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

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

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Generative optimization of bistable plates with deep learning

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Theoretical & Applied Mechanics Letters 2024年第1期14卷 35-38页

作者： hong Li Qingfeng wang School of Naval Architecture&Ocean Engineering Jiangsu University of Science and TechnologyZhenjiang 212003China

Bistate plates have found extensive applications in the domains of smart structures and energy harvesting *** bistable curved plates are characterized by a constant thickness ***,due to the inherent complexity of this problem,relatively little attention has been devoted to this *** this study,we demonstrate how deep learning can facilitate the discovery of novel plate profiles that cater to multiple objectives,including maximizing stiffness,forward snapping force,and backward snapping *** proposed approach is distinguished by its efficiency in terms of low computational energy consumption and high *** holds promise for future applications in the design and optimization of multistable structures with diverse objectives,addressing the requirements of various fields.

关键词： Bistable plate Nonlinear Microstructure Simulation Machine learning

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Laser manufacturing of spatial resolution approaching quantum limit

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Light(Science & Applications) 2024年第3期13卷 421-428页

作者： Xiao-Jie wang hong-Hua Fang Zhen-Ze Li Dan wang hong-Bo Sun State Key Laboratory of Precision Measurement Technology and Instruments Department of Precision InstrumentTsinghua UniversityBeijing 100084China State Key Laboratory of Integrated Optoelectronics College of Electronic Science and EngineeringJilin University2699 Qianjin StreetChangchun 130012China

Atomic and close-to-atom scale manufacturing is a promising avenue toward single-photon emitters,single-electron transistors,single-atom memory,and quantum-bit devices for future communication,computation,and sensing *** manufacturing is outstanding to this end for ease of beam manipulation,batch production,and no requirement for *** is,however,suffering from optical diffraction ***,we report a spatial resolution improved to the quantum limit by exploiting a threshold tracing and lock-in method,whereby the two-order gap between atomic point defect complexes and optical diffraction limit is surpassed,and a feature size of<5 nm is *** underlying physics is that the uncertainty of local atom thermal motion dominates electron excitation,rather than the power density slope of the incident *** show that the colour centre yield in hexagonal boron nitride is transformed from stochastic to deterministic,and the emission from individual sites becomes polychromatic to *** a result,single colour centres in the regular array are deterministically created with a unity yield and high positional accuracy,serving as a step forward for integrated quantum technological applications.

关键词： quantum limit resolution

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Concerted Steric and Electronic Strategy in Thermostable Salicylaldiminato Nickel Catalysts for Ethylene(Co)polymerization

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Chinese Journal of Polymer Science 2024年第8期42卷 1085-1092页

作者： hong-yu Ji hong-Liang Mu Chun-Feng Tang yu-Xing Zhang yue Chi Zhong-Bao Jian Key Laboratory of Advanced Structural Materials Ministry of EducationSchool of Materials Science and EngineeringChangchun University of TechnologyChangchun 130012China State Key Laboratory of Polymer Physics and Chemistry Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchun 130022China

Olefin polymerization is one of the most im portant chemical reactions in *** work presents a strategy that emphasizes the synergistic meta/poro-steric hindrance of N-aryl groups and electronic effects in newly synthesized neutral salicylaldiminato nickel *** nickel(Ⅱ)catalysts exhibit exceptional thermostability,ranging from 30℃to 130℃,demonstrating enhanced catalytic activities and broadly regulated polyethylene molecular weights(3-341 kg·mol^(-1))and controlled polymer branch density(2-102 brs/1000C).The preferred catalyst Ni3 with concerted steric and electronic effects enables the production of solid-state semi-crystalline polyethylene materials at temperatures below 90℃.Notably,Ni3 exhibits an impressive tolerance of 110℃and can withstand even the challenging polymerization temperature of 130℃,leading to the production of polyethylene wax and ***,functionalized polyethylene is produced.

关键词： Polyolefin Salicylaldiminato ligand Nickel catalyst Oil Wax

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Immersive visualization of 3D subsurface ground model developed from sparse boreholes using virtual reality(VR)

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Underground Space 2024年第4期17卷 188-206页

作者： Borui Lyu yu wang Department of Architecture and Civil Engineering City University of Hong KongKowloon 999077Hong KongChina

Analytics and visualization of multi-dimensional and complex geo-data,such as three-dimensional(3D)subsurface ground models,is critical for development of underground space and design and construction of underground structures(e.g.,tunnels,dams,and slopes)in engineering *** complicated 3D subsurface ground models now can be developed from site investigation data(e.g.,boreholes)which is often sparse in practice,it remains a great challenge to visualize a 3D subsurface ground model with sophisticated stratigraphic variations by conventional two-dimensional(2D)geological *** reality(VR)technology,which has an attractive capability of constructing a virtual environment that links to the physical world,has been rapidly developed and applied to visualization in various disciplines *** on the rapid development of VR,this study proposes a framework for immersive visualization of 3D subsurface ground models in geo-applications using VR *** 3D subsurface model is first developed from limited borehole data in a data-driven ***,a VR system is developed using related software and hardware devices currently available in the markets for immersive visualization and interaction with the developed 3D subsurface ground *** results demonstrate that VR visualization of the 3D subsurface ground model in an immersive environment has great potential in revolutionizing the geo-practices from 2D cross-sections to a 3D immersive virtual environment in digital era,particularly for the emerging digital twins.

关键词： Immersive visualization 3D subsurface model Virtual reality Virtual environment Interaction

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Recent progress in all-inorganic tin-based perovskite solar cells:a review

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Science China Chemistry 2024年第4期67卷 1117-1136页

作者： Minghao wang yu Shi School of Electronics and Information Engineering Wuxi UniversityWuxi 214105China Institute of Advanced Materials Nanjing Tech UniversityNanjing 211816China

Recently,power conversion efficiency(PCE)of organic-inorganic hybrid perovskite solar cells(PSCs)has been improved to26.1%.However,the toxicity issue of lead still hinders the large-scale commercial production and application of lead(Pb)-based halide ***,environmentally friendly tin(Sn)-based perovskites have recently shown excellent *** them,the all-inorganic Sn-based perovskites,including CsSnX_(3) and Cs_(2)SnX_(6),have better stability,more suitable bandgap,and higher charge mobility,which have attracted more attention from researchers than organic-inorganic Sn-based hybrid ***,we review recent research progress on all-inorganic Sn-based perovskite materials and corresponding solar cell ***,we also summarize the current challenges and future research directions for this type of PSCs.

关键词： solar cells perovskite all-inorganic CsSnX_(3) Cs_(2)SnX_(6)

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LncRNA HCP5-encoded protein contributes to adriamycin resistance through ERK/mTOR pathway-mediated autophagy in breast cancer cells

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Genes & Diseases 2024年第4期11卷 69-72页

作者： Jia-Ni Xing Yi-Ni Shang Zheng-Ling yu Shun-Heng Zhou wang-Yang Chen Li-hong wang Department of Pathophysiology Medical College of Southeast UniversityNanjingJiangsu 210009China Department of Biomedical Engineering Nanjing University of Aeronautics and AstronauticsNanjingJiangsu 211106China School of Medicine Taizhou UniversityTaizhouZhejiang 318000China Jiangsu Provincial Key Laboratory of Critical Care Medicine NanjingJiangsu 210009China

Adriamycin(ADR),also known as doxorubicin,is an anthracycline anticancer drug and a chemotherapeutic drug commonly used in breast cancer treatments.1 However,breast cancer patients can gradually become tolerant to ***,improving the curative effect of ADR remains an urgent problem to be *** is a complex catabolic process;normal living cells break down damaged organelles or aggregated molecules and absorb energy to maintain homeostasis through autophagy.

关键词： breast cancer homeostasis

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Clinical efficacy of Gamma Knife® combined with transarterial chemoembolization and immunotherapy in the treatment of primary liver cancer

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World Journal of Gastrointestinal Surgery 2024年第6期16卷 1601-1608页

作者： Guo-Feng wang Chang-Xin Shu Xiao-Dong Cai hong-Bo wang Jian-hong Xu yu-Qing Jia Department of General Surgery Yangzhou Friendship Hospital Affiliated to Medical College of Yangzhou UniversityYangzhou 225000Jiangsu ProvinceChina

BACKGROUND This study was designed to investigate the clinical efficacy and safety of Gamma Knife®combined with transarterial chemoembolization(TACE)and immunotherapy in the treatment of primary liver *** To investigate the clinical efficacy and safety of Gamma Knife®combined with TACE and immune-targeted therapy in the treatment of primary liver *** Clinical data from 51 patients with primary liver cancer admitted to our hospital between May 2018 and October 2022 were retrospectively *** patients underwent Gamma Knife®treatment combined with TACE and *** clinical efficacy,changes in liver function,overall survival(OS),and progression-free survival(PFS)of patients with different treatment responses were evaluated,and adverse reactions were *** The last follow-up for this study was conducted on October 31,*** evaluation of the 51 patients with primary liver cancer revealed a partial response(PR)in 27 patients,accounting for 52.94%(27/51);stable disease(SD)in 16 patients,accounting for 31.37%(16/51);and progressive disease(PD)in 8 patients,accounting for 15.69%(8/51).The objective response rate was 52.94%,and the disease control rate was 84.31%.Alanine aminotransferase,aspartate aminotransferase,lactate dehydrogenase,and alpha-fetoprotein isoform levels decreased after treatment compared with pretreatment(all P=0.000).The median OS was 26 months[95%confidence interval(95%CI):19.946-32.054]in the PR group and 19 months(95%CI:14.156-23.125)in the SD+PD group,with a statistically significant difference(P=0.015).The median PFS was 20 months(95%CI:18.441-34.559)in the PR group and 12 months(95%CI:8.745-13.425)in the SD+PD group,with a statistically significant difference(P=0.002).Common adverse reactions during treatment included nausea and vomiting(39.22%),thrombocytopenia(27.45%),and leukopenia(25.49%),with no treatment-related deaths *** Gamma Knife®combined with TACE and immune-targeted th

关键词： Gamma Knife® Transarterial chemoembolization Immunotherapy Primary liver cancer Liver function

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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

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Low Concentration of Wenyang Tonglin Decoction Promotes Conjugation and Transfer of Drug-Resistant Plasmids among Heterologous Strains

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Chinese Journal of Integrative Medicine 2024年第8期30卷 721-728页

作者： wang Bi-yan BU hong-shi XIA Li-bo JIANG Xiang-yu TONG Yan-qing Department of Traditional Chinese Medicine Changchun University of Traditional Chinese MedicineChangchun130000China

Objective To investigate the effect of low concentration of Wenyang Tonglin Decoction(WTD)on the binding conditions of R45 plasmid conjugative transfer under liquid phase conjugation and its *** Escherichia coli CP9(R45)and Staphylococcus aureus RN450RF were cultured in medium containing WTD,and their minimum inhibitory concentration(MIC)values were *** promoter fusion technology,*** CP9(R45)containing a promoter fusion was obtained.β-Galactosidase activity of TrfAp and TrbBp was tested,and the mRNA expression of regulatory factors(TrbA,KorA,and KorB)was detected by real-time fluorescent quantitative polymerase chain *** The MIC of *** CP9(R45)was 400 g/L and that of *** RN450RF was 200 g/*** the drug concentration in the culture medium was 200 g/L,the highest number of conjugants was(3.47±0.20)×10^(7) CFU/mL At 90 h of conjugation,the maximum number of conjugants was(1.15±0.06)×10^(8) CFU/mL When the initial bacterial concentration was 10^(8) CFU/mL,the maximum number of conjugants was(3.47±0.20)×10^(7) CFU/*** the drug concentration was 200 g/L,theβ-galactosidase activity of TrfAp and TrbBp significantly increased;the relative quantification of TrbA,KorA and KorB were significantly *** Low concentration of WTD promoted the development of bacterial resistance by affecting promoters and inhibiting the expression of regulatory factors.

关键词： urinary tract infection Chinese medicine drug-resistant plasmid heterozygous strains conjugation transfer

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