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Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-seq Data via DeeReCT-TSS

Genomics, Proteomics & Bioinformatics 2022年第5期20卷 959-973页

作者： Juexiao Zhou Bin Zhang Haoyang Li Longxi Zhou Zhongxiao Li Yongkang Long Wenkai Han Mengran Wang Huanhuan Cui Jingjing Li Wei Chen Xin Gao Computer Science Program ComputerElectrical and Mathematical Sciences and Engineering DivisionKing Abdullah University of Science and TechnologyThuwal 23955-6900Saudi Arabia Computational Bioscience Research Center King Abdullah University of Science and TechnologyThuwal 23955-6900Saudi Arabia Department of Biology School of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China Shenzhen Key Laboratory of Gene Regulation and Systems Biology School of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China Academy for Advanced Interdisciplinary Studies Southern University of Science and TechnologyShenzhen 518055China

The accurate annotation of transcription start sites(TSSs)and their usage are critical for the mechanistic understanding of gene regulation in different biological *** fulfill this,specific high-throughput experimental technologies have been developed to capture TSSs in a genome-wide manner,and various computational tools have also been developed for in silico prediction of TSSs solely based on genomic *** of these computational tools cast the problem as a binary classification task on a balanced dataset,thus resulting in drastic false positive predictions when applied on the genome ***,we present Dee Re CT-TSS,a deep learningbased method that is capable of identifying TSSs across the whole genome based on both DNA sequence and conventional RNA sequencing *** show that by effectively incorporating these two sources of information,Dee Re CT-TSS significantly outperforms other solely sequence-based methods on the precise annotation of TSSs used in different cell ***,we develop a meta-learning-based extension for simultaneous TSS annotations on 10 cell types,which enables the identification of cell type-specific ***,we demonstrate the high precision of DeeReCT-TSS on two independent datasets by correlating our predicted TSSs with experimentally defined TSS chromatin *** source code for Dee Re CT-TSS is available at https://github.-com/Joshua Chou2018/Dee Re CT-TSS_release and https://***/biocode/tools/BT007316.

关键词： Transcription start site Machine learning Deep learning Meta-learning RNA sequencing

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Autonomous self-healing 3D micro-suction adhesives for multi-layered amphibious soft skin electronics

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InfoMat 2024年第10期6卷 65-79页

作者： Dohyun Lim Min Woo Jeong Hyeongho Min Yeon Soo Lee Gui Won Hwang Seung Hwan Jeon Kyu Ho Jung Ngoc Thanh Phuong Vo Min-Seok Kim Da Wan Kim Jin Young Oh Changhyun Pang School of Chemical Engineering Sungkyunkwan University(SKKU)SuwonGyeonggi-doRepublic of Korea Department of Chemical Engineering(Integrated Engineering Program) Kyung Hee UniversityYonginGyeonggiRepublic of Korea Convergence Research Group for Meta-Touch Korea Research Institute of Standards and ScienceDaejeonRepublic of Korea Department of Electronic Engineering Korea National University of TransportationChungju-siChungbukRepublic of Korea Samsung Advanced Institute for Health Sciences and Technology(SAIHST) Sungkyunkwan UniversitySuwonGyunggi-doRepublic of Korea

Autonomously self-healing, reversible, and soft adhesive microarchitecturesand structured electric elements could be important features in stable and versatilebioelectronic devices adhere to complex surfaces of the human body(rough, dry, wet, and vulnerable). In this study, we propose an autonomousself-healing multi-layered adhesive patch inspired by the octopus, which possessself-healing and robust adhesion properties in dry/underwater *** implement autonomously self-healing octopus-inspired architectures, adynamic polymer reflow model based on structural and material design suggestscriteria for three-dimensional patterning self-healing elastomers. In addition,self-healing multi-layered microstructures with different moduli endowsefficient self-healing ability, human-friendly reversible bio-adhesion, and stablemechanical deformability. Through programmed molecular behavior ofmicrolevel hybrid multiscale architectures, the bioinspired adhesive patchexhibited robust adhesion against rough skin surface under both dry andunderwater conditions while enabling autonomous adhesion restoring performanceafter damaged (over 95% healing efficiency under both conditions for24 h at 30℃). Finally, we developed a self-healing skin-mountable adhesiveelectronics with repeated attachment and minimal skin irritation by laminatingthin gold electrodes on octopus-like structures. Based on the robust adhesionand intimate contact with skin, we successfully obtained reliable measurements during dynamic motion under dry, wet, and damagedconditions.

关键词： biomimetics dry adhesive self-healing polymer stretchable electronics

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Quaternary ammonium-functionalized polysilsesquioxanes for antifogging coating

RSC Applied Polymers

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RSC Applied Polymers 2024年第1期3卷 92-96页

作者： Hamada, Takashi Sugimoto, Tetsuya Tanaka, Arata Maeda, Tetsuya Katsura, Daiji Koga, Hiroyuki Ohshita, Joji Collaborative Research Laboratory Graduate School of Advanced Science and Engineering Hiroshima University 1-4-1 Kagamiyama Higashi-Hiroshima Hiroshima 739-8527 Japan Quantum Materials and Applications Research Center Takasaki Institute for Advanced Quantum Science National Institutes for Quantum Science and Technology (QST) 1233 Watanuki-machi Takasaki Gunma 370-1292 Japan Technical Research Center Mazda Motor Corporation Aki-gun Hiroshima 730-8670 Japan Smart Innovation Program Graduate School of Advanced Science and Engineering Hiroshima University 1-4-1 Kagamiyama Higashi-Hiroshima Hiroshima 739-8527 Japan Division of Materials Model-Based Research Digital Monozukuri (Manufacturing) Education and Research Center Hiroshima University 3-10-32 Kagamiyama Higashi-Hiroshima Hiroshima 739-0046 Japan

Aiming to develop antifogging materials with enhanced antifogging properties and scratch resistance, polysilsesquioxane films containing quaternary ammonium groups were prepared via a sol-gel reaction and quaternization. Owing to their high water uptake, scratch hardness, and transparency, the prepared quaternary ammonium-functionalized polysilsesquioxane films are promising for application in antifogging coatings. © 2025 RSC.

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The core morning clock component CCA1 enhances UPR target gene expression to facilitate ER stress recovery

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Plant Communications 2025年第4期6卷 234-247页

作者： Gyeongik Ahn In Jung Jung Gyeong-Im Shin Song Yi Jeong Myung Geun Ji Jin-Sung Huh Ji-Won Hwang Jeongsik Kim Joon-Yung Cha Sang Yeol Lee Min Gab Kim Woe-Yeon Kim Division of Applied Life Science(BK21 Four) PBRRCPMBBRCRILS&IALSGyeongsang National UniversityJinju 52828Republic of Korea National Institute of Wildlife Disease Control and Prevention(NIWDC) Ministry of EnvironmentGwangju 62407Republic of Korea Faculty of Science Education and Interdisciplinary Graduate Program in Advanced Convergence Technology and Science Jeju National UniversityJeju 63243Republic of Korea College of Pharmacy and Research Institute of Pharmaceutical Science PMBBRCGyeongsang National UniversityJinju 52828Republic of Korea

The endoplasmic reticulum(ER)is a cellular organelle responsible for protein synthesis and *** its protein folding capacity is exceeded,unfolded or misfolded proteins accumulate,causing ER stress and triggering the unfolded protein response(UPR)to restore ER *** UPR gene expression in plants follows a diel cycle,the mechanisms by which the circadian clock regulates these genes remain ***,we demonstrate that sensitivity to ER stress in root growth exhibits time-of-day phases and that the circadian clock regulates UPR target gene expression during ER ***,mutations in the core morning clock component CIRCADIAN CLOCK ASSOCIATED 1(CCA1)impair ER stress ***1 forms a complex with the UPR modulator basic leucine zipper 28(bZIP28)and acts as an upstream regulator of ER stress *** ER stress,CCA1 is stabilized and associates with bZIP28 at the ER stress response element within the BiP3 promoter,enhancing the ER stress ***,CCA1 and bZIP28 coordinate a time-dependent adaptive response to ER stress to maintain ER *** re-sults suggest that the circadian clock primes the timing and levels of ER chaperone expression to enhance ER stress tolerance.

关键词： circadian clock ER stress ER chaperone CCA1 bZIP28

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Thermal simulation of microwave kiln based on multiphysics

Thermal simulation of microwave kiln based on multiphysics

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2023 International Technical Conference on Circuits/Systems, Computers, and Communications, ITC-CSCC 2023

作者： Jansaengsuk, Thodsaphon Pattanapichai, Sorathon Poopanya, Piyawong Phimphakan, Nonthawat Thongsri, Jatuporn College of Advanced Manufacturing Innovation King Mongkut's Institute of Technology Ladkrabang Computer Simulation in Engineering Research Group Bangkok10520 Thailand Ubon Ratchathani Rajabhat University Program of Physics Faculty of Science Ubonratchatani34000 Thailand

ISBN: (纸本)9798350326413

A microwave kiln, made of silicon carbide and ceramic fiber, commonly employs in a household glassware production process. In this process, when the kiln was in a microwave oven, a microwave transmitted to the kiln generating a high temperature to fuse the glass inside. This article presents a thermal simulation to investigate the temperature inside the kiln based on multiphysics consisting of a high-frequency structure simulator (HFSS) and computational fluid dynamics (CFD). The multiphysics results revealed the temperature inside the kiln in a transient state, consistent with the experimental results. As expected, the temperature increased with the increasing time of the process. Significantly, the silicon carbide had higher temperatures than the ceramic fiber;therefore, silicon carbide is a crucial material for generating heat inside the kiln. In addition, the temperature-increasing rate (TIR) inside the kiln depended on the kiln's thickness (Th). As a result, the thinner Th provided better TIR. The research findings can be applied to develop a high-efficacy household glassware production process. © 2023 IEEE.

关键词： Multiphysics

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BiVO4-Decorated Graphite Felt as Highly Efficient Negative Electrode for All-Vanadium Redox Flow Batteries

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ACS Applied Energy Materials 2023年第6期6卷 3301-3311页

作者： Kabtamu, Daniel Manaye Li, Yu-Zhen Bayeh, Anteneh Wodaje Ou, Yun-Ting Huang, Zih-Jhong Chiang, Tai-Chin Huang, Hsin-Chih Wang, Chen-Hao Department of Materials Science and Engineering National Taiwan University of Science and Technology Taipei106335 Taiwan Department of Chemistry Debre Berhan University Po. Box 445 Debre Berhan Ethiopia King George VI Street Addis Ababa1000 Ethiopia King George VI Street Addis Ababa1000 Ethiopia Global Development Engineering Program National Taiwan University of Science and Technology Taipei106335 Taiwan Research Center National Cheng Kung University Tainan70101 Taiwan Advanced Manufacturing Research Center National Taiwan University of Science and Technology Taipei106335 Taiwan

Recently, discovering high-performance electrocatalytic materials for vanadium redox flow batteries (VRFBs) has been one of the most crucial tasks. This paper details the successful fabrication of a low-cost platelike bismuth vanadate (BiVO4) material through a simple one-step hydrothermal route, employed as an electrocatalyst to adorn graphite felt (GF) for use as the negative electrode in VRFBs. The experimental results show that BiVO4-3h exhibits the optimal electrocatalytic activity and reversibility for the vanadium redox couples among all samples. The energy efficiency of the VRFB cell assembled with BiVO4-decorated GF as the negative electrode is found to be 75.42% at 100 mA cm-2, which is about 10.24% more efficient than that of the cell assembled with a heat-treated graphite felt (HT-GF) electrode. The possible reasons for the activity enhancement can be ascribed to the existence of oxygen vacancies in the BiVO4 lattice structure and the relatively high surface area of BiVO4, which provide more active sites for facilitating the vanadium redox reactions. Furthermore, the BiVO4-GF electrode obstructs the competitive irreversible hydrogen evolution reaction on the negative side of the cell, and it also has better wettability. Impressively, BiVO4-GF as the negative electrode shows good stability over 100 cycles. © 2023 American Chemical Society.

关键词： Electrocatalysts

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Decoding EEG Signals Both During and After Offset of Small and Short-Time Visual Target Stimulus

Decoding EEG Signals Both During and After Offset of Small a...

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International Winter Workshop on Brain-Computer Interface (BCI)

作者： Jaehyun Kim Sungu Nam Sangjin Jang Youngjo Song Byunghyuk Choi Jaeseung Jeong Brain Cognitive Engineering Program Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea Life Science Research Institute Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea Department of Bio and Brain Engineering Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea Department of Brain Cognitive Science Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea

Conventional visual target detection with EEG signals has been experimented by exposing target objects that are large enough to be noticed without searching on visual image in order to average their corresponding responses such as event-related potentials (ERPs) to raise signal-to-noise ratio. Recent studies turn attention to decoding single-trial ERPs, while their experiments still minimize target object search time. In this paper, we studied the temporal aspects of target recognition of human brain including target object search by introducing the concept of semi-targets that are features posterior to offset of target visual stimuli, and applying it into a type of contrastive learning, Triplet MatchNet. The results showed that features five seconds posterior to target visual stimuli help increase in performance of EEG decoding.

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Selectivity of CO_(2)reduction reaction to CO on the graphitic edge active sites of Fe-single-atom and dual-atom catalysts:A combined DFT and microkinetic modeling

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Carbon Resources Conversion 2024年第1期7卷 21-31页

作者： Ahmad Nuruddin Adhitya Gandaryus Saputro Arifin Luthfi Maulana Febdian Rusydi Fiki Taufik Akbar Hadi Teguh Yudistira Hermawan Kresno Dipojono Advanced Functional Materials Research Group Faculty of Industrial TechnologyInstitut Teknologi BandungJl.Ganesha No.10Bandung 40132Indonesia Research Center for Nanosciences and Nanotechnology Institut Teknologi BandungJl.Ganesha No.10Bandung 40132Indonesia Research Center for Quantum Engineering Design Department of PhysicsFaculty of Science and TechnologyUniversitas AirlanggaSurabaya 60115Indonesia Theoretical High Energy Physics Research Division Faculty of Mathematics and Natural SciencesInstitut Teknologi BandungJl.Ganesha No.10Bandung 40132Indonesia Mechanical Engineering Study Program Institut Teknologi Sumatera(ITERA)South LampungLampungIndonesia Department of Materials Science and Engineering University of CaliforniaBerkeleyBerkeleyCA 94720United States

We study the carbon dioxide reduction reaction(CO_(2)RR)activity and selectivity of Fe single-atom catalyst(Fe-SAC)and Fe dual-atom catalyst(Fe-DAC)active sites at the interior of graphene and the edges of graphitic nanopore by using a combination of DFT calculations and microkinetic *** trend of limiting potentials for CO_(2)RR to produce CO can be described by using either the adsorption energy of COOH,CO,or their ***_(2)RR process with reasonable reaction rates can be achieved only on the active site configurations with weak tendencies toward CO *** efficiency of CO_(2)RR on a catalyst depends on its ability to suppress the parasitic hydrogen evolution reaction(HER),which is directly related to the behavior of H adsorption on the catalyst’s active *** find that the edges of the graphitic nanopore can act as potential adsorption sites for an H atom,and in some cases,the edge site can bind the H atom much stronger than the main Fe *** linear scaling between CO and H adsorptions is broken if this condition is *** condition also allows some edge active site configurations to have their CO_(2)RR limiting potential lower than the HER process favoring CO production over H2 production.

关键词： CO_(2)RR FexNy active site Fe-SAC Fe-DAC Graphitic edges DFT Microkinetic

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A Tensor Train based Multi-channel Fault Signal De-noising Method for Wind Turbine Generators 4

A Tensor Train based Multi-channel Fault Signal De-noising M...

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4th IEEE International Conference on Digital Twins and Parallel Intelligence, DTPI 2024

作者： Li, Keren Zhang, Wenqiang Xiao, Dandan Hou, Peng Shaltout, Mohamed L. Mao, Xuerui Beijing Institute of Technology Yangtze Delta Region Academy Jiaxing China Beijing Institute of Technology School of Mechatronical Engineering Beijing China Beijing Institute of Technology School of Aerospace Engineering Beijing China Baima Lake Laboratory Co. Ltd Hangzhou China Zewail City of Science and Technology Renewable Energy Engineering Program Giza Egypt Beijing Institute of Technology Advanced Research Institute-of Multidisciplinary Sciences Beijing China

ISBN: (纸本)9798350349252

With the continuous development of sensors and information collection related technologies, there are more and more types of data, and the amount of data of the same type is getting larger and larger. For mechanical components such as fan rotating gears, the use of a single sensor for fault diagnosis has limitations, and it is impossible to fully and simultaneously perform auxiliary fault diagnosis on gears, bearings and other components on each shaft. However, the use of multi-channel sensors can solve this problem well, but in actual engineering applications, there is noise interference when multi-channel sensors perform joint fault diagnosis, and it is impossible to accurately extract the fault characteristics of rotating machinery. This paper proposes a feature extraction method based on tensor train fused signal (TTFS) as a means of addressing noise interference in rotating machinery signals within wind farms. Initially, our focus is on data collection, during which we analyse data in tensor format across three dimensions: time, frequency, and channel. In order to emphasise the use of tensor train decomposition, we introduce a tensor reconstruction method with adaptive filter truncation. Subsequently, the continuous wavelet transform (CWT) method is employed to establish tensor data representation across these dimensions. Subsequently, the proposed adaptive filtering truncation tensor reconstruction method is employed to reconstruct the tensor by combining the aforementioned matrices. Finally, the continuous wavelet inverse transform is applied to the reconstructed tensor in order to obtain time-domain signals from different channels. The efficacy of the proposed method is demonstrated through experimental signals, which illustrate the advantages of the method and the improved convergence speed of the objective function. © 2024 IEEE.

关键词： Adaptive filtering

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An ultra thin,bright,and sensitive interactive tactile display based on organic mechanoluminescence for dual-mode handwriting identification

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InfoMat 2024年第6期6卷 76-87页

作者： Tingting Hou Wenlang Li Haoyu Wang Yuantian Zheng Chaojie Chen Haoran Zhang Kai Chen Huilin Xie Xin Li Shaoshuai He Siwei Zhang Dengfeng Peng Cheng Yang Jacky W.Y.Lam Ben Zhong Tang Yunlong Zi Department of Mechanical and Automation Engineering The Chinese University of Hong KongHong Kongthe People's Republic of China Department of Chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced StudyThe Hong Kong University of Science and TechnologyHong Kongthe People's Republic of China Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province College of Physics and Optoelectronic EngineeringShenzhen UniversityShenzhenthe People's Republic of China Thrust of Sustainable Energy and Environment The Hong Kong University of Science and Technology(Guangzhou)Guangzhouthe People's Republic of China The Hong Kong University of Science and Technology Interdisciplinary Program Office Hong Kong SARthe People's Republic of China Institute of Materials Research Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenthe People's Republic of China School of Science and Engineering Shenzhen Institute of Aggregate Science and TechnologyThe Chinese University of Hong KongShenzhenthe People's Republic of China HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute Shenzhenthe People's Republic of China Guangzhou HKUST Fok Ying Tung Research Institute Guangzhouthe People's Republic of China

Visible light-based human–machine interactive media is capable of transmitting electrical readouts to machines and providing intuitive feedback to users ***,many inorganic mechanoluminescent(ML)materials-based interactive media,typically ZnS-loaded phosphors(ZLPs),have been successfully ***,organic ML materials-based solutions were rarely exploited despite their huge merits of strong structural modification,abundant luminescence property,low cost,easy preparation,and so ***,we propose a novel interactive tactile display(ITD)based on organic ML materials(Cz-A6-dye)and triboelectric nanogenerator,with ultra-brightness(130%enhancement)and ultra-low threshold pressure(57%reduction)as compared to *** proposed ITD achieves the conversion of weak mechanical stimuli into visible light and electrical signals simultaneously,without extra power ***,the relationship between the luminous performance of organic ML materials and mechanical force is quantified,benefiting from the uniform ML layer *** by convolutional neural networks,the high-accuracy recognition(97.1%)for handwriting and identity of users is realized at the same ***,the ITD has great potential for intelligent wearable electronics and classified military applications.

关键词： interactive media organic mechanoluminescence triboelectric nanogenerators

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