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OcBSA:An NGS-based bulk segregant analysis tool for outcross populations

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Molecular Plant 2024年第4期17卷 648-657页

作者： Lingkui Zhang Yanfeng Duan Zewei Zhang Lei Zhang shumin Chen Chengcheng Cai Shaoguang Duan Kang Zhang Guangcun Li Feng Cheng State Key Laboratory of Vegetable Biobreeding Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsKey Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China

Constructing inbred lines for self-incompatible species and species with long generation times is challenging,making the use of F1 outcross/segregating populations the main strategy for genetic studies of such species.However,there is a lack of dedicated algorithms/tools for rapid quantitative trait locus(QTL)mapping using the F1 populations.To this end,we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 populations.OcBSA transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 population.Testing of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and accuracy.In addition,the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple,pear,peach,citrus,grape,tea,and rice.We also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this study.The OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene,which regulates potato flower color.Taken together,these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing species.For ease of use,we have developed both Windows and Linux versions of OcBSA,which are freely available at:https://***/Bioinformaticslab/OcBSA.

关键词： outcross BSA self-incompatible F1 population QTL mapping potato

Miniature tunable Airy beam optical meta-device

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Opto-Electronic Advances 2024年第2期7卷 5-12页

作者： Jing Cheng Zhang Mu Ku Chen Yubin Fan Qinmiao Chen Shufan Chen Jin Yao Xiaoyuan Liu shumin Xiao Din Ping Tsai Department of Electrical Engineering City University of Hong KongKowloonHong Kong SAR 999077China State Key Laboratory of Terahertz and Millimeter Waves City University of Hong KongKowloonHong Kong SAR 999077China Centre for Biosystems Neuroscienceand NanotechnologyCity University of Hong KongKowloonHong Kong SAR 999077China Ministry of Industry and Information Technology Key Lab of Micro-Nano Optoelectronic Information System Guangdong Provincial Key Laboratory of Semiconductor Optoelectronic Materials and Intelligent Photonic SystemsHarbin Institute of TechnologyShenzhen 518055China

Tunable Airy beams with controllable propagation trajectories have sparked interest in various fields,such as optical manipulation and laser fabrication.Existing research approaches encounter challenges related to insufficient compactness and integration feasibility,or they require enhanced tunability to enable real-time dynamic manipulation of the propagation trajectory.In this work,we present a novel method that utilizes a dual metasurface system to surpass these limitations,significantly enhancing the practical potential of the Airy beam.Our approach involves encoding a cubic phase profile and two off-axis Fresnel lens phase profiles across the two metasurfaces.The validity of the proposed strategy has been confirmed through simulation and experimental results.The proposed meta-device addresses the existing limitations and lays the foundation for broadening the applicability of Airy beams across diverse domains,encompassing light-sheet microscopy,laser fabrication,optical tweezers,etc.

关键词： metasurface miniature device tunable Airy beam tunable meta-device

Outage Probability Analysis for D2D-Enabled Heterogeneous Cellular Networks with Exclusion Zone:A Stochastic Geometry Approach

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工程与科学中的计算机建模(英文) 2024年第1期138卷 639-661页

作者： Yulei Wang Li Feng shumin Yao Hong Liang Haoxu Shi Yuqiang Chen School of Computer Science and Engineering Macao University of Science and TechnologyTaipaMacaoChina Department of Broadband Communication Peng Cheng LaboratoryShenzhenChina School of Artificial Intelligence Dongguan PolytechnicDongguanChina

Interference management is one of the most important issues in the device-to-device(D2D)-enabled heterogeneous cellular networks(HetCNets)due to the coexistence of massive cellular and D2D devices in which D2D devices reuse the cellular spectrum.To alleviate the interference,an efficient interference management way is to set exclusion zones around the cellular receivers.In this paper,we adopt a stochastic geometry approach to analyze the outage probabilities of cellular and D2D users in the D2D-enabled HetCNets.The main difficulties contain three aspects:1)how to model the location randomness of base stations,cellular and D2D users in practical networks;2)how to capture the randomness and interrelation of cellular and D2D transmissions due to the existence of random exclusion zones;3)how to characterize the different types of interference and their impacts on the outage probabilities of cellular and D2D users.We then run extensive Monte-Carlo simulations which manifest that our theoretical model is very accurate.

关键词： Device-to-device(D2D)-enabled heterogeneous cellular networks(HetCNets) exclusion zone stochastic geometry(SG) Matérn hard-core process(MHCP)

Control of defensive behavior by the nucleus of Darkschewitsch GABAergic neurons

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National Science Review 2024年第4期11卷 70-83页

作者： Huiying Zhao Jinrong Liu Yujin Shao Xiang Feng Binhan Zhao Li Sun Yijun Liu Linghui Zeng Xiao-ming Li Hongbin Yang shumin Duan Yan-qin Yu Department of Neurology of Second Affiliated Hospital and School of Brain Science and Brain Medicine Zhejiang University School of Medicine Nanhu Brain-Computer Interface Institute Liangzhu Laboratory MOE Frontier Science Center for Brain Science and Brain-Machine Integration State Key Laboratory of Brain-Machine Intelligence Zhejiang University NHC and CAMS Key Laboratory of Medical Neurobiology Zhejiang University Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province School of Medicine Hangzhou City University

The nucleus of Darkschewitsch(ND), mainly composed of GABAergic neurons, is widely recognized as a component of the eye-movement controlling system. However, the functional contribution of ND GABAergic neurons(NDGABA) in animal behavior is largely unknown. Here, we show that NDGABA neurons were selectively activated by different types of fear stimuli, such as predator odor and foot shock.Optogenetic and chemogenetic manipulations revealed that NDGABA neurons mediate freezing behavior.Moreover, using circuit-based optogenetic and neuroanatomical tracing methods, we identified an excitatory pathway from the lateral periaqueductal gray(l PAG) to the ND that induces freezing by exciting ND inhibitory outputs to the motor-related gigantocellular reticular nucleus, ventral part(Gi V). Together,these findings indicate the NDGABA population as a novel hub for controlling defensive response by relaying fearful information from the l PAG to Gi V, a mechanism critical for understanding how the freezing behavior is encoded in the mammalian brain.

关键词： nucleus of Darkschewitsch GABAergic population defensive behavior freezing neural circuitry

Boosting synergism of chemo- and immunotherapies via switching paclitaxel-induced apoptosis to mevalonate metabolism-triggered ferroptosis by bisphosphonate coordination lipid nanogranules

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Acta Pharmaceutica Sinica B 2024年第2期14卷 836-853页

作者： Ge Song Minghui Li shumin Fan Mengmeng Qin Bin Shao Wenbing Dai Hua Zhang Xueqing Wang Bing He Qiang Zhang Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems School of Pharmaceutical SciencesPeking UniversityBeijing 100191China State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical SciencesPeking UniversityBeijing 100191China Department of Medical Oncology Key Laboratory of Carcinogenesis and Translational Research(Ministry of Education)Peking University Cancer HospitalBeijing 100142China

Conventional chemotherapy based on cytotoxic drugs is facing tough challenges recently following the advances of monoclonal antibodies and molecularly targeted drugs.It is critical to inspire new potential to remodel the value of this classical therapeutic strategy.Here,we fabricate bisphosphonate coordination lipid nanogranules(BC-LNPs)and load paclitaxel(PTX)to boost the chemo-and immuno-therapeutic synergism of cytotoxic drugs.Alendronate in BC-LNPs@PTX,a bisphosphonate to block mevalonate metabolism,works as both the structure and drug constituent in nanogranules,where alendronate coordinated with calcium ions to form the particle core.The synergy of alendronate enhances the efficacy of paclitaxel,suppresses tumor metastasis,and alters the cytotoxic mechanism.Differing from the paclitaxel-induced apoptosis,the involvement of alendronate inhibits the mevalonate metabolism,changes the mitochondrial morphology,disturbs the redox homeostasis,and causes theaccumulation of mitochondrial ROS and lethal lipid peroxides(LPO).These factors finally trigger the ferroptosis of tumor cells,an immunogenic cell death mode,which remodels the suppressive tumor immune microenvironment and synergizes with immunotherapy.Therefore,by switching paclitaxel-induced apoptosis to mevalonate metabolism-triggered ferroptosis,BC-LNPs@PTX provides new insight into the development of cytotoxic drugs and highlights the potential of metabolism regulation in cancer therapy.

关键词： Bisphosphonate coordinationlipid nanogranules Ferroptosis Mevalonatemetabolism Mitochondrial metabolism Nano-systematic biology

Temporal-spatial Generation of Astrocytes in the Developing Diencephalon

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Neuroscience Bulletin 2024年第1期40卷 1-16页

作者： Wentong Hong Pifang Gong Xinjie Pan Zhonggan Ren Yitong Liu Guibo Qi Jun-Liszt Li Wenzhi Sun Woo-Ping Ge Chun-Li Zhang shumin Duan Song Qin Department of Anatomy Histology and EmbryologySchool of Basic Medical SciencesFudan UniversityShanghai 200032China Academy for Advanced Interdisciplinary Studies Peking UniversityBeijing 100871China Chinese Institute for Brain Research Beijing 102206China School of Basic Medical Sciences Capital Medical UniversityBeijing 100069China Department of Molecular Biology University of Texas Southwestern Medical CenterDallasTexas 75390-9148USA Department of Neurobiology Key Laboratory of Medical Neurobiology of Ministry of Health of ChinaZhejiang University School of MedicineHangzhou 310058China State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science Fudan UniversityShanghai 200032China

tAstrocytes are the largest glial population in the mammalian brain.However,we have a minimal understanding of astrocyte development,especially fate specification in different regions of the brain.Through lineage tracing of the progenitors of the third ventricle(3V)wall via in-utero electroporation in the embryonic mouse brain,we show the fate specification and migration pattern of astrocytes derived from radial glia along the 3V wall.Unexpectedly,radial glia located in different regions along the 3V wall of the diencephalon produce distinct cell types:radial glia in the upper region produce astrocytes and those in the lower region produce neurons in the diencephalon.With genetic fate mapping analysis,we reveal that the first population of astrocytes appears along the zona incerta in the diencephalon.Astrogenesis occurs at an early time point in the dorsal region relative to that in the ventral region of the developing diencephalon.With transcriptomic analysis of the region-specific 3V wall and lateral ventricle(LV)wall,we identified cohorts of differentially-expressed genes in the dorsal 3V wall compared to the ventral 3V wall and LV wall that may regulate astrogenesis in the dorsal diencephalon.Together,these results demonstrate that the generation of astrocytes shows a spatiotemporal pattern in the developing mouse diencephalon.

关键词： Radial glia Astrocyte specification Lineage tracing Diencephalon Third ventricle

Modulating the alloying mode in the doping-induced synthesis of Au-Pd nanowires

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Nano Research 2024年第4期17卷 3334-3343页

作者： Hui Jin Xiaoliang Wei Lecheng Zhao Jialong Yu Qiao Pan shumin Li Qian Wang Zhaotong Yuan Dan Yang Donghui Zhao Hongyu Chen Yawen Wang Institute of Advanced Synthesis School of Chemistry and Molecular EngineeringJiangsu National Synergistic Innovation Center for Advanced MaterialsNanjing Tech UniversityNanjing 211816China School of Science Westlake UniversityHangzhou 310064China Institute of Natural Sciences Westlake Institute for Advanced StudyHangzhou 310064China

Heterogeneous doping is one effective strategy for synthesizing metal alloy nanowires.Herein,the heterogeneous doping processes of Pd on the ultrathin Au nanowires were systematically modulated and investigated.Au-Pd alloy nanowires with various morphologies and lattice structures can be obtained by adjusting the morphology of the precursor Au nanowires and the kinetics of the heterogeneous doping processes.The effects of the rate of Pd reduction and the concentration of the ligand oleylamine(OAm)on the Pd deposition and alloying mode were articulated.Generally,as the Pd deposition rate decreases,the Pd deposition and alloying mode switches from the island-forming Stransky–Krastanov(SK)mode to the epitaxial Frank-van der Merwe(FM)mode,and eventually to an unconventional twisting alloying mode,where the interdiffusion of Pd and Au causes drastic rearrangement of the lattice structure and formation of helical structures.The kinetics-related variation of alloying mode could also be observed in the Au-Ag nanowires,demonstrating a general design principle for the synthesis of alloy nanostructures.In addition,the electrocatalytic performance of various Au-Pd nanowires was evaluated,and the alloy nanowire formed via the SK mode was found to be an excellent electrocatalyst for oxygen reduction and ethanol oxidation.

关键词： gold nanowires Au-Pd alloy oleylamine post-synthetic modification

Immunology reshapes neuroscience,and neuroscience reshapes immunology

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Fundamental Research 2024年第2期4卷 199-200页

作者： Bo Peng Yanxia Rao Yun Wang shumin Duan Hai Qi Jing Yang Hongliang Zhang Department of Neurosurgery Huashan HospitalInstitute for Translational Brain ResearchState Key Laboratory of Medical NeurobiologyMOE Frontiers Center for Brain ScienceMOE Innovative Center for New Drug Development of Immune Inflammatory DiseasesFudan UniversityShanghai 200040China Department of Laboratory Animal Science MOE Frontiers Center for Brain ScienceFudan UniversityShanghai 200032China Neuroscience Research Institute and Department of Neurobiology School of Basic Medical SciencesKey Laboratory for NeuroscienceMinistry of Education/National Health Commission and State Key Laboratory of Natural and Biomimetic DrugsPeking UniversityBeijing 100083China PKU-IDG/McGovern Institute for Brain Research Peking UniversityBeijing 100871China Faculty of Medicine and Pharmaceutical Sciences Zhejiang UniversityHangzhou 310014China School of Medicine Tsinghua UniversityBeijing 100084China IDG/McGovern Institute for Brain Research Center for Life SciencesSchool of Life SciencesPeking UniversityBeijing 100871China Chinese Institute for Brain Research Beijing 102206China Department of Life Sciences National Natural Science Foundation of ChinaBeijing 100085China

As a result of evolution,our body has evolved into a sophisticated system in which various tissues and organs cooperate in a highly orchestrated manner.Few tissues or organs operate in isolation.The brain serves as the command center of our body and is relatively isolated from the peripheral system due to the presence of the blood-brain barrier(BBB).This barrier prevents direct and extensive interaction between blood cells,plasma molecules,and brain cells,contributing to the longstanding perception of the brain as an“immune-privileged”area.Consequently,neuroscientists and immunologists historically conducted separate research with minimal overlap between these two disciplines.However,this perspective has undergone reconsideration over the past few decades.

关键词： organs overlap contributing

Discourse Analysis of the Belt and Road Initiative From the Perspective of Central Asian Countries: A Case Study of the Republic of Kazakhstan

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Journalism and Mass Communication 2024年第2期14卷 96-100页

作者： CHEN Jia LIU shumin FU Da’an SHAO Di North China Institute of Aerospace Engineering LangfangChina

This study employs Norman Fairclough’s Critical Discourse Analysis(CDA)three-dimensional model,using the Republic of Kazakhstan as a case study,to delve into the discourse construction of China’s Belt and Road Initiative(BRI)in Central Asian countries.Through detailed analysis of policy documents,media reports,and public discussions in Central Asian countries,this paper reveals how the BRI constructs specific social practices,discourse events,and textual meanings within these nations.The findings indicate that through this global development strategy,China has not only strengthened its economic ties with Central Asian countries but has also exerted profound influences on political,cultural,and social levels.

关键词： Belt and Road Initiative Central Asian countries discourse analysis Norman Fairclough’s three-dimensional model