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Using a hybrid neural network architecture for DNA sequence representation: A study on N4-methylcytosine sites

computers in Biology and Medicine 2024年 178卷 108664-108664页

作者： Nguyen, Van-Nui Ho, Trang-Thi Doan, Thu-Dung Le, Nguyen Quoc Khanh University of Information and Communication Technology Thai Nguyen University Thai Nguyen Viet Nam Department of Computer Science and Information Engineering TamKang University New Taipei251301 Taiwan International Degree Program in Animal Vaccine Technology International College National Pingtung University of Science and Technology Pingtung Taiwan Professional Master Program in Artificial Intelligence in Medicine College of Medicine Taipei Medical University Taipei110 Taiwan Research Center for Artificial Intelligence in Medicine Taipei Medical University Taipei110 Taiwan AIBioMed Research Group Taipei Medical University Taipei110 Taiwan Translational Imaging Research Center Taipei Medical University Hospital Taipei110 Taiwan

N4-methylcytosine (4mC) is a modified form of cytosine found in DNA, contributing to epigenetic regulation. It exists in various genomes, including the Rosaceae family encompassing significant fruit crops like apples, cherries, and roses. Previous investigations have examined the distribution and functional implications of 4mC sites within the Rosaceae genome, focusing on their potential roles in gene expression regulation, environmental adaptation, and evolution. This research aims to improve the accuracy of predicting 4mC sites within the genome of Fragaria vesca, a Rosaceae plant species. Building upon the original 4mc-w2vec method, which combines word embedding processing and a convolutional neural network (CNN), we have incorporated additional feature encoding techniques and leveraged pre-trained natural language processing (NLP) models with different deep learning architectures including different forms of CNN, recurrent neural networks (RNN) and long short-term memory (LSTM). Our assessments have shown that the best model is derived from a CNN model using fastText encoding. This model demonstrates enhanced performance, achieving a sensitivity of 0.909, specificity of 0.77, and accuracy of 0.879 on an independent dataset. Furthermore, our model surpasses previously published works on the same dataset, thus showcasing its superior predictive capabilities. © 2024 Elsevier Ltd

关键词： Embeddings

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Multidimensional analysis of sensory perception and neurophysiological responses to marinated beef cooked by diverse methods

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Innovative Food Science and Emerging Technologies 2025年 103卷

作者： Yang, Tianyi Jiang, Wei Luo, Chencheng Hu, Jin Xu, Wei Zhang, Peng Jin, Xiaofei Zhou, Yuxuan Liu, Rui Qian, Zhiyu Yang, Yamin Department of Biomedical Engineering Key Laboratory of Multi-modal Brain-Computer Precision Drive Ministry of Industry and Information Technology Key Laboratory of Brain-Machine Intelligence Technology Ministry of Education Key Laboratory of Digital Medical Equipment and Technology of Jiangsu Province Nanjing University of Aeronautics and Astronautics Nanjing210016 China Program in Neuroscience & Behavioral Disorders Duke-NUS Medical School National University of Singapore Singapore169857 Singapore Department of Neurosurgery Huashan Hospital Shanghai Medical College Fudan University National Center for Neurological Disorders National Key Laboratory of Medical Neurobiology Institutes of Brain Science Shanghai Key Laboratory of Brain Function and Regeneration Institute of Neurosurgery Shanghai200040 China School of Biomedical Engineering and Informatics Nanjing Medical University Nanjing211166 China College of Food Science and Engineering Yangzhou University Yangzhou225127 China

The cooking process significantly influences consumer perception and preference for meat. This study systematically compares the sensory and neurophysiological responses elicited by beef processed via five cooking methods, including boiling (BO), sous-vide (SV), roasting (RO), pan-frying (PF), and deep-frying (DF). Sensory evaluations combining a check-all-that-apply (CATA) questionnaire and hedonic scaling revealed that RO, PF, and DF treatments produced richer flavors and more intense aromas, linked to higher hedonic ratings. In contrast, SV and BO yielded milder sensory profiles with lower flavor intensity and less consumer preference. Electroencephalography (EEG) analysis supported these findings by showing that high-heat methods elicited stronger neural responses, especially in the α, β, and γ frequency bands, which are associated with pleasure, appetite, and cognitive engagement, particularly prominent during olfactory and gustatory tests. Source localization further revealed greater activation in brain regions involved in sensory, reward, memory, emotion, and motivation for high-heat treated beef, demonstrating the connection between enhanced flavor complexity of high-temperature process and consumer appeal. Converging evidence from subjective sensory evaluation and neurophysiological analysis highlights the central role of thermal processing in enhancing food palatability and consumer satisfaction, offering practical insights for improving beef preparation in the food industry. © 2025 Elsevier Ltd

关键词： Neurons

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Estimation of the main air pollutants from different biomasses under combustion atmospheres by artificial neural networks

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Chemosphere 2024年 352卷 141484页

作者： Monteiro, Thalyssa Oliveira Alves, Pedro Augusto Araújo da Silva de Almeida Nava Barradas Filho, Alex Oliveira Villa-Vélez, Harvey Alexander Cruz, Glauber Postgraduate Program in Mechanical Engineering (PPGMEC) Department of Mechanics and Materials Federal Institute of Education Science and Technology of Maranhão (IFMA) Maranhão São Luís Brazil Postgraduate Program in Computer Science and Computational Mathematics (PPG-CCMC) Department of Computer Science University of São Paulo (USP) São Carlos São Paulo Brazil Data Analysis and Artificial Intelligence Laboratory (DARTi) Department of Computational Engineering Federal University of Maranhão (UFMA) Maranhão São Luís Brazil Department of Chemical Engineering Federal University of Maranhão (UFMA) Maranhão São Luís Brazil Processes and Thermal Systems Laboratory (LPSisTer) Department of Mechanical Engineering Federal University of Maranhão (UFMA) Maranhão São Luís Brazil

The production of biofuels to be used as bioenergy under combustion processes generates some gaseous emissions (CO, CO2, NOx, SOx, and other pollutants), affecting living organisms and requiring careful assessments. H... 详细信息

The production of biofuels to be used as bioenergy under combustion processes generates some gaseous emissions (CO, CO₂, NO_x, SO_x, and other pollutants), affecting living organisms and requiring careful assessments. However, obtaining such information experimentally for data evaluation is costly and time-consuming and its in situ obtaining for regional biomasses (e.g., those from Northeast Brazil (NEB) is still a major challenge. This paper reports on the application of artificial neural networks (ANNs) for the prediction of the main air pollutants (CO, CO₂, NO, and SO₂) produced during the direct biomass combustion (N₂/O₂:80/20%) with the use of ultimate analysis (carbon, hydrogen, nitrogen, sulfur, and oxygen). 116 worldwide biomasses were used as input data, which is a relevant alternative to overcome the lack of experimental resources in NEB and obtain such information. Cross-validation was conducted with k-fold to optimize the ANNs and performance was analyzed with the use of statistical errors for accuracy assessments. The results showed an acceptable statistical performance for all architectures of ANNs, with 0.001–12.41% MAPE, 0.001–5.82 mg Nm⁻³ MAE, and 0.03–52.30 mg Nm⁻³ RMSE, highlighting the high precision of the emissions studied. On average, the differences between predicted and real values for CO, CO₂, NO, and SO₂ emissions from NEB biomasses were approximately 0.01%, 10⁻⁶%, 0.14%, and 0.05%, respectively. Pearson coefficient provided consistent results of concentration of the ultimate analysis in relation to the emissions studied and effectiveness of the test set in the developed models. © 2024 Elsevier Ltd

关键词： Brazilian northeastern Environmental statistics Evaluation metrics Gaseous emissions Predictive models Thermoconversion

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Terahertz spin dynamics in rare-earth orthoferrites

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Photonics Insights 2022年第2期1卷 1-56页

作者： Xinwei Li Dasom Kim Yincheng Liu Junichiro Kono Department of Physics California Institute of TechnologyPasadenaUSA Department of Electrical and Computer Engineering Rice UniversityHoustonUSA Applied Physics Graduate Program Smalley-Curl InstituteRice UniversityHoustonUSA Department of Physics and Astronomy Rice UniversityHoustonUSA Department of Materials Science and NanoEngineering Rice UniversityHoustonUSA

Recent interest in developing fast spintronic devices and laser-controllable magnetic solids has sparked tremendous experimental and theoretical efforts to understand and manipulate ultrafast dynamics in *** of spin dynamics in the terahertz(THz)frequency range are particularly important for elucidating microscopic pathways toward novel device ***,we review THz phenomena related to spin dynamics in rare-earth orthoferrites,a class of materials promising for antiferromagnetic *** expand this topic into a description of four key elements.(1)We start by describing THz spectroscopy of spin excitations for probing magnetic phase transitions in thermal *** acoustic magnons are useful indicators of spin reorientation transitions,electromagnons that arise from dynamic magnetoelectric couplings serve as a signature of inversion-symmetry-breaking phases at low temperatures.(2)We then review the strong laser driving scenario,where the system is excited far from equilibrium and thereby subject to modifications to the free-energy *** pathways for ultrafast laser manipulation of magnetic order are discussed.(3)Furthermore,we review a variety of protocols to manipulate coherent THz magnons in time and space,which are useful capabilities for antiferromagnetic spintronic applications.(4)Finally,new insights into the connection between dynamic magnetic coupling in condensed matter and the Dicke superradiant phase transition in quantum optics are *** presenting a review on an array of THz spin phenomena occurring in a single class of materials,we hope to trigger interdisciplinary efforts that actively seek connections between subfields of spintronics,which will facilitate the invention of new protocols of active spin control and quantum phase engineering.

关键词： terahertz spin dynamics magnetism orthoferrite ultrafast spectroscopy magneto-optics

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Manipulating Fano coupling in an opto-thermoelectric field

arXiv

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arXiv 2024年

作者： Lin, Linhan Lepeshov, Sergey Krasnok, Alex Huang, Yu Jiang, Taizhi Peng, Xiaolei Korgel, Brian A. Alu, Andrea Zheng, Yuebing State Key Laboratory of Precision Measurement Technology and Instruments Department of Precision Instrument Tsinghua University Beijing100084 China Department of Electrical and Photonics Engineering DTU Electro Technical University of Denmark Building 343 Kgs. LyngbyDK-2800 Denmark Department of Electrical and Computer Engineering Florida International University MiamiFL33174 United States School of Physics and Electronics Hunan University Changsha410082 China Mc Ketta Department of Chemical Engineering The University of Texas at Austin AustinTX78712 United States Materials Science & Engineering Program Texas Materials Institute The University of Texas at Austin AustinTX78712 United States Department of Electrical and Computer Engineering The University of Texas at Austin AustinTX78712 United States Advanced Science Research Center City University of New York New YorkNY10031 United States Physics Program Graduate Center City University of New York NY10016 United States Walker Department of Mechanical Engineering The University of Texas at Austin AustinTX78712 United States

Fano resonances in photonics arise from the coupling and interference between two resonant modes in structures with broken symmetry. They feature an uneven and narrow and tunable lineshape, and are ideally suited for optical spectroscopy. Many Fano resonance structures have been suggested in nanophotonics over the last ten years, but reconfigurability and tailored design remain challenging. Herein, we propose an all-optical "pick-and-place" approach aimed at assemble Fano metamolecules of various geometries and compositions in a reconfigurable manner. We study their coupling behavior by in-situ dark-field scattering spectroscopy. Driven by a light-directed opto-thermoelectric field, silicon nanoparticles with high quality-factor Mie resonances (discrete states) and low-loss BaTiO3 nanoparticles (continuum states) are assembled into all-dielectric heterodimers, where distinct Fano resonances are observed. The Fano parameter can be adjusted by changing the resonant frequency of the discrete states or the light polarization. We also show tunable coupling strength and multiple Fano resonances by altering the number of continuum states and discrete states in dielectric heterooligomers. Our work offers a general design rule for Fano resonance and an all-optical platform for controlling Fano coupling on demand. Copyright © 2024, The Authors. All rights reserved.

关键词： Light polarization

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Developing a medical artificial intelligence course for high school students

Developing a medical artificial intelligence course for high...

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International Forum on Medical Imaging in Asia 2021, IFMIA 2021

作者： Huang, Chao-Jung Wu, Tinghui Lu, Jui-Ting Lin, Beatrice Chang, Dawei Wang, Pochuan Wang, Mei-Chi Lee, Peijung Wang, Weichung National Taiwan University-Stanford Joint Program Office of AI in Biotechnology Ministry of Science and Technology Joint Research Center for Artificial Intelligence Technology and All Vista Healthcare Taipei Taiwan Institute of Applied Mathematical Sciences National Taiwan University Taipei Taiwan Department of Mathematics Ecole Normale Supérieure de Lyon Lyon France Department of Computer Science and Information Engineering National Taiwan University Taipei Taiwan Department of Electronic and Computer Engineering National Taiwan University of Science and Technology Taipei Taiwan Department of Mathematics National Taiwan University Taipei Taiwan

ISBN: (数字)9781510644212

ISBN: (纸本)9781510644205

Artificial intelligence (AI) training courses often require prerequisites such as calculus or statistics. It is hence challenging to design and develop an introductory AI course for students of secondary education. This research intends to develop a medical AI course, provide high school students with an overview of deep learning applications in medical image analysis, and inspire them to pursue careers in the field of medical AI. We designed a 20-hour course, including lectures and two hands-on projects based on medical image classification. The proposed courses provided medical AI disciplines and built up their knowledge from basic to advanced levels. During the ten-day online courses, all the students were fully engaged and gave us positive feedback. The students endeavored to complete the experimental study in training, testing, and hypothesis of medical images application in the course. Their performance exceeded all expectations, for they did further analysis by tuning different hyperparameters. We designed a course evaluation form, which suggested that the students found it essential and expected to interact with the instructors. The results indicate that combining lectures with hands-on sessions would lead to evidently better achievement in terms of high school students' medical AI knowledge and positive attitudes while addressing real-world problems in the projects. Through this innovative education model, high school students regained their enthusiasm and were encouraged to cultivate their medical AI skills through self-learning while finishing the project. We conclude that this course could be successfully applied to interdisciplinary education in high school. © 2021 SPIE.

关键词： Students

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Shaping Integrity: Why Generative Artificial Intelligence Does Not Have to Undermine Education

arXiv

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arXiv 2024年

作者： Tan, Myles Joshua Toledo Maravilla, Nicholle Mae Amor Tan Department of Electrical and Computer Engineering Herbert Wertheim College of Engineering University of Florida GainesvilleFL32611 United States Department of Epidemiology College of Public Health & Health Professions College of Medicine University of Florida GainesvilleFL32610 United States Biology Program College of Arts and Sciences University of St. La Salle Negros Occidental Bacolod City6100 Philippines Department of Natural Sciences College of Arts and Sciences University of St. La Salle Negros Occidental Bacolod City6100 Philippines Department of Chemical Engineering College of Engineering and Technology University of St. La Salle Negros Occidental Bacolod City6100 Philippines Department of Electronics Engineering College of Engineering and Technology University of St. La Salle Negros Occidental Bacolod City6100 Philippines Yo-Vivo Corporation Negros Occidental Bacolod City6100 Philippines

This paper examines the role of generative artificial intelligence (GAI) inpromoting academic integrity within educational settings. It explores how AIcan be ethically integrated into classrooms to enhance learning experiences,foster intrinsic motivation, and support voluntary behavior change amongstudents. By analyzing established ethical frameworks and educational theoriessuch as deontological ethics, consequentialism, constructivist learning, andSelf-Determination Theory (SDT), the paper argues that GAI, when usedresponsibly, can enhance digital literacy, encourage genuine knowledgeconstruction, and uphold ethical standards in education. This researchhighlights the potential of GAI to create enriching, personalized learningenvironments that prepare students to navigate the complexities of the modernworld ethically and effectively. © 2024, CC BY-NC-SA.

关键词： Contrastive Learning

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Measurement of Water Diffusion Coefficient in Cross-Linked Gelatins Using the Terahertz Time-Domain Spectroscopy Technique

Measurement of Water Diffusion Coefficient in Cross-Linked G...

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Conference on Lasers and Electro-Optics (CLEO)

作者： D. Walden D. Chakraborty J. Cheng A. Straksys A. Stirke W. CMA Melo A. Jukna I. Komissarov Roman Sobolewski Department of Physics and Astronomy University of Rochester Rochester New York USA Laboratory for Laser Energetics University of Rochester Rochester New York USA Materials Science Graduate Program University of Rochester Rochester New York USA State Research Institute Center for Physical Sciences & Technology Vilnius Lithuania Department of Physics Vilnius Gediminas Technical University Vilnius Lithuania Department of Electrical and Computer Engineering University of Rochester Rochester New York USA

A novel method has been developed to evaluate the water diffusion dynamics in gelatin-based gels, based on transient terahertz time-domain spectroscopy measurements. Such gels are widely used models for human skin.

ISBN: (纸本)9798350369311

关键词： Spectroscopy Measurement by laser beam Lasers and electrooptics Laser modes Skin Time-domain analysis Transient analysis Electro-optical waveguides

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Automated Diagnosis of Heart-Lung Diseases in Chest X-ray Images

Automated Diagnosis of Heart-Lung Diseases in Chest X-ray Im...

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International Conference on engineering technology and their Applications (IICETA)

作者： Mohammad Alslatie Hiam Alquran Wan Azani Mustafa Isam Abu-Qasmieh Ali Mohammad Alqudah Ahmed Alkhayyat King Hussein Medical Center Royal Jordanian Medical Service The Institute of Biomedical Technology Amman Jordan Biomedical Systems and Medical Informatics Engineering Yarmouk University Irbid Jordan Faculty of Electrical Engineering Technology Univerisiti Malaysia Perlis (UniMAP) Arau Perlis Malaysia Department of Electrical and Computer Engineering Biomedical Engineering Program University of Manitoba Canada Faculty of Engineering The Islamic University Najaf Iraq

ISBN: (数字)9781665472159

ISBN: (纸本)9781665472166

The state of the art of artificial intelligence (AI) for various medical imaging applications leads to enhanced accuracy, analysis, visualization, and interpretation of chest Xray (CXR) images for diagnosis. Many diseases are diagnosed based on CXR images. In this paper, two types of abnormalities are diagnosed based on AI techniques. The two classes are atelectasis and cardiomegaly. The acquired images are segmented to localize the chest region and then enhanced using gray-level transformation methods. The enhanced images are passed to two pretrained convolutional neural networks (CNNs): shuffle and mobile net. The transfer learning approach is utilized in this stage. The automated features are extracted from the last fully connected layer. Each CNN deserves to have the two most representative features for the two classes. These four features are passed to support the vector machine classifier. The training accuracy reached 100% and the test accuracy was 96.7%. The proposed method can be extended to be a milestone in the classification of all heart-lung diseases that can be diagnosed using chest X-ray images.

关键词： Image segmentation Visualization Transfer learning Feature extraction Convolutional neural networks Artificial intelligence X-ray imaging

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Room-temperature multiple ligands-tailored SnO_(2) quantum dots endow in situ dual-interface binding for upscaling efficient perovskite photovoltaics with high V_(OC)

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Light(Science & Applications) 2021年第12期10卷 2467-2481页

作者： Zhiwei Ren Kuan Liu Hanlin Hu Xuyun Guo Yajun Gao Patrick W.K.Fong Qiong Liang Hua Tang Jiaming Huang Hengkai Zhang Minchao Qin Li Cui Hrisheekesh Thachoth Chandran Dong Shen Ming-Fai Lo Annie Ng Charles Surya Minhua Shao Chun-Sing Lee Xinhui Lu Frédéric Laquai Ye Zhu Gang Li Department of Electronic and Information Engineering Research Institute for Smart Energy(RISE)Guangdong-Hong Kong-Macao(GHM)Joint Laboratory for Photonic-Thermal-Electrical Energy Materials and DevicesThe Hong Kong Polytechnic UniversityHung HomKowloonHong KongChina Department of Electrical and Computer Engineering Nazarbayev UniversityNur-SultanKazakhstan The Hong Kong Polytechnic University Shenzhen Research Institute Shenzhen 518057China Hoffmann Institute of Advanced Materials Shenzhen Polytechnic7098 Liuxian BoulevardShenzhen 518055China Department of Applied Physics The Hong Kong Polytechnic UniversityHung HomKowloonHong KongChina Department of Chemical and Biological Engineering The Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina King Abdullah University of Science and Technology(KAUST) KAUST Solar Center(KSC)Physical Sciences and Engineering Division(PSE)Material Science and Engineering Program(MSE)Thuwal 23955-6900Kingdom of Saudi Arabia Department of Physics The Chinese University of Hong KongShatin 999077 Hong KongChina Center of Super-Diamond and Advanced Films(COSDAF) Department of ChemistryCity University of Hong KongHong KongChina

The benchmark tin oxide(SnO_(2))electron transporting layers(ETLs)have enabled remarkable progress in planar perovskite solar cell(PSCs).However,the energy loss is still a challenge due to the lack of“hidden interface”*** report a novel ligand-tailored ultrafine SnO_(2) quantum dots(QDs)via a facile rapid room temperature ***,the ligand-tailored SnO_(2) QDs ETL with multi-functional terminal groups in situ refines the buried interfaces with both the perovskite and transparent electrode via enhanced interface binding and perovskite *** novel ETLs induce synergistic effects of physical and chemical interfacial modulation and preferred perovskite crystallization-directing,delivering reduced interface defects,suppressed non-radiative recombination and elongated charge carrier *** conversion efficiency(PCE)of 23.02%(0.04 cm^(2))and 21.6%(0.98 cm^(2),V_(OC) loss:0.336 V)have been achieved for the blade-coated PSCs(1.54 eV E_(g))with our new ETLs,representing a record for SnO_(2) based blade-coated ***,a substantially enhanced PCE(V_(OC))from 20.4%(1.15 V)to 22.8%(1.24 V,90 mV higher V_(OC),0.04 cm^(2) device)in the blade-coated 1.61 eV PSCs system,via replacing the benchmark commercial colloidal SnO_(2) with our new ETLs.

关键词： perovskite interface quantum

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