Jiahao Guan Chen Li Zhikang Wang Zixin Deng Robin BGasser Jiangning Song hong-yu Ou state Key Laboratory of Microbial Metabolism Joint International Laboratory on Metabolic&Developmental SciencesSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China Shanghai Key Laboratory of Veterinary Biotechnology Shanghai Jiao Tong UniversityShanghai 200240China Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology Monash UniversityMelbourneViC 3800Australia Monash Data Futures Institute Monash UniversityMelbourneViC 3800Australia Melbourne Veterinary School Faculty of ScienceThe University of MelbourneParkvilleVIC 3010Australia.

Proteins secreted by Gram-negative bacteria are tightly linked to the virulence and adaptability of these microbes to environmental *** identification of such secreted proteins can facilitate the investigations of infections and diseases caused by these bacterial ***,current bioinformatic methods for predicting bacterial secreted substrate proteins have limited computational efficiency and application scope on a genome-wide ***,we propose a novel deep-learning-based framework—DeepSecE—for the simultaneous inference of multiple distinct groups of secreted proteins produced by Gram-negative *** remarkably improves their classification from nonsecreted proteins using a pretrained protein language model and transformer,achieving a macro-average accuracy of 0.883 on 5-fold *** benchmarking suggests that DeepSecE achieves competitive performance with the state-of-the-art binary predictors specialized for individual types of secreted *** attention mechanism corroborates salient patterns and motifs at the N or C termini of the protein *** this pipeline,we further investigate the genome-wide prediction of novel secreted proteins and their taxonomic distribution across~1,000 Gram-negative bacterial *** present analysis demonstrates that DeepSecE has major potential for the discovery of disease-associated secreted proteins in a diverse range of Gram-negative *** online web server of DeepSecE is also publicly available to predict and explore various secreted substrate proteins via the input of bacterial genome sequences.

关键词： Deep server competitive

Multi-state system reliability:An emerging paradigm for sophisticated engineered systems

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Frontiers of Engineering Management 2024年第3期11卷 568-575页

作者： yu LIU Tangfan XIAHOU Qin zhang Liudong XING hong-Zhong HUANG School of Mechanical and Electrical Engineering University of Electronic Science and Technology of ChinaChengdu 611731China Center for System Reliability and Safety University of Electronic Science and Technology of ChinaChengdu 611731China Department of Electrical&Computer Engineering University of Massachusetts DartmouthMA 02747USA

1 Introduction Reliability is defined as the probability that a system or component will perform its required function for a specified period of time under specified operating conditions(Ebeling,2019).Traditional reliability theory assumes that both a system and its components have only two possible states in the operation stage,either perfectly functioning or completely ***,as engineered systems become more sophisticated,involving larger sizes,increased functionality,and greater intelligence,and with advancements in sensing technologies,it has been extensively observed that systems and components exhibit multiple distinct states as they deteriorate over *** failure behavior,damage severity,performance capacity,and operational efficiency of the system and components vary among these states(Lisnianski et al.,2018).It,therefore,necessitates the development of advanced reliability theories and methodologies that are capable of characterizing these systems and components with multi-state nature.

关键词： system state specified

Single-atom catalysts for neutral zinc-air batteries

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Science China Materials 2024年第5期67卷 1674-1675页

作者： Jiaxu zhang Minghao yu Faculty of Chemistry and Food Chemistry&Center for Advancing Electronics Dresden(CfAED) Technische Universität DresdenDresden01062Germany

The escalating global energy demand underscores the urgency of developing sustainable battery ***-air batteries(ZABs)have emerged as promising candidates due to their costeffectiveness,safety,and high energy density[1-4].Conventional ZABs typically rely on a four-electron(4e-)oxygen reduction reaction(ORR)in strongly alkaline electrolytes.

关键词： battery neutral typically

Cross section determination of^(27)Al(n,2n)^(26)Al reaction induced by 14-MeV neutrons uniting with D-T neutron activation and AMS techniques

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Nuclear Science and Techniques 2024年第6期35卷 78-89页

作者： Xian-Lin Yang Chang-Lin Lan yu-Ting Wei Yi zhang Gong Jiang Bo Xie yu Liu hong-Tao Shen Xiao-Jun Sun School of Nuclear Science and Technology Lanzhou UniversityLanzhou 730000China MOE Frontiers Science Center for Rare Isotopes Lanzhou UniversityLanzhou 730000China State Key Laboratory of Environmental Geochemistry Institute of GeochemistryChinese Academy of SciencesGuiyang 550081China Guangxi Key Laboratory of Nuclear Physics and Nuclear Technology Guangxi Normal UniversityGuilin 541004China

Aluminum is the primary structural material in nuclear engineering,and its cross section induced by 14-MeV neutrons is of great *** address the issue of insufficient accuracy for the^(27)Al(n,2n)^(26)Al reaction cross section,the activation method and accelerator mass spectrometry(AMS)technique were used to determine the^(27)Al(n,2n)^(26)Al cross section,which could be used as a D-T plasma ion temperature monitor in fusion *** the China Academy of Engineering Physics,neutron activation was performed using a K-400 neutron generator produced by the T(d,n)4He ***^(26)Al∕^(27)Al isotope ratios were measured using the newly installed GYIG 1 MV AMS at the Institute of Geochemistry,Chinese Academy of *** neutron flux was monitored by measuring the activity of 92mNb produced by the 93Nb(n,2n)92mNb *** measured results were compared with available data in the experimental nuclear reaction database,and the measured values showed a reasonable degree of consistency with partially available literature *** newly acquired cross-sectional data at 12 neutron energy points through systematic measurements clarified the divergence,which has two different growth trends from the existing experimental *** obtained results are also compared with the corresponding evaluated database,and the newly calculated excitation functions with TALYS−1.95 and EMPIRE−3.2 codes,the agreement with CENDL−3.2,TENDL-2021 and EMPIRE−3.2 results are generally acceptable.A substantial improvement in the knowledge of the^(27)Al(n,2n)^(26)Al reaction excitation function was obtained in the present work,which will lay the foundation for the diagnosis of the fusion ion temperature,testing of the nuclear physics model,evaluation of nuclear data,etc.

关键词： 14-MeV neutron ^(27)Al(n,2n)^(26)Al Cross section AMS

Characterizations of semihoops based on derivations

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Applied Mathematics(A Journal of Chinese Universities) 2024年第2期39卷 291-310页

作者： WANG Mei zhang Xiao-hong School of Electrical and Control Engineering Shaanxi University of Science and TechnologyXi'an 710021China School of Arts and Sciences Shaanxi University of Science and TechnologyXi'an 710021China School of Mathematics and Statistics Weinan Normal UniversityWeinan 714099China

In this paper,we discuss the related properties of some particular derivations in semihoops and give some characterizations of ***,we prove that every Heyting algebra is isomorphic to the algebra of all multiplicative derivations and show that every Boolean algebra is isomorphic to the algebra of all implicative ***,we show that the sets of multiplicative and implicative derivations on bounded regular idempotent semihoops are in oneto-one correspondence.

关键词： (prelinear)semihoop derivation Heyting algebra Galois connection

Implications for fault reactivation and seismicity induced by hydraulic fracturing

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Petroleum Science 2024年第2期21卷 1081-1098页

作者： Zi-Han Sun Ming-Guang Che Li-hong Zhu Shu-Juan zhang Ji-yuan Lu Chang-yu Jin Key Laboratory of Ministry of Education on Safe Mining of Deep Metal Mines School of Resources and Civil Engineering and Key Laboratory of Liaoning Province on Deep Engineering and Intelligent TechnologyNortheastern UniversityShenyang110819LiaoningChina Research Institute of Petroleum Exploration&Development PetroChina Company LimitedBeijing100084China The Exploration and Development Research Institute of Daqing Oilfield Limited Company Daqing163458HeilongjiangChina

Evaluating the physical mechanisms that link hydraulic fracturing(HF) operations to induced earthquakes and the anticipated form of the resulting events is significant in informing subsurface fluid injection operations. Current understanding supports the overriding role of the effective stress magnitude in triggering earthquakes, while the impact of change rate of effective stress has not been systematically addressed. In this work, a modified critical stiffness was brought up to investigate the likelihood, impact,and mitigation of induced seismicity during and after hydraulic fracturing by developing a poroelastic model based on rate-and-state fraction law and linear stability analysis. In the new criterion, the change rate of effective stress was considered a key variable to explore the evolution of this criterion and hence the likelihood of instability slip of fault. A coupled fluid flow-deformation model was used to represent the entire hydraulic fracturing process in COMSOL Multiphysics. The possibility of triggering an earthquake throughout the entire hydraulic fracturing process, from fracturing to cessation, was investigated considering different fault locations, orientations, and positions along the fault. The competition between the effects of the magnitude and change rate of effective stress was notable at each fracturing stage. The effective stress magnitude is a significant controlling factor during fracturing events, with the change rate dominating when fracturing is suddenly started or stopped. Instability dominates when the magnitude of the effective stress increases(constant injection at each fracturing stage) and the change rate of effective stress decreases(the injection process is suddenly stopped). Fracturing with a high injection rate, a fault adjacent to the hydraulic fracturing location and the position of the junction between the reservoir and fault are important to reduce the Coulomb failure stress(CFS) and enhance the critical stiffness as

关键词： Hydraulic fracturing Coulomb failure stress Rate-and-state fraction model Linear stability analysis Critical stiffness Seismically induced fault

Symbiotic bacteria attenuate Drosophila oviposition repellence to alkaline through acidification

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Insect Science 2021年第2期28卷 403-414页

作者： Wei Liu Jie Wang hong-yu zhang Ying-Chun Yang Ru-Xue Kang Peng Bai Hui Fu Li-Rong Chen Yan-Ping Gao Eng King Tan Department of Medical Laboratory Science Fenyang CollegeShanxi Medical UniversityShanxiChina Department of Neurology National Neuroscience InstituteSingapore General Hospital CampusSingapore Department of Basic Medical Fenyang CollegeShanxi Medical UniversityShanxiChina

Metazoans harbor a wealth of symbionts that are ever-changing the environment by taking up resources and/or excreting *** such common environmental modification is a change in *** wisdom holds that symbionts facilitate the survival and production of their hosts in the wild,but this notion lacks empirical ***,we report that symbiotic bacteria in the genus Enterococcus attenuate the oviposition avoidance of alkaline environments in *** studied the effects of alkalinity on oviposition preference for the first time,and found that flies are robustly disinclined to oviposit on alkali-containing *** innate repulsion to alkaline environments is explained,in part,by the fact that alkalinity compromises the health and lifespan of both offspring and parent *** dramatically diminished or even completely reversed the ovipositional avoidance of alkalinity in ***,Enterococcus generate abundant lactate during fermentation,which neutralizes the residual alkali in an egg-laying *** conclusion,Enterococcus protects Drosophila from alkali stress by acidifying the ovipositional substrate,and ultimately improves the fitness of the Drosophila *** results demonstrate that symbionts are profound factors in the Drosophila ovipositional decision,and extend our understanding of the intimate interactions between Drosophila and their symbionts.

关键词： acidification alkaline Drosophila,Enterococcus fitness oviposition

Unveiling quality of clinical trial in China:from concern to confirmation

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Cancer Communications 2024年第5期44卷 576-579页

作者： Huiyao Huang Yiru Hou hong Fang Ling Xu yue yu Huifang zhang Jing zhang yu Tang Gongtao Lan Wenbao zhang Ning Li Clinical Trials Center National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP.R.China School of Basic Medicine and Clinical Pharmacy China Pharmaceutical UniversityNanjingJiangsuP.R.China Department of Quality Medicine Boehringer Ingelheim(China)Investment Co LtdShanghaiP.R.China Department of Clinical Development Quality Pfizer Research and Development(China)BeijingP.R.China Department of Drug Registration National Medical Products AdministrationBeijingP.R.China Bureau of Medical Administration National Health CommissionBeijingP.R.China

The cornerstone of scientifically valid and ethically sound clinical trials is in compliance with established global quality *** China has made significant progress over the past 20 years in terms of the clinical trial quantity[1],quality and participation in multiregional trials[2],there still remain concerns regarding the trial quality,which could be associated with the self-inspection initiative in 2015[3].

关键词： clinical corners confirmation

Rapid lithium-ion insertion/extraction and migration behavior of Na_(2)WO_(4)-encapsulated lithium-rich layered oxide cathode

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Rare Metals 2024年第8期43卷 3647-3660页

作者： yu-Shen Zhao Fan-Fan Wang Jian-Cang Wang Peng-Fei Wang Ting-Feng Yi Jun-hong zhang School of Materials Science and Engineering Northeastern UniversityShenyangShenyang 110819China Key Laboratory of Dielectric and Electrolyte Functional Material Hebei Province School of Resources and MaterialsNortheastern University at QinhuangdaoQinhuangdao 066004China Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology College of Chemistry and Chemical EngineeringLiaocheng UniversityLiaocheng 252059China

Due to the low cost,high working voltage and high storage capacity,Li-rich Mn-based layered compounds show promise as the cathode materials for lithiumion batteries(LIBs).However,the side reactions at the solid-liquid interface of the cathode will lead to rapid capacity decay and inferior rate ***,this article proposes a liquid-phase dispersion strategy to introduce a Na_(2)WO_(4)layer on the Li_(1.2)Ni_(0.13)-Co_(0.13)Mn_(0.54)O_(2) cathode,which can reduce the side effects between raw materials and electrolyte and promote the insertion/extraction rate of Li^(+),thus enhancing the material stability and rate *** a result,the capacity retention rate is 96.9%after 200 cycles under ***,the capacities are 177.5,149.5,111.1 and58.3 mAh·g^(-1)at 1C,2C,5C and 10C,implying a superior fast charging *** exceptional performance can be ascribed to both the increased conductivity and enhanced structural stability of the cathode ***'s more,based on the investigation of ion insertion/extraction behavior in electrode materials and the ion migration kinetics in the electrolyte,this study suggests that coating Li-rich Mn-based materials with Na_(2)WO_(4)can be a promising strategy to improve their performance in LIBs.

关键词： Li-ion battery Coating Rate performance Li_(1.2)Ni_(0.13)Co_(0.13)Mn_(0.54)O_(2) Reaction kinetics