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Author Correction: AIVariant: a deep learning-based somatic variant detector for highly contaminated tumor samples

Experimental & molecular medicine 2025年第1期57卷 284页

作者： Hyeonseong Jeon Junhak Ahn Byunggook Na Soona Hong Lee Sael Sun Kim Sungroh Yoon Daehyun Baek Interdisciplinary Program in Bioinformatics Seoul National University Seoul Republic of Korea. Genome4me Inc. Seoul Republic of Korea. School of Biological Sciences Seoul National University Seoul Republic of Korea. Department of Electrical and Computer Engineering Seoul National University Seoul Republic of Korea. AIGENDRUG Co. Ltd. Seoul Republic of Korea. Department of Software and Computer Engineering Ajou University Suwon Republic of Korea. Department of Computer Science and Engineering Seoul National University Seoul Republic of Korea. Interdisciplinary Program in Artificial Intelligence Seoul National University Seoul Republic of Korea. Interdisciplinary Program in Bioinformatics Seoul National University Seoul Republic of Korea. baek@snu.ac.kr. Genome4me Inc. Seoul Republic of Korea. baek@snu.ac.kr. School of Biological Sciences Seoul National University Seoul Republic of Korea. baek@snu.ac.kr. Interdisciplinary Program in Artificial Intelligence Seoul National University Seoul Republic of Korea. baek@snu.ac.kr.

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Abnormal association between neural activity and genetic expressions of impulsivity in attention deficit hyperactivity disorder: an Adolescent Brain Cognitive Development study

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Biological Psychiatry: Cognitive Neuroscience and Neuroimaging 2025年

作者： Soohyun Jeon Jae-eon Kang Jundong Hwang Vince D. Calhoun Jong-Hwan Lee Department of Brain and Cognitive Engineering Korea University Seoul South Korea Center for Translational Research in Neuroimaging and Data Science (TReNDS): Georgia State University Georgia Institute of Technology and Emory University Atlanta USA Department of Electrical and Computer Engineering Georgia Institute of Technology Atlanta USA Interdisciplinary Program in Precision Public Health Korea University Seoul South Korea McGovern Institute for Brain Research Massachusetts Institute of Technology Boston MA

Background Impulsivity in highly heritable attention deficit hyperactivity disorder (ADHD) has been studied using neural activity via fMRI or genetic data, but rarely with multivariate methods linking both. We investigated coupled neural activity and gene expression signatures, using parallel independent component analysis (pICA) and Adolescent Brain Cognitive Development data. Methods Children with ADHD ( n = 394; 63% males) and healthy controls ( n = 1,000; 47% males) of European ancestry were included. The subjects were randomly divided into 80% discovery and 20% replication datasets with demographic stratification. We analyzed neural activity and gene expressions from the discovery datasets using pICA and extracted paired independent components (pICs). The loading coefficients of the pICs were utilized to predict behavioral and cognitive data for stop signal task (SST) in replication datasets. Results We identified three pICs estimated from gene expression in the cortex, cerebellum, and nucleus accumbens. Significant neural activity was mainly localized to the orbital/inferior/middle frontal gyri, rectal gyrus, precuneus, inferior temporal gyrus, inferior parietal lobule, and cerebellum. Significant gene components were associated with immunoglobulin, taste receptor, and immunity-related terms and were overlapped with ADHD-related genes. The extracted fMRI-/Gene-ICs were significantly correlated with mean reaction time, stop signal reaction time of SST, and behavioral inhibition with a large boost in sensitivity when both the paired fMRI-/Gene-ICs and their interaction were used in a multimodal regression analysis. Conclusion We reported biologically plausible pairs of neural activity and gene sets using pICA, which were significantly associated with ADHD impulsivity-related behavioral and cognitive data.

关键词： Attention deficit hyperactivity disorder functional magnetic resonance imaging gene expression imaging genetics parallel independent component analysis stop signal task

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Investigation of the Electronic, Magnetic, Exchange Interactions, and Magnetocaloric Properties in Orthotitanate Oxides Rtio3 (R = Er, Ho)

SSRN

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SSRN 2023年

作者： Jmal, Sohail Ait Tamerd, Mohamed Ait Mounkachi, Omar Salvestrini, Jean Paul Balli, Mohamed AMEEC Team LERMA International University of Rabat Parc Technopolis Rocade de Rabat- Salé 11100 Morocco Laboratory of Condensed Matter and Interdisciplinary Sciences Department of Physics Faculty of Sciences Mohammed V University in Rabat PO Box 1014 Rabat Morocco Modeling Simulation & Data Analysis Program Mohammed VI Polytechnic University Ben Guerir43150 Morocco Institute of Applied Physics Mohammed VI Polytechnic University Lot 660 Hay Moulay Rachid BP 43150 Ben Guerir Morocco CNRS IRL 2958 Georgia Tech CNRS 2 rue Marconi Metz57070 France Georgia Institute of Technology School of Electrical and Computer Engineering AtlantaGA30332-0250 United States

Strong correlated materials are emerging materials in low magnetocaloric cooling applications. The development of these fields necessitates materials with appealing magnetic, and magnetocaloric features. In this context, Density Functional Theory (DFT) combined with Monte Carlo simulations (MCs) are performed to comprehensively examine various physical, and magnetic features of the orthorhombic perovskite-type RTiO3. A metallic behavior of (Ho, Er)TiO3 has been found via the density of state using GGA+U approach. X-ray magnetic circular dichroism (XMCD) was carried out to identify the magnetic contributions of Ho, Er, and Ti atoms in HoTiO3, and ErTiO3 compounds. The spin-orbit coupling was added in our calculations to study and evaluate the magnetocrystalline anisotropies of RTiO3 with (R= Ho, Er). We noticed an easy magnetization axis along the b-direction for HoTiO3, and along the c-direction for ErTiO3. Low magnetocrystalline anisotropy energies were found compared to other perovskite oxides such as RVO3, and RMnO3indicating that a weak rotating magnetocaloric effect (RMCE) is expected in (Ho, Er)TiO3. Moreover, the exchange coupling interactions were calculated using Ising model, the (Ti-Ti) interaction coupling is ferromagnetic, and larger than the other exchange interactions in (Ho, Er)TiO3. Furthermore, these exchange coupling interactions were utilized within the Heisenberg model for MCs, allowing us to understand the driving mechanisms underlying magnetocaloric and magnetic behaviors in (Ho, Er)TiO3. © 2023, The Authors. All rights reserved.

关键词： Perovskite

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A PARALLEL VARIATIONAL MESH QUALITY IMPROVEMENT METHOD FOR TETRAHEDRAL MESHES 28

A PARALLEL VARIATIONAL MESH QUALITY IMPROVEMENT METHOD FOR T...

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28th International Meshing Roundtable, IMR 2019

作者： Shontz, Suzanne M. Varilla, M.A.L. Huang, Weizhang Department of Electrical Engineering and Computer Science Bioengineering Program Information and Telecommunication Technology Center University of Kansas LawrenceKS United States Husky Injection Molding Systems Ltd. Luxembourg Luxembourg Department of Mathematics University of Kansas LawrenceKS United States

ISBN: (纸本)9781733489003

There are numerous large-scale applications requiring mesh adaptivity, e.g., computational uid dynamics and weather prediction. Parallel processing is needed for simulations involving large-scale adaptive meshes. In this paper, we propose a parallel variational mesh quality improvement algorithm for use with distributed memory machines. Our method parallelizes the serial variational mesh quality improvement method by Huang and Kamenski. Their approach is based on the use of the Moving Mesh PDE method to adapt the mesh based on the minimization of an energy functional for mesh equidistribution and alignment. This leads to a system of ordinary differential equations (ODEs) to be solved which determine where to move the interior mesh nodes. An efficient solution is obtained by solving the ODEs on subregions of the mesh with overlapped communication and computation. Strong and weak scaling experiments on up to 128 cores for meshes with up to 160M elements demonstrate excellent results. © 2019 Proceedings of the 28th International Meshing Roundtable, IMR 2019. All rights reserved.

关键词： Ordinary differential equations

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Bulk-plasmon-mediated free-electron radiation beyond the conventional formation time

arXiv

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arXiv 2022年

作者： Tay, Fuyang Lin, Xiao Shi, Xihang Chen, Hongsheng Kaminer, Ido Zhang, Baile Interdisciplinary Center for Quantum Information State Key Laboratory of Modern Optical Instrumentation ZJUHangzhou Global Science and Technology Innovation Center College of Information Science and Electronic Engineering Zhejiang University Hangzhou310027 China Department of Electrical and Computer Engineering Rice University HoustonTX77005 United States Applied Physics Graduate Program Smalley–Curl Institute Rice University HoustonTX77005 United States International Joint Innovation Center The Electromagnetics Academy Zhejiang University Zhejiang University Haining314400 China Department of Electrical Engineering Technion-Israel Institute of Technology Haifa32000 Israel Jinhua Institute of Zhejiang University Zhejiang University Jinhua321099 China Division of Physics and Applied Physics School of Physical and Mathematical Sciences Nanyang Technological University 637371 Singapore Centre for Disruptive Photonic Technologies Nanyang Technological University 637371 Singapore

Free-electron radiation is a fundamental photon emission process that is induced by fast-moving electrons interacting with optical media. Historically, it has been understood that, just like any other photon emission process, free-electron radiation must be constrained within a finite time interval known as the "formation time", whose concept is applicable to both Cherenkov radiation and transition radiation, the two basic mechanisms describing radiation from a bulk medium and from an interface, respectively. Here we reveal an alternative mechanism of free-electron radiation far beyond the previously defined formation time. It occurs when a fast electron crosses the interface between vacuum and a plasmonic medium supporting bulk plasmons. While emitted continuously from the crossing point on the interface — thus consistent with the features of transition radiation — the extra radiation beyond the conventional formation time is supported by a long tail of bulk plasmons following the electron’s trajectory deep into the plasmonic medium. Such a plasmonic tail mixes surface and bulk effects, and provides a sustained channel for electron-interface interaction. These results also settle the historical debate in Ferrell radiation, regarding whether it is a surface or bulk effect, from transition radiation or plasmonic oscillation. Copyright © 2022, The Authors. All rights reserved.

关键词： Plasmonics

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Taming cluster synchronization

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Chaos, Solitons and Fractals 2025年 199卷

作者： Tomaselli, Cinzia Gambuzza, Lucia Valentina Sun, Gui-Quan Boccaletti, Stefano Frasca, Mattia Modeling and Engineering Risk and Complexity Program Scuola Superiore Meridionale Naples80138 Italy Department of Electrical Electronics and Computer Science Engineering University of Catania Catania95125 Italy Complex Systems Research Center Shanxi University Shanxi Taiyuan030006 China Sino-Europe Complex Science Center North University of China Shanxi Taiyuan030051 China Institute of Interdisciplinary Intelligent Science Ningbo Univ. of Technology Ningbo China CNR - Institute of Complex Systems Sesto FiorentinoI-50019 Italy

Synchronization is a widespread phenomenon observed across natural and artificial networked systems. It often manifests itself by clusters of units exhibiting coincident dynamics. These clusters are a direct consequence of the organization of the Laplacian matrix eigenvalues into spectral localized blocks. We show how the concept of spectral blocks can be leveraged to design straightforward yet powerful controllers able to fully manipulate cluster synchronization of a generic network, thus shaping at will its parallel functioning. Specifically, we demonstrate how to induce the formation of spectral blocks in networks where such structures would not exist, and how to achieve precise mastering over the synchronizability of individual clusters by dictating the sequence in which each of them enters or exits the synchronization stability region as the coupling strength varies. Our results underscore the pivotal role of cluster synchronization control in shaping the parallel operation of networked systems, thereby enhancing their efficiency and adaptability across diverse applications. © 2025 The Authors

关键词： Networked control systems

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Sub-picosecond all-optical switching in a hybrid VO2:silicon waveguide at 1550 nm

arXiv

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arXiv 2020年

作者： Hallman, Kent A. Miller, Kevin J. Baydin, Andrey Weiss, Sharon M. Haglund, Richard F. Department of Physics and Astronomy Vanderbilt University NashvilleTN37235 United States Interdisciplinary Graduate Program in Materials Science NashvilleTN37235 United States Department of Electrical Engineering and Computer Science Vanderbilt University NashvilleTN37235 United States AEgis Technologies Group 410 Jan Davis Drive HuntsvilleAL35803 United States Department of Electrical and Computer Engineering Rice University HoustonTX70005 United States

Achieving ultrafast all-optical switching in a silicon waveguide geometry is a key milestone on the way to an integrated platform capable of handling the increasing demands for higher speed and higher capacity for information transfer. Given the weak electro-optic and thermo-optic effects in silicon, there has been intense interest in hybrid structures in which that switching could be accomplished by integrating another material into the waveguide, including the phase-changing material, vanadium dioxide (VO2). It has long been known that the phase transition in VO2 can be triggered by ultrafast laser pulses, and that pump-laser fluence is a critical parameter governing the recovery time of thin films irradiated by femtosecond laser pulses near 800 nm. However, thin-film experiments are not a priori reliable guides to using VO2 for all-optical switching in on-chip silicon photonics because of the large changes in VO2 optical constants in the telecommunications band, the requirement of low insertion loss, and the limits on switching energy permissible in integrated photonic systems. Here we report the first measurements to show that the reversible, ultrafast photo-induced phase transition in VO2 can be harnessed to achieve sub-picosecond switching when small VO2 volumes are integrated in a silicon waveguide as a modulating element. Switching energies above threshold are of order 600 fJ/switch. These results suggest that VO2 can now be pursued as a strong candidate for all-optical switching with sub-picosecond on-off times. Copyright © 2020, The Authors. All rights reserved.

关键词： Optical switches

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Exploration of the Impact of Physical Integration Schemes on Soft Errors in 3D ICs Using Monte Carlo Simulation

Exploration of the Impact of Physical Integration Schemes on...

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Annual International Symposium on Reliability Physics

作者： M. L. Breeding R. A. Reed K. M. Warren M. L. Alles Interdisciplinary Materials Science and Engineering Program Vanderbilt University Nashville TN USA Electrical Engineering and Computer Science Department Vanderbilt University Nashville TN USA

The complex vertical structures of 2.5D/3D integrated circuits present new challenges for the simulation, experimentation, and analysis of soft errors. Each added layer of circuitry in vertically integrated technologies increases the requirement for interconnect metallization. The proximity of these metal layers to sensitive regions may result in materials-dependent responses to radiation. Monte-Carlo simulations offer flexibility and utility in exploring the impact of geometry and material selection on the resulting radiation response characteristics in 3D IC structures. As the fabrication and experimentation of such technologies at this point follows no universal standard or guidelines, various configuration possibilities are advantageously thus considered in order to minimize cost and waste. Simulations indicate important differences in relative responses to radiation effects; in the discussed parametrizations, copper and cobalt interconnects behave similarly, while tungsten interconnects exhibit better properties than ruthenium.

关键词： Three-dimensional displays Metals Neutrons Radiation effects Integrated circuit interconnections Reliability

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GeoT: A Geometry-aware Transformer for Reliable Molecular Property Prediction and Chemically Interpretable Representation Learning

arXiv

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arXiv 2021年

作者： Kwak, Bumju Park, Jiwon Kang, Taewon Jo, Jeonghee Lee, Byunghan Yoon, Sungroh Recommendation Team Kakao Corporation Gyeonggi13529 Korea Republic of LG Chem Seoul07795 Korea Republic of Interdisciplinary Program in Artificial Intelligence Seoul National University Seoul08826 Korea Republic of Daejeon34141 Korea Republic of Institute of New Media and Communications Seoul National University Seoul08826 Korea Republic of Department of Electronic Engineering Seoul National University of Science and Technology Seoul01811 Korea Republic of Department of Electrical and Computer Engineering Seoul National University Seoul08826 Korea Republic of Artificial Intelligence Institute Seoul National University Seoul08826 Korea Republic of

In recent years, molecular representation learning has emerged as a key area of focus in various chemical tasks. However, many existing models fail to fully consider the geometric information of molecular structures, resulting in less intuitive representations. Moreover, the widely used message-passing mechanism is limited to provide the interpretation of experimental results from a chemical perspective. To address these challenges, we introduce a novel Transformer-based framework for molecular representation learning, named the Geometry-aware Transformer (GeoT). GeoT learns molecular graph structures through attention-based mechanisms specifically designed to offer reliable interpretability, as well as molecular property prediction. Consequently, GeoT can generate attention maps of interatomic relationships associated with training objectives. In addition, GeoT demonstrates comparable performance to MPNN-based models while achieving reduced computational complexity. Our comprehensive experiments, including an empirical simulation, reveal that GeoT effectively learns the chemical insights into molecular structures, bridging the gap between artificial intelligence and molecular sciences. © 2021, CC BY.

关键词： Geometry

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Publisher’s Note: “Ultraviolet nanosecond laser ablation of polyimide with thermal and nonthermal effects near threshold fluence” [J. Laser Appl. 34, 032004 (2022)]

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Journal of Laser Applications 2022年第3期34卷

作者： ChangSoon Han Muhammad Aleem Zahid Byungwoo Lee Jae-Yong Oh Youngkuk Kim Junsin Yi 1Laser Advanced System Industrialization Center Jeonnam Technopark Stiftung Jeollanam-do Jangseong-gun 57248 Republic of Korea 2Interdisciplinary Program in Photovoltaic System Engineering Sungkyunkwan University Suwon Gyeonggi-Do Suwon 16419 Republic of Korea 3Department of Electrical and Computer Engineering Sungkyunkwan University Suwon Gyeonggi-Do 16419 South Korea

This article was published online on 17 June 2022 with an error in the affiliations and corresponding author information. The affiliations and footnote appear c

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