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An Exploratory Computational Approach for Elucidating a Nonstructural Protein Interaction in Dengue Virus 2

Procedia computer science 2024年 245卷 470-479页

作者： Alam Ahmad Hidayat Rudi Nirwantono Bens Pardamean Mathematics Department School of Computer Science Bina Nusantara University Indonesia 11480 Biotechnology Department Faculty of Engineering Bina Nusantara University Indonesia 11480 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta Indonesia 11480

As the dengue infection still impacts hundreds of millions of people globally, unprecedented efforts in dengue drug development have been more progressive in recent decades. Computational methods provide a fast, sustainable, and efficient screening of active compounds and newly created drug molecules, including those specifically targeting nonstructural proteins (NS) of dengue viruses. In this work, protein modeling for the NS proteins of DENV-2/16681 strain was performed using a template-based homology modeling for the NS3 protein and an Artificial Intelligence (AI)-based prediction via AlphaFold for the NS4B protein. Moreover, the protein-protein interaction between the two structures was predicted using the HADDOCK server, which employs information about active and passive residues of the interaction interface to guide the docking process. After the modeling and its respective refinement process, the predicted structures of NS3 and NS4B improved their steric clashing scoring from MolProbity assessment. The refined models were then docked, and the resulting docking pose was analyzed to extract the interacting residues based on the polar contacts within the interface of the two proteins. Our result presents a preliminary study to create a dataset related to in silico molecular interactions of the NS3-NS4B interaction of different DENV types. It is helpful for building a computational pipeline for elucidating protein-ligand problems in dengue drug screenings.

关键词： bioinformatics computational biology dengue protein docking structural biology

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Joint Source Decomposition of Concurrent EEG-FMRI Data in Epilepsy and Control Groups

Joint Source Decomposition of Concurrent EEG-FMRI Data in Ep...

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IEEE International Symposium on Biomedical Imaging

作者： J. Mason Harding Haatef Pourmotabbed Yamin Li Kimberly Rogge-Obando Kate Wang Sarah E. Goodale Shiyu Wang Camden Bibro Bergen Allee Caroline Martin Victoria L. Morgan Dario J. Englot Catie Chang Department of Electrical and Computer Engineering Vanderbilt University Department of Biomedical Engineering Vanderbilt University Department of Computer Science Vanderbilt University Neuroscience Graduate Program Vanderbilt University Vanderbilt Memory and Alzheimer's Center Vanderbilt University Medical Center Department of Neurological Surgery Vanderbilt University Medical Center Department of Radiology Vanderbilt University Medical Center

ISBN: (数字)9798331520526

ISBN: (纸本)9798331520533

EEG and fMRI are complementary, noninvasive technologies for investigating human brain function. These modalities have been used to uncover large-scale functional networks and their disruptions in clinical populations. Given the high temporal resolution of EEG and high spatial resolution of fMRI, integrating these modalities can provide a more holistic understanding of brain activity. This work explores a multimodal source decomposition technique for extracting shared modes of temporal variation between fMRI BOLD signals and EEG spectral power fluctuations in the resting state. The resulting components are then compared between patients with focal epilepsy and controls, revealing multimodal network differences between groups.

关键词： Neuroimaging Brain Fluctuations Epilepsy Functional magnetic resonance imaging Electroencephalography Pattern recognition Hemodynamics Spatial resolution Signal resolution

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The Deep Learning Approach For American Sign Language Detection

The Deep Learning Approach For American Sign Language Detect...

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Creative Communication and Innovative Technology (ICCIT), IEEE

作者： Gusti Pangestu Yaya Heryadi Lukas Wayan Suparta Yulyani Arifin Computer Science Department BINUS Graduate Program Computer Science. Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program Computer Science Bina Nusantara University Jakarta Indonesia Cognitive Engineering Research (CERG) Faculty of Engineering Universitas Katolik Indonesia Atma Jaya Jakarta Indonesia Department of Electrical Engineering Faculty of Industrial Technology Institut Teknologi Nasional Yogyakarta Yogyakarta Indonesia

Sign language has importance rule to deal with communication process especially with impairments hearing people. Sign language detection also attract lot of researchers to join the challenge of research to detect and recognize the sign language in the field of computer science. Hence, there is still no any standard approach and method to recognize the meaning in every pose of sign language. This research proposed a mechanism to detect Alphabet American Sign Language by utilizing Convolutional Neural Network (CNN) process. The CNN approach was chosen based on the ability and capability to recognize image. In this research, MNIST dataset is used for traning and testing process. The proposed CNN architecture produced 97% of accuracy that outperform the previous research using the same dataset which made this architecture promising.

关键词： Deep learning computer science Image recognition Gesture recognition computer architecture Auditory system Assistive technologies

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Arabic text sentiment analysis and emotion classification using transformers

Arabic text sentiment analysis and emotion classification us...

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Electronics, Communications, and Computations (JAC-ECC), International Japan-Africa Conference on

作者： Nada Mossad Youssef Mohamed A Fares Ahmed B. Zaky Egypt-Japan University of Science and Technology (E-JUST) Alexandria Egypt The Department of Electrical Engineering The Computer Systems Engineering Program Faculty of Engineering at Shoubra Benha University

Sentiment analysis and emotion classification are two crucial components of natural language processing (NLP), which have been widely explored in recent years due to their broad applications. Sentiment analysis aims to identify the polarity of written texts, ranging from positive to negative. Meanwhile, emotion classification is focused on recognizing and categorizing the emotional states expressed in the text. To achieve a deeper understanding of sentiments and emotions, it's essential to utilize models like BERT transformers that can effectively interpret the context. The process begins with data preprocessing, including tokenization and noise removal, followed by fine-tuning techniques to adapt the BERT model to the proposed tasks. We employed the BERT model on four datasets obtained from various sources, including Twitter, news websites, and restaurant reviews, where each dataset represents a distinct Arabic dialect. Our proposed model outperforms commonly used techniques like LSTM and CNN, yielding superior results. Despite the progress made, there are still challenges to overcome, such as dealing with Arabic diacritics, the new Arabic Arabizi, which uses Latin characters, and handling Arabic idioms. Further research is required to address these challenges adequately.

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Signature Analysis of SRAM-PUF for IoT Decentralized Identifier in Large-Scale Networks

Signature Analysis of SRAM-PUF for IoT Decentralized Identif...

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International Conference on Ubiquitous and Future Networks, ICUFN

作者： Seungnam Han Jeein Kim Haewon Lee Euiseok Hwang School of Electrical Engineering and Computer Science Gwangju South Korea Artificial Intelligence Graduate School Gwangju Institute of Science and Technology (GIST) Gwangju South Korea

In this paper, we extract hardware signatures from numerous static random access memory (SRAM) and analyze the feasibility as a signature for Internet of Things (IoT) decentralized identifier (DID). Due to uncontrollable variations in the manufacturing process, SRAM contains inherent randomness that can serve as a physical unclonable function (PUF) to identify the device uniquely. In particular, with the massive deployment of IoT devices, research on SRAM-PUF based distributed device identification is being actively investigated. However, conventional SRAM-PUF research has mainly focused on application to a small-scale IoT environment, so a limited number of SRAM have been analyzed. To generalize the signature utilization, we investigate uniqueness of the PUF from a number of SRAMs. We employed commercial SRAMs and off-the-shelf development boards to extract SRAM-PUFs. Evaluation results demonstrate that SRAM-PUFs are suitable for DIDs even in large-scale IoT networks, considering both chip-by-chip and block-by-block uniqueness.

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Algorithms of Sampling-Frequency-Independent Layers for Non-integer Strides

Algorithms of Sampling-Frequency-Independent Layers for Non-...

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European Signal Processing Conference (EUSIPCO)

作者： Kanami Imamura Tomohiko Nakamura Norihiro Takamune Kohei Yatabe Hiroshi Saruwatari Graduate School of Information Science and Technology The University of Tokyo Tokyo Japan Department of Electrical Engineering and Computer Science Tokyo University of Agriculture and Technology Tokyo Japan

In this paper, we propose algorithms for handling non-integer strides in sampling-frequency-independent (SFI) convolutional and transposed convolutional layers. The SFI layers have been developed for handling various sampling frequencies (SFs) by a single neural network. They are replaceable with their non-SFI counterparts and can be introduced into various network architectures. However, they could not handle some specific configurations when combined with non-SFI layers. For example, an SFI extension of Conv-TasNet, a standard audio source separation model, cannot handle some pairs of trained and target SFs because the strides of the SFI layers become non-integers. This problem cannot be solved by simple rounding or signal resampling, resulting in the significant performance degradation. To overcome this problem, we propose algorithms for handling non-integer strides by using windowed sinc inter-polation. The proposed algorithms realize the continuous-time representations of features using the interpolation and enable us to sample instants with the desired stride. Experimental results on music source separation showed that the proposed algorithms outperformed the rounding- and signal-resampling-based methods at SFs lower than the trained SF.

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Statistical 3D Device Simulation of Full Fluctuations of Gate-All-Around Silicon Nanosheet MOSFETs at Sub-3-nm Technology Nodes

Statistical 3D Device Simulation of Full Fluctuations of Gat...

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2022 International Symposium on VLSI Technology, Systems and Applications, VLSI-TSA 2022

作者： Kola, Sekhar Reddy Li, Yiming Chen, Chieh-Yang Chuang, Min-Hui National Yang-Ming Chiao Tung University Electrical Engineering and Computer Science International Graduate Program Hsinchu300 Taiwan National Yang-Ming Chiao Tung University Institute of Communications Engineering Hsinchu300 Taiwan National Yang-Ming Chiao Tung University Department of Electrical Engineering and Computer Engineering Hsinchu300 Taiwan National Yang-Ming Chiao Tung University Institute of Biomedical Engineering Hsinchu300 Taiwan National Yang-Ming Chiao Tung University Parallel and Scientific Computing Laboratory Hsinchu300 Taiwan

ISBN: (纸本)9781665409230

We for the first time study characteristic fluctuation of gate-all-around silicon nanosheet MOSFETs induced by random dopants fluctuation (RDF), interface trap fluctuation (ITF), and work function fluctuation (WKF), and their combinations. The explored devices affected by the WKF and its combination result in sizeable variability. Because of enigmatical interactions among the aforementioned random factors, overestimated variabilities occur if we only consider one random source each time, compared with the statistical 3D device simulation for full RDF, ITF and WKF at the same time. Notably, 10.78% and 103% overestimations are found for the threshold voltage and off-state current fluctuations. © 2022 IEEE.

关键词： Nanosheets

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ReRobo Walker: Robotic Walker with Fall Detection and Active Safety

ReRobo Walker: Robotic Walker with Fall Detection and Active...

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IEEE Conference on Industrial Electronics and Applications (ICIEA)

作者： Damin Ding Yagang Wang Houji Zhang Qiaoling Meng Hongliu Yu Yanzhao Lin Qiu Chen Rehabilitation Engineering and Technology Institute School of Optical-Electrical and Computer Engineering University of Shanghai for Science and Technology Shanghai China Rehabilitation Engineering and Technology Institute School of Optical-Electrical School of Optical-Electrical and Computer Engineering University of Shanghai for Science and Technology Shanghai China Guangzhou Foreign Language School Guangzhou China Rehabilitation Engineering and Technology Institute University of Shanghai for Science and Technology Shanghai China School of Optical-Electrical and Computer Engineering University of Shanghai for Science and Technology Shanghai China Major of Electrical Engineering and Electronics Graduate School of Engineering Kogakuin University Tokyo Japan

In recent years, Chinese society has become increasingly ageing while the fertility rate continues to decline. This situation has led to a growing public demand for rehabilitation devices such as walking aids. A novel intelligent robotic walker named ReRobo Walker is proposed which can assist groups of elderly people with dysfunctional legs with rehabilitation training and indoor and outdoor walking. We design robust mechanical structures for robotic walker, install special 3D force sensor, 2D LIDAR and other sensors, and design new algorithms to enable intelligent functionality while guaranteeing the safety of robotic walker.(1) Real-time monitoring of the user’s physical status, such as falls, through laser range sensors and 3D force sensor; (2) Modelling of the scene through 2D LIDAR for path planning, obstacle avoidance and navigation functions; (3) Precise control through LADRC-based algorithm for uphill assistance, downhill control and prevention of sharp shifts of the robotic walker. Experiment results demonstrate the solid mechanical structure, stable reliability and the effectiveness of intelligent control algorithms of the intelligent robotic walker.

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Comparison of Coherent and Incoherent Donut Beams for Deep Tissue STED Microscopy

Comparison of Coherent and Incoherent Donut Beams for Deep T...

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2023 Conference on Lasers and Electro-Optics, CLEO 2023

作者： Shanavas, Thariq McLeod, Robert R. Siemens, Mark E. Gopinath, Juliet T. Department of Physics University of Colorado BoulderCO80309 United States Department of Electrical Computer and Energy Engineering University of Colorado BoulderCO80309 United States Department of Physics University of Denver DenverCO80204 United States Materials Science Engineering Program University of Colorado BoulderCO80309 United States

We numerically compare the null quality for STED microscopy generated by Laguerre-Gaussian beams with orbital angular momentum and donut beams generated by incoherent addition of orthogonal Hermite Gaussian beams when... 详细信息

ISBN: (纸本)9781957171258

关键词： Tissue

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Algorithms of Sampling-Frequency-Independent Layers for Non-integer Strides

arXiv

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arXiv 2023年

作者： Imamura, Kanami Nakamura, Tomohiko Takamune, Norihiro Yatabe, Kohei Saruwatari, Hiroshi Graduate School of Information Science and Technology The University of Tokyo Tokyo Japan Department of Electrical Engineering and Computer Science Tokyo University of Agriculture and Technology Tokyo Japan

In this paper, we propose algorithms for handling non-integer strides in sampling-frequency-independent (SFI) convolutional and transposed convolutional layers. The SFI layers have been developed for handling various sampling frequencies (SFs) by a single neural network. They are replaceable with their non-SFI counterparts and can be introduced into various network architectures. However, they could not handle some specific configurations when combined with non-SFI layers. For example, an SFI extension of Conv-TasNet, a standard audio source separation model, cannot handle some pairs of trained and target SFs because the strides of the SFI layers become non-integers. This problem cannot be solved by simple rounding or signal resampling, resulting in the significant performance degradation. To overcome this problem, we propose algorithms for handling non-integer strides by using windowed sinc interpolation. The proposed algorithms realize the continuous-time representations of features using the interpolation and enable us to sample instants with the desired stride. Experimental results on music source separation showed that the proposed algorithms outperformed the rounding- and signal-resampling-based methods at SFs lower than the trained SF. © 2023, CC BY-SA.

关键词： Network architecture

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