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A Dual-Capture and Dual-Output 3D DNA Walker System Integrated with Ligases Enables Ultrasensitive Detection of Single-Nucleotide Polymorphisms

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Analytical Chemistry 2025年第17期97卷 9316-9325页

作者： Zhang, Yunshan Tan, Qianglong Yang, Fang Huang, Tuo Yu, Siyu Ye, Jing Zeng, Jianxian Feng, Xianzhong Zhang, Diming Key Laboratory of Soybean Molecular Design Breeding National Key Laboratory of Black Soils Conservation and Utilization Northeast Institute of Geography and Agroecology Chinese Academy of Sciences Changchun130102 China Research Center for Novel Computing Sensing and Intelligent Processing Zhejiang Laboratory Hangzhou311121 China Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences Zhejiang Hangzhou310024 China School of Chemistry and Chemical Engineering Hunan University of Science and Technology Hunan Xiangtan411201 China

DNA walkers, as structurally and functionally programmable signal amplification tools, exhibit great potential for application in the field of biosensing. Traditional DNA walkers often rely on enzymes for operation, posing compatibility challenges, while the handful of existing enzyme-free DNA walkers demonstrate limited performance. To address this, we innovatively developed an efficient enzyme-free 3D DNA walker with dual capture and dual output capabilities. Coupled with ligase chain reaction (LCR), this system facilitates highly sensitive and specific detection of single nucleotide polymorphisms (SNPs). Specifically, LCR precisely identifies single-base mutations, effectively transmitting biological information. The 3D DNA walker system is based on entropy-driven circuit cycling reaction technology. In this system, LCR products serve as the driving strands for the DNA walker, independently binding to track strands and walking legs immobilized on gold nanoparticles, forming a unique dual signal capture mechanism. Each track strand carries two signal chains, significantly enhancing signal amplification efficiency. Benefiting from this novel enzyme-free 3D DNA walker strategy, our biosensing system exhibits exceptional sensitivity to mutant targets (MT), detecting MT at concentrations as low as 30.3 aM and distinguishing heterozygous samples with a 0.01% mutation frequency. Furthermore, this system has been successfully applied to genotyping and mutation abundance assessment of genomes from fresh soybean leaves, demonstrating its vast potential for practical applications. In summary, this research pioneers a novel enzyme-free 3D DNA walker with dual capture and dual output capabilities, and develops an ultrasensitive genotyping tool. This provides strong technical support for the advancement of genetic research. © 2025 American Chemical Society.

关键词： Nucleotides

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MBF-DTI: A Fused Multi-dimensional Biochemical Feature-Based Drug Target Prediction Method Based on Heterogeneous Graph Attention Networks 10th

MBF-DTI: A Fused Multi-dimensional Biochemical Feature-Based...

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10th China Health Information Processing Conference, CHIP 2024

作者： Zhao, Haixue Yao, Kui Liu, Yunjiong Che, Chao Tang, Lin Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education Dalian University Dalian116622 China School of Software Engineering Dalian University Dalian116622 China

ISBN: (纸本)9789819637515

Drug-target interaction prediction help reduce the cost and time of drug development. However, existing research often overlooks the complexity of biological interactions. To address this issue, this paper proposes a DTI prediction model that integrates multi-dimensional biochemical features. Specifically, the model utilizes a heterogeneous graph attention network to capture the topological relationships among biological entities from diverse data, providing a deep understanding of the interactions among drugs, proteins, diseases, and side effects. A molecular attention Transformer network and a CBiNet module are used to extract the key structural features of drugs and targets. By automatically optimizing the weight distribution between drugs and targets, the model enhances the information transfer during network training, significantly improving model performance. Experimental results on real-world datasets demonstrate that the proposed model outperforms the current state-of-the-art methods in the field. Among the top 50 novel COVID-19 therapeutic drugs predicted by our model, 30 have been supported by clinical trials or scientific literature, further demonstrating the effectiveness of our proposed method in drug repurposing. Experimental data and supplementary materials are available online at: https://***/Eadog/MBF-DTI. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2025.

关键词： COVID-19

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A sequential mixing fusion network for enhanced feature representations in multimodal sentiment analysis

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Knowledge-Based Systems 2025年 320卷

作者： Wang, Chenchen Zhang, Qiang Dong, Jing Fang, Hui Schaefer, Gerald Liu, Rui Yi, Pengfei The Key Laboratory of Advanced Design and Intelligent Computing DaLian University Dalian China Department of Computer Science Loughborough University Loughborough United Kingdom

Multimodal sentiment analysis exploits multiple modalities to understand a user's sentiment state from video content. Recent work in this area integrates features derived from different modalities. However, current multimodal sentiment datasets are typically small with limited cross-modal interaction diversity, for which simple feature fusion mechanisms can lead to modality dependence and model overfitting. Consequently, how to augment diverse cross-modal samples and use non-verbal modalities to dynamically enhance text feature representations is still under-explored. In this paper, we propose a sequential mixing fusion network to tackle this research challenge. Using speech text content as a primary source, we design a sequential fusion strategy to maximise the feature expressiveness enhanced by auxiliary modalities, namely facial movements and audio features, and a random feature-level mixing algorithm to augment diverse cross-modality interactions. Experimental results on three benchmark datasets show that our proposed approach significantly outperforms current state-of-the-art methods, while demonstrating strong robustness capability when dealing with a missing modality. © 2025 Elsevier B.V.

关键词： Emotion Recognition

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Rsta: A Reversible Signal Transmission Architecture for Breaking the Limitation of Unidirectional Transmission

SSRN

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SSRN 2025年

作者： Liu, Xin Cui, Shuang Zhang, Xun Zhou, Fuxing Sheng, Kaikai Wang, Bin Zhang, Qiang School of Computer Science and Technology Dalian University of Technology Dalian116024 China Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education School of Software Engineering Dalian University Dalian116622 China

Molecular circuits are essential tools for biosensing and molecular information processing. However, the long-distance and reversible transmission of orthogonal signals remains a significant challenge in molecular circuits, preventing molecular signals from achieving reversible transmission similar to that of electrical signals in wires. To overcome the limitations of unidirectional signal transmission and facilitate the integration of antagonistic circuits. We propose a reversible signal transmission architecture (RSTA) with wire-like characteristics to achieve reversible signal transmission based on fundamental molecular devices known as reversible signal fan-out devices (RSFDs). The polarity of the input signal dictates the transmission direction, establishing the initial condition for the output signals. Cascaded RSFDs within RSTA offer two key advantages. First, the temporal response to signals. Second, the reversible transformation of opposite circuit types without structural modification. We experimentally validated the principles and functionality of RSTA using temporal logic device and integrated molecular circuits. This work advances the field of reversible molecular signal transmission, enabling the rational design of complex molecular circuits and molecular information processing systems. We envision applications of this technology in nanomachines, molecular computing, and biosensing. © 2025, The Authors. All rights reserved.

关键词： Temporal logic

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Family of Mutually Uncorrelated Codes for DNA Storage Address design

IEEE Transactions on Nanobioscience

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IEEE Transactions on Nanobioscience 2025年 PP卷 PP页

作者： Liu, Zhenlu Cao, Ben Shao, Qi Zheng, Yanfen Wang, Bin Zhou, Shihua Zheng, Pan Dalian University Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education School of Software Engineering Dalian116622 China Dalian University of Technology School of Computer Science and Technology Dalian116024 China University of Canterbury Upper Riccarton Department of Accounting and Information Systems Christchurch8140 New Zealand

Deoxyribonucleic acid (DNA) has become an ideal medium for long-term storage and retrieval due to its extremely high storage density and long-term stability. But access efficiency is an existing bottleneck in DNA storage, especially the lack of high-quality random access address sequences. Therefore, in this paper, we report a series of approaches based on k-weakly mutually uncorrelated (k-WMU) codes to design the address sequence to improve the access efficiency of DNA storage. To address the problem of DNA sequences that are poorly scalable at the base level, we propose a 0-m-ruling coding scheme combined with k-WMU codes that can make address sequences avoid generating secondary structure with stem lengths ranging from 3 to 9. Based on the decoupled structure, We further extend the k-WMU codes with error correction function while satisfying combinatorial biological constraints. In order to investigate the performance of the designed address sequences for real-world applications, we perform simulation experiments based on thermodynamic properties and error correction capability as well as compared the minimum free energy (MFE), melting temperature (TM), and average decoding success rate (ADSR) with previous work. The results show that designed address sequences have a high MFE value and ADSR and a substantial reduction in TM-variance while satisfying the combinatorial biological constraints. As the quality of address sequences improves, this will help to achieve accurate random access as well as enhance the robustness of the DNA storage system. © 2002-2011 IEEE.

关键词： DNA sequences

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A novel ECT image reconstruction method based on the deblurring diffusion model

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Flow Measurement and Instrumentation 2025年 104卷

作者： Liu, Yan-Dong Wu, Xin-Jie Liu, Shi-Xing Wang, Yi-Fan Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education Dalian University Liaoning Dalian116622 China School of Software Engineering Dalian University Liaoning Dalian116622 China College of Physics Liaoning University Liaoning Shenyang110036 China School of Information Science and Engineering Shenyang University of Technology Liaoning Shenyang110870 China

To address the challenge of low reconstruction accuracy in Electrical Capacitance Tomography (ECT) images, we propose an imaging method based on a deblurring diffusion model, transforming the image reconstruction into image generation. In cases where the noise type affecting the ECT image reconstruction cannot be determined, inspired by the cold diffusion model, we use an alpha kernel instead of Gaussian noise to perform the image blurring process. During the deblurring process, we utilize the U-Net as the backbone network and incorporated the Linear Attention module to improve imaging accuracy. Additionally, recognizing the similarity between image error metrics and the Dice function, we integrate the Dice function into the loss. Simulation experiments demonstrate that the image errors and correlation coefficients using the proposed method outperform those achieved with the LBP, Tikhonov, Landweber, and classic CNNs. Finally, we deploy the proposed algorithm to the actual ECT system. © 2025 Elsevier Ltd

关键词： Image denoising

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Dynamic Simulation Analysis of the Flexible Swap Device

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Journal of Donghua University(English Edition) 2015年第2期32卷 300-304页

作者：崔艳波赵腊生张强张建新 Key Laboratory of Advanced Design and Intelligent Computing Dalian University

With the development of space science and technology,the on-orbit servicing technologies of spacecraft get more and more *** to the design criterion of existing spacecraft in orbit module replacement technology,the flexible swap device is designed and the dynamics simulation of institutions by the automatic dynamic analysis of mechanical systems(ADAMS)simulation software is *** the analysis process,this paper studies the effect of collision force of flexible mechanism and provides a basis for the optimization of flexible plug agencies.

关键词： collision swap spacecraft institutions trajectory freedom kinematic criterion constraints replacement

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Ladle Furnace Temperature Prediction Model Based on Large-scale Data With Random Forest

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IEEE/CAA Journal of Automatica Sinica 2017年第4期4卷 770-774页

作者： Xiaojun Wang Key Laboratory of Advanced Design and Intelligent Computing Ministry of EducationDalian UniversityDalian 116622 China

In ladle furnace, the prediction of the liquid steel temperature is always a hot topic for the researchers. The most of the existing temperature prediction models use small sample set. Today, the precision of them can not satisfy practical production. Fortunately, the large sample set is accumulated from the practical production process. However, a large sample set makes it difficult to build a liquid steel temperature model. To deal with the issue, the random forest method is preferred in this paper, which is a powerful regression method with low complexity and can be designed very quickly. It is with the parallel ensemble structure,uses sample subsets,and employs a simple learning algorithm of sub-models. Then, the random forest method is applied to establish a temperature model by using the data sampled from the production process. The experiments show that the random forest temperature model is more precise than other temperature models.

关键词： Ladle furnace random forest regression tree temperature prediction

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Motion Planning for Minimizing Base Disturbance of Space Manipulators

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Journal of Donghua University(English Edition) 2015年第2期32卷 252-256页

作者：纪路周东生张强 Key Laboratory of Advanced Design and Intelligent Computing(Dalian University) Ministry of Education

A simulated annealing particle swarm optimization(PSO)algorithm is utilized in this paper to plan the motion of space manipulators with minimized base disturbance,not only its attitude but also its *** space manipulators must meet the Law of Momentum Conservation,any motion of manipulators will disturb the spacecraft which is free-float in the space *** paper tries to limit this effect to the ***,this paper establishes the mathematical model for space manipulators by generalized Jacobian matrix(GJM) and analyzes its inverse kinematics by Theory of ***,a polynomial function of seventh degree is used to parameterize the joint motion and quaternion representation is also used to represent attitude of ***,this paper designs a proper objective function and depicts this algorithm detailedly and ***,the results of numerical simulation are verified by the proposed algorithm.

关键词： utilized kinematics verified disturbance inverse annealing attitude polynomial effector spacecraft

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On the simulation of expressional animation based on facial MoCap

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Science China(Information Sciences) 2013年第10期56卷 265-276页

作者： FANG XiaoYong WEI XiaoPeng ZHANG Qiang ZHOU ChangJun Key Laboratory of Advanced Design and Intelligent Computing (Dalian University) Ministry of Education School of Management Dalian University of Technology

MoCap(motion capture)-based animation is a hot issue in computer animation research *** on the optical MoCap system,this paper proposes a novel cross-mapping based facial expression simulating *** overcome the problem of the false upper and lower jaw correlation derived from the facial global RBFbased cross-mapping method,we construct a functional partition based RBF cross-mapping *** model animating,enhanced markers are added and animated by our proposed skin motion *** addition,based on the enhanced markers,an improved RBF-based animating approach is raised to derive realistic facial *** more,a pre-computing algorithm is presented to reduce computational cost for real-time *** experiments proved that the method can not only map the MoCap data of one subject to diferent personalized faces but generate realistic facial animation.

关键词： facial animation cross-mapping functional partition motion mechanism RBF

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