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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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Anomaly-Resistant Decentralized State Estimation Under Minimum Error Entropy With Fiducial Points for Wide-Area Power systems

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IEEE/CAA Journal of Automatica Sinica 2024年第1期11卷 74-87页

作者： Bogang Qu Zidong Wang Bo Shen Hongli Dong Hongjian Liu the College of Automation Engineering Shanghai University of Electric PowerShanghai 200090China IEEE the Department of Computer Science Brunel University LondonUxbridgeMiddiesex UB83PHUK the College of Information Science and Technology Donghua UniversityShanghai 200051 the Engineering Research Center of Digitalized Textile and Fashion Technology Ministry of EducationShanghai 201620China the Artificial Intelligence Energy Research Institute Northeast Petroleum UniversityDaqing 163318 the Heilongjiang Provincial Key Laboratory of Networking and Intelligent Control Northeast PetroleumDaqing 163318 the Sanya Offshore Oil&Gas Research Institute Northeast Petroleum UniversitySanya 572024China the Key Laboratory of Advanced Perception and Intelligent Control of High-End Equipment Ministry of EducationAnhui Polytechnic UniversityWuhu 2410000 the School of Mathematics and Physics Anhui Polytechnic UniversityWuhu 241000China

This paper investigates the anomaly-resistant decentralized state estimation(SE) problem for a class of wide-area power systems which are divided into several non-overlapping areas connected through transmission lines. Two classes of measurements(i.e., local measurements and edge measurements) are obtained, respectively, from the individual area and the transmission lines. A decentralized state estimator, whose performance is resistant against measurement with anomalies, is designed based on the minimum error entropy with fiducial points(MEEF) criterion. Specifically, 1) An augmented model, which incorporates the local prediction and local measurement, is developed by resorting to the unscented transformation approach and the statistical linearization approach;2) Using the augmented model, an MEEF-based cost function is designed that reflects the local prediction errors of the state and the measurement;and 3) The local estimate is first obtained by minimizing the MEEF-based cost function through a fixed-point iteration and then updated by using the edge measuring information. Finally, simulation experiments with three scenarios are carried out on the IEEE 14-bus system to illustrate the validity of the proposed anomaly-resistant decentralized SE scheme.

关键词： Decentralized state estimation(SE) measurements with anomalies minimum error entropy unscented Kalman filter wide-area power systems

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The Peridigm Meshfree Peridynamics Code

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Journal of Peridynamics and Nonlocal Modeling 2024年第1期6卷 118-148页

作者： Littlewood, David J. Parks, Michael L. Foster, John T. Mitchell, John A. Diehl, Patrick Center for Computing Research Sandia National Laboratories Albuquerque NM United States Hildebrand Department of Petroleum and Geosystems Engineering University of Texas at Austin Austin TX United States Center of Computation & Technology and Department of Physics and Astronomy Louisiana State University Baton Rouge LA United States Computer Science and Mathematics Division Oak Ridge National Laboratory Oak Ridge TN United States

Peridigm is a meshfree peridynamics code written in C++ for use on large-scale parallel computers. It was originally developed at Sandia National Laboratories and is currently managed as an open-source, community driven software project. Its primary features include bond-based, state-based, and non-ordinary state-based constitutive models, bond failure laws, contact, and support for explicit and implicit time integration. To date, Peridigm has been used primarily by methods developers focused on solid mechanics and material failure. Peridigm utilizes foundational software components from Sandia’s Trilinos project and was designed for extensibility. This paper provides an overview of the solution methods implemented in Peridigm, a discussion of its software infrastructure, and demonstrates the use of Peridigm for the solution of several example problems. © 2023, The Author(s).

关键词： Meshfree methods Open source software Peridynamics

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Effect of quenching rate on microstructure formation in Al-Zn-Mg alloy sheet

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Keikinzoku/Journal of Japan Institute of Light Metals 2023年第12期73卷 616-621页

作者： Aisu, Yuki Ichitani, Koji Tanaka, Hiroki Saito, Genki Muto, Shunsuke Okajima, Toshihiro Research & Development Center Marketing & Technology Division UACJ Corporation 3-1-12 Chitose Minato-ku Aichi Nagoya-shi455-8670 Japan Department of Materials Physics Graduate School of Engineering Nagoya University Aichi Nagoya-shi Japan Advanced Measurement Technology Center Institute of Materials and Systems for Sustainability Nagoya University Aichi Nagoya-shi Japan Aichi Synchrotron Radiation Center Aichi Science & Technology Foundation Aichi Seto-shi Japan

A phenomenon that Al-6.0%Zn-0.75%Mg alloy sheets furnace-cooled after solution heat treatment had higher strength than water-quenched sheets under specific aging condition was reported. However, the strengthening mechanism related to furnace-cooling had been not clarified yet. In this research, replication test of the strengthening phenomenon of furnace-cooled sheets and the microstructural change during natural aging and artificial aging at 200°C after furnace-cooling after solution heat treatment was investigated by tensile tests, SAXS measurements, STEM observation and electrical conductivity measurement. The strengthen phenomenon of furnace-cooled sheets was reproduced. In as-furnace-cooled sheets, 2-5 nm clusters which induced lattice strain were observed in LAADF-STEM image apart from atomic number contrast in HAADF-STEM image. The clusters seemed to be generated during furnace cooling. The clusters seemed to cause suppression of reversion and promotion of age hardening in furnace-cooled material. © 2023 The Japan Institute of Light Metals.

关键词： Zinc alloys

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Application of Data science and Machine Learning in the Prediction of College Dropout: A Data-Driven Predictive Approach

Application of Data Science and Machine Learning in the Pred...

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International Conference on Software Process Improvement (CIMPS)

作者： Axel Frederick Félix Jiménez Vania Stephany Sanchéz Lee Isaul Ibarra Belmonte Ezra Federico Parra González Engineering in Computer Systems National Polytechnic Institute Zacatecas México Software Engineer Center for Research in Mathematics Zacatecas México Computer Science Department Center for Research in Mathematics Zacatecas México

ISBN: (数字)9798350358568

ISBN: (纸本)9798350358575

This paper presents a study on the prediction of student graduation or failure using two predictive models: K-Nearest Neighbors (KNN) and a forward sequential Artificial Neural Network (ANN). The models, built with a well-chosen set of independent variables, were assessed using metrics like precision and accuracy. The results obtained revealed that both the KNN model and the sequential forward ANN model achieved high efficiency in predicting student graduation or failure, achieving accuracies of 0.9133% (K=3) and 0.9312% (after 50 epochs), respectively. Providing a valuable tool to identify early on students at risk of not graduating and to take preventive measures to improve their academic performance. Comparisons with related research showed consistent outcomes, underscoring the credibility and importance of the employed predictive models.

关键词： Measurement Artificial neural networks Machine learning Predictive models Data science Software

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Blockchain and Web of Things for Structural Health Monitoring Applications: A Proof of Concept 19

Blockchain and Web of Things for Structural Health Monitorin...

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19th IEEE Annual Consumer Communications and Networking Conference, CCNC 2022

作者： Gigli, Lorenzo Sciullo, Luca Montori, Federico Marzani, Alessandro Di Felice, Marco University of Bologna Department of Computer Science and Engineering Italy University of Bologna Department of Civil Chemical Environmental and Materials Engineering Italy University of Bologna Advanced Research Center on Electronic Systems Ercole de Castro Italy

ISBN: (纸本)9781665431620

Interoperable and secure data management techniques are fundamental for most of large-scale Structural Health Monitoring (SHM) systems. Indeed, given the relevance of SHM critical measurements, data integrity must be protected against tampering or falsifications. In this paper, we propose a four-layer SHM architecture that allows to build an effective data pipeline from sensors to consumer applications, passing through the cloud. The architecture is built on top of the MODRON platform and exploits the recent advances of the W3C Web of Things (WoT) standard for interoperability. We then discuss how third-party services can take benefit of the W3C WoT architecture to retrieve the SHM critical data and to publish them on the Ethereum Blockchain through an SHM-specific Smart Contract, for data protection and traceability purposes. We test the effectiveness of the Smart Contract implementation in terms of latency and costs under simulated workloads. © 2022 IEEE.

关键词： Smart contract

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Critical nonlinear aspects of hopping transport for reconfigurable logic in disordered dopant networks

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Physical Review Applied 2024年第2期22卷 024063页

作者： Henri Tertilt Jonas Mensing Marlon Becker Wilfred G. van der Wiel Peter A. Bobbert Andreas Heuer Institute for Physical Chemistry Department of Physics NanoElectronics Group Faculty of Electrical Engineering Mathematics and Computer Science MESA+ Institute for Nanotechnology and Center for Brain-Inspired Nano Systems (BRAINS) Department of Applied Physics Center for Computational Energy Research (CCER)

Nonlinear behavior in the hopping transport of interacting charges enables reconfigurable logic in disordered dopant network devices, where voltages applied at control electrodes tune the relation between voltages applied at input electrodes and the current measured at an output electrode. From kinetic Monte Carlo simulations we analyze the critical nonlinear aspects of variable-range hopping transport for realizing Boolean logic gates in these devices on three levels. First, we quantify the occurrence of individual gates for random choices of control voltages. We find that linearly inseparable gates such as the xor gate are less likely to occur than linearly separable gates such as the and gate, despite the fact that the number of different regions in the multidimensional control voltage space for which and or xor gates occur is comparable. Second, we use principal-component analysis to characterize the distribution of the output current vectors for the (00,10,01,11) logic input combinations in terms of eigenvectors and eigenvalues of the output covariance matrix. This allows a simple and direct comparison of the behavior of different simulated devices and a comparison to experimental devices. Third, we quantify the nonlinearity in the distribution of the output current vectors necessary for realizing Boolean functionality by introducing three nonlinearity indicators. The analysis provides a physical interpretation of the effects of changing the hopping distance and temperature and is used in a comparison with data generated by a deep neural network trained on a physical device.

关键词： Carrier dynamics Dynamics of networks Electrical conductivity Fitness Hopping transport Network optimization Optimization problems Temperature

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Electro-magneto-hydrodynamic Eyring-Powell fluid flow through micro-parallel plates with heat transfer and non-Darcian effects

Electro-magneto-hydrodynamic Eyring-Powell fluid flow throug...

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作者： Bhatti, Muhammad Mubashir Doranehgard, Mohammad Hossein Ellahi, Rahmat College of Mathematics and Systems Science Shandong University of Science and Technology Qingdao China Department of Mechanical and Aerospace Engineering Hong Kong University of Science and Technology Clear Water Bay Hong Kong Center for Modeling & Computer Simulation Research Institute King Fahd University of Petroleum and Minerals Dhahran Saudi Arabia Department of Mathematics and Statistics International Islamic University Islamabad Pakistan

The Eyring-Powell fluid flow between two micro-parallel plates in the context of electro-magneto-hydrodynamic is the focus of the article. The Lorentz force, which is generated by the interactions of a vertical magnetic field and an externally imposed horizontal electrical field, is presumed to be unilateral and one-dimensional. Using the Darcy-Brinkman-Forchheimer model, the medium of the micro-parallel plates is assumed to be porous. The energy equation evaluates the effect of viscous dissipation and joule heating as well. To solve the nonlinear coupled differential equations, analytical solutions are derived using the multi-step differential transform method. For the velocity and temperature profiles, the impact of all evolving variables is explored and illustrated in graphs and tables. It can be seen from the graphical results that the Darcy parameter, and also the magnetic field, are oppositional to both fluid motion and temperature profile. Additionally, the thermal Grashof number improves the velocity and temperature profiles of the system. On the velocity and temperature profiles, the outcomes for both fluid parameters are nearly identical. © 2022 John Wiley & Sons Ltd.

关键词： Temperature control

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Self-Immolative Electrochemical Redox Substrates: Emerging Artificial Receptors in Sensing and Biosensing

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ACS Measurement science Au 2024年第2期4卷 163-183页

作者： Manibalan, Kesavan Arul, Ponnusamy Wu, Hsin-Jay Huang, Sheng-Tung Mani, Veerappan Department of Materials Science and Engineering National Yang Ming Chiao Tung University Hsinchu 30010 Taiwan Institute of Biochemical and Biomedical Engineering Department of Chemical Engineering and Biotechnology National Taipei University of Technology Taipei 10608 Taiwan Advanced Membranes and Porous Materials Center (AMPMC) Computer Electrical and Mathematical Science and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia High-Value Biomaterials Research and Commercialization Center National Taipei University of Technology No. 1 Sec. 3 Zhongxiao E. Rd. Taipei 10608 Taiwan

The development of artificial receptors has great significance in measurement science and technology. The need for a robust version of natural receptors is getting increased attention because the cost of natural receptors is still high along with storage difficulties. Aptamers, imprinted polymers, and nanozymes are some of the matured artificial receptors in analytical chemistry. Recently, a new direction has been discovered by organic chemists, who can synthesize robust, activity-based, self-immolative organic molecules that have artificial receptor properties for the targeted analytes. Specifically designed trigger moieties implant selectivity and sensitivity. These latent electrochemical redox substrates are highly stable, mass-producible, inexpensive, and eco-friendly. Combining redox substrates with the merits of electrochemical techniques is a good opportunity to establish a new direction in artificial receptors. This Review provides an overview of electrochemical redox substrate design, anatomy, benefits, and biosensing potential. A proper understanding of molecular design can lead to the development of a library of novel self-immolative redox molecules that would have huge implications for measurement science and technology. © 2024 The Authors. Published by American Chemical Society.

关键词： alkaline phosphatase artificial receptors electrochemical mediators electrochemical sensors and biosensors galactosidase hydrogen peroxide neuraminidase organic electrochemistry ratiometric sensors self-immolative sensors

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Investigation on Structures of Axial Gap Type Magnetic Multiple Spur Gear for In-Wheel Motor System of Electric Vehicle

Investigation on Structures of Axial Gap Type Magnetic Multi...

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2023 IEEE Transportation Electrification Conference and Expo, Asia-Pacific, ITEC Asia-Pacific 2023

作者： Kamijo, Taiga Aiso, Kohei Akatsu, Kan Aoyama, Yasuaki Shibaura Institute of Technology Electrical Engineering and Computer Science Tokyo Japan Shibaura Institute of Technology Department of Electrical Engineering Tokyo Japan Yokohama National University Division of Intelligent Systems Engineering Department of Faculty of Engineering Yokohama Japan Center for Technology Innovation - Materials Hitachi Ltd. Research & Development Group Ibaraki Japan

ISBN: (纸本)9798350314274

A novel drive system using Magnetic Multiple Spur Gear (MMSG) and multiple high-speed motors is characterized by small size, lightweight, and high efficiency even at high-speed region, it is expected to apply to in-wheel motor systems. However, there is a risk of contact between the rotors when applied to in-wheel motor system. In this study, a novel axial-gap MMSG is proposed to solve this problem, stabilize the air gap between the high-speed and low-speed rotors, and effectively utilize the magnets, and its performance is evaluated by finite element analysis. © 2023 IEEE.

关键词： Electric vehicles

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