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Upgraded durian genome reveals the role of chromosome reshuffling during ancestral karyotype evolution,lignin biosynthesis regulation,and stress tolerance

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Science China(Life Sciences) 2024年第6期67卷 1266-1279页

作者： wanwan Li Xin Chen Jianing Yu Yuxian Zhu College of Life Sciences Shaanxi Normal UniversityXi’an 710119China The State Key Laboratory of Protein and Gene Research College of Life SciencesPeking UniversityBeijing 100871China The Institute for Advanced Studies Wuhan UniversityWuhan 430072China

Durian(Durio zibethinus)is a tropical fruit that has a unique flavor and aroma.It occupies a significant phylogenetic position within the Malvaceae family.Extant core-eudicot plants are reported to share seven ancestral karyotypes that have undergone reshuffling,resulting in an abundant genomic diversity.However,the ancestral karyotypes of the Malvaceae family,as well as the evolution trajectory leading to the28 chromosomes in durian,remain poorly understood.Here,we report the high-quality assembly of the durian genome with comprehensive comparative genomic analyses.By analyzing the collinear blocks between cacao and durian,we inferred 11 Malvaceae ancestral karyotypes.These blocks were present in a single-copy form in cacao and mainly in triplicates in durian,possibly resulting from a recent whole genome triplication(WGT)event that led to hexaploidization of the durian genome around 20(17–24)million years ago.A large proportion of the duplicated genes in durian,such as those involved in the lignin biosynthesis module for phenylpropane biosynthesis,are derived directly from whole genome duplication,which makes it an important force in reshaping its genomic architecture.Transcriptome studies have revealed that genes involved in feruloyl-Co A formations were highly preferentially expressed in fruit peels,indicating that the thorns produced on durian fruit may comprise guaiacyl and syringyl lignins.Among all the analyzed transcription factors(TFs),members of the heat shock factor family(HSF)were the most significantly upregulated under heat stress.All subfamilies of genes encoding heat shock proteins(HSPs)in the durian genome appear to have undergone expansion.The potential interactions between HSF Dzi05.397 and HSPs were examined and experimentally verified.Our study provides a high-quality durian genome and reveals the reshuffling mechanism of ancestral Malvaceae chromosomes to produce the durian genome.We also provide insights into the mechanism underlying lignin biosynthesis and heat stress tolerance.

关键词： Durio zibethinus whole genome duplication whole genome triplication Malvaceae ancestral karyotypes chromosome reshuffling lignin biosynthesis heat stress

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Time-Resolved Imaging in Short-Wave Infrared Region

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Journal of Shanghai Jiaotong university(Science) 2024年第1期29卷 29-36页

作者：徐杨李万万 School of Materials Science and Engineering Shanghai Jiao Tong UniversityShanghai 200240China

Compared with the conventional first near-infrared(NIR-I,700900 nm)window,the short-wave infrared region(SWIR,900—1700nm)possesses the merits of the increasing tissue penetration depths and the suppression of scattering background,leading to great potential for in vivo imaging.Based on the limitations of the common spectral domain,and the superiority of the time-dimension,time-resolved imaging eliminates the auto-fuorescence in the biological tissue,thus supporting higher signal-to-noise ratio and sensitivities.The imaging technique is not affected by the difference in tissue composition or thickness and has the practical value of quan-titative in vivo detection.Almost all the relevant time-resolved imaging was carried out around lanthanide-doped upconversion nanomaterials,owing to the advantages of ultralong luminescence lifetime,excellent photostability,controllable morphology,easy surface modification and various strategies of regulating lifetime.Therefore,this review presents the research progress of SWIR time-resolved imaging technology based on nanomaterials doped with lanthanide ions as luminescence centers in recent years.

关键词： time-resolved imaging short-wave infrared fluorescence probe lanthanide ions

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Early Warning and Monitoring of Coronavirus Disease 2019 Using Baidu Search Index and Baidu Information Index in Guangxi,China

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Infectious Microbes & Diseases 2022年第4期4卷 168-174页

作者： Yihong Xie wanwan zhou Jinhui Zhu Yuhua Ruan Xiaomin Wang Tengda Huang Department of Epidemiology and Biostatistics Guangxi Medical UniversityNanningGuangxiChina Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response Guangxi Center for Disease Control and PreventionNanningGuangxiChina

Coronavirus disease 2019(COVID-19)is an emerging infectious disease,and it is important to detect early and monitor the disease trend for policymakers to make informed decisions.We explored the predictive utility of Baidu Search Index and Baidu Information Index for early warning of COVID-19 and identified search keywords for further monitoring of epidemic trends in Guangxi.A time-series analysis and Spearman correlation between the daily number of cases and both the Baidu Search Index and Baidu Information Index were performed for seven keywords related to COVID-19 from January 8 to March 9,2020.The time series showed that the temporal distributions of the search terms“coronavirus,”“pneumonia”and“mask”in the Baidu Search Index were consistent and had 2 to 3 days'lead time to the reported cases;the correlation coefficients were higher than 0.81.The Baidu Search Index volume in 14 prefectures of Guangxi was closely related with the number of reported cases;it was not associated with the local GDP.The Baidu Information Index search terms“coronavirus”and“pneumonia”were used as frequently as 192,405.0 and 110,488.6 per million population,respectively,and they were also significantly associated with the number of reported cases(rs>0.6),but they fluctuated more than for the Baidu Search Index and had 0 to 14 days'lag time to the reported cases.The Baidu Search Index with search terms“coronavirus,”“pneumonia”and“mask”can be used for early warning and monitoring of the epidemic trend of COVID-19 in Guangxi,with 2 to 3 days'lead time.

关键词： COVID-19 Baidu Search Index Baidu Information Index early warning monitoring epidemic trend

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基于FBG-FPI光纤传感器的岩石含水率光纤超声检测

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光学学报 2024年第8期44卷 19-26页

作者：康弯弯邵志华周旷羽乔学光西北大学物理学院陕西西安710127 陕西省油气资源光纤探测工程技术研究中心陕西西安710065

提出了一种基于光纤超声传感技术的岩石含水率检测新方法。在实验中,以压电换能器(PZT)发出的1 MHz超声波作为声源,采用超声波透射法,通过刻写在细芯光纤中的一对光纤光栅检测岩石的超声波信息(包括时域以及频域的结果),并与相同条件下... 详细信息

提出了一种基于光纤超声传感技术的岩石含水率检测新方法。在实验中,以压电换能器(PZT)发出的1 MHz超声波作为声源,采用超声波透射法,通过刻写在细芯光纤中的一对光纤光栅检测岩石的超声波信息(包括时域以及频域的结果),并与相同条件下的PZT接收结果进行比较。随着岩石含水率的增加,光纤传感器表现出与PZT相似的响应趋势,且测得的含水率绝对偏差较小,充分证明了光纤探测岩石含水信息的可行性和优越性。

关键词：光纤光学红砂岩含水率超声波光纤检测

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Parallel Physics-Informed Neural Networks Method with Regularization Strategies for the Forward-Inverse Problems of the Variable Coefficient Modified KdV Equation

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Journal of Systems Science & Complexity 2024年第2期37卷 511-544页

作者： zhou Huijuan School of Science Shanghai Maritime UniversityShanghai 201306China

This paper mainly introduces the parallel physics-informed neural networks(PPINNs)method with regularization strategies to solve the data-driven forward-inverse problems of the variable coefficient modified Korteweg-de Vries(VC-MKdV)equation.For the forward problem of the VC-MKdV equation,the authors use the traditional PINN method to obtain satisfactory data-driven soliton solutions and provide a detailed analysis of the impact of network width and depth on solving accuracy and speed.Furthermore,the author finds that the traditional PINN method outperforms the one with locally adaptive activation functions in solving the data-driven forward problems of the VC-MKdV equation.As for the data-driven inverse problem of the VC-MKdV equation,the author introduces a parallel neural networks to separately train the solution function and coefficient function,successfully addressing the function discovery problem of the VC-MKdV equation.To further enhance the network’s generalization ability and noise robustness,the author incorporates two regularization strategies into the PPINNs.An amount of numerical experimental data in this paper demonstrates that the PPINNs method can effectively address the function discovery problem of the VC-MKdV equation,and the inclusion of appropriate regularization strategies in the PPINNs can improves its performance.

关键词： Data-driven forward-inverse problems parallel physics-informed neural networks regularization strategies variable coefficient modified KdV equation

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An Environment‑Tolerant Ion‑Conducting Double‑Network Composite Hydrogel for High‑Performance Flexible Electronic Devices

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Nano-Micro Letters 2024年第5期16卷 352-369页

作者： Wenchao Zhao Haifeng zhou Wenkang Li Manlin Chen Min zhou Long Zhao State Key Laboratory of Advanced Electromagnetic Technology School of Electrical and Electronic EngineeringHuazhong University of Science and TechnologyWuhan 430074People’s Republic of China School of Chemistry and Chemical Engineering Huazhong University of Science and TechnologyWuhan 430074People’s Republic of China

High-performance ion-conducting hydrogels(ICHs)are vital for developing flexible electronic devices.However,the robustness and ion-conducting behavior of ICHs deteriorate at extreme tempera-tures,hampering their use in soft electronics.To resolve these issues,a method involving freeze–thawing and ionizing radiation technology is reported herein for synthesizing a novel double-network(DN)ICH based on a poly(ionic liquid)/MXene/poly(vinyl alcohol)(PMP DN ICH)system.The well-designed ICH exhibits outstanding ionic conductivity(63.89 mS cm^(-1) at 25℃),excellent temperature resistance(-60–80℃),prolonged stability(30 d at ambient temperature),high oxidation resist-ance,remarkable antibacterial activity,decent mechanical performance,and adhesion.Additionally,the ICH performs effectively in a flexible wireless strain sensor,thermal sensor,all-solid-state supercapacitor,and single-electrode triboelectric nanogenerator,thereby highlighting its viability in constructing soft electronic devices.The highly integrated gel structure endows these flexible electronic devices with stable,reliable signal output performance.In particular,the all-solid-state supercapacitor containing the PMP DN ICH electrolyte exhibits a high areal specific capacitance of 253.38 mF cm^(-2)(current density,1 mA cm^(-2))and excellent environmental adaptability.This study paves the way for the design and fabrication of high-performance mul-tifunctional/flexible ICHs for wearable sensing,energy-storage,and energy-harvesting applications.

关键词： Ionic liquids Double-network hydrogels Temperature tolerance Multifunctionality Flexible electronic devices

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Perturbation of autophagy pathways in murine alveolar macrophage by 2D TMDCs is chalcogen-dependent

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Journal of Environmental Sciences 2024年第1期135卷 97-107页

作者： Xiaofei zhou Weitao Jin Rui Zhang Xuan Mao Jianbo Jia Hongyu zhou College of Science&Technology Hebei Agricultural UniversityHuanghua 061100China Institute of Environmental Research at Greater Bay Area Key Laboratory for Water Quality and Conservation of the Pearl River DeltaMinistry of EducationGuangzhou UniversityGuangzhou 510006China

Increasing risks of incidental and occupational exposures to two-dimensional transition metal dichalcogenides(2D TMDCs)due to their broad application in various areas raised their public health concerns.While the composition-dependent cytotoxicity of 2D TMDCs has been well-recognized,how the outer chalcogenide atoms and inner transition metal atoms differentially contribute to their perturbation on cell homeostasis at non-lethal doses remains to be identified.In the present work,we compared the autophagy induction and related mechanisms in response to WS_(2),NbS_(2),WSe_(2)and Nb Se_(2)nanosheets exposures in MH-S murine alveolar macrophages.All these 2D TMDCs had comparable physicochemical properties,overall cytotoxicity and capability in triggering autophagy in MH-S cells,but showed outer chalcogen-dependent subcellular localization and activation of autophagy pathways.Specifically,WS_(2)and NbS_(2)nanosheets adhered on the cell surface and internalized in the lysosomes,and triggered m TOR-dependent activation of autophagy.Meanwhile,WSe_(2)and Nb Se_(2)nanosheets had extensive distribution in cytoplasm of MH-S cells and induced autophagy in an m TOR-independent manner.Furthermore,the 2D TMDCs-induced perturbation on autophagy aggravated the cytotoxicity of respirable benzo[a]pyrene.These findings provide a deeper insight into the potential health risk of environmental 2D TMDCs from the perspective of homeostasis perturbation.

关键词： Chalcogen group Autophagy pathway Cell function Endosomal escape Inhalation toxicity

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The role of proteasomes in tumorigenesis

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Genes & Diseases 2024年第4期11卷 155-169页

作者： Xiangyi zhou Ruqing Xu Yue Wu Li zhou Tingxiu Xiang Department of Oncology The First Affliated Hospital of Chongqing Medical UniversityChongqing 400016China Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment Chongqing University Cancer HospitalChongqing 400030China

Protein homeostasis is the basis of normal life activities,and the proteasomefamily plays an extremely important function in this process.The proteasome 2os is a concentric circle structure with twoαrings and twoβrings overlapped.The proteasome 2os can perform both ATP-dependent and non-ATP-dependent ubiquitination proteasome degradation by binding to various subunits(such as 19S,11S,and 200 PA),which is performed by its active subunitβ1,β2,andβ5.The proteasome can degrade misfolded,excess proteins tomaintain homeostasis.At the same time,it can be utilized by tumors to degrade over-proliferate and unwanted proteins to support their growth.Proteasomes can affect the development of tumors from several aspects including tumor signaling pathways such as NF-kB and p53,cell cycle,immune regulation,and drug resistance.Proteasome-encoding genes have been found to be overexpressed in a variety of tumors,providing a potential novel target for cancer therapy.In addition,proteasome inhibitors such as bortezomib,carfilzomib,and ixazomib have been put into clinical application as the first-line treatment of multiple myeloma.More and more studies have shown that it also has different therapeutic effects in other tumors such as hepatocellular carcinoma,non-small cell lung cancer,glioblastoma,and neuroblastoma.However,proteasome inhibitors are not much effective due to their tolerance and singleness in other tumors.Therefore,further studies on their mechanisms of action and drug interactions are needed to investigate their therapeutic potential.

关键词： Bortezomib Cancer therapy Immunoproteasome Multiplemyeloma Proteasome 20S Proteasome inhibitor Thymoproteasom

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Deep-reinforcement-learning-based UAV autonomous navigation and collision avoidance in unknown environments

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Chinese Journal of Aeronautics 2024年第3期37卷 237-257页

作者： Fei WANG Xiaoping ZHU zhou zhou Yang TANG School of Astronautics Northwestern Polytechnical UniversityXi’an 710072China School of Aeronautics Northwestern Polytechnical UniversityXi’an 710072China

In some military application scenarios,Unmanned Aerial Vehicles(UAVs)need to perform missions with the assistance of on-board cameras when radar is not available and communication is interrupted,which brings challenges for UAV autonomous navigation and collision avoidance.In this paper,an improved deep-reinforcement-learning algorithm,Deep Q-Network with a Faster R-CNN model and a Data Deposit Mechanism(FRDDM-DQN),is proposed.A Faster R-CNN model(FR)is introduced and optimized to obtain the ability to extract obstacle information from images,and a new replay memory Data Deposit Mechanism(DDM)is designed to train an agent with a better performance.During training,a two-part training approach is used to reduce the time spent on training as well as retraining when the scenario changes.In order to verify the performance of the proposed method,a series of experiments,including training experiments,test experiments,and typical episodes experiments,is conducted in a 3D simulation environment.Experimental results show that the agent trained by the proposed FRDDM-DQN has the ability to navigate autonomously and avoid collisions,and performs better compared to the FRDQN,FR-DDQN,FR-Dueling DQN,YOLO-based YDDM-DQN,and original FR outputbased FR-ODQN.

关键词： Faster R-CNN model Replay memory Data Deposit Mechanism(DDM) Two-part training approach Image-based Autonomous Navigation and Collision Avoidance(ANCA) Unmanned Aerial Vehicle(UAV)

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Oxidation of emerging organic contaminants by in-situ H_(2)O_(2) fenton system

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Green Energy & Environment 2024年第3期9卷 417-434页

作者： Yuqin Ni Chuxiang zhou Mingyang Xing Yi zhou State Environmental Protection Key Lab of Environmental Risk Assessment and Control on Chemical Processes School of Resources&Environmental EngineeringEast China University of Science and TechnologyShanghai200237China Key Laboratory for Advanced Materials and Institute of Fine Chemicals National Engineering Laboratory for Industrial Wastewater TreatmentSchool of Chemistry and Molecular EngineeringEast China University of Science and Technology130 Meilong RoadShanghai200237China Department of Applied Natural Sciences Technische Hochschule LubeckMonkhofer Weg 23923562 LubeckGermany

The existence and risk of emerging organic contaminants(EOCs)have been under consideration and paid much effort to degrade these pollutants.Fenton system is one of the most widely used technologies to solve this problem.The original Fenton system relies on the hydroxyl radicals produced by Fe(Ⅱ)/H_(2)O_(2) to oxidize the organic contaminants.However,the application of the Fenton system is limited by its low iron cycling efficiency and the high risks of hydrogen peroxide transportation and storage.The introduction of external energy(including light and electricity etc.)can effectively promote the Fe(Ⅲ)/Fe(Ⅱ)cycle and the reduction of oxygen to produce hydrogen peroxide in situ.This review introduces three in-situ Fenton systems,which are electro-Fenton,Photo-Fenton,and chemical reaction.The mechanism,influencing factors,and catalysts of these three in-situ Fenton systems in degrading EOCs are discussed systematically.This review strengthens the understanding of Fenton and in-situ Fenton systems in degradation,offering further insight into the real application of the in-situ Fenton system in the removal of EOCs.

关键词： In-situ H_(2)O_(2)production Fenton Emerging organic contaminants Photocatalysis Electrocatalysis

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