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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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Comparative analysis of deep learning models for detecting face mask 7

Comparative analysis of deep learning models for detecting f...

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7th International Conference on computer science and Computational Intelligence, CSCI 2022

作者： Ramadhan, M. Vickya Muchtar, Kahlil Nurdin, Yudha Oktiana, Maulisa Fitria, Maya Maulina, Novi Elwirehardja, Gregorius Natanael Pardamean, Bens Department of Electrical and Computer Engineering Universitas Syiah Kuala Banda Aceh23111 Indonesia Universitas Syiah Kuala Banda Aceh23111 Indonesia Microbiology Department School of Medicine Universitas Syiah Kuala Banda Aceh23111 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department BINUS Graduate Program-Master of Computer Science Program Bina Nusantara University Jakarta 11480 Indonesia

The spread of Corona Virus Disease 19 (COVID-19) in Indonesia is still relatively high and has not shown a significant decrease. One of the main reasons is due to the lack of supervision on the implementation of health protocols such as wearing masks in daily activities. Recently, state-of-The-Art algorithms were introduced to automate face mask detection. To be more specific, the researchers developed various kinds of architectures for the detection of masks based on computer vision methods. This paper aims to evaluate well-known architectures, namely the ResNet50, VGG11, InceptionV3, EfficientNetB4, and YOLO (You Only Look Once) to recommend the best approach in this specific field. By using the MaskedFace-Net dataset, the experimental results showed that the EfficientNetB4 architecture has better accuracy at 95.77% compared to the YOLOv4 architecture of 93.40%, InceptionV3 of 87.30%, YOLOv3 of 86.35%, ResNet50 of 84.41%, VGG11 of 84.38%, and YOLOv2 of 78.75%, respectively. It should be noted that particularly for YOLO, the model was trained using a collection of MaskedFace-Net images that had been pre-processed and labelled for the task. The model was initially able to train faster with pre-Trained weights from the COCO dataset thanks to transfer learning, resulting in a robust set of features expected for face mask detection and classification. © 2022 Elsevier B.V.. All rights reserved.

关键词： Face recognition

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Metal-organic framework derived Mn0.2Zn0.8Se/C amalgamated with nitrogen-doped graphene hydrogel for antioxidant trolox detection in food, environmental, and biological samples

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Chemical engineering Journal 2024年 496卷

作者： Ashokrao Jagtap, Akash Sakthivel, Rajalakshmi Kubendhiran, Subbiramaniyan Lin, Lu-Yin Kannan Ramaraj, Sayee Liu, Xinke Pattappan, Dhanaprabhu Hsu-Wei Lai, Yi-Ting Tung, Ching-Wei Chung, Ren-Jei Taipei Taiwan PG& Research Department of Chemistry Thiagarajar College Tamilnadu Madurai India College of Materials Science and Engineering Chinese Engineering and Research Institute of Microelectronics Shenzhen University Shenzhen China Department of Electrical and Computer Engineering National University of Singapore Singapore Department of Materials Engineering Ming Chi University of Technology New Taipei City Taiwan Taipei Taiwan

Determining the optimum level of trolox, an antioxidant, is crucial, as excessive consumption can harm human health. This study proposes a highly sensitive electrode material, manganese zinc selenide with carbon (Mn0.2Zn0.8Se/C) decorated on a nitrogen-doped graphene hydrogel (NGH) for trolox detection. The Mn–ZIF-8-derived Mn0.2Zn0.8Se/C was prepared via a simple selenization process, and the NGH@Mn0.2Zn0.8Se/C composite was prepared via sonication. Structural, morphological, and spectroscopic analyses of the prepared NGH@Mn0.2Zn0.8Se/C composite material were performed. This sensing platform is cost-effective, and its rapid preparation time renders it highly effective. The synergistic effect between NGH and the Mn0.2Zn0.8Se/C composite resulted in enhanced electrochemical performance, with a lower Rct value than that of the control materials. The proposed sensor exhibited a good linear range of 0.01–103.79 μM with a lower detection limit of 0.08 μM. Real-time monitoring confirmed the reliability of trolox for detecting food, environmental, and biological samples. © 2024 Elsevier B.V.

关键词： Graphene

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Synthetic materials with high pockels coefficient for plasmonic modulators

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Optical materials Express 2025年第6期15卷 1356-1370页

作者： Keller, Killian Dober, Marco Winiger, Joel Schneuwly, Arnaud Yu, Zhuoyang Baumann, Michael Doderer, Michael Nishiwaki, Shiro Romanyuk, Yaroslav E. Khurgin, Jacob B. Leuthold, Juerg ETH Zürich Gloriastrasse 35 Zurich8092 Switzerland Department of Materials Science and Engineering National University of Singapore 9 Engineering Drive 1 #03-09 EA 117575 Singapore Laboratory of Thin Films and Photovoltaics Empa Swiss Federal Laboratories for Materials Science and Technology Überlandstrasse 129 Dübendorf8600 Switzerland Department of Electrical and Computer Engineering John Hopkins Whiting School of Engineering 3400 North Charles Street BaltimoreMD21218 United States

We present simulations of Pockels materials based on nonlinearities arising from intersubband transitions (ISBT). To elevate the Pockels coefficient to the order of nm/V, the ISBT resonance is tuned close to the operation point. This comes at the expense of increased material losses due to quasi-resonant operation. Such Pockels materials are of high interest for implementation in plasmonic modulators. In these modulators the higher material losses do not significantly impact the device performance, as overall losses are dominated by plasmonic waveguide losses. With this approach, voltage-loss-length (VπLα) products on the order of ∼15 V dB may be achieved with plasmonic losses. Such efficiencies are comparable to those with photonic modulators. The Pockels effect coefficient calculations have been performed using self-consistent Schrödinger-Poisson simulations with consideration of many-body effects. Furthermore, we investigated the influence of RF field screening and surface roughness on the efficiency of the ISB transition-mediated Pockels materials. © 2025 Optica Publishing Group (formerly OSA). All rights reserved.

关键词： Light modulation

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Overcoming Secondary Nucleation of Misoriented Domains during Wafer-Scale Epitaxy of Single-Crystal Graphene on Ge(110)

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ACS Nano 2025年第22期19卷 21046-21056页

作者： Jacobberger, Robert M. Miao, Zichun Yu, Ka-Man Lam, Yin Hei Li, Zizhong He, Yangchen Wang, Jia Su, Katherine A. Pathaare, Yashwrdhan Saraswat, Vivek Rhodes, Daniel A. Lagally, Max G. Altman, Michael S. Arnold, Michael S. Department of Materials Science and Engineering University of Wisconsin-Madison MadisonWI53706 United States Department of Electrical and Computer Engineering University of Wisconsin-Madison MadisonWI53706 United States Department of Physics Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong Department of Physics University of Wisconsin-Madison MadisonWI53706 United States

The wafer-scale synthesis of single-crystal graphene on technologically important substrates is a major challenge inhibiting the development of next-generation devices that harness the exceptional electronic, thermal, and mechanical properties of single-crystal graphene. Here, the factors controlling the domain orientation of graphene grown epitaxially on Ge(110) are elucidated, and this insight is utilized to produce graphene with minimal polycrystallinity. In the early stages of growth, most graphene islands have unidirectionally aligned lattices. However, we discover a secondary nucleation phenomenon in which misoriented graphene domains nucleate near/from the island edges, introducing defective grain boundaries and significantly increasing polycrystallinity throughout growth. We find that secondary nucleation occurs when islands grow over Ge steps, which form because of an interplay between the island growth and Ge surface topography evolution. Strategies for suppressing secondary nucleation are developed, enabling the synthesis of graphene in which the predominant crystal orientation has high coverage >99% and low rotational spread © 2025 American Chemical Society.

关键词： Plasma CVD

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Assessment of ATH-Filled Silicone Rubber Under DC Dry Band Arcing 24

Assessment of ATH-Filled Silicone Rubber Under DC Dry Band A...

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24th International Middle East Power System Conference, MEPCON 2023

作者： Mehmood, Basharat Ghunem, Refat El-Hag, Ayman Hassan, Mohammad K. Al-Sulaiti, Leena Abdala, Ahmed University of Waterloo Electrical & Computer Engineering Department 200 University Avenue W WaterlooONN2L 3G1 Canada OttawaONK1A0R6 Canada Qatar University Center for Advanced Materials Qatar Texas A&m University at Qatar Chemical Engineering Program Doha Qatar

ISBN: (纸本)9798350358469

This paper investigates the tracking and erosion performance of silicone rubber filled with alumina trihydrate under DC dry band arcing in the inclined plane tracking and erosion test (IPT). Alumina trihydrate is incorporated into silicone rubber at 50 wt.% loading level for preparing silicone rubber composites, which are exposed to DC dry band arcing under mild and severe voltage levels in the inclined plane tracking and erosion test. Test outcomes indicate that the mechanism of silicone rubber deterioration changes with respect to the severity of the DC dry band arcing. It is found that dry band arcing tends to stimulate surface tracking under mild voltage levels and erosion due to thermal degradation under relatively higher voltage levels (critical). Moreover, test results indicate that silicone rubber erosion is not solely influenced by the dry band arcing power derived from the leakage current, but also dependent on additional contributing mechanisms leading to elevated surface temperatures and severe erosion. © 2023 IEEE.

关键词： Erosion

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electrically tunable VO2-metal metasurface for mid-infrared switching, limiting, and nonlinear isolation

arXiv

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arXiv 2023年

作者： King, Jonathan Wan, Chenghao Park, Tae Joon Deshpande, Sanket Zhang, Zhen Ramanathan, Shriram Kats, Mikhail A. Department of Electrical and Computer Engineering University of Wisconsin-Madison United States Department of Materials Science and Engineering University of Wisconsin-Madison United States School of Materials Engineering Purdue University West LafayetteIN United States Department of Electrical and Computer Engineering Rutgers The State University of New Jersey New BrunswickNJ08854 United States

We demonstrate an electrically controlled metal-VO2 metasurface for the mid-wave infrared that simultaneously functions as a tunable optical switch, an optical limiter with a tunable limiting threshold, and a nonlinear optical isolator with a tunable operating range. The tunability is achieved via Joule heating through the metal comprising the metasurface, resulting in an integrated optoelectronic device. As an optical switch, the device has an experimental transmission ratio of ~100 when varying the bias current. Operating as an optical limiter, we demonstrated tunability of the limiting threshold from 20 mW to 180 mW of incident laser power. Similar degrees of tunability are also achieved for nonlinear optical isolation, which enables asymmetric (nonreciprocal) transmission. Copyright © 2023, The Authors. All rights reserved.

关键词： Vanadium dioxide

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Spleen-preserving distal pancreatectomy from multi-port to reducedport surgery approach

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World Journal of Gastrointestinal Surgery 2023年第7期15卷 1501-1511页

作者： Ching-Lung Hsieh Tung-Sheng Tsai Cheng-Ming Peng Teng-Chieh Cheng Yi-Jui Liu Department of Computer Science and Information Engineering Feng Chia UniversityTaichung 40724TaiwanChina Department of Surgery Chung Shan Medical University HospitalTaichung 40201TaiwanChina PhD Program of Electrical and Communications Engineering Feng Chia UniversityTaichung 40724Taiwan School of Medicine Chung Shan Medical UniversityTaichung 40201Taiwan Da Vinci Minimally Invasive Surgery Center Chung Shan Medical University HospitalTaichung 40201Taiwan Department of Automatic Control Engineering Feng Chia UniversityTaichung 407Taiwan

BACKGROUND Minimally invasive pancreatic surgery via the multi-port approach has become a primary surgical method for distal pancreatectomy(DP)due to its advantages of lower wound pain and superior cosmetic *** studies have applied reduced-port techniques for DP in an attempt to enhance cosmetic outcomes due to the minimally invasive *** recent review studies have compared multi-port laparoscopic DP(LDP)and multi-port robotic DP(RDP);most of these studies concluded multi-port RDP is more beneficial than multi-port LDP for spleen ***,there have been no comprehensive reviews of the value of reduced-port LDP and reduced-port *** To search for and review the studies on spleen preservation and the clinical outcomes of minimally invasive DP that compared reduced-port DP surgery with multi-port DP *** The PubMed medical database was searched for articles published between 2013 and *** search terms were implemented using the following Boolean search algorithm:(“distal pancreatectomy”OR“left pancreatectomy”OR“peripheral pancreatic resection”)AND(“reduced-port”OR“single-site”OR“single-port”OR“dual-incision”OR“single-incision”)AND(“spleen-preserving”OR“spleen preservation”OR“splenic preservation”).A literature review was conducted to identify studies that compared the perioperative outcomes of reduced-port LDP and reduced-port *** Fifteen articles published in the period from 2013 to 2022 were retrieved using three groups of search *** studies were added after manually searching the related ***,10 papers were selected after removing case reports(n=3),non-English language papers(n=1),technique papers(n=1),reviews(n=1),and animal studies(n=1).The common items were defined as items reported in more than five papers,and data on these common items were extracted from all *** ten studies included a total of 337 patients(females/males:231/106)who underwent *** total,166 patients(females/male

关键词： Minimally invasive surgery Robotic distal pancreatectomy Laparoscopic distal pancreatectomy Spleen preservation Reduced-port Multi-port

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Analytical Methods for Determining High Frequency Winding Loss for Toroidal Inductors

Analytical Methods for Determining High Frequency Winding Lo...

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IEEE Electric Ship Technologies Symposium, ESTS

作者： Todd J. Marzec Ravisekhar Raju Brandon Grainger Paul R. Ohodnicki Department of Electrical and Computer Engineering University of Pittsburgh Pittsburgh USA Fastwatt LLC Clifton Park USA Department of Mechanical Engineering and Materials Science University of Pittsburgh Pittsburgh USA

Inductors are energy storage devices that serve as key components in power conversion technology. The advent of wide-bandgap (WBG) semiconductor devices has led to high frequency operation of power converters at higher voltage and current levels. In the range of 20kHz-1MHz, additional sources of loss in magnetic components interfacing to these WBG semiconductors are introduced due to high-frequency electromagnetic phenomena. Finite element analysis can capture these effects to a high degree of accuracy but require extensive computation time precluding their application in robust optimization and design schemes. There exist several analytical models for winding loss in literature that can evaluate multiple designs with minimal computation cost. In this work, popular models are reviewed, investigated, and expanded on in the context of various toroidal winding geometries. The goal of this work is to analyze well-known winding loss models and demonstrate their accuracies at high frequency (beyond 20kHz) as they pertain to toroidal inductors while maintaining the low computation cost required for integration into optimization and design schemes.

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A Fingerprint Based Indoor Visible Light Positioning System for Tilted Receivers Equipped with a Single Photo Detector

A Fingerprint Based Indoor Visible Light Positioning System ...

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IEEE Conference on Wireless Communications and Networking

作者： Ibrahim M. Abou-Shehada Ali H. Muqaibel Wessam Mesbah Ki-Hong Park Mohamed-Slim Alouini Electrical Engineering Department King Fahd University of Petroleum and Minerals Dhahran Saudi Arabia Electrical Engineering Department Center for Communication Systems and Sensing King Fahd University of Petroleum and Minerals Dhahran Saudi Arabia Electrical and Computer Engineering Program King Abdullah University of Science and Technology Thuwal Saudi Arabia

ISBN: (数字)9798350303582

ISBN: (纸本)9798350303599

Indoor positioning systems (IPS) are gaining higher attention recently due to the increased demand for indoor location aware services. Visible light communication (VLC) is a promising technology to use for IPS. In particular, received signal strength (RSS) based visible light positioning (VLP) systems are gaining high attention due to their low complexity and cost, in addition to higher positioning accuracy compared to their radio frequency (RF) counterparts. One of the main challenges in RSS based VLP systems is encountered when the receiver (the target) is tilted and not placed in parallel with the transmitters (the anchors). RSS based trilateration techniques require a computationally expensive and time-consuming process to solve the nonlinear problem of tilted receivers. Fingerprint based systems generally provide high positioning accuracy with short positioning time, and maybe used to circumvent the need to deal with the high complexity associated with tilted receivers. However, the design of a fingerprinting VLP system for tilted receiver has not been explored yet as far as receivers with a single photodetector (PD) are concerned. In this work, a fingerprint based VLP system for tilted receivers using artificial neural networks (ANN) is proposed, where different types of input features for training the positioning algorithm are studied. We show that using the components of the normal vector to the PD's surface in addition to RSS values provides an excellent positioning accuracy with an average positioning error of 25.41 cm and a remarkably low average positioning time less than $\mathbf{5} \boldsymbol{\mu} \boldsymbol{s}$ . In addition, important research directions for future work are discussed.

关键词： Training Accuracy Receivers Artificial neural networks Fingerprint recognition Vectors Real-time systems

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