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Integrating machine learning and genome editing for crop improvement

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aBIOTECH 2024年第2期5卷 262-277页

作者： long Chen Guanqing Liu Tao Zhang Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education Agricultural College of Yangzhou UniversityYangzhou 225009China Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology Yangzhou UniversityYangzhou 225009China

Genome editing is a promising technique that has been broadly utilized for basic gene function studies and trait ***,the exponential growth of computational power and big data now promote the application of machine learning for biological *** this regard,machine learning shows great potential in the refinement of genome editing systems and crop ***,we review the advances of machine learning to genome editing optimization,with emphasis placed on editing efficiency and specificity ***,we demonstrate how machine learning bridges genome editing and crop breeding,by accurate key site detection and guide RNA ***,we discuss the current challenges and prospects of these two techniques in crop *** integrating advanced genome editing techniques with machine learning,progress in crop breeding will be further accelerated in the future.

关键词： Machine learning Genome editing Crop improvement Molecular design breeding

Classifying hepatitis B therapies with insights from covalently closed circular DNA dynamics

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Virologica Sinica 2024年第1期39卷 9-23页

作者： Jie-Li Hu Ai-long Huang Key Laboratory of Molecular Biology on Infectious Diseases Ministry of EducationChongqing Medical UniversityChongqing400016China

The achievement of a functional cure for chronic hepatitis B(CHB)remains limited to a minority of patients treated with currently approved *** primary objective in developing new anti-HBV drugs is to enhance the functional cure rates for CHB.A critical prerequisite for the functional cure of CHB is a substantial reduction,or even eradication of covalently closed circular DNA(cccDNA).Within this context,the changes in cccDNA levels during treatment become as a pivotal *** have previously analyzed the factors influencing cccDNA dynamics and introduced a preliminary classification of hepatitis B treatment strategies based on these *** this review,we employ a systems thinking perspective to elucidate the fundamental aspects of the HBV replication cycle and to rationalize the classification of treatment strategies according to their impact on the dynamic equilibrium of *** upon this foundation,we categorize current anti-HBV strategies into two distinct groups and advocate for their combined use to significantly reduce cccDNA levels within a well-defined timeframe.

关键词： Hepatitis B cccDNA Functional cure Dynamics Treatment Strategy

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基于应力转换的内螺纹高周疲劳强度分析方法

机械工程学报 2016年第21期52卷 166-174页

作者：龙旦风黄成海向东徐卫国王一江江伟一汽解放汽车有限公司无锡柴油机厂无锡214026 清华大学机械工程系北京100084

螺纹具有特征尺寸小、结构复杂的特点,其非线性接触的有限元分析具有很高的难度,因此机械零件强度仿真分析时螺纹通常被忽略,只根据经验对螺纹作保守设计。事实上承受循环重载的零件极容易从螺纹部位发生疲劳断裂,在设计阶段有必要进行... 详细信息

螺纹具有特征尺寸小、结构复杂的特点,其非线性接触的有限元分析具有很高的难度,因此机械零件强度仿真分析时螺纹通常被忽略,只根据经验对螺纹作保守设计。事实上承受循环重载的零件极容易从螺纹部位发生疲劳断裂,在设计阶段有必要进行疲劳强度校核。针对此问题,提出了一种基于应力转换的内螺纹高周疲劳强度分析方法。此方法把螺纹根部应力分解为近源应力和远源应力两部分,通过无螺纹简化模型仿真获得螺纹接触压力和摩擦力之后转换为近源应力和远源应力并叠加得到螺纹根部最大应力,最后考虑应力梯度、存活率和表面粗糙度等因素的影响系数,借助Haigh图计算各扣内螺纹的疲劳安全系数。把这种方法与带螺纹的细节模型有限元仿真和疲劳强度分析结果进行对比,所提方法的安全系数结果与细节模型的相应结果相差–7.6%;把这种方法应用于某型号缸体主轴承壁,其分析结果与疲劳试验结果相差–8.2%,证明了它的可行性。

关键词：内螺纹应力集中疲劳强度安全系数

PARP1-DNA co-condensation:the driver of broken DNA repair

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Signal Transduction and Targeted Therapy 2024年第6期9卷 2351-2353页

作者： Xiang Wei Fangfang Zhou long Zhang Life Sciences Institute The Second Affiliated Hospital of the Zhejiang University School of MedicineThe MOE Key Laboratory of Biosystems Homeostasis&Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell BiologyZhejiang UniversityHangzhouChina The First Affiliated Hospital the Institutes of Biology and Medical SciencesSuzhou Medical CollegeSoochow UniversitySuzhouJiangsu 215123China

A recent study published by Simon Alberti1 in Cell has revealed that DNA double-strand break(DSB)sites that prevent the disjunction of broken DNA ends are formed through poly(ADPribose)(PAR)polymerase 1(PARP1)-DNA co-condensation.1(Fig.1).Here,a comprehensive and novel model was provided for the ordered assembly of PARP1-DNA condensates,which can rationally make clear broken DNA end synapses and how repair effectors are recruited to repair DSB.

关键词： PARP1 repair rational

Anchoring heterometallic cluster on P-doped carbon nitride for efficient photocatalytic nitrogen fixation in water and air ambient

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Chinese Chemical Letters 2024年第4期35卷 176-180页

作者： Chao-long Chen Rong Chen La-Sheng long Lan-Sun Zheng Xiang-Jian Kong Collaborative Innovation Center of Chemistry for Energy Materials State Key Laboratory of Physical Chemistry of Solid Surfaces and Department of ChemistryCollege of Chemistry and Chemical EngineeringXiamen UniversityXiamen 361005China

Light-driven nitrogen fixation to produce ammonia is a green and economical technology of nitrogen reduction but is still quite challenging, especially in an air atmosphere without any sacrificial ***, we demonstrate efficient photocatalytic nitrogen fixation using water and air directly by loading lanthanide–transition metal(4f–3d) cluster NdCo_(3) on two-dimensional P-doped graphitic carbon nitrides(PCN) material surface. Benefiting from the increase in the number of nitrogen vacancies(NVs) and highly matched band gap structure and excellent hole trapping ability of clusters, the NdCo_(3)/PCN photocatalyst exhibits efficient nitrogen reduction activity with 371(in air) and 825 μmol h^(-1)g^(-1)(in pure nitrogen)without any sacrificial reagents. The introduction of potassium sulfate inhibits hydrogen production and promotes nitrogen reduction activation. This work suggests that anchoring precisely structured clusters on 2D materials may enhance photocatalytic nitrogen reduction under normal temperature and pressure.

关键词： Photocatalytic Nitrogen fixation 4f-3d Cluster Air atmosphere

A novel and promising engineering application of carbon dots:Enhancing the chloride binding performance of cement

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Chinese Chemical Letters 2024年第6期35卷 409-416页

作者： Wu-Jian long Yang Yu Chuang He Guangdong Provincial Key Laboratory of Durability for Marine Civil Engineering Key Lab of Coastal Urban Resilient InfrastructureMOECollege of Civil and Transportation EngineeringShenzhen UniversityShenzhen 518060China

Corrosion of reinforcement induced by chloride invasion is extensively considered as the dominating deterioration mechanism of reinforced concrete(RC)structures,leading to serious safety hazards and tremendous economic ***,it still lacks well dispersive and cost-efficient nanomaterials to improve the anti-chloride-corrosion ability of RC ***,specific carbon dots(CDs)with high dispersity and low cost are deliberately designed,successfully prepared by hydrothermal processing,and then firstly applied to immensely enhance chloride binding performance of cement,thereby contributing to suppressing the corrosion of ***,the tailored CDs are composed of the carbon core with highly crystalline sp^(2)C structures and oxygen-containing groups connecting on the carbon core;The typical equilibrium test confirms that with respect to that of the blank cement paste,the chloride binding capacity of cement paste involving 0.2 wt%(by weight of cement)CDs is increased by 109% after 14-day exposure to 3 mol/L Na Cl solution;according to comprehensive analyses of phase compositions,the chloride binding mechanism of CDs-modified cement is rationally attributed to the fact that the incorporation of CDs advances the formation of calcium silicate hydrate(C-S-H)gels and Friedel's salt(Fs),thus enormously enhancing the physically adsorbed and chemically bound chloride ions of cement *** work not only firstly provides a novel high-dispersity and low-cost nanomaterial toward the durability enhancement of RC structures,but also broadens the application of CDs in the field of engineering,conducing to stimulating their industrialization development.

关键词： Carbon dots Chloride binding Cement Chloride binding mechanism Friedel’s salt

The Novel long QT Syndrome Type 2-associated F129I Mutation in the KCNH2 Gene Significantly Affects IKr Through the hERG1 Homomeric and Heteromeric Potassium Channels

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Cardiology Discovery 2024年第2期4卷 174-182页

作者： Li Feng Kejuan Ma Xin Li Nian Liu Deyong long Changsheng Ma Department of Cardiology Beijing Anzhen HospitalCapital Medical UniversityNational Clinical Research Center for Cardiovascular DiseasesBeijing 100029China Community Health Service Center of Beijing Nomal University Beijing 100875China.

Objective:The long QT syndrome type 2 is caused by the loss-of-function mutations in the KCNH2 gene,which encodes hERG1,the voltage-gated potassium *** hERG1 channels conduct rapid delayed rectifier K^(+)currents(I_(Kr))in the human cardiac ***2 encodes 2 main isoforms-hERG1a and hERG1b,which assemble to form the homomeric or heteromeric hERG1 ***,the functional characteristics of the heteromeric hERG1 channels in long QT syndrome type 2 are not *** this study,a novel mutation in the N-terminus of hERG1a(F129l)was identified in a proband of long QT syndrome type *** purpose of this study was to identify the electrophysiological change of homomeric and heteromeric hERG1 channels with ***:Candidate genes were screened by direct sequencing.F129l-hERG1a was cloned in the pcDNA3.1 vector by site-directed ***,the wild-type(WT)hERG1a and/or F129l-hERG1a were transiently expressed in the HEK293 cells with or without hERG1b *** expression levels of the transgenes,cellular distribution of hERG1a and hERG1b,and the electrophysiological features of the homomeric and the heteromeric hERG1 channels with the WT-hERG1a or F129l-hERG1a were analyzed using whole-cell patch-clamp electrophysiology,western blotting,and immunofluorescence ***:The proband was clinically diagnosed with long QT syndrome type 2 and carried a heterozygous mutation c.385T>A(F1291)in the KCNH2 *** study proved that the F129l substitution in hERG1a significantly decreased I_(Kr) in both the homomeric and heteromeric hERG1channels by 86%and 70%,respectively(WT-hERG1a(54.88±18.74)pA/pF vs.F129l-hERG1a(7.34±1.90)pA/pF,P<0.001;WT-hERG1a/hERG1b(89.92±24.51)pA/pF vs.F129l-hERG1a/hERG1b(26.54±9.83)pA/pF,P<0.001).The voltage dependence of I_(Kr) activation(V_(1/2) and k)was not affected by the mutation in both the homomeric and heteromeric hERG1 *** peak current densities and the kinetic charact

关键词： long QT syndrome Arrhythmia lon channels hERG

Hyperbolic Tangent Function-Based Protocols for Global/Semi-Global Finite-Time Consensus of Multi-Agent Systems

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IEEE/CAA Journal of Automatica Sinica 2024年第6期11卷 1381-1397页

作者： Zongyu Zuo Jingchuan Tang Ruiqi Ke Qing-long Han Seventh Research Division Beihang University(BUAA)Beijing 100191China School of Science Computing and Engineering TechnologiesSwinburne University of TechnologyMelbourne VIC 3122Australia IEEE

This paper investigates the problem of global/semi-global finite-time consensus for integrator-type multi-agent *** hyperbolic tangent function-based protocols are pro-posed to achieve global and semi-global finite-time consensus for both single-integrator and double-integrator multi-agent systems with leaderless undirected and leader-following directed commu-nication *** new protocols not only provide an explicit upper-bound estimate for the settling time,but also have a user-prescribed bounded control *** addition,compared to some existing results based on the saturation function,the pro-posed approach considerably simplifies the protocol design and the stability *** examples and an application demonstrate the effectiveness of the proposed protocols.

关键词： Consensus protocol finite-time consensus hyper-bolic tangent function multi-agent systems.

Phase behavior of gas condensate in porous media using real-time computed tomography scanning

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Petroleum Science 2024年第2期21卷 1032-1043页

作者： Wen-long Jing Lei Zhang Ai-Fen Li Jun-Jie Zhong Hai Sun Yong-Fei Yang Yu-long Cheng Jun Yao Institute of Petroleum Engineering China University of Petroleum(East China)Qingdao266580ShandongChina National Key Laboratory of Deep Oil and Gas China University of Petroleum(East China)Qingdao266580ShandongChina

The phase behavior of gas condensate in reservoir formations differs from that in pressure-volume-temperature(PVT)cells because it is influenced by porous media in the reservoir *** was used as a sample to investigate the influence of porous media on the phase behavior of the gas *** pore structure was first analyzed using computed tomography(CT)scanning,digital core technology,and a pore network *** sandstone core sample was then saturated with gas condensate for the pressure depletion *** each pressure-depletion state was stable,realtime CT scanning was performed on the *** scanning results of the sample were reconstructed into three-dimensional grayscale images,and the gas condensate and condensate liquid were segmented based on gray value discrepancy to dynamically characterize the phase behavior of the gas condensate in porous *** network models of the condensate liquid ganglia under different pressures were built to calculate the characteristic parameters,including the average radius,coordination number,and tortuosity,and to analyze the changing mechanism caused by the phase behavior change of the gas *** types of condensate liquid(clustered,branched,membranous,and droplet ganglia)were then classified by shape factor and Euler number to investigate their morphological changes dynamically and *** results show that the dew point pressure of the gas condensate in porous media is 12.7 MPa,which is 0.7 MPa higher than 12.0 MPa in PVT *** average radius,volume,and coordination number of the condensate liquid ganglia increased when the system pressure was between the dew point pressure(12.7 MPa)and the pressure for the maximum liquid dropout,Pmax(10.0 MPa),and decreased when it was below *** volume proportion of clustered ganglia was the highest,followed by branched,membranous,and droplet *** study provides crucial experimental evidence for the phase behavior chan

关键词： Gas condensate Pressure depletion Real-time micro-computed tomography scanning Distribution of condensate liquid