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Inside-out assembly of viral antigens for the enhanced vaccination

Signal Transduction and Targeted Therapy 2023年第6期8卷 3144-3157页

作者： Fengqiang Cao Sha Peng Yaling An Kun Xu Tianyi Zheng Lianpan Dai Kenji Ogino To Ngai Yufei Xia Guanghui Ma State Key Laboratory of Biochemical Engineering Institute of Process EngineeringChinese Academy of SciencesBeijing100190PR China Graduate School of Bio-Applications and Systems Engineering Tokyo University of Agriculture and Technology2-24-16 NakachoKoganeiTokyo184-8588Japan Institute of Global Innovation Research Tokyo University of Agriculture and Technology2-24-16 NakachoKoganei-shiTokyo184-8588Japan CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing100101PR China Savaid Medical School University of Chinese Academy of SciencesBeijingPR China Key Laboratory of Tropical Translational Medicine of Ministry of Education School of Tropical Medicine and Laboratory MedicineThe First Affiliated HospitalHainan Medical UniversityHainan571199PR China Zhejiang University School of Medicine Hangzhou310058PR China Department of Chemistry The Chinese University of Hong KongShatinN.T.Hong Kong999077PR China University of Chinese Academy of Sciences Beijing100049PR China Innovation Academy for Green Manufacture Chinese Academy of Sciences Beijing100190PR China

Current attempts in vaccine delivery systems concentrate on replicating the natural dissemination of live pathogens,but neglect that pathogens evolve to evade the immune system rather than to provoke *** the case of enveloped RNA viruses,it is the natural dissemination of nucleocapsid protein(NP,core antigen)and surface antigen that delays NP exposure to immune ***,we report a multi-layered aluminum hydroxide-stabilized emulsion(MASE)to dictate the delivery sequence of the *** this manner,the receptor-binding domain(RBD,surface antigen)of the spike protein was trapped inside the nanocavity,while NP was absorbed on the outside of the droplets,enabling the burst release of NP before *** with the natural packaging strategy,the inside-out strategy induced potent type I interferon-mediated innate immune responses and triggered an immune-potentiated environment in advance,which subsequently boosted CD40+DC activations and the engagement of the lymph *** both H1N1 influenza and SARS-CoV-2 vaccines,rMASE significantly increased antigen-specific antibody secretion,memory T cell engagement,and Th1-biased immune response,which diminished viral loads after lethal *** simply reversing the delivery sequence of the surface antigen and core antigen,the inside-out strategy may offer major implications for enhanced vaccinations against the enveloped RNA virus.

关键词： vaccination outside evolve

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Towards a Predictive Approach for Omni-channel Retailing Supply Chains

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IFAC-PapersOnLine 2019年第13期52卷 844-850页

作者： Pereira, Marina Meireles Frazzon, Enzo Morosini Graduate Program in Production Engineering Industrial and Systems Engineering Department Technology Center Federal University of Santa Catarina Florianópolis Santa Catarina Brazil

The adoption of omni-channel strategy has changed the relation between retailers and customers and brought more complexity to the retailing supply chains. To address the increasing complexity, it is necessary to adopt innovative approaches based on information technologies and intelligent decision methods. The challenges to retailers are improving the accuracy of offline and online channels demand forecasting, better managing offline and online customer's needs, thus reducing the uncertainties of the omni-channel retailing supply chain. In this context, this research paper aims to propose a predictive approach for omni-channel retailing supply chain combining clustering with artificial neural network to handle demand uncertainty. © 2019, IFAC (International Federation of Automatic Control) Hosting by Elsevier Ltd. All rights reserved.

关键词： Neural networks Complex networks Learning systems Sales Supply chain management Channel strategies Clustering Demand forecasting Demand uncertainty Innovative approaches Intelligent decisions Omni channel Retail supply chain

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Adaptive Contextual Caching for Mobile Edge Large Language Model Service

arXiv

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arXiv 2025年

作者： Liu, Guangyuan Liu, Yinqiu Wang, Jiacheng Du, Hongyang Niyato, Dusit Kang, Jiawen Xiong, Zehui College of Computing and Data Science The Energy Research Institute @ NTU Interdisciplinary Graduate Program Nanyang Technological University Singapore College of Computing and Data Science Nanyang Technological University Singapore Department of Electrical and Electronic Engineering University of Hong Kong Hong Kong School of Automation Guangdong University of Technology China Pillar of Information Systems Technology and Design Singapore University of Technology and Design Singapore

Mobile edge Large Language Model (LLM) deployments face inherent constraints, such as limited computational resources and network bandwidth. Although Retrieval-Augmented Generation (RAG) mitigates some challenges by integrating external knowledge bases, inefficient cache management can still result in high retrieval latency and frequent cache updates. To address these issues, we propose an Adaptive Contextual Caching (ACC) framework that anticipates user needs by proactively caching semantically relevant data for mobile-edge LLMs. ACC utilizes a deep reinforcement learning (DRL) module to refine cache replacement policies, balancing user context, document similarity, and the overhead associated with cache misses. Experimental results demonstrate that ACC increases cache hit rates to over 80% after only 11 training episodes, outperforming FIFO, LRU, and semantic-only caching while reducing retrieval latency by up to 40%. In particular, ACC also reduces local caching overhead (i.e., the cost of updating the cache when a miss occurs) by as much as 55%, enabling scalable, low-latency LLM services in resource-constrained edge environments. © 2025, CC BY.

关键词： Deep reinforcement learning

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3D bioprinting of scaffold structure using micro-extrusion technology 28

3D bioprinting of scaffold structure using micro-extrusion t...

引用

28th Annual International Solid Freeform Fabrication Symposium - An Additive Manufacturing Conference, SFF 2017

作者： Xing, Juan Luo, Xianli Bermudez, Juliana Moldthan, Matthew Li, Bingbing Department of Manufacturing Systems Engineering and Management California State University NorthridgeCA91330-8332 United States

Scaffold-based techniques are a vital assistance tool to support main structure and enhance the resolution of target structure. In this study, a custom-made micro-extrusion bioprinting system was built and utilized to fabricate different scaffold structures such as log-pile scaffold and two-ring scaffold. This approach showed tremendous potential because of its ability to produce microscale channels with almost any shape. We were able to fabricate these scaffolds by using a custom-made 3D bioprinter to print hydrogel solution, mostly composed of Pluronic F-127, then wash away hydrogen by phosphate buffer saline (PBS) after crosslinking of main structure. We were able to achieve the desired scaffold structure by feeding G-codes data into user interface (Pronterface) and then translating that model into a program that utilizes a customized programming language, which instructs the microfabrication printer nozzles to dispense the hydrogel at specific locations. This fundamental study will be used to print increasingly viable and complex tissue shapes with living cells. Copyright © SFF *** rights reserved.

关键词： Hydrogels

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Reliable network design considering endogenous customers’ choices under probabilistic arc failures

A I I E Transactions

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A I I E Transactions 2024年第2期56卷

作者： Pengcheng Dong Yang Liu Qingchun Meng Guodong Yu a School of Management Shandong University Jinan China b Department of Civil and Environmental Engineering and the Department of Industrial Systems Engineering and Management National University of Singapore Singapore

We consider a reliable network design where the facility location and road ban decisions are jointly optimized to minimize the total expected costs and risks against uncertain exogenous arc-dependent failures and customers’ endogenous interactions. We formulate endogenous customers’ choices by incorporating an expressive measure, Cumulative prospect theory, into the widely used multinomial logit model. Additionally, we use a well-known downside measure, Conditional value-at-risk, for the designer to control integrated risks from exogenous arc failures and endogenous customers’ choices. Accordingly, a mixed-integer trilinear program is developed. To solve the model, we first transform it into a class of mixed-integer linear programs based on the separable structure. Then, a customized branch-and-Benders-cut algorithm is proposed to solve these mixed-integer linear programs. We devise a set of novel valid inequalities based on the endogenous transition of choice probability to strengthen the weak relaxation of the master problem. Moreover, by aggregating the grouping and dual iterations shrinking techniques for solving sub-problems, the branch-and-Benders-cut algorithm can converge within 30 seconds and the whole problem can be solved within 15 minutes for a network with 90 nodes and 149 road segments. Some managerial insights for balancing risk and cost are finally extracted.

关键词： Network design endogenous interactions mixed-integer trilinear program branch-and-Benders-cut

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Improving Land Cover Segmentation Using Multispectral Dataset

Improving Land Cover Segmentation Using Multispectral Datase...

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International Conference on Informatics and Computing (ICIC)

作者： Herlawati Herlawati Rahmadya Trias Handayanto Yaya Heryadi Edi Abdurachman Haryono Soeparno Edy Irwansyah Eka Miranda Informatics Universitas Bhayangkara Jakarta Raya Jakarta Indonesia Computer Engineering Universitas Islam 45 Bekasi Indonesia Computer Science Department BINUS Graduate Program – Doctor of Computer Science Bina Nusantara University Jakarta Indonesia Trisakti Institute of Transportation and Logistic Jakarta Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia Information Systems Department School of Information Systems Bina Nusantara University Jakarta Indonesia

Computer vision has been used in many areas such as medical, transportation, military, geography, etc. The fast development of sensor devices inside camera and satellite provides not only red-greed-blue (RGB) images but also multispectral dataset with some channels including RGB, infrared, short-wave, and thermal wave. Most of the dataset is panchromatic (black and white) and RGB, for example Google Map and other satellite-based map applications. This study examines the effects of multispectral dataset for semantic segmentation of land cover. The comparison between RGB with band 2 to band 7 of Landsat 8 Satellite shows an improvement of accuracy from 90.283 to 94.473 for U-Net and from 91.76 to 95.183 for DeepLabV3+. In addition, this research also compares two well-known semantic segmentation methods, namely U-Net and DeepLabV3+, that shown that DeepLabV3+ outperformed U-Net regarding to speed and accuracy. Testing was conducted in the Karawang Regency area, West Java, Indonesia.

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Specific pupylation as IDEntity reporter(SPIDER)for the identification of protein-biomolecule interactions

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Science China(Life Sciences) 2023年第8期66卷 1869-1887页

作者： He-Wei Jiang Hong Chen Yun-Xiao Zheng Xue-Ning Wang Qingfeng Meng Jin Xie Jiong Zhang ChangSheng Zhang Zhao-Wei Xu Zi-Qing Chen Lei Wang Wei-Sha Kong Kuan Zhou Ming-Liang Ma Hai-Nan Zhang Shu-Juan Guo Jun-Biao Xue Jing-Li Hou Zhe-Yi Liu Wen-Xue Niu Fang-Jun Wang Tao Wang Wei Li Rui-Na Wang Yong-Jun Dang Daniel MCzajkowsky JianFeng Pei Jia-Jia Dong Sheng-Ce Tao Shanghai Center for Systems Biomedicine Key Laboratory of Systems Biomedicine(Ministry of Education)Shanghai Jiao Tong UniversityShanghai 200240China Center for Quantitative Biology Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijing 100871China Inflammation and Immune Mediated Diseases Laboratory of Anhui Province School of PharmacyAnhui Medical UniversityHefei 230032China Key Laboratory of Organofluorine Chemistry Center for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryUniversity of the Chinese Academy of SciencesChinese Academy of SciencesShanghai 200240China College of Chemistry and Molecular Engineering Peking UniversityBeijing 100871China Key Laboratory of Gastrointestinal Cancer(Fujian Medical University) Ministry of EducationFuzhou 350122China Department of Molecular Biology Princeton UniversityNew Jersey 08540USA Instrumental Analysis Center Shanghai Jiao Tong UniversityShanghai 200240China CAS Key Laboratory of Separation Sciences for Analytical Chemistry Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalian 116023China Institute of Systems Biology Shenzhen Bay LaboratoryPeking University Shenzhen Graduate SchoolShenzhen 518055China Department of Medicinal Chemistry School of PharmacyChina Pharmaceutical UniversityNanjing 211198China Key Laboratory of Metabolism and Molecular Medicine the Ministry of EducationDepartment of Biochemistry and Molecular BiologySchool of Basic Medical SciencesFudan UniversityShanghai 200240China Center for Novel Target and Therapeutic Intervention Chongqing Medical UniversityChongqing 400016China School of Biomedical Engineering Shanghai Jiao Tong UniversityShanghai 200240China

Protein-biomolecule interactions play pivotal roles in almost all biological *** a biomolecule of interest,the identification of the interacting protein(s)is *** this need,although many assays are available,highly robust and reliable methods are always *** combining a substrate-based proximity labeling activity from the pupylation pathway of Mycobacterium tuberculosis and the streptavidin(SA)-biotin system,we developed the Specific Pupylation as IDEntity Reporter(SPIDER)method for identifying protein-biomolecule *** SPIDER,we validated the interactions between the known binding proteins of protein,DNA,RNA,and small *** successfully applied SPIDER to construct the global protein interactome for m^(6)A and m RNA,identified a variety of uncharacterized m^(6)A binding proteins,and validated SRSF7 as a potential m^(6)A *** globally identified the binding proteins for lenalidomide and Cob ***,we identified SARS-CoV-2-specific receptors on the cell ***,SPIDER is powerful and highly accessible for the study of proteinbiomolecule interactions.

关键词： proximity labeling protein-biomolecule interaction proteomics pupylation

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An Analysis Method for Metric-Level Switching in Beat Tracking

arXiv

引用

arXiv 2022年

作者： Chiu, Ching-Yu Müller, Meinard Davies, Matthew E.P. Su, Alvin Wen-Yu Yang, Yi-Hsuan Graduate Program of Multimedia Systems and Intelligent Computing National Cheng Kung University Academia Sinica Taiwan International Audio Laboratories Erlangen Germany Department of Informatics Engineering Centre for Informatics and Systems The University of Coimbra University of Coimbra Portugal Department of CSIE National Cheng Kung University Taiwan Taiwan AI Labs Taiwan

For expressive music, the tempo may change over time, posing challenges to tracking the beats by an automatic model. The model may first tap to the correct tempo, but then may fail to adapt to a tempo change, or switch between several incorrect but perceptually plausible ones (e.g., half- or double-tempo). Existing evaluation metrics for beat tracking do not reflect such behaviors, as they typically assume a fixed relationship between the reference beats and estimated beats. In this paper, we propose a new performance analysis method, called annotation coverage ratio (ACR), that accounts for a variety of possible metric-level switching behaviors of beat trackers. The idea is to derive sequences of modified reference beats of all metrical levels for every two consecutive reference beats, and compare every sequence of modified reference beats to the subsequences of estimated beats. We show via experiments on three datasets of different genres the usefulness of ACR when being utilized alongside existing metrics, and discuss the new insights that can be gained. © 2022, CC BY.

关键词： Taps

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Towards understanding structure–property relations in materials with interpretable deep learning

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npj Computational Materials 2023年第1期9卷 157-168页

作者： Tien-Sinh Vu Minh-Quyet Ha Duong-Nguyen Nguyen Viet-Cuong Nguyen Yukihiro Abe Truyen Tran Huan Tran Hiori Kino Takashi Miyake Koji Tsuda Hieu-Chi Dam Japan Advanced Institute of Science and Technology NomiIshikawaJapan HPC SYSTEMS Inc. MinatoTokyoJapan Applied Artificial Intelligence Institute Deakin UniversityGeelongVICAustralia School of Materials Science and Engineering Georgia Institute of TechnologyAtlantaGAUSA Research and Services Division of Materials Data and Integrated System National Institute for Materials ScienceTsukubaIbarakiJapan Research Center for Computational Design of Advanced Functional Materials National Institute of Advanced Industrial Science and TechnologyTsukubaIbarakiJapan Department of Computational Biology and Medical Sciences Graduate School of Frontier SciencesUniversity of TokyoKashiwa-shiChiba-kenJapan International Center for Synchrotron Radiation Innovation Smart(SRIS) Tohoku UniversityAoba-kuSendaiJapan

Deep learning(DL)models currently employed in materials research exhibit certain limitations in delivering meaningful information for interpreting predictions and comprehending the relationships between structure and material *** address these limitations,we propose an interpretable DL architecture that incorporates the attention mechanism to predict material properties and gain insights into their structure–property *** proposed architecture is evaluated using two well-known datasets(the QM9 and the Materials Project datasets),and three in-house-developed computational materials ***–test–split validations confirm that the models derived using the proposed DL architecture exhibit strong predictive capabilities,which are comparable to those of current state-of-the-art ***,comparative validations,based on first-principles calculations,indicate that the degree of attention of the atoms’local structures to the representation of the material structure is critical when interpreting structure–property relationships with respect to physical *** properties encompass molecular orbital energies and the formation energies of *** proposed architecture shows great potential in accelerating material design by predicting material properties and explicitly identifying crucial features within the corresponding structures.

关键词： properties property structure

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A Unified View of Allostery.

arXiv

引用

arXiv 2024年

作者： Rouviere, Eric Rivoire, Olivier Ranganathan, Rama Center for Physics of Evolving Systems Department of Biochemistry & Molecular Biology University of Chicago ChicagoIL60637 United States Graduate Program in Biophysical Sciences University of Chicago ChicagoIL60637 United States Gulliver ESPCI Paris CNRS Université PSL Paris75005 France The Pritzker School for Molecular Engineering University of Chicago ChicagoIL60637 United States

Allostery is a fundamental property of proteins that represents the functional coupling between distantly located sites. In different manifestations, this property underlies signal transduction, gene expression, and regulation-elementary reactions in networks comprising cellular information and metabolic processing systems. In this work, we present a reduced theoretical model for allostery that encompasses the many diverse mechanisms described in past work. What emerges is a basic classification of different forms of allostery into two groups : those that couple distant sites through soft normal modes within a single state, and those that possess multiple states, with effective interactions between sites emerging only upon transitioning between these states. This work serves to unify the extensive past theoretical work on the phenomenology and machinery of allostery in proteins. Copyright © 2024, The Authors. All rights reserved.

关键词： Gene expression regulation

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