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Whole-genome sequencing in medicinal plants:current progress and prospect

Science China(Life Sciences) 2024年第2期67卷 258-273页

作者： Yifei Pei Liang Leng Wei Sun Baocai Liu xue feng Xiwen Li Shilin Chen Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China Institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu 611137China Innovative Institute of Chinese Medicine and Pharmacy Chengdu University of Traditional Chinese MedicineChengdu 611137China Institute of Agricultural Bioresource Fujian Academy of Agricultural SciencesFuzhou 350003China

Advancements in genomics have dramatically accelerated the research on medicinal plants,and the development of herbgenomics has promoted the“Project of 1K Medicinal Plant Genome”to decipher their genetic code.However,it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity.Whole genomes of 123 medicinal plants were published until September 2022.These published genome sequences were investigated in this review,covering their classification,research teams,ploidy,medicinal functions,and sequencing strategies.More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes.Diploid species account for a majority of sequenced medicinal plants.The whole genomes of plants in the Poaceae family are the most studied.Almost 40%of the published papers studied species with tonifying,replenishing,and heat-cleaning medicinal effects.Medicinal plants are still in the process of domestication as compared with crops,thereby resulting in unclear genetic backgrounds and the lack of pure lines,thus making their genomes more difficult to complete.In addition,there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome.Herein,a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants.Moreover,whole genome-based biological studies of medicinal plants,including breeding and biosynthesis,were reviewed.We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.

关键词： herbgenomics whole genome high throughput sequencing research strategy model species application

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Reversal of the immunosuppressive tumor microenvironment via platinum-based neoadjuvant chemotherapy in cervical cancer

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Cancer Pathogenesis and Therapy 2024年第1期2卷 38-49页

作者： xue feng Xiaolin Meng Dihong Tang Shuaiqingying Guo Qiuyue Liao Jing Chen Qin Xie fengyuan Liu Yong Fang Chaoyang Sun Yingyan Han Jihui Ai Kezhen Li Department of Gynecological Oncology Tongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei 430000China National Clinical Research Center for Obstetrics and Gynecology Cancer Biology Research Center(Key Laboratory of the Ministry of Education)Tongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei 430000China Department of Gynecologic Oncology Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaHunan 410000China

Background Immunotherapy favors patients with tumors;however,only 3-26.3%of patients with cervical cancer benefit from single-agent immune checkpoint inhibitors.Combined immunotherapy and chemotherapy has been explored against tumor;however,the combination remains controversial.This study aimed to investigate the tumor immune microenvironment(TIME)and the effects of platinum-based neoadjuvant chemotherapy(NACT)in cervical cancer to identify the clinical value of combining chemotherapy with immunotherapy.Methods Multiplex immunohistochemistry(IHC)with 11 markers(cluster of differentiation[CD]3,CD8,CD4,CD11c,CD68,forkhead box P3[Foxp3],programmed cell death 1[PD-1],programmed cell death 1 ligand 1[PD-L1],indoleamine 2,3-dioxygenase[IDO],cyclin-dependent kinase inhibitor 2A[p16],and cytokeratin[CK])was performed to evaluate TIME from 108 matched pre-and post-NACT cervical cancer samples.The mechanism of antitumor immunity triggered by NACT was explored using RNA sequencing(RNA-seq)from four paired samples and subsequently verified in 41 samples using IHC.Results The infiltration rate of the CD8^(+)T cells in treatment-naive cervical cancer was 0.73%,and those of Foxp3^(+)regulatory T cells(Tregs)and IDO^(+)cells were 0.87%and 17.15%,respectively.Moreover,immunoreactive T cells,dendritic cells,and macrophages were more in the stromal than the intratumor region.NACT increased dendritic,CD3^(+)T,CD8^(+)T,and CD4^(+)T cells and decreased Tregs.The aforementioned alterations occurred predominantly in the stromal region and were primarily in responders.Non-responders primarily showed decreased Tregs and no increase in CD8^(+)T or dendritic cell infiltration.Furthermore,dendritic cells interacted more closely with CD3^(+)T cells after NACT,an effect primarily observed in responders.RNA-seq data revealed activation of the antigen receptor-mediated signaling pathway and upregulation of major histocompatibility complex(MHC)I and MHC II after chemotherapy,validated using IHC.Conclusions NACT can reduce Tregs,and when tumor cel

关键词： Neoadjuvant chemotherapy Cervical cancer Tumor immune microenvironment Spatial architecture CD8 Regulatory T cells

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通智测试——基于动态具身物理社会交互环境的通用人工智能测试

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Engineering 2024年第3期34卷 12-22页

作者： Yujia Peng Jiaheng Han Zhenliang Zhang Lifeng Fan Tengyu Liu Siyuan Qi xue feng Yuxi Ma Yizhou Wang Song-Chun Zhu National Key Laboratory of General Artificial Intelligence Beijing Institute for General Artificial IntelligenceBeijing 100086China Institute for Artificial Intelligence Peking UniversityBeijing 100871China Beijing Key Laboratory of Behavior and Mental Health School of Psychological and Cognitive SciencesPeking UniversityBeijing 100871China School of Intelligence Science and Technology Peking UniversityBeijing 100871China School of Computer Science Peking UniversityBeijing 100871China

The release of the generative pre-trained transformer(GPT)series has brought artificial general intelligence(AGI)to the forefront of the artificial intelligence(AI)field once again.However,the questions of how to define and evaluate AGI remain unclear.This perspective article proposes that the evaluation of AGI should be rooted in dynamic embodied physical and social interactions(DEPSI).More specifically,we propose five critical characteristics to be considered as AGI benchmarks and suggest the Tong test as an AGI evaluation system.The Tong test describes a value-and ability-oriented testing system that delineates five levels of AGI milestones through a virtual environment with DEPSI,allowing for infinite task generation.We contrast the Tong test with classical AI testing systems in terms of various aspects and propose a systematic evaluation system to promote standardized,quantitative,and objective benchmarks and evaluation of AGI.

关键词： Artificial general intelligence Artificial intelligence benchmark Artificial intelligence evaluation Embodied artificial intelligence Value alignment Turing test Causality

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Achieving a remarkable low-temperature tensile ductility in a high-strength tungsten alloy

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Tungsten 2024年第1期6卷 150-161页

作者： Xiang Cheng Zhuo-Ming Xie xue-feng Xie Long-Fei Zeng Rui Liu Jun-feng Yang xue-Bang Wu Xian-Ping Wang Chang-Song Liu Qiang-feng Fang Key Laboratory of Materials Physics Institute of Solid State PhysicsHFIPSChinese Academy of SciencesHefei 230031China University of Science and Technology of China Hefei 230026China Faculty of Materials Metallurgy and Chemistry Jiangxi University of Science and TechnologyGanzhou 341000China

Hot-swaging yields a high ultimate tensile strength of 712 MPa but a limited tensile ductility with the total elongation of3.6%at a testing temperature of 200℃in a representative W-0.5wt.%ZrC alloy.In this work,the evolution of Vickers microhardness with annealing temperatures is investigated in detail,which contributes to a rough index chart to guide the search for an optimized post-annealing temperature.Through the post-annealing around 1300℃,an outstanding tensile ductility at200℃,including a uniform elongation of 14%and a total elongation of~25%,has been achieved without the sacrifice of its strength.The evolution of dislocations and grain structures with the annealing temperatures accessed through backscattered scanning electron microscope and transmission electron microscope analysis reveals that the improved low-temperature tensile ductility has resulted from the reduction of residual dislocations and dislocation tanglement via the static recovery,which provides more room to accommodate dislocations,and hence stronger strain hardening ability and tensile ductility.

关键词： Tungsten Low-temperature ductility Annealing Dislocations

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Dynamic cooperations between lattice oxygen and oxygen vacancies for photocatalytic ethane dehydrogenation by a self-restoring LaVO_(4)catalyst

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Chinese Chemical Letters 2024年第3期35卷 171-176页

作者： Fen Wei Weichao xue Zhiyang Yu xue feng Lu Sibo Wang Wei Lin Xinchen Wang State Key Laboratory of Photocatalysis on Energy and Environment College of ChemistryFuzhou UniversityFuzhou 350108China

Thermocatalytic nonoxidative ethane dehydrogenation(EDH)is a promising strategy for ethene production but suffers from intense energy consumption and poor catalyst durability;exploring technology that permits efficient EDH by solar energy remains a giant challenge.Herein,we present that an oxygen vacancy(O_v)-rich LaVO_(4)(LaVO_(4)-O_v)catalyst is highly active and stable for photocatalytic EDH,through a dynamic lattice oxygen(O_(latt.))and O_(v)co-mediated mechanism.Irradiated by simulated sunlight at mild conditions,LaVO_(4)-O_(v)effectively dehydrogenates undiluted ethane to produce C_(2)H_(4)and CO with a conversion of 2.3%.By loading a small amount of Pt cocatalyst,the evolution and selectivity of C_(2)H_(4)are enhanced to 275μmol h^(-1)g^(-1)and 96.8%.Of note,LaVO_(4)-O_(v)appears nearly no carbon deposition after the reaction.The isotope tracked reactions reveal that the consumed O_(latt.)recuperates by exposing the used catalyst with O_(2),thus establishing a dynamic cycle of O_(latt.)and achieving a facile catalyst regeneration to preserve its intrinsic activity.The refreshed LaVO_(4)-O_(v)exhibits superior reusability and delivers a turnover number of about 305.The O_(v)promotes photo absorption,boosts ethane adsorption/activation,and accelerates charge separation/transfer,thus improving the photocatalytic efficiency.The possible photocatalytic EDH mechanism is proposed,considering the key intermediates predicted by density functional theory(DFT)and monitored by in-situ diffuse reflectance infrared Fourier transform spectroscopy(DRIFTS).

关键词： Photocatalysis Ethane dehydrogenation Ethene LaVO_(4) Oxygen vacancy

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Risk Factors of Depression Screened by Two-Sample Mendelian Randomization Analysis:A Systematic Review

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Biomedical and Environmental Sciences 2024年第1期37卷 85-95页

作者： WANG Han Lin xue Yan feng CUI Bao Qiu LIU Hong SHEN Xin Xin Shandong Provincial Research Center for Bioinformatic Engineering and Technique School of Life SciencesShandong University of TechnologyZibo 255049ShandongChina Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuan 030013ShanxiChina State Key Laboratory of Infectious Disease Prevention and Control National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China

Objective This study explored the potentially modifiable factors for depression and major depressive disorder(MDD)from the MR-Base database and further evaluated the associations between drug targets with MDD.Methods We analyzed two-sample of Mendelian randomization(2SMR)using genetic variant depression(n=113,154)and MDD(n=208,811)from Genome-Wide Association Studies(GWAS).Separate calculations were performed with modifiable risk factors from MR-Base for 1,001 genomes.The MR analysis was performed by screening drug targets with MDD in the DrugBank database to explore the therapeutic targets for MDD.Inverse variance weighted(IVW),fixed-effect inverse variance weighted(FE-IVW),MR-Egger,weighted median,and weighted mode were used for complementary calculation.Results The potential causal relationship between modifiable risk factors and depression contained 459 results for depression and 424 for MDD.Also,the associations between drug targets and MDD showed that SLC6A4,GRIN2A,GRIN2C,SCN10A,and IL1B expression are associated with an increased risk of depression.In contrast,ADRB1,CHRNA3,HTR3A,GSTP1,and GABRG2 genes are candidate protective factors against depression.Conclusion This study identified the risk factors causally associated with depression and MDD,and estimated 10 drug targets with significant impact on MDD,providing essential information for formulating strategies to prevent and treat depression.

关键词： Risk factors Drug targets Depression Major depressive disorder Two-sample Mendelian randomization

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Tunable quantum anomalous Hall effects in ferromagnetic van der Waals heterostructures

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National Science Review 2024年第3期11卷 100-107页

作者： feng xue Yusheng Hou Zhe Wang Zhiming Xu Ke He Ruqian Wu Yong Xu Wenhui Duan Beijing Academy of Quantum Information Sciences State Key Laboratory of Low Dimensional Quantum Physics Department of Physics Tsinghua University Guangdong Provincial Key Laboratory of Magnetoelectric Physics and Devices Center for Neutron Science and Technology School of Physics Sun Yat-sen University State Key Laboratory of Surface Physics Key Laboratory of Computational Physical Sciences and Department of PhysicsFudan University Frontier Science Center for Quantum Information Department of Physics and Astronomy University of California-Irvine Tencent Quantum Laboratory Tencent Technology(Shenzhen)Co.Ltd RIKEN Center for Emergent Matter Science(CEMS) Institute for Advanced Study Tsinghua University

The quantum anomalous Hall effect（QAHE） has unique advantages in topotronic applications, but it is still challenging to realize the QAHE with tunable magnetic and topological properties for building functional devices. Through systematic first-principles calculations, we predict that the in-plane magnetization induced QAHE with Chern numbers C = ±1 and the out-of-plane magnetization induced QAHE with high Chern numbers C = ±3 can be realized in a single material candidate, which is composed of van der Waals（vdW）coupled Bi and MnBi2Te4monolayers. The switching between different phases of QAHE can be controlled in multiple ways, such as applying strain or（weak） magnetic field or twisting the vdW materials. The prediction of an experimentally available material system hosting robust, highly tunable QAHE will stimulate great research interest in the field. Our work opens a new avenue for the realization of tunable QAHE and provides a practical material platform for the development of topological electronics.

关键词： quantum anomalous Hall effect topological quantum phase transition van der Waals heterostructures tunable Chern number high Chern number

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Potential and application of abortive transcripts as a novel molecular marker of cancers

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World Journal of Experimental Medicine 2024年第2期14卷 53-61页

作者： Tian-Miao Zhang Xiao-Nian Zhu Shao-Wei Qin xue-feng Guo xue-Kun Xing Li-feng Zhao Sheng-Kui Tan Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health Guilin Medical UniversityGuilin 541199Guangxi Zhuang Autonomous RegionChina School of Leisure and Health Guilin Tourism UniversityGuilin 541006Guangxi Zhuang Autonomous RegionChina

Abortive transcript(AT)is a 2-19 nt long non-coding RNA that is produced in the abortive initiation stage.Abortive initiation was found to be closely related to RNA polymerase through in vitro experiments.Therefore,the distribution of AT length and the scale of abortive initiation are correlated to the promoter,discriminator,and transcription initiation sequence,and can be affected by transcription elongation factors.AT plays an important role in the occurrence and development of various diseases.Here we summarize the discovery of AT,the factors responsible for AT formation,the detection methods and biological functions of AT,to provide new clues for finding potential targets in the early diagnosis and treatment of cancers.

关键词： Abortive transcript Abortive initiation RNA polymerase Transcription Tumor marker

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Engineering yolk-shell CuCo_(2)S_(4)@Cu_(2)O Z-scheme nanoreactors for accelerating generation of value-added chemicals and of degradation multi-organic contaminants

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Journal of Materials Science & Technology 2023年第25期156卷 54-63页

作者： xue feng Lei Zhang College of Chemistry Liaoning University66 Chongshan Middle RoadShenyang 110036China

The synthesis of solar-driven chemical value-added products and the degradation of pollutants is a promising approach for sustainable development. However, achieving these works via photocatalysts with efficient charge-separation, photo-absorption is challenging. A yolk-shell CuCo_(2)S_(4)@Cu_(2)O Z-scheme nanoreactor (YS-CuCo_(2)S_(4)@Cu_(2) O-NR) with octahedron Cu_(2)O as the core and tubular CuCo2 S4 as the shell, has been synthesized by regulating composition and morphology. YS-CuCo_(2)S_(4)@Cu_(2)O-NR shows superior photocatalytic activities for producing H_(2) O_(2) collaborates by selective oxidation of benzyl alcohol (BA) to high value-added benzaldehyde (BAD)/utilized Fenton-like reaction to degrade multi-pollutants through space-confinement effect, reaching 80% conversion and 99% selectivity of BA, a yield of 12 mM g^(−1) for H_(2)O_(2) and above 90% degradation efficiency for multi-pollutants. A photocatalysis nanoconfinement reactor system is proposed and demonstrated by using yolk-shell to enhance the performance of the chemical reaction. Mechanism studies show that the yolk-shell provides confined space to accelerate redox reaction kinetics;while the inner void promotes light harvesting and keeps yolk Cu_(2) O from deactivation;combined with the Z-scheme charge transfer, engineering Cu^(+) /Cu^(2+) active composition, they are favorable for enhancing the H_(2) O_(2) generation and Fenton-like activity. These findings provide new opportunities for application of yolk-shell Z-scheme metal-oxide-based photocatalysts.

关键词： Octahedron yolk-shell structure catalyzer Z-scheme charge transfer H2O_(2)generation Selective oxidation of BA Fenton-like reaction

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Fully sprayed MXene-based high-performance flexible piezoresistive sensor for image recognition

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Nano Materials Science 2024年第1期6卷 77-85页

作者： Zhi-Dong Zhang xue-feng Zhao Qing-Chao Zhang Jie Liang Hui-Nan Zhang Tian-Sheng Zhang Chen-Yang xue Key Laboratory of Instrumentation Science&Dynamic Measurement of Ministry of Education North University of ChinaTaiyuan030051People's Republic of China State Key Laboratory of ASIC and System Shanghai Institute of Intelligent Electronics&SystemsSchool of MicroelectronicsFudan UniversityShanghai200433People's Republic of China Shanxi Hosipital of Acupuncture and Moxibustion Taiyuan030006People's Republic of China

High-performance flexible pressure sensors provide comprehensive tactile perception and are applied in human activity monitoring,soft robotics,medical treatment,and human-computer interface.However,these flexible pressure sensors require extensive nano-architectural design and complicated manufacturing and are timeconsuming.Herein,a highly sensitive,flexible piezoresistive tactile sensor is designed and fabricated,consisting of three main parts:the randomly distributed microstructure on T-ZnOw/PDMS film as a top substrate,multilayer Ti_(3)C_(2)-MXene film as an intermediate conductive filler,and the few-layer Ti_(3)C_(2)-MXene nanosheetbased interdigital electrodes as the bottom substrate.The MXene-based piezoresistive sensor with randomly distributed microstructure exhibits a high sensitivity over a broad pressure range(less than 10 kPa for 175 kPa^(-1))and possesses an out-standing permanence of up to 5000 cycles.Moreover,a 16-pixel sensor array is designed,and its potential applications in visualizing pressure distribution and an example of tactile feedback are demonstrated.This fully sprayed MXene-based pressure sensor,with high sensitivity and excellent durability,can be widely used in,electronic skin,intelligent robots,and many other emerging technologies.

关键词： Piezoresistive sensor Ti_(3)C_(2)-MXene T-ZnOw/PDMS film Randomly distributed microstructure

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