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Plant RNA-binding proteins:Phase separation dynamics and functional mechanisms underlying plant development and stress responses

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Molecular Plant 2024年第4期17卷 531-551页

作者： Sheng Fan Yu Zhang Shaobo Zhu Lisha Shen Temasek Life Sciences laboratory 1 Research LinkNational University of Singapore1 Research LinkSingapore 117604Singapore Department of Biological Sciences National University of Singapore14 Science Drive 4Singapore 117543Singapore

RNA-binding proteins(RBPs)accompany RNA from synthesis to decay,mediating every aspect of RNA metabolism and impacting diverse cellular and developmental processes in *** RBPs undergo phase separation along with their bound RNA to form and function in dynamic membraneless biomolecular condensates for spatiotemporal coordination or regulation of RNA *** evidence suggests that phase-separating RBPs with RNA-binding domains and intrinsically disordered regions play important roles in plant development and stress ***,we summarize the current knowledge about how dynamic partitioning of RBPs into condensates controls plant development and enables sensing of experimental changes to confer growth plasticity under stress conditions,with a focus on the dynamics and functional mechanisms of RBP-rich nuclear condensates and cytoplasmic granules in mediating RNA *** also discuss roles of multiple factors,such as environmental signals,protein modifications,and N6-methyladenosine RNA methylation,in modulating the phase separation behaviors of RBPs,and highlight the prospects and challenges for future research on phase-separating RBPs in crops.

关键词： RNA-binding proteins phase separation biomolecular condensates RNA metabolism development stress resilience

Nano-enhanced solid-state hydrogen storage:Balancing discovery and pragmatism for future energy solutions

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Nano Research 2024年第10期17卷 8729-8753页

作者： Chaochao Dun Xinyi Wang Linfeng Chen Sichi Li Hanna M.Breunig Jeffrey J.Urban The Molecular Foundry Lawrence Berkeley National Laboratory BerkeleyBerkeleyCA 94720USA Energy Analysis and Environmental Impacts Division Lawrence Berkeley National LaboratoryBerkeleyCA 94720USA Lawrence Livermore national {1. LivermoreCA 94550USA

Nanomaterials have revolutionized the battery industry by enhancing energy storage capacities and charging speeds,and their application in hydrogen(H_(2))storage likewise holds strong potential,though with distinct challenges and mechanisms.H_(2) is a crucial future zero-carbon energy vector given its high gravimetric energy density,which far exceeds that of liquid ***,its low volumetric energy density in gaseous form currently requires storage under high pressure or at low *** review critically examines the current and prospective landscapes of solid-state H_(2) storage technologies,with a focus on pragmatic integration of advanced materials such as metal-organic frameworks(MOFs),magnesium-based hybrids,and novel sorbents into future energy *** materials,enhanced by nanotechnology,could significantly improve the efficiency and capacity of H_(2) storage systems by optimizing H_(2) adsorption at the nanoscale and improving the kinetics of H_(2) uptake and *** discuss various H_(2) storage mechanisms—physisorption,chemisorption,and the Kubas interaction—analyzing their impact on the energy efficiency and scalability of storage *** review also addresses the potential of“smart MOFs”,single-atom catalyst-doped metal hydrides,MXenes and entropy-driven alloys to enhance the performance and broaden the application range of H_(2) storage systems,stressing the need for innovative materials and system integration to satisfy future energy ***-throughput screening,combined with machine learning algorithms,is noted as a promising approach to identify patterns and predict the behavior of novel materials under various conditions,significantly reducing the time and cost associated with experimental *** closing,we discuss the increasing involvement of various companies in solid-state H_(2) storage,particularly in prototype vehicles,from a techno-economic *** forward-looking perspective underscores t

关键词： nanomaterials nanotechnology solid-state H_(2)storage techno-economic analysis model-driven material development processes

Functional genomics of Brassica napus:Progresses,challenges,and perspectives

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Journal of Integrative Plant Biology 2024年第3期66卷 484-509页

作者： Zengdong Tan Xu Han Cheng Dai Shaoping Lu Hanzi He Xuan Yao Peng Chen Chao Yang Lun Zhao Qing-Yong Yang Jun Zou Jing Wen Dengfeng Hong Chao Liu Xianhong Ge Chuchuan Fan Bing Yi Chunyu Zhang Chaozhi Ma Kede Liu Jinxiong Shen Jinxing Tu Guangsheng Yang Tingdong Fu Liang Guo Hu Zhao national Key {1. of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China Yazhouwan national {1. Sanya 572025China

Brassica napus,commonly known as rapeseed or canola,is a major oil crop contributing over 1.%to the stable supply of edible vegetable oil *** and understanding the gene functions in the *** genome is crucial for genomic breeding.A group of genes controlling agronomic traits have been successfully cloned through functional genomics studies in *** this review,we present an overview of the progress made in the functional genomics of ***,including the availability of germplasm resources,omics databases and cloned functional *** on the current progress,we also highlight the main challenges and perspectives in this *** advances in the functional genomics of *** contribute to a better understanding of the genetic basis underlying the complex agronomic traits in *** and will expedite the breeding of high quality,high resistance and high yield in *** varieties.

关键词： accelerate breeding Brassica napus functional genomics high resistance high yield

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Learnware:small models do big

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Science China(Information Sciences) 2024年第1期67卷 39-50页

作者： Zhi-Hua ZHOU Zhi-Hao TAN national Key {1. for Novel Software Technology Nanjing University

There are complaints about current machine learning techniques such as the requirement of a huge amount of training data and proficient training skills,the difficulty of continual learning,the risk of catastrophic forgetting,and the leaking of data privacy/*** research efforts have been focusing on one of those concerned issues separately,paying less attention to the fact that most issues are entangled in *** prevailing big model paradigm,which has achieved impressive results in natural language processing and computer vision applications,has not yet addressed those issues,whereas becoming a serious source of carbon *** article offers an overview of the learnware paradigm,which attempts to enable users not to need to build machine learning models from scratch,with the hope of reusing small models to do things even beyond their original purposes,where the key ingredient is the specification which enables a trained model to be adequately identified to reuse according to the requirement of future users who know nothing about the model in advance.

关键词： artificial intelligence machine learning learnware

Balancing the Quantum Speed Limit and Instantaneous Energy Cost in Adiabatic Quantum Evolution

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Chinese Physics Letters 2024年第4期41卷 7-12页

作者：徐建文张宇佳郑文蔡浩阳周浩宇李先科廖绪东张钰李邵雄兰栋谭新生于扬 national {1. of Solid State Microstructures School of PhysicsNanjing UniversityNanjing 210093China Shishan laboratory Suzhou Campus of Nanjing UniversitySuzhou 215163China Hefei national {1. Hefei 230088China

Adiabatic time-optimal quantum controls are extensively used in quantum technologies to break the constraints imposed by short coherence ***,practically it is crucial to consider the trade-off between the quantum evolution speed and instantaneous energy cost of process because of the constraints in the available control ***,we experimentally show that using a transmon qubit that,even in the presence of vanishing energy gaps,it is possible to reach a highly time-optimal adiabatic quantum driving at low energy cost in the whole evolution *** validates the recently derived general solution of the quantum Zermelo navigation problem,paving the way for energy-efficient quantum control which is usually overlooked in conventional speed-up schemes,including the well-known counter-diabatic *** designing the control Hamiltonian based on the quantum speed limit bound quantified by the changing rate of phase in the interaction picture,we reveal the relationship between the quantum speed limit and instantaneous energy ***,we demonstrate fast and high-fidelity quantum adiabatic processes by employing energy-efficient driving strengths,indicating a promising strategy for expanding the applications of time-optimal quantum controls in superconducting quantum circuits.

关键词： process quantum adiabatic

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A dephosphorylation-dependentmolecular switch for FT repression mediates flowering in Arabidopsis

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Plant Communications 2024年第3期5卷 167-178页

作者： Yu Zhang Changmei Hua Jian Xuan Kiang Lisha Shen Temasek Life Sciences laboratory 1 Research LinkNational University of SingaporeSingapore 117604Singapore Department of Biological Sciences Faculty of ScienceNational University of SingaporeSingapore 117543Singapore

The reproductive success offlowering plants relies greatly on precise timing of thefloral transition,which isnely modulated by a complex network offloral *** a mainfloral integrator,FLOWERING LOCUS T(FT)is also an essential constituent of theflorigen that is transported from leaves to shoot apices to *** is specically transcribed in leaf vascular tissues,where its production is suppressed by manyflowering repressors,including the MYB transcription factor EARLY FLOWERING MYB PROTEIN(EFM).Here,we show that a plant CTD phosphatase,C-TERMINAL DOMAIN PHOSPHATASE-LIKE 2(CPL2),suppresses FT expression in leaf vascular tissues by modulating the binding activity of ***2 interacts with and dephosphorylates EFM to facilitate the binding of dephosphorylated EFM to FT chromatin,thereby *** results suggest that CPL2-mediated dephosphorylation of thefloral repressor EFM serves as a molecular switch,adding another layer of regulation tone-tune FT transcription and ensure thatflowering occurs at an appropriate time.

关键词： CTD phosphatase MYB protein florigen FT flowering Arabidopsis

The quantum Ising model for perfect matching and solving it with variational quantum eigensolver

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Science China(Information Sciences) 2024年第9期67卷 306-320页

作者： Qilin ZHENG Pingyu ZHU Chao WU Miaomiao YU Weihong LUO Ping XU Institute for Quantum Information and State Key laboratory of High Performance Computing College of Computer Science and Technology National University of Defense Technology Hefei national {1.

Obtaining all perfect matchings of a graph is a tough problem in graph theory, and its complexity belongs to the #P-Complete class. The problem is closely related to combinatorics, marriage matching problems, dense subgraphs, the Gaussian boson sampling, chemical molecular structures, and dimer *** this paper, we propose a quadratic unconstrained binary optimization formula of the perfect matching problem and translate it into the quantum Ising model. We can obtain all perfect matchings by mapping them to the ground state of the quantum Ising Hamiltonian and solving it with the variational quantum eigensolver. Adjusting the model's parameters can also achieve the maximum or minimum weighted perfect matching. The experimental results on a superconducting quantum computer of the Origin Quantum Computing Technology Company show that our model can encode 2~n dimensional optimization space with only O（n） qubits consumption and achieve a high success probability of the ground state corresponding to all perfect matchings. In addition, the further simulation results show that the model can support a scale of more than 1. qubits, effectively resist the adverse effects of noise, and obtain a high success probability at a shallow variational depth. This method can be extended to other combinatorial optimization problems.

关键词： perfect matching Ising model quantum Hamiltonian variational quantum eigensolver quadratic unconstrained binary optimization

Rts: learning robustly from time series data with noisy label

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Frontiers of Computer Science 2024年第06期18卷 186332-186332页

作者： ZHOU Zhi JIN Yi-Xuan Li Yu-Feng national Key {1. for Novel Software Technology Nanjing University

Significant progress has been made in machine learning with large amounts of clean labels and static data. However, in many real-world applications, the data often changes with time and it is difficult to obtain massive clean annotations, that is, noisy labels and time series are faced simultaneously. For example, in product-buyer evaluation, each sample records the daily time behavior of users, but the long transaction period brings difficulties to analysis, and salespeople often erroneously annotate the user’s purchase behavior. Such a novel setting, to our best knowledge, has not been thoroughly studied yet, and there is still a lack of effective machine learning methods. In this paper, we present a systematic approach RTS both theoretically and empirically, consisting of two components, Noise-Tolerant Time Series Representation and Purified Oversampling Learning. Specifically, we propose reducing label noise’s destructive impact to obtain robust feature representations and potential clean samples. Then, a novel learning method based on the purified data and time series oversampling is adopted to train an unbiased model. Theoretical analysis proves that our proposal can improve the quality of the noisy data set. Empirical experiments on diverse tasks, such as the house-buyer evaluation task from real-world applications and various benchmark tasks, clearly demonstrate that our new algorithm robustly outperforms many competitive methods.

关键词： weakly-supervised learning time-series classification class-imbalanced learning

New Opportunities for Neutrons in Environmental and Biological Sciences

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Frontiers of Environmental Science & Engineering 2024年第7期18卷 179-186页

作者： Alexander Johs Shuo Qian Leighton Coates Brian H.Davison James G.Elkins Xin Gu Jennifer Morrell-Falvey Hugh O'Neill Jeffrey M.Warren Eric M.Pierce Kenneth Herwig Oak Ridge national {1. Oak RidgeTN37831USA

The use of neutron methods in environmental and biological sciences is rapidly emerging and accelerating with the development of new instruments at neutron user *** article,based on a workshop held at Oak Ridge national {1.(ORNL),offers insights into the application of neutron techniques in environmental and biological *** highlight recent advances and identify key challenges and potential future research *** include soil and rhizosphere processes,root water dynamics,plant-microbe interactions,structure and dynamics of biological systems,applications in synthetic biology and enzyme engineering,next-generation bioproducts,biomaterials and bioenergy,nanoscale structure,and fluid dynamics of porous materials in *** provide an outlook on emerging opportunities with an emphasis on new capabilities that will be enabled at the Spallation Neutron Source Second Target Station currently under design at *** mission of scientific neutron user facilities worldwide is to enable science using state-of-the-art neutron *** aim to encourage researchers in the environmental and biological research community to explore the unique capability afforded by neutrons at these facilities.

关键词： Neutrons Environment Biology Neutron imaging Neutron scattering Second Target Station(STS)