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ATP_mCNN: Predicting ATP binding sites through pretrained language models and multi-window neural networks

Computers in Biology and Medicine 2025年 185卷 109541-109541页

作者： Le, Van-The Malik, Muhammad-Shahid Lin, Yi-Jing Liu, Yu-Chen Chang, Yan-Yun Ou, Yu-Yen Department of Computer Science and Engineering Yuan Ze University Chung-Li32003 Taiwan Graduate Program in Biomedical Informatics Yuan Ze University Chung-Li32003 Taiwan Department of Computer Sciences Karakoram International University Gilgit-Baltistan 15100 Pakistan

Adenosine triphosphate plays a vital role in providing energy and enabling key cellular processes through interactions with binding proteins. The increasing amount of protein sequence data necessitates computational methods for identifying binding sites. However, experimental identification of adenosine triphosphate-binding residues remains challenging. To address the challenge, we developed a multi-window convolutional neural network architecture taking pre-trained protein language model embeddings as input features. In particular, multiple parallel convolutional layers scan for motifs localized to different window sizes. Max pooling extracts salient features concatenated across windows into a final multi-scale representation for residue-level classification. On benchmark datasets, our model achieves an area under the ROC curve of 0.95, significantly improving on prior sequence-based models and outperforming convolutional neural network baselines. This demonstrates the utility of pre-trained language models and multi-window convolutional neural networks for advanced sequence-based prediction of adenosine triphosphate-binding residues. Our approach provides a promising new direction for elucidating binding mechanisms and interactions from primary structure. © 2024 Elsevier Ltd

关键词： Convolutional neural networks

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High-Resolution Hydrogen Molecule Detection Utilizing a Nanocandle-Based Optical Sensor 16

High-Resolution Hydrogen Molecule Detection Utilizing a Nano...

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16th Pacific Rim Conference on Lasers and Electro-Optics, CLEO-PR 2024

作者： Park, Nu-Ri Kim, Min-Joong Lee, Jongsu Seo, Minah Ryu, Yong-Sang Kim, Myung-Ki KU-KIST Graduate School of Converging Science and Technology Korea University Seoul02841 Korea Republic of Korea Institute of Science and Technology Sensor System Research Center Seoul02792 Korea Republic of Northwestern University Department of Electrical Engineering and Computer Science EvanstonIL60208 United States School of Biomedical Engineering Korea University Seoul02481 Korea Republic of Interdisciplinary Program in Precision Public Health Korea University Seoul02481 Korea Republic of

Our research introduces a novel method for safe hydrogen detection. We've developed an advanced nano-candle sensor, combining Pd with nano-candles, enabling accurate detection of low-concentration hydrogen ( ©... 详细信息

ISBN: (纸本)9798350372076

关键词： Nanoclay

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Development of Automated Detection Methods for Calculating Blood Vessel Width and Stenosis Rate in Cardiac Catheterization Imaging 24

Development of Automated Detection Methods for Calculating B...

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8th International Conference on Medical and Health Informatics, ICMHI 2024

作者： Huang, Hsien-Cheng Chang, Hsiao-Huang Ke, Xiang-Wei Chien, Ting-Ying Department of Computer Science and Engineering Yuan Ze University Taoyuan City Taiwan Cardiovascular Surgery Department Taipei Veterans General Hospital Taipei City Taiwan Taipei Medical University Taipei City Taiwan Graduate Program in Biomedical Informatics Yuan Ze University Taoyuan City Taiwan Innovation Center for Big Data and Digital Convergence Yuan Ze University Taoyuan City Taiwan

ISBN: (纸本)9798400716874

Coronary artery disease is the most prevalent type of heart disease and has a considerable mortality rate. In diagnosing and assessing coronary artery disease, physicians must integrate a variety of clinical information and test results to evaluate the degree of coronary artery obstruction and continually learn and improve their skills in clinical practice to ensure the most accurate assessment of patients. Currently, the use of information technology to assist medical staff allows more effective and accurate analysis of symptoms. This approach not only serves as an auxiliary standard for physician diagnosis, thereby reducing the possibility of misdiagnosis, but also significantly improves patient treatment outcomes and medical quality while reducing the time burden on physicians for diagnosing patients. This study utilized image processing techniques and thinning algorithms to automate the detection of coronary artery width and, following the recommended methods of physicians in related fields, used specific vessel widths to calculate the degree of coronary artery narrowing. This provides a more accurate and efficient assessment method for evaluating the degree of vascular constriction in patients with coronary artery disease. © 2024 Copyright ACM.

关键词： Patient treatment

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Three-Dimensional Variable Slab-Selective Projection Acquisition Imaging

arXiv

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arXiv 2023年

作者： Park, Jinil Shin, Taehoon Park, Jang-Yeon The Department of Intelligent Precision Healthcare Convergence Sungkyunkwan University Suwon Korea Republic of Division of Mechanical and Biomedical Engineering Graduate Program in Smart Factory Ewha Woman University Seoul Korea Republic of The Department of Biomedical Engineering Sungkyunkwan University Suwon Korea Republic of

Three-dimensional (3D) projection acquisition (PA) imaging has recently gained attention because of its advantages, such as achievability of very short echo time, less sensitivity to motion, and undersampled acquisition of projections without sacrificing spatial resolution. However, larger subjects require a stronger Nyquist criterion and are more likely to be affected by outer-volume signals outside the field of view (FOV), which significantly degrades the image quality. Here, we proposed a variable slab-selective projection acquisition (VSS-PA) method to mitigate the Nyquist criterion and effectively suppress aliasing streak artifacts in 3D PA imaging. The proposed method involves maintaining the vertical orientation of the slab-selective gradient for frequency-selective spin excitation and the readout gradient for data acquisition. As VSS-PA can selectively excite spins only in the width of the desired FOV in the projection direction during data acquisition, the effective size of the scanned object that determines the Nyquist criterion can be reduced. Additionally, unwanted signals originating from outside the FOV (e.g., aliasing streak artifacts) can be effectively avoided. The mitigation of the Nyquist criterion owing to VSS-PA was theoretically described and confirmed through numerical simulations and phantom and human lung experiments. These experiments further showed that the aliasing streak artifacts were nearly suppressed. © 2023, CC BY-NC-ND.

关键词： Data acquisition

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Injectable cross-linked hyaluronic acid hydrogels with epigallocatechin gallate loading as vitreous substitutes

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International Journal of Biological Macromolecules 2024年第Part1期275卷 133467页

作者： Chen, Huai-An Tai, Yi-Ning Hsieh, Erh-Hsuan Thacker, Minal Lin, I-Chan Tseng, Ching-Li Lin, Feng-Huei Graduate Institute of Biomedical Materials and Tissue Engineering College of Biomedical Engineering Taipei Medical University Shuang-Ho Campus New Taipei City Taiwan Institute of Biomedical Engineering College of Medicine & College of Engineering National Taiwan University Taipei City Taiwan 17W Hong Kong Science Park Hong Kong Department of Ophthalmology Wan Fang Hospital Taipei Medical University Taipei City Taiwan Department of Ophthalmology School of Medicine College of Medicine Taipei Medical University Taipei City Taiwan International Ph. D. Program in Biomedical Engineering College of Biomedical Engineering Taipei Medical University Shuang-Ho Campus New Taipei City Taiwan Research Center of Biomedical Device College of Biomedical Engineering Taipei Medical University Taipei City Taiwan International Ph. D. Program in Cell Therapy and Regenerative Medicine College of Medicine Taipei Medical University Taipei City Taiwan National Health Research Institutes Miaoli County Taiwan

Hyaluronic acid (HA) serves as a vitreous substitute owing to its ability to mimic the physical functions of native vitreous humor. However, pure HA hydrogels alone do not provide sufficient protection against potential inflammatory risks following vitrectomy. In this study, HA was crosslinked with 1,4-butanediol diglycidyl ether (BDDE) to form HA hydrogels (HB). Subsequently, the anti-inflammatory agent epigallocatechin gallate (EGCG) was added to the hydrogel (HBE) for ophthalmic applications as a vitreous substitute. The characterization results indicated the successful preparation of HB with transparency, refractive index, and osmolality similar to those of native vitreous humor, and with good injectability. The anti-inflammatory ability of HBE was also confirmed by the reduced expression of inflammatory genes in retinal pigment epithelial cells treated with HBE compared with those treated with HB. In a New Zealand white rabbit model undergoing vitreous substitution treatment, HBE 50 (EGCG 50 μM addition) exhibited positive results at 28 days post-surgery. These outcomes included restored intraocular pressure, improved electroretinogram responses, minimal increase in corneal thickness, and no inflammation during histological examination. This study demonstrated the potential of an injectable HA-BDDE cross-linked hydrogel containing EGCG as a vitreous substitute for vitrectomy applications, offering prolonged degradation time and anti-inflammatory effects postoperatively. © 2024 The Authors

关键词： Hyaluronic acid

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Single-cell RNA-sequencing and subcellular spatial transcriptomics facilitate the translation of liver microphysiological systems for regulatory application

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Journal of Pharmaceutical Analysis 2023年第7期13卷 691-693页

作者： Dan Li Zhou Fang Qiang Shi Nicholas Zhang Binsheng Gong Weida Tong Ahmet F.Coskun Joshua Xu Division of Bioinformatics and Biostatistics National Center for Toxicological ResearchU.S.Food and Drug AdministrationJeffersonAR72079USA Wallace H.Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory UniversityAtlantaGA30332USA Machine Learning Graduate Program Georgia Institute of TechnologyAtlantaGA30332USA Division of Systems Biology National Center for Toxicological ResearchU.S.Food and Drug AdministrationJeffersonAR72079USA Interdisciplinary Bioengineering Graduate Program Georgia Institute of TechnologyAtlantaGA30332USA Parker H.Petit Institute for Bioengineering and Bioscience Georgia Institute of TechnologyAtlantaGA30332USA

Reducing the use of animal models in drug development and safety assessment has long been supported by the *** and Drug Administration(FDA).The report by Royal Society for the Prevention of Cruelty to Animals indicates that in 2020,experiments involved the use of over 100 million animals,with the United States leading the list by utilizing 20 million *** ethical considerations associated with animal testing and the costs in terms of time and money,animal models are not always effective in predicting human reactions to drug *** animal testing has been the traditional method for assessing the safety and efficacy of drugs.

关键词： money utilizing testing

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Peripheral pulse harmonic analysis and its clinical application: A systematic review

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Journal of Traditional and Complementary Medicine 2024年第2期14卷 223-236页

作者： Hsiao, Kun-Yuan Kang, Jiunn-Horng Wu, Yeong-Shing Chang, Hen-Hong Yang, Cheng-Ta Institute of Allied Health Sciences National Cheng Kung University Tainan Taiwan Department of Chinese Medicine Cishan Hospital Ministry of Health and Welfare Kaohsiung Taiwan Professional Master Program in Artificial Intelligence in Medicine College of Medicine Taipei Medical University Taipei Taiwan Graduate Institute of Nanomedicine and Medical Engineering College of Biomedical Engineering Taipei Medical University Taipei Taiwan Department of Physical Medicine and Rehabilitation Taipei Medical University Hospital Taipei Taiwan Graduate Institute of Integrated Medicine College of Chinese Medicine and Chinese Medicine Research Center China Medical University Taichung Taiwan Department of Chinese Medicine China Medical University Hospital Taichung Taiwan Department of Psychology National Cheng Kung University Tainan Taiwan Graduate Institute of Mind Brain and Consciousness Taipei Medical University Taipei Taiwan Graduate Institute of Health and Biotechnology Law Taipei Medical University Taipei City Taiwan

Introduction: Pulse harmonic analysis is a quantitative and objective methodology within traditional Chinese medicine (TCM) used to evaluate pulse characteristics. However, interpreting pulse wave data is challenging due to its inherent complexity. This study aims to provide a comprehensive review and comparison of existing human pulse wave harmonic analysis methods to elucidate their patterns and characteristics. Methods: A systematic review of clinical research reports published from 1990 to 2021 was conducted, focusing on variations in harmonic characteristics across different medical conditions and physiological states. Keyword searches included terms related to analysis methods (e.g., “Pulse Spectrum,” "harmonic analysis," “harmonic index”) and measured indicators (e.g., “vascular response,” "PPG," “Photoplethysmography,” "aortic," “arterial,” "blood pressure"). Supplementary research using PubMed's Mesh terms specifically targeted “Pulse wave analysis” within the methods and statistical analysis domain. Articles were filtered based on predefined criteria, including human participants and research related to pulse pressure or vascular volume changes. Conference papers, animal studies, and irrelevant research were excluded, with literature evaluation scales selected based on the retrieved research reports. Results: Initially, 6487 research reports were identified, and after screening, 50 reports were included in the review. The analysis revealed that low-frequency harmonics increase following vigorous activity or sympathetic excitation but decrease during rest or parasympathetic excitation. Cardiovascular patients exhibited elevated first harmonics associated with the liver meridian, while diabetes patients displayed weakened third harmonics related to the spleen meridian. Liver dysfunction was linked to changes in the first harmonic, and cancer patients showed signs of liver and kidney yin deficiency in the first and second harmonics. These findings underscore

关键词： Diagnostic tools Harmonic characteristics Pulse diagnosis Pulse harmonic analysis Traditional Chinese medicine

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Identifying Prognostic Markers of Non-small Cell Lung Carcinoma Using Bioinformatics

Identifying Prognostic Markers of Non-small Cell Lung Carcin...

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International Conference on Industrial Instrumentation and Control,ICI2C 2021

作者： Khan, Siladitya Chakraborty, Debamitra Department of Biomedical Engineering University of Rochester RochesterNY14627 United States Goergen Institute for Data Science University of Rochester RochesterNY14627 United States Materials Science Graduate Program University of Rochester RochesterNY14627 United States

ISBN: (纸本)9789811670107

We present a transcriptomics pipeline for performing the functional analysis of array expression profiling data of normal and adenocarcinoma lung tissue. Our aims are twofold, firstly to elucidate molecular processes that transform normal tissue, to a lung adenocarcinoma. Following this, we perform functional analysis to screen potential hub genes and demonstrate their value in cancer prognosis. Analysis was performed on a total of 500 differentially expressed genes (DEG), screened for their regulation and transcriptional modulation in a female population carrying non–small cell lung carcinoma (NSCLC). Key pathways like cytokine-cytokine receptors, ECM receptor interactions, and TNF signaling were identified suggesting a potential role in lung tumorigenesis. © 2022, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

关键词： Bioinformatics

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Unitig-centered pan-genome machine learning approach for predicting antibiotic resistance and discovering novel resistance genes in bacterial strains

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Computational and Structural Biotechnology Journal 2024年 23卷 1864-1876页

作者： Do, Duyen Thi Yang, Ming-Ren Vo, Tran Nam Son Le, Nguyen Quoc Khanh Wu, Yu-Wei Graduate Institute of Biomedical Informatics College of Medical Science and Technology Taipei Medical University Taipei Taiwan Department of Electrical Engineering National Taiwan University of Science and Technology Taipei Taiwan Department of Business Administration College of Management Lunghwa University of Science and Technology Taoyuan City Taiwan Professional Master Program in Artificial Intelligence in Medicine College of Medicine Taipei Medical University Taipei Taiwan Clinical Big Data Research Center Taipei Medical University Hospital Taipei Taiwan TMU Research Center for Digestive Medicine Taipei Medical University Taipei Taiwan

In current genomic research, the widely used methods for predicting antimicrobial resistance (AMR) often rely on prior knowledge of known AMR genes or reference genomes. However, these methods have limitations, potentially resulting in imprecise predictions owing to incomplete coverage of AMR mechanisms and genetic variations. To overcome these limitations, we propose a pan-genome-based machine learning approach to advance our understanding of AMR gene repertoires and uncover possible feature sets for precise AMR classification. By building compacted de Brujin graphs (cDBGs) from thousands of genomes and collecting the presence/absence patterns of unique sequences (unitigs) for Pseudomonas aeruginosa, we determined that using machine learning models on unitig-centered pan-genomes showed significant promise for accurately predicting the antibiotic resistance or susceptibility of microbial strains. Applying a feature-selection-based machine learning algorithm led to satisfactory predictive performance for the training dataset (with an area under the receiver operating characteristic curve (AUC) of > 0.929) and an independent validation dataset (AUC, approximately 0.77). Furthermore, the selected unitigs revealed previously unidentified resistance genes, allowing for the expansion of the resistance gene repertoire to those that have not previously been described in the literature on antibiotic resistance. These results demonstrate that our proposed unitig-based pan-genome feature set was effective in constructing machine learning predictors that could accurately identify AMR pathogens. Gene sets extracted using this approach may offer valuable insights into expanding known AMR genes and forming new hypotheses to uncover the underlying mechanisms of bacterial AMR. © 2024 The Authors

关键词： Genes

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Improved camptothecin encapsulation and efficacy by environmentally sensitive block copolymer/chitosan/fucoidan nanoparticles for targeting lung cancer cells

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International Journal of Biological Macromolecules 2024年第Part2期277卷 133901页

作者： Don, Trong-Ming Hong, Yu-Ting Jheng, Pei-Ru Chuang, Er-Yuan Huang, Yi-Cheng Department of Chemical and Materials Engineering Tamkang University New Taipei City Taiwan College of Life Sciences Department of Food Science National Taiwan Ocean University Keelung Taiwan Graduate Institute of Biomedical Materials and Tissue Engineering International PhD Program in Biomedical Engineering Taipei Medical University Taipei Taiwan Cell Physiology and Molecular Image Research Center Taipei Medical University–Wan Fang Hospital Taipei Taiwan

In this study, thermo-sensitive poly(N-isopropyl acrylamide) (PNP) was polymerized with pH-sensitive poly(acrylic acid) (PAA) to prepare a PAA-b-PNP block copolymer. Above its cloud point, the block copolymer self-assembled into nanoparticles (NPs), encapsulating the anticancer drug camptothecin (CPT) in situ. Chitosan (CS) and fucoidan (Fu) further modified these NPs, forming Fu-CPT-NPs to enhance biocompatibility, drug encapsulation efficiency (EE), and loading content (LC), crucially facilitating P-selectin targeting of lung cancer cells through a drug delivery system. The EE and LC reached 82 % and 3.5 %, respectively. According to transmission electron microscope observation, these Fu-CPT-NPs had uniform spherical shapes with an average diameter of ca. 250 nm. They could maintain their stability in a pH range of 5.0–6.8. In vitro experimental results revealed that the Fu-CPT-NPs exhibited good biocompatibility and had anticancer activity after encapsulating CPT. It could deliver CPT to cancer cells by targeting P-selectin, effectively increasing cell uptake and inducing cell apoptosis. Animal study results showed that the Fu-CPT-NPs inhibited lung tumor growth by increasing tumor cell apoptosis without causing significant tissue damage related to generating reactive oxygen species in lung cancer cells. This system can effectively improve drug-delivery efficiency and treatment effects and has great potential for treating lung cancer. © 2024 Elsevier B.V.

关键词： Nanoparticles

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