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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

Synthesis of carbon dots with predictable photoluminescence by the aid of machine learning

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Nano Research 2024年第3期17卷 1984-1989页

作者： Chenyu Xing Gaoyu Chen Xia Zhu Jiakun An Jianchun Bao Xuan Wang Xiuqing Zhou Xiuli Du Xiangxing Xu Jiangsu key laboratory of Biofunctional Materials Jiangsu Key Laboratory of New Power BatteriesSchool of Chemistry and Materials ScienceNanjing Normal UniversityNanjing 210023China School of Mathematical Sciences Nanjing Normal UniversityNanjing 210023China State key laboratory of Coordination Chemistry School of Chemistry and Chemical EngineeringNanjing UniversityNanjing 210093China

Carbon dots(CDs)have wide application potentials in optoelectronic devices,biology,medicine,chemical sensors,and quantum techniques due to their excellent fluorescent ***,synthesis of CDs with controllable spectrum is challenging because of the diversity of the CD components and *** this report,machine learning(ML)algorithms were applied to help the synthesis of CDs with predictable photoluminescence(PL)under the excitation wavelengths of 365 and 532 *** combination of precursors was used as the *** PL peaks of the strongest intensity(λ_(s))and the longest wavelength(λ_(l))were used as target *** six investigated ML models,the random forest(RF)model showed outstanding)performance in the prediction of the PL peaks.

关键词： carbon dots(CDs) synthesis photoluminescence(PL) machine learning(ML) PL prediction

Hydrogen sulfide responsive nanoplatforms: Novel gas responsive drug delivery carriers for biomedical applications

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Asian Journal of Pharmaceutical Sciences 2024年第1期19卷 1-17页

作者： Jiafeng Zou Zeting Yuan Xiaojie Chen You Chen Min Yao Yang Chen Xiang Li Yi Chen Wenxing Ding Chuanhe Xia Yuzheng Zhao Feng Gao Shanghai Frontier Science Research Base of Optogenetic techniques for Cell Metabolism School of PharmacyEast China University of Science and TechnologyShanghai 200237China key laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province School of Pharmaceutical SciencesZhejiang Chinese Medical UniversityHangzhou 310053China Shanghai key laboratory of Functional Materials Chemistry East China University of Science and TechnologyShanghai 200237China Shanghai key laboratory of New Drug Design School of PharmacyEast China University of Science and TechnologyShanghai 200237China Optogenetics and Synthetic Biology Interdisciplinary Research Center State Key Laboratory of Bioreactor EngineeringEast China University of Science and TechnologyShanghai 200237China CAS Center for Excellence in Brain Science Shanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai 200031China Research Unit of New techniques for Live-cell Metabolic Imaging Chinese Academy of Medical SciencesBeijing 100050China

Hydrogen sulfide(H_(2)S)is a toxic,essential gas used in various biological and physical processes and has been the subject of many targeted studies on its role as a new gas *** studies have mainly focused on the production and pharmacological side effects caused by H_(2)***,effective strategies to remove H_(2)S has become a key research ***,the development of novel nanoplatforms has provided new tools for the targeted removal of H_(2)*** paper was performed to review the association between H_(2)S anddisease,relatedH_(2)S inhibitory drugs,aswell as H_(2)S responsive nanoplatforms(HRNs).This review first analyzed the role of H_(2)S in multiple tissues and ***,common drugs used to eliminate H_(2)S,as well as their potential for combination with anticancer agents,were *** only the existing studies on HRNs,but also the inhibition H_(2)S combined with different therapeutic methods were both sorted out in this ***,this review provided in-depth analysis of the potential of HRNs about treatment or detection in ***,potential challenges of HRNs were *** study demonstrates the excellent potential of HRNs for biomedical applications.

关键词： Hydrogen sulfide Disease mechanisms Removal of hydrogen sulfide Responsive nanoplatforms Challenges Biomedical applications

Simultaneous quantification of trace heavy metals in mushrooms using a three-dimensional highly reduced graphene oxide/FeOnanocomposite-based electrochemical sensor

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Food Science and Human Wellness 2024年

作者： Yiming Tian Pingsheng Zhong Kai Zhou Lufei Zheng Jiali Ren Hunan key laboratory of Forestry Edible Resources safety and Processing Hunan key laboratory of Grain-oil Deep Process and Quality Control Central South University of Forestry and Technology Institute of Quality Standard and Testing Technology for Agro-Products of CAAS

The accumulation of heavy metals in mushrooms has presented a significant risk to human health， underscoring the importance of devising a portable and cost-effective method for detecting heavy metals. Thus， we have developed an electrochemical sensor based on 3-dimensional highly reduced graphene oxide (3D-HRGO) in conjunction with Fe3O4nanoparticles， enabling the simultaneous quantification of Cd2+， Pb2+， Cu2+， and Hg2+. The 3D-HRGO/Fe3O4nano-particles material prepared in this study was characterized and confirmed by multiple techniques， then dispersed in a simple and environmental dispersant， consist of 75% ethanol and 0.1% Nafion， and coating on a glass carbon electrode (GCE) to preparing a 3D-HRGO/Fe3O4/GCE sensor. The limit of detection (LOD) of 3D-HRGO/Fe3O4/GCE sensor for Cd2+， Pb2+， Cu2+， and Hg2+in simultaneous detection were 0.2 μg/L， 0.6 μg/L， 0.6 μg/L， and 0.9 μg/L， respectively. The sensor demonstrates exceptional stability， reproducibility， anti-interference， and recovery rate. Furthermore， the electrochemical sensor was employed to detect heavy metals in actual mushrooms and validated through conventional methodologies. This study represents the pioneering utilization of 3D-HRGO/Fe3O4as a foundational material for an electrochemical sensor capable of simultaneous detection of multiple metals， thereby advancing the progress of on-site and expeditious detection techniques.

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Time-resolution enhanced multi-path OTD measurement using an adaptive filter based incoherent OFDR

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Chinese Optics Letters 2024年第1期22卷 153-158页

作者：王立晗任凌云王祥传潘时龙 National key laboratory of Microwave Photonics Nanjing University of Aeronautics and AstronauticsNanjing 210016China

High accuracy and time resolution optical transfer delay(OTD)measurement is highly desired in many multi-path applications,such as optical true-time-delay-based array systems and distributed optical ***,the time resolution is usually limited by the frequency range of the probe signal in frequency-multiplexed OTD measurement ***,we proposed a time-resolution enhanced OTD measurement method based on incoherent optical frequency domain reflectometry(I-OFDR),where an adaptive filter is designed to suppress the spectral leakage from other paths to break the resolution limitation.A weighted least square(WLS)cost function is first established,and then an iteration approach is used to minimize the cost ***,the appropriate filter parameter is obtained according to the convergence *** a proof-of-concept experiment,the time-domain response of two optical links with a length difference of 900 ps is successfully estimated by applying a probe signal with a bandwidth of 400 *** time resolution is improved by 2.78times compared to the theoretical resolution limit of the inverse discrete Fourier transform(iDFT)*** addition,the OTD measurement error is below±0.8 *** proposed algorithm provides a novel way to improve the measurement resolution without applying a probe signal with a large bandwidth,avoiding measurement errors induced by the dispersion effect.

关键词： optical transfer delay measurement time resolution enhancement incoherent OFDR adaptive filtering

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Iron–doped bismuth oxybromides as visible-light-responsive Fenton catalysts for the degradation of atrazine in aqueous phases

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Journal of Environmental Sciences 2024年第3期137卷 321-332页

作者： Yong-Li Cai Yu-Hang Xu Ji-Zun Xiang Zhi-Qiang Zhang Qiu-Xiang He Ya-Feng Li Jian Lü Fujian Provincial key laboratory of Soil Environmental Health and Regulation College of Resources and EnvironmentFujian Agriculture and Forestry UniversityFuzhou 350002China State key laboratory of Photocatalysis on Energy and Environment Fuzhou UniversityFuzhou 350116China

Pesticides and its degradation products,being well–known residues in soil,have recently been detected in many water bodies as pollutants of emerging concerns,and thus there is a contemporary demand to develop viable and cost–effective techniques for the removal of related organic pollutants in aqueous ***,a visible-light-responsive Fenton system was constructed with iron–doped bismuth oxybromides(Fe–BiOBr)as the *** the advantage of sustainable Fe(Ⅲ)/Fe(Ⅱ)conversion and optimized H_(2)O_(2)utilization,the optimal Fe–BiOBr–2 catalyst showed an excellent atrazine removal efficiency of 97.61%in 120 min,which is superior than the traditional homogeneous Fenton and the majority of heterogeneous processes documented in the *** this photo–Fenton system,hydroxyl(·OH)and superoxide(·O_(2)^(-))radicals were dominant active species contributed to the oxidative degradation of *** to the production of various active radicals,five degradation pathways were proposed based on the identification of intermediates and degradation ***,this work not only demonstrates a fundamental insight into creating highly efficient and atom economic photo-Fenton systems,but also provides a complementary strategy for the treatment of organic pollutants in water.

关键词： Bismuth oxybromide Photo–Fenton Atrazine Catalytic degradation

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Learning in games:a systematic review

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Science China(Information Sciences) 2024年第7期67卷 133-159页

作者： Rong-Jun QIN Yang YU National key laboratory for Novel Software Technology Nanjing University Polixir Technologies

Game theory studies the mathematical models for self-interested individuals. Nash equilibrium is arguably the most central solution in game theory. While finding the Nash equilibrium in general is known as polynomial parity arguments on directed graphs(PPAD)-complete, learning in games provides an alternative to approximate Nash equilibrium, which iteratively updates the player's strategy through interactions with other players. Rules and models have been developed for learning in games, such as fictitious play and no-regret learning. Particularly, with recent advances in online learning and deep reinforcement learning,techniques from these fields greatly boost the breakthroughs in learning in games from theory to *** a result, we have witnessed many superhuman game AI systems. The techniques used in these systems evolve from conventional search and learning to purely reinforcement learning(RL)-style learning methods,gradually getting rid of the domain knowledge. In this article, we systematically review the above techniques,discuss the trend of basic learning rules towards a unified framework, and recap applications in large ***, we discuss some future directions and make the prospect of future game AI systems. We hope this article will give some insights into designing novel approaches.

关键词： non-cooperative games learning in games no-regret learning reinforcement learning superhuman AI

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Experimental demonstration of a quantum downstream access network in continuous variable quantum key distribution with a local local oscillator

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Photonics Research 2024年第6期12卷 1262-1273页

作者： DENGKE QI XIANGYU WANG ZHENGHUA LI JIAYU MA ZIYANG CHEN YUEMING LU SONG YU State key laboratory of Information Photonics and Optical Communications Beijing University of Posts and TelecommunicationsBeijing 100876China key laboratory of Trustworthy Distributed Computing and Service(MoE) Beijing University of Posts and TelecommunicationsBeijing 100876China State key laboratory of Advanced Optical Communication Systems and Networks School of Electronicsand Center for Quantum Information TechnologyPeking UniversityBeijing 100871China

Quantum networks provide opportunities and challenges across a range of intellectual and technical frontiers,including quantum computation,communication,and *** traditional communication networks,quantum networks utilize quantum bits rather than classical bits to store and transmit *** key distribution(QKD)relying on the principles of quantum mechanics is a key component in quantum networks and enables two parties to produce a shared random secret key,thereby ensuring the security of data *** this work,we propose a cost-effective quantum downstream access network structure in which each user can get their corresponding key information through terminal *** on this structure,we demonstrate the first four-end-users quantum downstream access network in continuous variable QKD with a local local *** contrast to point-to-point continuous variable QKD,the network architecture reevaluates the security of each user and accounts for it accordingly,and each user has a lower tolerance for excess noise as the overall network expands with more ***,the feasibility of the experiment is based on the analysis of the theoretical model,noise analysis,and multiple techniques such as the particle filter and adaptive equalization algorithm used to suppress excess *** results show that each user can get a low level of excess noise and can achieve secret key rates of 546 kbps,535 kbps,522.5 kbps,and 512.5 kbps under a transmission distance of 10 km,respectively,with the finite-size block of 1×10^(8).This not only verifies the good performance but also provides the foundation for the future multi-user quantum downstream access networks.

关键词： quantum oscillator local

Engineering the future cereal crops with big biological data:toward intelligence-driven breeding by design

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Journal of Genetics and Genomics 2024年第8期51卷 781-789页

作者： Lei Liu Jimin Zhan Jianbing Yan National key laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubei 430070China

How to feed 10 billion human populations is one of the challenges that need to be addressed in the following decades,especially under an unpredicted climate *** breeding,initiating from the phenotype-based selection by local farmers and developing into current biotechnology-based breeding,has played a critical role in securing the global food ***,regarding the changing environment and ever-increasing human population,can we breed outstanding crop varieties fast enough to achieve high productivity,good quality,and widespread adaptability?This review outlines the recent achievements in understanding cereal crop breeding,including the current knowledge about crop agronomic traits,newly developed techniques,crop big biological data research,and the possibility of integrating them for intelligence-driven breeding by design,which ushers in a new era of crop breeding practice and shapes the novel architecture of future *** review focuses on the major cereal crops,including rice,maize,and wheat,to explain how intelligence-driven breeding by design is becoming a reality.

关键词： Crop Big biological data Multi-omic Artificial intelligence Crop design breeding