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Genome assembly and transcriptome analysis provide insights into the antischistosome mechanism of Microtus fortis

Journal of Genetics and Genomics 2020年第12期47卷 743-755页

作者： Hong Li Zhen Wang Shumei Chai Xiong Bai Guohui Ding Yuanyuan Li Junyi Li Qingyu Xiao Benpeng Miao Weili Lin Jie Feng Mingyue Huang Cheng Gao Bin Li Wei Hu Jiaojiao Lin Zhiqiang Fu Jianyun Xie Yixue Li Bio-Med Big Data Center CAS Key Laboratory of Computational BiologyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200031China Shanghai Veterinary Research Institute Chinese Academy of Agricultural SciencesKey Laboratory of Animal ParasitologyMinistry of AgricultureShanghai 200241China Shanghai Laboratory Animal Research Center Shanghai 201203China Institute for Digital Health International Human Phenome Institutes(Shanghai)Shanghai 200433China Shanghai Center for Bioinformation Technology Shanghai Academy of Science and TechnologyShanghai 201203China School of Computer Science and Technology Harbin Institute of Technology(Shenzhen)ShenzhenGuangdong 518055China Shanghai Institute of Immunology Department of Immunology and MicrobiologyShanghai JiaoTong University School of MedicineShanghai 200025China State Key Laboratory of Genetic Engineering Ministry of Education Key Laboratory of Contemporary AnthropologyCollaborative Innovation Center for Genetics and DevelopmentSchool of Life SciencesFudan UniversityShanghai 200438China Hangzhou Institute for Advanced Study University of Chinese Academy of SciencesHangzhouZhejiang 330106China

Microtus fortis is the only mammalian host that exhibits intrinsic resistance against Schistosoma japonicum ***,the underlying molecular mechanisms of this resistance are not yet ***,we perform the first de novo genome assembly of ***,comprehensive gene annotation analysis,and evolution ***,we compare the recovery rate of schistosomes,pathological changes,and liver transcriptomes between *** and mice at different time points after *** observe that the time and type of immune response in *** are different from those in *** activates immune and inflammatory responses on the 10th day post infection,such as leukocyte extravasation,antibody activation,Fc-gamma receptor-mediated phagocytosis,and the interferon signaling cascade,which play important roles in preventing the development of *** contrast,an intense immune response occurrs in mice at the late stages of infection and could not eliminate *** mice suffer severe pathological injury and continuous decreases in cell cycle,lipid metabolism,and other *** findings offer new insights into the intrinsic resistance mechanism of *** against schistosome *** genome sequence also provides the basis for future studies of other important traits in ***.

关键词： Genome assembly Microtus fortis Schistosome Immune Transcriptome

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Optimizing blood-brain barrier permeability in KRAS inhibitors: A Structure-constrained molecular generation approach

引用

Journal of Pharmaceutical Analysis 2025年

作者： Xia Sheng Yike Gui Jie Yu Yitian Wang Zhenghao Li Xiaoya Zhang Yuxin Xing Yuqing Wang Zhaojun Li Mingyue Zheng Liquan Yang Xutong Li Drug Discovery and Design Center State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China University of Chinese Academy of Sciences Beijing 100049 China Nanjing University of Chinese Medicine Nanjing 210023 China Lingang Laboratory Shanghai 200031 China School of Information Science and Technology ShanghaiTech University Shanghai 201210 China Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology ShanghaiTech University Shanghai 201210 China School of Pharmaceutical Science and Technology Hangzhou Institute for Advanced Study Hangzhou 330106 China College of Computer and Information Engineering Dezhou University Dezhou Shandong 253023 China College of Agriculture and Biological Science Dali University Dali Yunnan 671003 China

Kirsten rat sarcoma viral oncogene homolog (KRAS) protein inhibitors are a promising class of therapeutics, but research on molecules that effectively penetrate the blood-brain barrier (BBB) remains limited, which is crucial for treating central nervous system (CNS) malignancies. Although molecular generation models have recently advanced drug discovery, they often overlook the complexity of biological and chemical factors, leaving room for improvement. In this study, we present a structure-constrained molecular generation workflow designed to optimize lead compounds for both drug efficacy and drug absorption properties. Our approach utilizes a variational autoencoder (VAE) generative model integrated with reinforcement learning for multi-objective optimization. This method specifically aims to enhance BBB permeability while maintaining high-affinity substructures of KRAS inhibitors. To support this, we incorporate a specialized KRAS BBB predictor based on active learning and an affinity predictor employing comparative learning models. Additionally, we introduce two novel metrics, the knowledge-integrated reproduction score (KIRS) and the composite diversity score (CDS), to assess structural performance and biological relevance. Retrospective validation with KRAS inhibitors, AMG510 and MRTX849, demonstrates the framework’s effectiveness in optimizing BBB permeability and highlights its potential for real-world drug development applications. This study provides a robust framework for accelerating the structural enhancement of lead compounds, advancing the drug development process across diverse targets.

关键词： KRAS inhibitors Drug design Blood-brain barrier permeability Molecular optimization Deep learning Generation models

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Recycling qubits for the generation of Bell nonlocality between independent sequential observers

arXiv

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arXiv 2021年

作者： Cheng, Shuming Liu, Lijun Baker, Travis J. Hall, Michael J.W. The Department of Control Science and Engineering Tongji University Shanghai 201804 China Shanghai Institute of Intelligent Science and Technology Tongji University Shanghai 201804 China Institute for Advanced Study Tongji University Shanghai 200092 China College of Mathematics and Computer Science Shanxi Normal University Linfen041000 China Centre for Quantum Dynamics Griffith University BrisbaneQLD4111 Australia Department of Theoretical Physics Research School of Physics Australian National University CanberraACT0200 Australia

There is currently much interest in the recycling of entangled systems, for use in quantum information protocols by sequential observers. In this work, we study the sequential generation of Bell nonlocality via recycling one or both components of two-qubit states. We first give a description of two-valued qubit measurements in terms of measurement bias, strength, and reversibility, and derive useful tradeoff relations between them. Then, we derive one-sided monogamy relations for unbiased observables, that strengthen the recent Conjecture in [S. Cheng et al., Phys. Rev. A 104, L060201 (2021) ] that if the first pair of observers violate Bell nonlocality then a subsequent independent pair cannot, and give semi-analytic results for the best possible monogamy relation. We also extend the construction in [P. J. Brown and R. Colbeck, Phys. Rev. Lett. 125, 090401 (2020)] to obtain (i) a broader class of two-qubit states that allow the recycling of one qubit by a given number of observers on one side, and (ii) a scheme for generating Bell nonlocality between arbitrarily many independent observers on each side, via the two-sided recycling of multiqubit states. Our results are based on a formalism that is applicable to more general problems in recycling entanglement, and hence is expected to aid progress in this field. Copyright © 2021, The Authors. All rights reserved.

关键词： Recycling

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Reentrant quantum anomalous Hall effect in molecular beam epitaxy-grown MnBi2Te4 thin films

arXiv

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arXiv 2024年

作者： Li, Yuanzhao Bai, Yunhe Feng, Yang Luan, Jianli Gao, Zongwei Chen, Yang Tong, Yitian Liu, Ruixuan Chong, Su Kong Wang, Kang L. Zhou, Xiaodong Shen, Jian Zhang, Jinsong Wang, Yayu Chen, Chui-Zhen Xie, XinCheng Feng, Xiao He, Ke Xue, Qi-Kun Beijing Academy of Quantum Information Sciences Beijing100193 China State Key Laboratory of Low Dimensional Quantum Physics Department of Physics Tsinghua University Beijing100084 China Department of Electrical and Computer Engineering University of California Los Angeles Los AngelesCA90095 United States Department of Physics and Astronomy University of California Los Angeles Los AngelesCA90095 United States State Key Laboratory of Surface Physics Department of Physics Fudan University Shanghai200438 China Institute for Nanoelectronic Devices and Quantum Computing Fudan University Shanghai200438 China Zhangjiang Fudan International Innovation Center Fudan University Shanghai201210 China Shanghai Research Center for Quantum Sciences Shanghai201315 China Collaborative Innovation Center of Advanced Microstructures Nanjing210093 China School of Physical Science and Technology Soochow University Suzhou215006 China Institute for Advanced Study Soochow University Suzhou215006 China International Center for Quantum Materials School of Physics Peking University Beijing100871 China Southern University of Science and Technology Shenzhen518055 China Frontier Science Center for Quantum Information Beijing100084 China Hefei National Laboratory Hefei230088 China

In the realm of topological quantum physics, it is widely accepted that a global bandgap is necessary to achieve quantized Hall conductance, irrespective of its origin-magnetic field, exchange coupling or other mechanisms. A material exhibiting the quantum anomalous Hall (QAH) effect had been considered equivalent to a Chern insulator, a band insulator with non-zero Chern number. However, a Chern Anderson insulator (CAI), which arises in a conducting state with exchange-induced Berry curvature splitting and disorder-induced Anderson localization, can in principle exhibit the QAH effect. In this study, we investigate intrinsic magnetic topological insulator MnBi2Te4 thin films grown by molecular beam epitaxy (MBE). We observe a reentrant QAH effect when the Fermi energy enters the valance band and magnetic field equals zero, indicating the emergence of the CAI state. The discovery opens a new avenue for realizing the QAH effect and underscores the fundamental role of both Berry curvature and Anderson localization. © 2024, CC BY-NC-ND.

关键词： Molecular beam epitaxy

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An efficient adaptive online neural spikes detection and classification engine based on Bayesian inference 6

An efficient adaptive online neural spikes detection and cla...

引用

6th International Conference on Systems and Informatics, ICSAI 2019

作者： Li, Nan Sawan, Mohamad Wang, Lei College of Computer Science National University of Defense Technology Changsha China Polystim Neurotech. Lab Polytechnique Montreal Electrical Engineering Dept. Montreal Canada School of Engineering Westlake University Hangzhou310024 China Institute of Advanced Study Westlake Institute for Advanced Study Hangzhou310024 China

ISBN: (纸本)9781728152561

A new method, called Bayesian inference-based template matching (BIBTM) method, is proposed in this article, which is designed to detect and classify neural spikes from real neural signals. Through this spike detection and classification method, the templates do not need be given in advance, and they can be automatically generated. To evaluate the performance of our method, we built signals with diverse signal-to-noise ratios and firing rates, and also researched two spike template generation methods. Based on the experimental results and comparison, BIBTM method has excellent detection performance. The true positive rates (TPR) and false positive rates (FPR) of the spike detection can reach 0.92 and 0.05 respectively, and the average FPR and average TPR of the spike classification can reach 0.05 and 0.6 respectively. From the discussion and analysis, our proposed BIBTM method not only has high detection and classification accuracy, but also has a simple structure and low complexity. © 2019 IEEE.

关键词： Template matching

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Limitations on sharing bell nonlocality between sequential pairs of observers

arXiv

引用

arXiv 2021年

作者： Cheng, Shuming Liu, Lijun Baker, Travis J. Hall, Michael J.W. The Department of Control Science and Engineering Tongji University Shanghai201804 China Shanghai Institute of Intelligent Science and Technology Tongji University Shanghai201804 China Institute for Advanced Study Tongji University Shanghai200092 China College of Mathematics and Computer Science Shanxi Normal University Linfen041000 China Centre for Quantum Computation and Communication Technology Australian Research Council Centre for Quantum Dynamics Griffith University BrisbaneQLD4111 Australia Department of Theoretical Physics Research School of Physics Australian National University CanberraACT0200 Australia

We give strong analytic and numerical evidence that, under mild measurement assumptions, two qubits cannot both be recycled to generate Bell nonlocality between multiple independent observers on each side. This is surprising, as under the same assumptions it is possible to recycle just one of the qubits an arbitrarily large number of times [P. J. Brown and R. Colbeck, Phys. Rev. Lett. 125, 090401 (2020)]. We derive corresponding 'one-sided monogamy relations' that rule out two-sided recycling for a wide range of parameters, based on a general tradeoff relation between the strengths and maximum reversibilities of qubit measurements. We also show if the assumptions are relaxed to allow sufficiently biased measurement selections, then there is a narrow range of measurement strengths that allows two-sided recycling for two observers on each side, and propose an experimental test. Our methods may be readily applied to other types of quantum correlations, such as steering and entanglement, and hence to general information protocols involving sequential measurements. Copyright © 2021, The Authors. All rights reserved.

关键词： Recycling

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Time-domain identification of distinct mechanisms for competing charge density waves in a rare-earth tritelluride

arXiv

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arXiv 2025年

作者： Su, Yifan Lv, B.Q. Zong, Alfred Müller, Aaron Chattopadhyay, Sambuddha Dolgirev, Pavel E. Singh, Anisha G. Straquadine, Joshua A.W. Choi, Dongsung Azoury, Doron Mogi, Masataka Fisher, Ian R. Demler, Eugene Gedik, Nuh Massachusetts Institute of Technology Department of Physics CambridgeMA02139 United States Tsung-Dao Lee Institute School of Physics and Astronomy Zhangjiang Institute for Advanced Study Shanghai Jiao Tong University Shanghai200240 China Departments of Physics and of Applied Physics Stanford University StanfordCA94305 United States SIMES SLAC National Accelerator Laboratory Menlo ParkCA94025 United States Institute for Theoretical Physics ETH Zürich Zürich8093 Switzerland Lyman Laboratory Department of Physics Harvard University CambridgeMA02138 United States Geballe Laboratory for Advanced Materials Stanford University StanfordCA94305 United States Department of Applied Physics Stanford University StanfordCA94305 United States Massachusetts Institute of Technology Department of Electrical Engineering and Computer Science CambridgeMA02139 United States Department of Applied Physics University of Tokyo Bunkyo-ku Tokyo113-8656 Japan

Understanding the origin of phase transitions and the interactions between distinct phases remains a central task in condensed matter physics. Charge density wave (CDW) systems provide an ideal platform for investigating these phenomena. While the dominant CDW phases in many materials can be explained through Fermi surface nesting or electron-phonon interactions, certain CDW phase transitions remain poorly understood, challenging conventional paradigms. One notable example is rare-earth tritelluride ErTe3, which hosts two competing CDW orders. While the dominant CDW phase fits within the electron-phonon coupling framework, the formation mechanism of the subdominant CDW remains enigmatic. In this study, we combine time- and angle-resolved photoemission spectroscopy and time-dependent Ginzburg-Landau theory to establish a time-domain approach for probing phase transitions in solid-state systems. By analyzing the distinct recovery dynamics of the two CDW orders in ErTe3 following light excitation, we reveal a novel nucleation and growth mechanism that likely drives the secondary CDW phase transition. This work not only uncovers a previously unknown CDW formation mechanism in rare-earth tritellurides but also introduces a non-equilibrium framework for understanding phase transitions and phase competition in quantum materials. Copyright © 2025, The Authors. All rights reserved.

关键词： Charge density waves

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Mapping global lake dynamics reveals the emerging roles of small lakes (October, 10.1038/s41467-022-33239-3, 2022)

引用

NATURE COMMUNICATIONS 2022年第1期13卷 1-12页

作者： Pi, Xuehui Luo, Qiuqi Feng, Lian Xu, Yang Tang, Jing Liang, Xiuyu Ma, Enze Cheng, Ran Fensholt, Rasmus Brandt, Martin Cai, Xiaobin Gibson, Luke Liu, Junguo Zheng, Chunmiao Li, Weifeng Bryan, Brett A. Southern University of Science and Technology School of Environmental Science and Engineering Shenzhen China (GRID:grid.263817.9) (ISNI:0000 0004 1773 1790) The University of Hong Kong Department of Urban Planning and Design Hong Kong SAR China (GRID:grid.194645.b) (ISNI:***) The University of Hong Kong Urban Systems Institute Hong Kong SAR China (GRID:grid.194645.b) (ISNI:***) Southern University of Science and Technology School of Environmental Science and Engineering Shenzhen China (GRID:grid.263817.9) (ISNI:0000 0004 1773 1790) Southern University of Science and Technology School of Environmental Science and Engineering Shenzhen China (GRID:grid.263817.9) (ISNI:0000 0004 1773 1790) University of Copenhagen Department of Geosciences and Natural Resource Management Copenhagen Denmark (GRID:grid.5254.6) (ISNI:0000 0001 0674 042X) University of Copenhagen Department of Biology Copenhagen Denmark (GRID:grid.5254.6) (ISNI:0000 0001 0674 042X) Lund University Department of Physical Geography and Ecosystem Science Lund Sweden (GRID:grid.4514.4) (ISNI:0000 0001 0930 2361) Southern University of Science and Technology Guangdong Provincial Key Laboratory of Brain-inspired Intelligent Computation Department of Computer Science and Engineering Shenzhen China (GRID:grid.263817.9) (ISNI:0000 0004 1773 1790) University of Copenhagen Department of Geosciences and Natural Resource Management Copenhagen Denmark (GRID:grid.5254.6) (ISNI:0000 0001 0674 042X) Chinese Academy of Sciences Institute of Geodesy and Geophysics Wuhan China (GRID:grid.9227.e) (ISNI:***) Southern University of Science and Technology School of Environmental Science and Engineering Shenzhen China (GRID:grid.263817.9) (ISNI:0000 0004 1773 1790) North China University of Water Resources and Electric Power School of Water Conservancy Zhengzhou China (GRID:grid.412224.3) (ISNI:0000 0004 1759 6955) Southern University of Science and Technology School of Environmental Science and Engineering Shenzhen China (GRID:grid.263

Lakes are important natural resources and carbon gas emitters and are undergoing rapid changes worldwide in response to climate change and human activities. A detailed global characterization of lakes and their long-term dynamics does not exist, which is however crucial for evaluating the associated impacts on water availability and carbon emissions. Here, we map 3.4 million lakes on a global scale, including their explicit maximum extents and probability-weighted area changes over the past four decades. From the beginning period (1984–1999) to the end (2010–2019), the lake area increased across all six continents analyzed, with a net change of +46,278 km2, and 56% of the expansion was attributed to reservoirs. Interestingly, although small lakes (<1 km2) accounted for just 15% of the global lake area, they dominated the variability in total lake size in half of the global inland lake regions. The identified lake area increase over time led to higher lacustrine carbon emissions, mostly attributed to small lakes. Our findings illustrate the emerging roles of small lakes in regulating not only local inland water variability, but also the global trends of surface water extent and carbon *** are essential components of the hydrological and biogeochemical cycles. Here, Pi et al develop a global lake dataset called GLAKES via high-resolution satellite images and deep learning to examine global lake changes over four decades.

关键词： Hydrology Limnology

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Cooperative nanoparticle self-assembly and photothermal heating in a flexible plasmonic metamaterial

arXiv

引用

arXiv 2020年

作者： Phan, Anh D. Lam, Vu D. Wakabayashi, Katsunori Phenikaa Institute for Advanced Study Artificial Intelligence Laboratory Faculty of Computer Science Materials Science and Engineering Phenikaa University Hanoi12116 Viet Nam Department of Nanotechnology for Sustainable Energy School of Science and Technology Kwansei Gakuin University Sanda Hyogo669-1337 Japan Graduate University of Science and Technology Vietnam Academy of Science and Technology 18 Hoang Quoc Viet Hanoi Viet Nam

We theoretically investigate equilibrium behaviors and photothermal effects of a flexible plasmonic metamaterial composed of aramid nanofibers and gold nanoparticles. The fiber matrix is considered as an external field to reconfigure a nanoparticle assembly. We find that the heating process tunes particle-particle and fiber-particle interactions, which alter adsorption of nanoparticles on fiber surfaces or clustering in pore spaces. Thus, it is possible to control the nanoparticle self-assembly by laser illumination. Gold nanoparticles strongly absorb radiations and efficiently dissipate absorbed energy into heat. By solving the heat transfer equation associated with an effective medium approximation, we calculate the spatial temperature rise. Remarkably, our theoretical results quantitatively agree with prior experiments. This indicates that we can ignore plasmonic coupling effects induced by particle clustering. Effects of the laser spot size and intensity on the photothermal heating are also discussed. Copyright © 2020, The Authors. All rights reserved.

关键词： Metal nanoparticles

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Coexistence of interacting charge density waves in a layered semiconductor

arXiv

引用

arXiv 2024年

作者： Lv, B.Q. Zong, Alfred Wu, Dong Nie, Zhengwei Su, Yifan Choi, Dongsung Ilyas, Batyr Fichera, Bryan T. Li, Jiarui Baldini, Edoardo Mogi, Masataka Huang, Y.-B. Po, Hoi Chun Meng, Sheng Wang, Yao Wang, N.L. Gedik, Nuh Tsung-Dao Lee Institute Shanghai Jiao Tong University Shanghai200240 China Massachusetts Institute of Technology Department of Physics CambridgeMA02139 United States School of Physics and Astronomy Shanghai Jiao Tong University Shanghai200240 China Zhangjiang Institute for Advanced Study Shanghai Jiao Tong University Shanghai200240 China University of California at Berkeley Department of Chemistry BerkeleyCA94720 United States Beijing Academy of Quantum Information Sciences Beijing100913 China Beijing National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of Sciences Beijing100190 China Massachusetts Institute of Technology Department of Electrical Engineering and Computer Science CambridgeMA02139 United States SLAC National Accelerator Laboratory Menlo ParkCA94025 United States Department of Applied Physics Stanford University StanfordCA94305 United States Shanghai Synchrotron Radiation Facility Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai201204 China Department of Physics Hong Kong University of Science and Technology Clear Water Bay Hong Kong Department of Chemistry Emory University AtlantaGA30322 United States International Center for Quantum Materials School of Physics Peking University Beijing100871 China

Coexisting orders are key features of strongly correlated materials and underlie many intriguing phenomena from unconventional superconductivity to topological orders. Here, we report the coexistence of two interacting charge-density-wave (CDW) orders in EuTe4, a layered crystal that has drawn considerable attention owing to its anomalous thermal hysteresis and a semiconducting CDW state despite the absence of perfect FS nesting. By accessing unoccupied conduction bands with time- and angle-resolved photoemission measurements, we find that mono- and bi-layers of Te in the unit cell host different CDWs that are associated with distinct energy gaps. The two gaps display dichotomous evolutions following photoexcitation, where the larger bilayer CDW gap exhibits less renormalization and faster recovery. Surprisingly, the CDW in the Te monolayer displays an additional momentum-dependent gap renormalization that cannot be captured by density-functional theory calculations. This phenomenon is attributed to interlayer interactions between the two CDW orders, which account for the semiconducting nature of the equilibrium state. Our findings not only offer microscopic insights into the correlated ground state of EuTe4 but also provide a general non-equilibrium approach to understand coexisting, layer-dependent orders in a complex system. © 2024, CC BY.

关键词： Ground state

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