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Improved genome annotation of Brassica oleracea highlights the importance of alternative splicing

Horticultural Plant Journal 2024年第4期10卷 961-970页

作者： Yinqing Yang Lei Zhang qi Tang lingkui Zhang Xing li Shumin Chen Kang Zhang ying li Xilin Hou Feng Cheng State Key Laboratory of Crop Genetics and Germplasm Enhancement College of HorticultureNanjing Agricultural UniversityNanjing 210095China State Key Laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsBeijing 100081China

Brassica oleracea has been developed into many important crops,including cabbage,kale,cauliflower,broccoli and so *** genome and gene annotation of cabbage(cultivar JZS),a representative morphotype of ***,has been widely used as a common reference in biological *** its genome assembly has been updated twice,the current gene annotation still lacks information on untranslated regions(UTRs)and alternative splicing(AS).Here,we constructed a high-quality gene annotation(JZSv3)using a full-length transcriptome acquired by nanopore sequencing,yielding a total of 59452 genes and 75684 ***,we re-analyzed the previously reported transcriptome data related to the development of different tissues and cold response using JZSv3 as a reference,and found that 3843 out of 11908 differentially expressed genes(DEGs)underwent AS during the development of different tissues and 309 out of 903 cold-related genes underwent AS in response to cold ***,we also identified many AS genes,including BolLHCB5 and BolHSP70,that displayed distinct expression patterns within variant transcripts of the same gene,highlighting the importance of JZSv3 as a pivotal reference for AS ***,JZSv3 provides a valuable resource for exploring gene function,especially for obtaining a deeper understanding of AS regulation mechanisms.

关键词： Brassica oleracea Oxford nanopore technologies Gene annotation Alternative splicing

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Research advances in smart responsive-hydrogel dressings with potential clinical diabetic wound healing properties

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Military Medical Research 2024年第4期11卷 543-566页

作者： ying Chen Xing Wang Sheng Tao qi Wang Pan-qin Ma Zi-Biao li Yun-Long Wu Da-Wei li Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology School of Pharmaceutical SciencesXiamen UniversityXiamen 361102FujianChina Beijing National Laboratory for Molecular Sciences Institute of ChemistryChinese Academy of SciencesBeijing 100090China University of Chinese Academy of Sciences Beijing 100049China Senior Department of Orthopedics the Fourth Medical Center of Chinese PLA General HospitalBeijing 100091China Institute of Materials Research and Engineering A*STAR(Agency for ScienceTechnology and Research)Singapore 138634Singapore

The treatment of chronic and non-healing wounds in diabetic patients remains a major medical *** reports have shown that hydrogel wound dressings might be an effective strategy for treating diabetic wounds due to their excellent hydrophilicity,good drug-loading ability and sustained drug release *** a typical example,hyaluronic acid dressing(Healoderm)has been demonstrated in clinical trials to improve wound-healing efficiency and healing rates for diabetic foot ***,the drug release and degradation behavior of clinically-used hydrogel wound dressings cannot be adjusted according to the wound *** to the intricacy of diabetic wounds,antibiotics and other medications are frequently combined with hydrogel dressings in clinical practice,although these medications are easily hindered by the hostile *** this case,scientists have created responsive-hydrogel dressings based on the microenvironment features of diabetic wounds(such as high glucose and low pH)or combined with external stimuli(such as light or magnetic field)to achieve controllable drug release,gel degradation,and microenvironment improvements in order to overcome these clinical *** responsive-hydrogel dressings are anticipated to play a significant role in diabetic therapeutic wound ***,we review recent advances on responsive-hydrogel dressings towards diabetic wound healing,with focus on hydrogel structure design,the principle of responsiveness,and the behavior of *** but not least,the advantages and limitations of these responsive-hydrogels in clinical applications will also be *** hope that this review will contribute to furthering progress on hydrogels as an improved dressing for diabetic wound healing and practical clinical application.

关键词： Responsive-hydrogel Diabetic wound Anti-inflammation Tissue remodeling

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Simulation study on the security of consensus algorithms in DAG-based distributed ledger

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Frontiers of Computer Science 2024年第3期18卷 171-182页

作者： Shuzhe li Hongwei XU qiong li qi HAN Faculty of Computing Harbin Institute of TechnologyHarbin 150001China

Due to the advantages of high volume of transactions and low resource consumption,Directed Acyclic Graph(DAG)-based Distributed Ledger Technology(DLT)has been considered a possible next-generation alternative to ***,the security of the DAG-based system has yet to be comprehensively *** at verifying and evaluating the security of DAG-based DLT,we develop a Multi-Agent based IOTA Simulation platform called *** MAIOTASim,we model honest and malicious nodes and simulate the configurable network environment,including network topology and *** double-spending attack is a particular security issue related to *** perform the security verification of the consensus algorithms under multiple double-spending attack *** simulations show that the consensus algorithms can resist the parasite chain attack and partially resist the splitting attack,but they are ineffective under the large weight *** take the cumulative weight difference of transactions as the evaluation criterion and analyze the effect of different consensus algorithms with parameters under each attack ***,MAIOTASim enables users to perform largescale simulations with multiple nodes and tens of thousands of transactions more efficiently than state-of-the-art ones.

关键词： distributed ledger IOTA Multi-Agent system simulation

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Global research trends and hotspots in overweight/obese comorbid with depression among children and adolescents: A bibliometric analysis

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World Journal of Psychiatry 2024年第8期14卷 1267-1284页

作者： Ya-qi Wang Tao-Tao Wu Yan li Shi-En Cui ying-Shuai li College of Basic Medical Sciences Zhejiang Chinese Medical UniversityHangzhou 310051Zhejiang ProvinceChina National Institute of Traditional Chinese Medicine Constitution and Preventive Treatment of Diseases Beijing University of Chinese MedicineBeijing 100029China

BACKGROUND Overweight/obesity combined with depression among children and adolescents(ODCA)is a global *** bidirectional relationship between depression and overweight/obesity often leads to their *** and adolescence represent critical periods for physical and psychological development,during which the comorbidity of overweight/obesity and depression may increase the risk of adverse health *** To evaluate the relationship between ODCA,we conduct a bibliometric analysis to aid in formulating prevention and treatment *** From 2004 to 2023,articles related to ODCA were selected using the Science Citation Index Expanded from the Web of Science Core *** analysis of relevant publications,including countries/regions,institutions,authors,journals,references,and keywords,was conducted using the online bibliometric analysis platforms,CiteSpace,VOSviewer,and *** Between 2004 and 2023,a total of 1573 articles were published on *** United States has made leading contributions in this field,with Harvard University emerging as the leading contributor in terms of research output,and Tanofsky being the most prolific *** J Adolescent Health has shown significant activity in this *** on the results of the keyword and reference analyses,inequality,adverse childhood experiences,and comorbidities have become hot topics in ***,the impact of balancedrelated behavior and exploration of the biological mechanisms,including the potential role of key adipocytokines and lipokines,as well as inflammation in ODCA,have emerged as frontier *** The trend of a significant increase in ODCA publications is expected to *** research findings will contribute to elucidating the pathogenic mechanisms of ODCA and its prevention and treatment.

关键词： Children Adolescents Overweight Obesity Depression Bibliometric analysis Research trends

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Development of component stiffness equations for thread-fixed one-side bolt connections to an enclosed rectangular hollow section column under tension

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Frontiers of Structural and Civil Engineering 2024年第4期18卷 568-586页

作者： Fu-Wei WU Yuan-qi li Department of Structural Engineering Tongji UniversityShanghai 200092China State Key Laboratory of Disaster Reduction in Civil Engineering Tongji UniversityShanghai 200092China

The derivation and validation of analytical equations for predicting the tensile initial stiffness of threadfixed one-side bolts(TOBs),connected to enclosed rectangular hollow section(RHS)columns,is presented in this *** unknown stiffness components are considered:the TOBs connection and the enclosed RHS ***,the trapezoidal thread of TOB,as an equivalent cantilevered beam subjected to uniformly distributed loads,is analyzed to determine the associated *** on the findings,the thread-shank serial-parallel stiffness model of TOB connection is *** analysis of the tensile stiffness of the enclosed RHS face due to two bolt forces,the four sidewalls are treated as rotation constraints,thus reducing the problem to a two-dimensional plate *** to the load superposition method,the deflection of the face plate is resolved into three components under various boundary and load *** to the plate deflection theory of Timoshenko,the analytical solutions for the three deflections are derived in terms of the variables of bolt spacing,RHS thickness,height to width ratio,***,the validity of the above stiffness equations is verified by a series of finite element(FE)models of T-stub *** proposed component stiffness equations are an effective supplement to the component-based method.

关键词： initial stiffness component based method thread-fixed one-side bolt rectangular hollow sections analytical equation

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Structure-based development of potent and selective type-II kinase inhibitors of RIPK1

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Acta Pharmaceutica Sinica B 2024年第1期14卷 319-334页

作者： ying qin Dekang li Chunting qi Huaijiang Xiang Huyan Meng Jingli liu Shaoqing Zhou Xinyu Gong ying li Guifang Xu Rui Zu Hang Xie Yechun Xu Gang Xu Zheng Zhang Shi Chen lifeng Pan ying li li Tan Interdisciplinary Research Center on Biology and Chemistry Shanghai Institute of Organic ChemistryChinese Academy of SciencesShanghai 201210China University of Chinese Academy of Sciences Beijing 100049China State Key Laboratory of Chemical Biology Shanghai Institute of Organic ChemistryChinese Academy of SciencesShanghai 200032China School of Chinese Materia Medica Nanjing University of Chinese MedicineNanjing 210023China State Key Laboratory of Drug Research Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai 201203China Institute of Hepatology National Clinical Research Center for Infectious DiseaseShenzhen Third People’s Hospitalthe Second Affiliated HospitalSchool of MedicineSouthern University of Science and TechnologyShenzhen 518112China Department of Burn and Plastic Surgery Shenzhen Institute of Translational MedicineShenzhen University Medical SchoolShenzhen Second People’s Hospitalthe First Affiliated Hospital of Shenzhen UniversityShenzhen 518035China

Receptor-interacting serine/threonine-protein kinase 1(RIPK1)functions as a key regulator in inflammation and cell death and is involved in mediating a variety of inflammatory or degenerative diseases.A number of allosteric RIPK1 inhibitors(RIPK1i)have been developed,and some of them have already advanced into clinical ***,selective RIPK1i that interact with both the allosteric pocket and the ATP-binding site of RIPK1 have started to ***,we report the rational development of a new series of type-II RIPK1i based on the rediscovery of a reported but mechanistically atypical *** also describe the structure-guided lead optimization of a potent,selective,and orally bioavailable RIPK1i,62,which exhibits extraordinary efficacies in mouse models of acute or chronic inflammatory ***,62 provides a useful tool for evaluating RIPK1 in animal disease models and a promising lead for further drug development.

关键词： RIPK1 Necroptosis Type-II kinase inhibitors Rational design Lead optimization Structure‒activity relationship Anti-inflammation Preclinical drug discovery

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Comprehensive Evaluation Method for Traffic Flow Data Quality Based on Grey Correlation Analysis and Particle Swarm Optimization

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Journal of Systems Science and Systems Engineering 2024年第1期33卷 106-128页

作者： Wei Ba Baojun Chen qi li School of Automation and Electrical Engineering Dalian Jiaotong UniversityDalian116028China Faculty of Electronic Information and Electrical Engineering Dalian University of TechnologyDalian116023China

Nowadays,data are more and more used for intelligent modeling and prediction,and the comprehensive evaluation of data quality is getting more and more attention as a necessary means to measure whether the data are usable or ***,the comprehensive evaluation method of data quality mostly contains the subjective factors of the evaluator,so how to comprehensively and objectively evaluate the data has become a bottleneck that needs to be solved in the research of comprehensive evaluation *** order to evaluate the data more comprehensively,objectively and differentially,a novel comprehensive evaluation method based on particle swarm optimization(PSO)and grey correlation analysis(GCA)is presented in this *** first,an improved GCA evaluation model based on the technique for order preference by similarity to an ideal solution(TOPSIS)is ***,an objective function model of maximum difference of the comprehensive evaluation values is built,and the PSO algorithm is used to optimize the weights of the improved GCA evaluation model based on the objective function ***,the performance of the proposed method is investigated through parameter analysis.A performance comparison of traffic flow data is carried out,and the simulation results show that the maximum average difference between the evaluation results and its mean value(MDR)of the proposed comprehensive evaluation method is 33.24%higher than that of TOPSIS-GCA,and 6.86%higher than that of *** proposed method has better differentiation than other methods,which means that it objectively and comprehensively evaluates the data from both the relevance and differentiation of the data,and the results more effectively reflect the differences in data quality,which will provide more effective data support for intelligent modeling,prediction and other applications.

关键词： Data quality comprehensive evaluation particle swarm optimization grey correlation analysis traffic flow data

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Metal complexes of bipyridine-functionalized covalent organic frameworks as efficient electrocatalysts for oxygen evolution reaction

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Rare Metals 2024年第7期43卷 3096-3106页

作者： Zhuang-Zhuang Wu Tian Xia ying liang Yong-Peng li Zhu-Yin Sui li-Juan Feng Dao-Xiong Wu Xin-Long Tian qi Chen State Key Laboratory of Marine Resource Utilization in South China Sea School of Marine Science and EngineeringHainan UniversityHaikou 570228China School of Chemistry and Chemical Engineering Yantai UniversityZhuhai519041China School of Bioengineering Zhuhai Campus of Zunyi Medical UniversityZhuhai519041China

Electrocatalytic water splitting is considered a clean and practic al method for producing *** this study,COF-Bpy,a bipyridine-functionalized covalent organic framework(COF),was prepared via post-synthetic modification,after which electrocatalysts for the oxygen evolution reactions(OER)were formed through coordination to single-or double-transition metals(Fe,Co,Ni,FeCo,FeNi or CoNi).COF-Bpy@FeNi delivered the best OER performance among the studied electrocatalysts,with an overpotential of 399 mV at 10 mA·cm^(-2)in an alkaline electrolyte(1.0 mol·L^(-1)KOH aqueous).Notably,the electrocatalytic performance of COF-Bpy@FeNi showed slight degradation during durability testing,which is ascribable to its irreversible benzoquinoline structure and strong metal *** expected,COF-Bpy@FeNi exhibited a low overpotential of 347 mV at a turnover frequency(TOF)of 0.1 s^(-1),which suggests that COF-Bpy@FeNi possesses excellent intrinsic electroc atalytic OER ***,density functional theory(DFT)calculations reveal that the Ni site plays a major role,while the Fe site adjusts the electronic structure of the Ni ions,which rationalizes the excellent OER properties of COF-Bpy@*** study not only provides a simple and efficient method for complexing COFs with transition metals,but also offers a novel strategy for designing porous organic polymer electrocatalysts.

关键词： Covalent organic framework Oxygen evolution reactions(OER)electrocatalyst Nickel-iron synergy Water splitting

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Knockdown of SIRT2 Rescues YARS-induced Charcot-Marie-Tooth Neuropathy in Drosophila

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Neuroscience Bulletin 2024年第4期40卷 539-543页

作者： Xuedong li Mengrong Wang Xiang Gao Chenyu li Chunyu Chen Yun qi ying Wan Wei Yu State Key Laboratory of Genetic Engineering School of Life SciencesZhongshan HospitalFudan UniversityShanghai200438China School of Basic Medic Science Southwest Medical UniversityLuzhou64600China Department of Geriatrics Tongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China

Dear Editor,Charcot-Marie-Tooth disease,the most common inherited peripheral neuropathology,is highly heterogeneous among patients and associated with mutations in~100 different genes at an incidence of at least 1:2,500[1].Over 30 mutated genes have been identified in CMT2,which is characterized by peripheral axon degeneration and distal deficits in motor function[2].The aminoacyl-tRNA synthetase is the largest family in CMT2 and includes tyrosyl-tRNA synthetase(YARS,tyrosyl-tRNA synthetase).

关键词： Marie degeneration pathology

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An Example of Embedded Singular Continuous Spectrum for Discrete Schrödinger Operators

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Acta Mathematica Sinica,English Series 2024年第8期40卷 1837-1849页

作者： Zheng qi FU Xiong li Laboratory of Mathematics and Complex Systems(Ministry of Education) School of Mathematical SciencesBeijing Normal UniversityBeijing 100875P.R.China

We present an example of a potential such that the corresponding discrete Schrödinger operator has singular continuous spectrum embedded in the absolutely continuous spectrum.

关键词： Sparse potentials singular continuous spectrum Prüfer variables

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