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A sensitive sample preparation pipeline for adventitious virus detection using Oxford Nanopore sequencing

Molecular Therapy Methods and Clinical Development 2025年第2期33卷

作者： Tsinda, Emmanuel K. Swofford, Charles A. Strutt, James P.B. Sangerman, José Roushangar, Raeuf Li, Alexander Gomez, Lara M. Bousquet, Aidan N. Neufeld, Caleb Wolfrum, Jacqueline M. Han, Jongyoon Williams, Rohan B.H. Sinskey, Anthony J. Barone, Paul W. Springs, Stacy L. Center for Biomedical Innovation Massachusetts Institute of Technology Cambridge 02139 MA United States Critical Analytics for Manufacturing Personalized-Medicine Singapore-MIT Alliance for Research and Technology Singapore 138602 Singapore Research Laboratory of Electronics Massachusetts Institute of Technology Cambridge 02139 MA United States Department of Biological Engineering Massachusetts Institute of Technology Cambridge 02139 MA United States Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge 02139 MA United States Singapore Centre for Environmental Life Sciences Engineering National University of Singapore Singapore 119077 Singapore Department of Biology Massachusetts Institute of Technology Cambridge 02139 MA United States

Recent regulatory guidance now encourages the use of sequencing as an alternative adventitious agent testing assay to lengthy compendial in vivo assays used for cell line qualification. Most short-read sequencing assays, however, still require over a week to obtain a final test result since the sequencing must be completed before bioinformatic analysis can begin, which is still too long for some cell and gene therapy products that must be released as soon as possible to reach critically ill patients. Oxford Nanopore sequencing can address these issues, as it provides real-time basecalling and sequence alignment, which can reduce the overall assay time. Still, as with any sequencing platform, the abundance of background nucleic acid from the human or mammalian host can mask the signal from a low-level viral contaminant. To address this, we have developed a sensitive sample preparation workflow using concentration, nuclease treatment, and agnostic PCR methods to eliminate background signals and amplify viral contaminant reads, leading to a 3-log improvement in the limit of detection that is comparable to or better than short-read sequencing approaches. This approach will lead to more rapid and improved detection of viral contaminants in cell and gene therapy manufacturing. © 2025

关键词： adventitious agent detection biomanufacturing cell therapy long read sequencing Oxford Nanopore sequencing SISPA viral safety

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Fractional four-step finite element method for analysis of thermally coupled fluid-solid interaction problems

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Applied Mathematics and Mechanics(English Edition) 2012年第1期33卷 99-116页

作者： A. MALATIP N. WANSOPHARK P. DECHAUMPHAI Computer-Aided Research Unit National Metal and Materials Technology Center Department of Mechanical Engineering Faculty of Engineering Chulalongkorn University

An integrated fluid-thermal-structural analysis approach is presented. In this approach, the heat conduction in a solid is coupled with the heat convection in the viscous flow of the fluid resulting in the thermal stress in the solid. The fractional four-step finite element method and the streamline upwind Petrov-Galerkin （SUPG） method are used to analyze the viscous thermal flow in the fluid. Analyses of the heat transfer and the thermal stress in the solid axe performed by the Galerkin method. The second-order semi- implicit Crank-Nicolson scheme is used for the time integration. The resulting nonlinear equations are lineaxized to improve the computational efficiency. The integrated analysis method uses a three-node triangular element with equal-order interpolation functions for the fluid velocity components, the pressure, the temperature, and the solid displacements to simplify the overall finite element formulation. The main advantage of the present method is to consistently couple the heat transfer along the fluid-solid interface. Results of several tested problems show effectiveness of the present finite element method, which provides insight into the integrated fluid-thermal-structural interaction phenomena.

关键词： fluid-solid interaction finite element method fractional four-step method

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Spectral width of maximum deposition eigenchannels in diffusive media

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Physical Review B 2025年第14期111卷 144202-144202页

作者： Rohin E. McIntosh Arthur Goetschy Nicholas Bender Alexey Yamilov Chia Wei Hsu Hasan Yılmaz Hui Cao Department of Physics Yale University New Haven Connecticut 06511 USA Institut Langevin ESPCI Paris PSL University CNRS F-75005 Paris France School of Applied and Engineering Physics Cornell University Ithaca New York 14850 USA Physics Department Missouri University of Science & Technology Rolla Missouri 65409 USA Ming Hsieh Department of Electrical and Computer Engineering University of Southern California Los Angeles California 90089 USA Institute of Materials Science and Nanotechnology National Nanotechnology Research Center (UNAM) Bilkent University 06800 Ankara Turkey

The maximum deposition eigenchannel provides the largest possible power delivery to a target region inside a diffusive medium by optimizing the incident wavefront of a monochromatic beam. It originates from constructive interference of scattered waves, which is frequency sensitive. We investigate the spectral width of the maximum deposition eigenchannels over a range of target depths using numerical simulations of a 2D diffusive system. Compared to tight focusing into the system, power deposition to an extended region is more sensitive to frequency detuning. The spectral width of enhanced delivery to a large target displays a rather weak, nonmonotonic variation with target depth, in contrast to a sharp drop of focusing bandwidth with depth. While the maximum enhancement of power deposited within a diffusive system can exceed that of power transmitted through it, this comes at the cost of a narrower spectral width. We investigate the narrower deposition width in terms of the constructive interference of transmission eigenchannels within the target. We further observe that the spatial field distribution inside the target region decorrelates more slowly with spectral detuning than the power decay of the maximum deposition eigenchannel. Additionally, absorption increases the spectral width of deposition eigenchannels, but the depth dependence remains qualitatively identical to that without absorption. These findings hold for any diffusive waves, including electromagnetic waves, acoustic waves, pressure waves, mesoscopic electrons, and cold atoms.

关键词： Wavefronts

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Synergistic integration of dual Z-scheme Gd₂Sn₂O₇/Ag₃PO₄/SnS₂ heterojunction for accelerated visible-light photodegradation of sulfasalazine: Insights into DFT, toxicity, and antibacterial study

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Journal of Water Process engineering 2025年 75卷

作者： Jagtap, Akash Ashokrao Prasanna, Sanjay Ballur Ramanathan, Susaritha Shadakshari, Sandeep Ningappa, Kumara Swamy Lin, Yu-Chien Liu, Xinke Tung, Ching-Wei Chung, Ren-Jei Department of Chemical Engineering and Biotechnology National Taipei University of Technology (Taipei Tech) Taipei 10608 Taiwan Department of Chemistry SJCE JSS Science and Technology University Karnataka 570006 India School of Materials Science and Engineering Nanyang Technological University 50 Nanyang Avenue Singapore 639798 Singapore BIOBOND LTD 1 Abacus House Newlands Road Corsham Wiltshire SN13 0BH United Kingdom College of Materials Science and Engineering Chinese Engineering and Research Institute of Microelectronics Shenzhen University Shenzhen 518060 China Department of Electrical and Computer Engineering National University of Singapore Singapore 117583 Singapore Department of Materials Engineering Ming Chi University of Technology New Taipei City 24301 Taiwan High-value Biomaterials Research and Commercialization Center National Taipei University of Technology (Taipei Tech) Taipei 10608 Taiwan

The persistence of pharmaceutical contaminants sulfasalazine (SSZ) in aquatic environments poses significant ecological risks, necessitating efficient removal strategies. This study integrated novel double-Z-scheme photocatalysts (Gd₂Sn₂O₇/Ag₃PO₄/SnS₂) using a hydrothermal method and subsequently ultrasonicated. The prepared photocatalysts were systematically assessed for photocatalytic efficiency, degradation of sulfasalazine (SSZ), and actuation of persulfate (PS) under visible light. The impact of the initial antibiotic concentration, reaction pH, photocatalyst dosage, and PS concentration on the efficiency of photocatalysis was thoroughly examined. The synergistic action of reactive oxygen species (•OH, ¹O₂, SO₄•⁻) was confirmed through radical quenching and EPR analyses. GC–MS analysis and density functional theory (DFT) suggested potential degradation mechanisms and pathways. Additionally, based on projections from the Quantitative Structure-Activity Relationship (QSAR), the toxicity of the intermediates was evaluated. The photocatalyst achieved 86.47 % SSZ degradation within 70 min under visible light and persulfate (PS) activation, reducing byproduct toxicity as confirmed by QSAR analysis. The nanocomposite was tested under visible light to determine its bactericidal effectiveness toward the pathogenic bacteria Escherichia coli and Staphylococcus aureus. This study highlights a scalable solution for antibiotic removal in wastewater, advancing environmental pollution mitigation technologies. © 2025 Elsevier Ltd

关键词： DFT Gd2Sn2O7/Ag3PO4/SnS2 heterojunction Photocatalytic degradation Sulfasalazine Thermodynamics

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Observation of charge to spin conversion in p-orbital InBi alloy

arXiv

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arXiv 2025年

作者： Li, Gen Zhang, Ying Xu, Xiaoguang Shen, Lei Feng, Zheng Meng, Kangkang Li, Ang Cheng, Lu He, Kang Tan, Wei Wu, Yong Wu, Yihong Jiang, Yong Key Laboratory of Advanced Materials and Devices for Post-Moore Chips Ministry of Education School of Materials Science and Engineering University of Science and Technology Beijing Beijing100083 China Department of Electrical and Computer Engineering National University of Singapore 117576 Singapore Research Institute Chongqing Liang Jiang New Area Chongqing401123 China Department of Mechanical Engineering National University of Singapore 117575 Singapore Microsystem & Terahertz Research Center CAEP Chengdu610200 China Faculty of Materials and Manufacturing Beijing Key Lab of Microstructure and Properties of Advanced Materials Beijing University of Technology Beijing100124 China Institute of Quantum Materials and Devices School of Electronic and Information Engineering State Key Laboratory of Separation Membranes and Membrane Processes Tiangong University Tianjin300387 China

High density data storage and spin-logic devices require highly efficient all-electric control of spin moment. So far, charge-to-spin conversion through the spin Hall effect limits to d-orbital materials associated with strong spin-orbit coupling, especially heavy metals. However, d-orbital heavy metals with strong spin-orbit coupling results in a short spin diffusion length, which restricts the spin transport and accumulation in spintronic devices. Therefore, the conflict between charge-to-spin conversion efficiency and spin transport ability is irreconcilable in d-orbital materials. Here, we report a large charge to spin conversion experimentally observed in the p-orbital In2Bi alloy, exhibiting the coexistence of a large spin Hall angle comparable to heave metal Pt and a long spin diffusion length (4 times that of Pt). First-principles calculations reveal that topological symmetry-protected gap opening near the Fermi level results in large Berry curvature-related spin Hall conductivity. Due to the delocalized nature of p-orbitals and semimetal properties of In2Bi, its spin current can overcome the physical barriers between spin Hall angle and spin diffusion length in d-orbital metals, thereby advancing the development of high-performance spintronic devices. Copyright © 2025, The Authors. All rights reserved.

关键词： Heavy metals

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SAND: semi-automated adaptive network defense via programmable rule generation and deployment

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Science China(Information Sciences) 2022年第7期65卷 121-138页

作者： Haoyu CHEN Deqing ZOU Hai JIN Shouhuai XU Bin YUAN National Engineering Research Center for Big Data Technology and System Services Computing Technology and System LabCluster and Grid Computing Lab School of Computer Science and TechnologyHuazhong University of Science and Technology National Engineering Research Center for Big Data Technology and System Services Computing Technology and System LabHubei Engineering Research Center on Big Data Security School of Cyber Science and EngineeringHuazhong University of Science and Technology Department of Computer Science University of Colorado at Colorado Springs

Cyber security is dynamic as defenders often need to adapt their defense postures. The state-ofthe-art is that the adaptation of network defense is done manually(i.e., tedious and error-prone). The ideal solution is to automate adaptive network defense, which is however a difficult problem. As a first step towards automation, we propose investigating how to attain semi-automated adaptive network defense(SAND). We propose an approach extending the architecture of software-defined networking, which is centered on providing defenders with the capability to program the generation and deployment of dynamic defense rules enforced by network defense tools. We present the design and implementation of SAND, as well as the evaluation of the prototype implementation. Experimental results show that SAND can achieve agile and effective dynamic adaptations of defense rules(less than 15 ms on average for each operation), while only incurring a small performance overhead.

关键词： network defense adaptive defense automated defense programmable defense security services software-defined networking security management

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Diff9D: Diffusion-Based Domain-Generalized Category-Level 9-DoF Object Pose Estimation

arXiv

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arXiv 2025年

作者： Liu, Jian Sun, Wei Yang, Hui Deng, Pengchao Liu, Chongpei Sebe, Nicu Rahmani, Hossein Mian, Ajmal National Engineering Research Center for Robot Visual Perception and Control Technology College of Electrical and Information Engineering School of Robotics State Key Laboratory of Advanced Design and Manufacturing for Vehicle Body Hunan University Changsha410082 China Institute of Artificial Intelligence and Robotics Xi’an Jiaotong University Xi’an710049 China Department of Information Engineering and Computer Science University of Trento Trento38123 Italy School of Computing and Communications Lancaster University LA1 4YW United Kingdom Department of Computer Science The University of Western Australia WA6009 Australia

Nine-degrees-of-freedom (9-DoF) object pose and size estimation is crucial for enabling augmented reality and robotic manipulation. Category-level methods have received extensive research attention due to their potential for generalization to intra-class unknown objects. However, these methods require manual collection and labeling of large-scale real-world training data. To address this problem, we introduce a diffusion-based paradigm for domain-generalized category-level 9-DoF object pose estimation. Our motivation is to leverage the latent generalization ability of the diffusion model to address the domain generalization challenge in object pose estimation. This entails training the model exclusively on rendered synthetic data to achieve generalization to real-world scenes. We propose an effective diffusion model to redefine 9-DoF object pose estimation from a generative perspective. Our model does not require any 3D shape priors during training or inference. By employing the Denoising Diffusion Implicit Model, we demonstrate that the reverse diffusion process can be executed in as few as 3 steps, achieving near real-time performance. Finally, we design a robotic grasping system comprising both hardware and software components. Through comprehensive experiments on two benchmark datasets and the real-world robotic system, we show that our method achieves state-of-the-art domain generalization performance. Our code will be made public at https://***/CNJianLiu/Diff9D. Copyright © 2025, The Authors. All rights reserved.

关键词： Augmented reality

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Visualization of flatness pattern recognition based on T-S cloud inference network

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Journal of Central South University 2015年第2期22卷 560-566页

作者：张秀玲赵亮臧佳音樊红敏 Key Laboratory of Industrial Computer Control Engineering of Hebei Province (Yanshan University) National Engineering Research Center for Equipment and Technology of Cold Strip Rolling

Flatness pattern recognition is the key of the flatness control. The accuracy of the present flatness pattern recognition is limited and the shape defects cannot be reflected intuitively. In order to improve it, a novel method via T-S cloud inference network optimized by genetic algorithm(GA) is proposed. T-S cloud inference network is constructed with T-S fuzzy neural network and the cloud model. So, the rapid of fuzzy logic and the uncertainty of cloud model for processing data are both taken into account. What's more, GA possesses good parallel design structure and global optimization characteristics. Compared with the simulation recognition results of traditional BP Algorithm, GA is more accurate and effective. Moreover, virtual reality technology is introduced into the field of shape control by Lab VIEW, MATLAB mixed programming. And virtual flatness pattern recognition interface is ***, the data of engineering analysis and the actual model are combined with each other, and the shape defects could be seen more lively and intuitively.

关键词： pattern recognition T-S cloud inference network cloud model mixed programming virtual reality visual recognition

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Extended Dissipativity Analysis and Synthesis for Discrete-Time Lur'e Delayed Systems: Matrix-Separation-Based Lyapunov Functional Method

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IET Control Theory and Applications 2025年第1期19卷

作者： Xie, Ke-You Lee, Sangmoon Zhang, Chuan-Ke Jin, Li Liu, Yajuan He, Yong School of Automation China University of Geosciences Wuhan China Hubei Key Laboratory of Advanced Control and Intelligent Automation for Complex Systems Wuhan China Engineering Research Center of Intelligent Technology for Geo-Exploration Ministry of Education Wuhan China School of Electronic and Electrical Engineering Kyungpook National University Daegu Korea Republic of School of Control and Computer Engineering North China Electric Power University Beijing China

This paper develops a matrix-separation-based Lyapunov functional method to study the extended dissipativity analysis and synthesis issue of discrete-time Lur'e-type delayed systems. The advanced idea of matrix-separation is reflected in Lyapunov functional candidates and estimates summation terms as precisely as feasible. First, we introduce a novel summation inequality based on the matrix-separation method to provide a bound for the augmented summation that involves common state variables. An improved delay-product-type Lyapunov functional is devised by extending non-positive definite summations as separate subblocks of the state-augmented summation. Then, by using the matrix injection method to handle the cubic delay term in the functional forward difference, a delay-variation-dependent stability criterion and an extended dissipativity criterion are developed under the matrix-separation-based method. Subsequently, sufficient conditions for the control design of Lur'e-type systems are derived. Finally, the effectiveness and superiority of the proposed method are verified through its application to Chua's circuits, neural networks, and a stochastic numerical example. © 2025 The Author(s). IET Control Theory & Applications published by John Wiley & Sons Ltd on behalf of The Institution of engineering and technology.

关键词： Stability criteria

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Radiologist-in-the-Loop Self-Training for Generalizable CT Metal Artifact Reduction

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IEEE Transactions on Medical Imaging 2025年 PP卷 PP页

作者： Ma, Chenglong Li, Zilong Li, Yuanlin Han, Jing Zhang, Junping Zhang, Yi Liu, Jiannan Shan, Hongming Fudan University Institute of Science and Technology for Brain-inspired Intelligence Moe Frontiers Center for Brain Science Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Shanghai200433 China Fudan University Shanghai Key Laboratory of Intelligent Information Processing School of Computer Science Shanghai200433 China Shanghai Ninth People's Hospital Department of Oral Maxillofacial Head and Neck Oncology China Shanghai Jiao Tong University School of Medicine College of Stomatology China Shanghai Key Laboratory of Stomatology Shanghai Research Institute of Stomatology National Center for Stomatology National Clinical Research Center for Oral Diseases Shanghai200011 China Sichuan University School of Cyber Science and Engineering Chengdu Sichuan610065 China

Metal artifacts in computed tomography (CT) images can significantly degrade image quality and impede accurate diagnosis. Supervised metal artifact reduction (MAR) methods, trained using simulated datasets, often struggle to perform well on real clinical CT images due to a substantial domain gap. Although state-of-the-art semi-supervised methods use pseudo ground-truths generated by a prior network to mitigate this issue, their reliance on a fixed prior limits both the quality and quantity of these pseudo ground-truths, introducing confirmation bias and reducing clinical applicability. To address these limitations, we propose a novel radiologist-in-the-loop self-training framework for MAR, termed RISE-MAR, which can integrate radiologists' feedback into the semi-supervised learning process, progressively improving the quality and quantity of pseudo ground-truths for enhanced generalization on real clinical CT images. For quality assurance, we introduce a clinical quality assessor model that emulates radiologist evaluations, effectively selecting high-quality pseudo ground-truths for semi-supervised training. For quantity assurance, our self-training framework iteratively generates additional high-quality pseudo groundtruths, expanding the clinical dataset and further improving model generalization. Extensive experimental results on multiple clinical datasets demonstrate the superior generalization performance of our RISE-MAR over state-of-the-art methods, advancing the development of MAR models for practical application. © 2025 IEEE.

关键词： computerized tomography

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