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Advances in genotypic antimicrobialresistance testing: a comprehensive review

Science China Life Sciences 2025年第1期68卷 130-143页

作者： Boheng Duan Xianjun Zeng Junping Peng Huan Kui College of Nanchang University Department of Imaging The Second Affiliated Hospital of Nanchang University NHC key laboratory of Systems biology of Pathogens National Institute of Pathogen BiologyChinese Academy of Medical Sciences & Peking Union Medical College key laboratory of Respiratory Disease Pathogenomics Chinese Academy of Medical Sciences & Peking Union Medical College key laboratory of Pathogen Infection Prevention and Control (Ministry of Education) State Key Laboratory of Respiratory Health and MultimorbidityNational Institute of Pathogen BiologyChinese Academy of Medical Sciences & Peking Union Medical College

Antimicrobial resistance(AMR) represents a substantial threat to global public health, complicating the treatment of common infections and leading to prolonged illness and escalated healthcare expenses. To effectively combat AMR, timely and accurate detection is crucial for AMR surveillance and individual-based therapy. Phenotypic antibiotic resistance testing(AST) has long been considered the gold standard in clinical applications, serving as the foundation for clinical AMR diagnosis and optimized therapy. It has significantly contributed to ensuring patients′ health and the development of novel antimicrobials. Despite advancements in automated culture-based AST technologies,inherent limitations impede the widespread use of phenotypic AST in AMR surveillance. Genotypic AST technologies offer a promising alternative option, exhibiting advantages of rapidity, high sensitivity, and specificity. With the continuous advancement and expanding applications of genotypic AST technologies, such as microfluidics, mass spectrometry, and high-resolution melting curve analysis, new vigor has been injected into the development and clinical implementation of genotypic AST technologies. In this narrative review, we discuss the principles, applications, and advancements of emerging genotypic AST methods in clinical settings. The comprehensive review aims to highlight the significant scientific potential of emerging genotypic AST technologies in clinical AMR diagnosis, providing insights to enhance existing methods and explore novel approaches.

关键词： antimicrobial resistance (AMR) genotypic antibiotic resistance testing (AST) AST technologies review

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Deciphering fungal metabolon coupling tandem inverse-electrondemand Diels-Alder reaction and semipinacol rearrangement for the biosynthesis of spiro polycyclic alkaloids

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Science China Chemistry 2025年第1期68卷 288-296页

作者： Shuai Liu Wen-Qiang Xu Ying-Tong Di Man-Cheng Tang Ding-Kang Chen Ming-Ming Cao Yao-Wen Chang Hong-Yu Tang Chun-Mao Yuan Jun-Bo Yang Zhi-Li Zuo Han Guo Zi-Fei Xu Ying Zeng Yun-Dong Wu Xiao-Jiang Hao key laboratory of Phytochemistry and Natural Medicines (Chinese Academy of Sciences) Kunming Institute of Botany Chinese Academy of Sciences University of Chinese Academy of Sciences lab of Computational Chemistry and Drug Design State Key Laboratory of Chemical Oncogenomics Peking University Shenzhen Graduate School Shenzhen Bay laboratory State key laboratory of Microbial Metabolism School of Life Sciences & Biotechnology Shanghai Jiao Tong University State key laboratory of Functions and Applications of Medicinal Plants Guizhou Medical University Molecular biology Experimental Center Germplasm Bank of Wild Species in Southwest China Kunming Institute of Botany Chinese Academy of Sciences Yunnan key laboratory for Wild Plant Resources Kunming Institute of Botany Chinese Academy of Sciences Research Unit of Chemical biology of Natural Anti-Virus Products Chinese Academy of Medical Sciences

In the intricate process of natural product biosynthesis, a metabolon can enhance metabolic flux by associating sequential enzymes. A fungal metabolon, comprising of flavin-dependent monooxygenase Spe F and P450 monooxygenase Spe G, is identified in the biosynthesis of spiro polycyclic alkaloids(+)-notoamide B and its diastereomer(+)-versicolamide B. Using notoamide E as a substance, Spe F/Spe G metabolon can control the stereoselectivity of its 2,3-epoxidation, followed by hydrogen atom ion at C-17 to generate reactive epoxide tau-m A with dienyl iminium unit. Subsequently,(+)-notoamide B and(+)-versicolamide B are produced via tandem nonenzymatic inverse-electron-demand Diels-Alder reaction and semipinacol rearrangement. This provides the first example of metabolon in the biosynthesis of spiro-prenylated indole alkaloids.

关键词： metabolon Diels-Alder reaction semipinacol rearrangement biosynthesis notoamides spiro polycyclic alkaloids

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Cobalamin-dependent radical S-adenosyl-L-methionine protein functions with a partner to successively methylate tricyclic indole alkaloid for chuangxinmycin maturation and derivatization

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Science China Chemistry 2025年第1期68卷 308-316页

作者： Sili Wang Jiancheng Huang Yanan Du Wei Huang Yufeng Xue Xiaokun Xu Guannan Zhong Yuanyuan Shi Bin Hong Xiaoying Bian Wen Liu State key laboratory of Chemical biology Shanghai Institute of Organic Chemistry University of Chinese Academy of SciencesChinese Academy of Sciences State key laboratory of Microbial Technology Shandong University National Health Commission (NHC) key laboratory of Biotechnology for Microbial Drugs Institute of Medicinal BiotechnologyChinese Academy of Medical Science & Peking Union Medical College

Cobalamin(Cbl)-dependent radical S-adenosyl-L-methionine(SAM) proteins constitute the largest collection of the radical SAM superfamily that has hundreds of thousands of individual members. Many of these proteins are involved in the biosynthesis of pharmaceutically important natural products to catalyze chemically demanding reactions. In the biosynthetic pathway of chuangxinmycin(CXM), a unique indole alkaloid antibiotic with potent anti-infective activity, functionalization of the characteristic thiopyrano[4,3,2-cd]indole scaffold by regio-and stereoselective C3-methylation is believed to rely on a Cbl-dependent radical process, which, however, remained to be reconstituted biochemically. We here report the dissection of this enzymatic process, which requires the incorporation of Cxm8, a Cbl-dependent radical SAM protein, with Cxm9, a DUF5825family protein that shares no homology to any proteins of known functions. Cxm8 and Cxm9 function together by forming an unexpected heterodimeric complex that selectively catalyzes C3-methylation of the tricyclic indole-S-hetero ring system in a successive manner, achieving CXM and a recently identified, C3-dimethylated congener. Detailed biochemical characterization,isotope labeling, structural simulation and bioinformatics analysis rationalized the catalysis of the Cxm8/Cxm9 complex and particularly the necessity of the DUF5825 protein for C3-methylase activity. This is the first example that a Cbl-dependent protein acts with a partner to exhibit radical SAM activity.

关键词： cbl-dependent radical SAM protein biosynthesis chuangxinmycin stereoselective methylation

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Propagating subduction initiation of the Caroline Plate at the Mussau Trench

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Science China Earth Sciences 2025年第1期68卷 253-269页

作者： Chun-Feng LI Yongkang DENG Tao WU Dongdong DONG Guoliang ZHANG Jiazheng ZHANG Yutao LIU Yaqing LI Fugui TANG Lulu ZHANG Department of Marine Sciences Zhejiang University laboratory of Marine Mineral Resources Laoshan Laboratory key lab of Marine Geology and Environment Institute of Oceanology Chinese Academy of Sciences key lab of Ocean and Marginal Sea Geology South China Sea Institute of Oceanology Chinese Academy of Sciences Science & Technology on Integrated Information System lab Institute of Software Chinese Academy of Sciences

New seismic imaging from the Mussau Trench confirms that, under horizontal compression on an oceanic plate boundary, it is within the young and weak oceanic plate that a trench will develop, and it is the young plate, not so long after its birth, that starts to subduct toward the old plate. The Mesozoic Pacific Plate cannot easily bend, under the joint horizontal compression and vertical gravity pull, even with a pre-existing weak zone in place and with a large age offset across the plate boundary. The bending of the Caroline Plate near the northern end of the Mussau Trench started only after a long-time span of trench migration, and/or after a prolonged transition from initial compression to trench development. Highly contrasting trench deformation and sedimentary accretion between two parallel seismic sections support an evident migration of underthrusting or significant longitudinal heterogeneity along the trench. The swift transition from underthrusting to non-thrusting can be explained by a counter-clockwise rotation of the Caroline Plate. That miniature accretionary wedges develop even before the subduction initiates imply strong compression and uplifting before the underthrusting can kick-start. Rotation of the Caroline Plate have been halted as the Mussau Trench is seismically rather quiet and the Lyra Trough to the east shows relaxational extension.

关键词： Mussau Trench Subduction initiation Seismic reflection Caroline Plate

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Experimental Study on Geometry Characteristics of Turbulent Premixed Flames for Natural Gas/Air Mixtures

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Journal of Thermal Science 2025年第1期34卷 268-282页

作者： ZHENG Weilin WANG Qijiao XIAO Huahua CHEN Xiaoxiao XIE Fan ZENG Wen Liaoning key lab of Advanced Test Technology for Aerospace Propulsion System Shenyang Aerospace University State key laboratory of Fire Science University of science and Technology of China AVIC Shenyang Aircraft Design and Research Institute

In this study,focusing on the geometry characteristics of spherical expanding flame,the turbulent premixed flames of natural gas/air mixtures were investigated in a fan-stirred turbulent *** effects of initial temperature（T=300-400 K）,initial pressure（P=0.1-0.3 MPa）,turbulence intensity（u'=1.0-2.7 m/s）,oxygen volumetric percentage(φ（O2）=15%-21%) and carbon dioxide volumetric percentage(φ（CO2）=0-20%)were delved *** flame profile under the Cartesian coordinate system was derived from the schlieren images taken by the high-speed ***,from both macroscopic and microscopic perspectives,the influence of experimental conditions on the flame geometry characteristics was explored through flame front extraction,wavelet decomposition and network *** results demonstrate that for significant flame wrinkling,changes in species concentrations and turbulence intensity have more pronounced effects on the flame wrinkling *** wrinkling of the flame front maintains a certain degree of similarity,as evidenced by the locally concentrated distribution of the angles of the maximum fluctuation *** disturbance energy under large-scale（D6-D8） disturbances exhibits relatively high values with a similar trend,exerting a significant impact on the geometry characteristics of the flame *** peaks of correlation degree are scattered either with the decomposition scale or the development of flame radius,indicating no linear correlation between different detail ***,the probability distribution of node degrees in key wrinkled regions exhibits different trends with that of large-scale wrinkling and disturbance energy,especially with changes in initial *** occurs because the number of key wrinkles varies based on the perturbation's strength or the region's ***,an increase in the fluctuation frequency of the flame's local radius may not necessarily lead to an increase in the number of key folded regions.

关键词： fan-stirred turbulent combustor geometry characteristics large-scale wrinkling network topology wavelet decomposition

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Genes and proteins expressed at different life cycle stages in the model protist Euplotes vannus revealed by both transcriptomic and proteomic approaches

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Science China Life Sciences 2025年第1期68卷 232-248页

作者： Yaohan Jiang Xiao Chen Chundi Wang Liping Lyu Saleh A.Al-Farraj Naomi A.Stover Feng Gao key laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity Ocean University of China Marine College Shandong University Zoology Department College of ScienceKing Saud University Department of biology Bradley University laboratory for Marine biology and Biotechnology Qingdao Marine Science and Technology Center

Sexual reproduction first appeared in unicellular protists and has continued to be an essential biological process in almost all *** protists, which contain both germline and somatic genomes within a single cell, have evolved a special form of sexual reproduction called conjugation that involves mitosis, meiosis, fertilization, nuclear differentiation, genome rearrangement, and the development of unique cellular structures. The molecular basis and mechanisms of conjugation vary dramatically among ciliates, and many details of the process and its regulation are still largely unknown. In order to better comprehend these processes and mechanisms from an evolutionary perspective, this study provides the first comprehensive overview of the transcriptome and proteome profiles during the entire life cycle of the newly-established marine model ciliate Euplotes vannus. Transcriptome analyses from 14 life cycle stages(three vegetative stages and 11 sexual stages) revealed over 26,000 genes that are specifically expressed at different stages, many of which are related to DNA replication,transcription, translation, mitosis, meiosis, nuclear differentiation, and/or genome rearrangement. Quantitative proteomic analyses identified 338 proteins with homologs associated with conjugation and/or somatic nuclear development in other ciliates, including dicer-like proteins, Hsp90 proteins, RNA polymerase Ⅱ and transcription elongation factors, ribosomal-associated proteins, and ubiquitin-related proteins. Four of these homologs belong to the PIWI family, each with different expression patterns identified and confirmed by RT-qPCR,which may function in small RNA-mediated genome rearrangement. Proteins involved in the nonhomologous end-joining pathway are induced early during meiosis and accumulate in the developing new somatic nucleus, where more than 80% of the germline sequences are eliminated from the somatic genome. A number of new candidate genes and proteins likely t

关键词： sexual reproduction transcriptomic proteomic genome rearrangement PIWI NHEJ

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Optimizing battery deployment: Aging trajectory prediction enabling homogenous performance grouping

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Journal of Energy Chemistry 2025年第1期100卷 565-577页

作者： Shuquan Wang Feng Gao Zhan Ma Hao Tian Yusen Zhang School of Control Science and Engineering Shandong University key lab of Power System Intelligent Dispatch and Control of Ministry of Education Shandong University

As battery deployments in electric vehicles and energy storage systems grow, ensuring homogeneous performance across units is crucial. We propose a multi-derivative imaging fusion(MDIF) model, employing advanced imaging and machine learning to predict battery aging trajectories from minimal initial data, thus facilitating effective performance grouping before deployment. Utilizing a derivative strategy and Gramian Angular Difference Field for dimensional enhancement, the MDIF model uncovers subtle predictive features from discharge curve data after only ten cycles. The architecture includes a parallel convolutional neural network with lateral connections to enhance feature integration and *** on a self-developed dataset, the model achieves an average root-mean-square error of 0.047 Ah and an average mean absolute percentage error of 1.60%, demonstrating high precision and *** robustness is further validated through transfer learning on two publicly available datasets, adapting with minimal retraining. This approach significantly reduces the testing cycles required, lowering both time and costs associated with battery testing. By enabling precise battery behavior predictions with limited data, the MDIF model optimizes battery utilization and deployment strategies, enhancing system efficiency and sustainability.

关键词： Lithium-ion battery Battery prognostics Fusion model Convolutional neural network Transfer learning

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Nanoscale and hollow inorganic sulfide@porous organic network doped intelligent hydrogels for accelerating diabetes wound therapeutics

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Science China Chemistry 2025年

作者： Yanhong Li Qiang Zhang Quanbo Wang Junping Wang Xiaomei Zhang Caixia Yin School of Chemistry and Chemical Engineering Shandong University key laboratory of Chemical biology and Molecular Engineering of Ministry of Education Shanxi University

Diabetic wound healing remains a major challenge due to the excess hyperglycemia microenvironment,massively bacterial infections,macrophage dysfunction,and persistent *** comprehensively solve these problems,novel multifunctional materials are highly ***,a versatile and intelligent hydrogel (Cu2S@FePPOPTPM@GOx@Gel) is ***2S@FePPOPTPM@GOx with hollow morphology and controllable size was rationally designed and fabricated by using Cu2S nanocubes as a template,followed by in situ growth of FePPOPTPMand loading glucose oxidase （GOx）,*** infection occurs,the Schiff base bonds in Cu2S@FePPOPTPM@GOx@Gel can controllably release Cu2S@FePPOPTPM@GOx based on its excellent dynamic pH-responsiveness,thereby synergically reducing blood glucose levels and killing bacteria achieved relying on the excellent catalytic activity of GOx towards glucose and its promoted peroxidelike activity of *** experiments on diabetic wound model in vivo demonstrated that Cu2S@FePPOPTPM@GOx@Gel promoted wound healing and skin regeneration,which was attributed to its antibacterial properties,alleviating inflammation,stimulating vascular regeneration,and encouraging M2 polarization of *** work provides a novel strategy for the construction of a microenvironment-responsive and antibiotics-free drug delivery platform to treat diabetic wounds,as well as broad prospects of nanomaterials in the clinical treatment of chronic wounds.

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Local-contrastive-learning machine with both generalization and adversarial robustness: A statistical physics analysis

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 109-123页

作者： Mingshan Xie Yuchen Wang Haiping Huang PMI lab School of Physics Sun Yat-sen University Guangdong Provincial key laboratory of Magnetoelectric Physics and Devices Sun Yat-sen University

Distinct from human cognitive processing, deep neural networks trained by backpropagation can be easily fooled by adversarial examples. To design a semantically meaningful representation learning, we discard backpropagation, and instead, propose a local contrastive learning, where the representations for the inputs bearing the same label shrink(akin to boson) in hidden layers,while those of different labels repel(akin to fermion). This layer-wise learning is local in nature, being biologically plausible.A statistical mechanics analysis shows that the target fermion-pair-distance is a key parameter. Moreover, the application of this local contrastive learning to MNIST benchmark dataset demonstrates that the adversarial vulnerability of standard perceptron can be greatly mitigated by tuning the target distance, i.e., controlling the geometric separation of prototype manifolds.

关键词： machine learning statistical mechanics adversarial robustness neural networks

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Ultrastrong MXene films for bone regeneration

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Science China Materials 2025年

作者： Jinghong Li Department of Chemistry Center for Bioanalytical Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education) Tsinghua University

Guided bone regeneration (GBR),as an important clinical treatment of bone defects,has long been a great challenge in modern *** addition to biological scaffolds,growth factors,and stem cells,barrier membranes for GBR application also play a key role in preventing the invasion of cells from the surrounding epithelium and connective tissue[1–3],to favor osteoprogenitor cells to proliferate and form new bone tissue in the site of *** commercial GBR membranes,such as polytetrafluoroethylene,titanium,collagen,and polyesters,exhibit low osteogenesis performance because of the lack of suitable antioxidant ability.

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