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arXiv 2023年

作者： Doumani, Jacques Lou, Minhan Dewey, Oliver Hong, Nina Fan, Jichao Baydin, Andrey Yomogida, Yohei Yanagi, Kazuhiro Pasquali, Matteo Saito, Riichiro Kono, Junichiro Gao, Weilu Department of Electrical and Computer Engineering Rice University HoustonTX United States Applied Physics Graduate Program Smalley–Curl Institute Rice University HoustonTX United States Department of Electrical and Computer Engineering The University of Utah Salt Lake CityUT United States Carbon Hub Rice University HoustonTX United States Department of Chemical and Biomolecular Engineering Rice University HoustonTX United States J.A. Woollam Co. Inc. LincolnNE United States Smalley–Curl Institute Rice University HoustonTX United States Department of Physics Tokyo Metropolitan University Tokyo Japan Department of Chemistry Rice University HoustonTX United States Department of Materials Science and NanoEngineering Rice University HoustonTX United States Department of Physics Tohoku University Sendai Japan Department Physics and Astronomy Rice University HoustonTX United States

There is an emerging recognition that successful utilization of chiral degrees of freedom can bring new scientific and technological opportunities to diverse research areas. Hence, methods are being sought for creating artificial matter with controllable chirality in an uncomplicated and reproducible manner. Here, we report the development of two straightforward methods for fabricating wafer-scale chiral architectures of ordered carbon nanotubes (CNTs) with tunable and giant circular dichroism (CD). Both methods employ simple approaches, (i) mechanical rotation and (ii) twist-stacking, based on controlled vacuum filtration and do not involve any sophisticated nanofabrication processes. We used a racemic mixture of CNTs as the starting material, so the intrinsic chirality of chiral CNTs is not responsible for the observed chirality. In particular, by controlling the stacking angle and handedness in (ii), we were able to maximize the CD response and achieve a record-high deep-ultraviolet ellipticity of 40 ± 1 mdeg/nm. Our theoretical simulations using the transfer matrix method reproduce the salient features of the experimentally observed CD spectra and further predict that a film of twist-stacked CNTs with an optimized thickness will exhibit an ellipticity as high as 150 mdeg/nm. The created wafer-scale objects represent a new class of synthetic chiral matter consisting of ordered quantum wires whose macroscopic properties are governed by nanoscopic electronic signatures such as van Hove singularities. These artificial structures with engineered chirality will not only provide playgrounds for uncovering new chiral phenomena but also open up new opportunities for developing high-performance chiral photonic and optoelectronic devices. © 2023, CC BY.

关键词： Carbon nanotubes

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Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks

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Nucleic acids research 2023年第13期51卷 6578-6592页

作者： Yongjian Yang Guanxun Li Yan Zhong Qian Xu Bo-Jia Chen Yu-Te Lin Robert S Chapkin James J Cai Department of Electrical and Computer Engineering Texas A&M University College Station TX 77843 USA. Department of Statistics Texas A&M University College Station TX 77843 USA. Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of Statistics East China Normal University 3663 North Zhongshan Road Shanghai 200062 China. Department of Veterinary Integrative Biosciences Texas A&M University College Station TX 77843 USA. Graduate Institute of Microbiology and Public Health College of Veterinary Medicine National Chung Hsing University Taichung 402 Taiwan. Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan. Program in Integrative & Complex Diseases Department of Nutrition Texas A&M University College Station TX 77843 USA. Interdisciplinary Program of Genetics Texas A&M University College Station TX 77843 USA.

In this paper, we introduce Gene Knockout Inference (GenKI), a virtual knockout (KO) tool for gene function prediction using single-cell RNA sequencing (scRNA-seq) data in the absence of KO samples when only wild-type (WT) samples are available. Without using any information from real KO samples, GenKI is designed to capture shifting patterns in gene regulation caused by the KO perturbation in an unsupervised manner and provide a robust and scalable framework for gene function studies. To achieve this goal, GenKI adapts a variational graph autoencoder (VGAE) model to learn latent representations of genes and interactions between genes from the input WT scRNA-seq data and a derived single-cell gene regulatory network (scGRN). The virtual KO data is then generated by computationally removing all edges of the KO gene-the gene to be knocked out for functional study-from the scGRN. The differences between WT and virtual KO data are discerned by using their corresponding latent parameters derived from the trained VGAE model. Our simulations show that GenKI accurately approximates the perturbation profiles upon gene KO and outperforms the state-of-the-art under a series of evaluation conditions. Using publicly available scRNA-seq data sets, we demonstrate that GenKI recapitulates discoveries of real-animal KO experiments and accurately predicts cell type-specific functions of KO genes. Thus, GenKI provides an in-silico alternative to KO experiments that may partially replace the need for genetically modified animals or other genetically perturbed systems.

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Electrochemical biosensor based on an atomic layered composite of graphene oxide/graphene as an electrode material towards selective and sensitive detection of miRNA-21

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Microchemical Journal 2024年 199卷

作者： Huang, Min-Shin Govindasamy, Mani Chinnapaiyan, Sathishkumar Lin, Yi-Ting Lu, Shao-Yang Samukawa, Seiji Huang, Chi-Hsien Department of Materials Engineering Ming Chi University of Technology New Taipei City 243303 Taiwan International Ph.D. Program in Innovative Technology of Biomedical Engineering and Medical Devices Ming Chi University of Technology New Taipei City 24303 Taiwan Centre for Applied Research Saveetha School of Engineering Saveetha Institute of Medical and Technical Sciences (SIMATS) Chennai-602105 Tamil Nadu India Institute of Fluid Science Tohoku University Sendai 980-8577 Japan College of Electrical and Computer Engineering National Yang Ming Chiao Tung University Hsinchu 300093 Taiwan Division of Rheumatology Allergy and Immunology Chang Gung Memorial Hospital Taoyuan City 33305 Taiwan College of Engineering Chang Gung University Taoyuan City 33302 Taiwan

Development of an efficient technique towards the detection of miRNAs is highly significant for the timely diagnosis and prognosis of cancers. In this study, we utilized the chemical vapor deposition (CVD) technique to grow bilayer graphene (BLG) on copper foil and subsequently transferred the BLG to fluorine doped tin oxide (FTO) substrate via a facile wet transfer technique. The upper layer of the BLG was modified to graphene oxide (GO) with a low damage plasma treatment (LDPT) process to serve as a biomolecule receiving layer and the lower graphene layer (G) serves as an electron transport layer. The developed GO/G/FTO platform offers superior sensing ability towards the miRNA-21. The results demonstrated that the proposed GO/G/FTO substrate detect the miRNA-21 with a wide linear range (10 fM ∼ 1 nM), low limit of detection (3.18 fM), high sensitivity (0.6 mApM⁻¹cm⁻²), selectivity and stability via the differential pulse voltammetry method. Additionally, the sensors can efficiently discriminate the target miRNA-21 from its complementary base mismatched counterparts. The proposed approach serves as an excellent tool for the early diagnosis of diseases. © 2024 Elsevier B.V.

关键词： Atomic layer oxidation Biosensor Cancer biomarkers Electrochemical Graphene oxide Plasma treatment

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ZETA: a library for Zonotope-based EsTimation and fAult diagnosis of discrete-time systems

arXiv

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arXiv 2025年

作者： Rego, Brenner S. Scott, Joseph K. Raimondo, Davide M. Terra, Marco H. Raffo, Guilherme V. Department of Electrical and Computer Engineering University of São Paulo SP São Carlos13566-590 Brazil Department of Chemical and Biomolecular Engineering Georgia Institute of Technology 311 Ferst Dr. AtlantaGA30318 United States Department of Engineering and Architecture University of Trieste Trieste34127 Italy Department of Electronics Engineering Graduate Program in Electrical Engineering Federal University of Minas Gerais MG Belo Horizonte31270-901 Brazil

This paper introduces ZETA, a new MATLAB library for Zonotope-based EsTimation and fAult diagnosis of discrete-time systems. It features user-friendly implementations of set representations based on zonotopes, namely zonotopes, constrained zonotopes, and line zonotopes, in addition to a basic implementation of interval arithmetic. This library has capabilities starting from the basic set operations with these sets, including propagations through nonlinear functions using various approximation methods. The features of ZETA allow for reachability analysis and state estimation of discrete-time linear, nonlinear, and descriptor systems, in addition to active fault diagnosis of linear systems. Efficient order reduction methods are also implemented for the respective set representations. Some examples are presented in order to illustrate the functionalities of the new library. © 2025, CC BY.

关键词： Digital arithmetic

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Set-based state estimation and fault diagnosis of linear discrete-time descriptor systems using constrained zonotopes

arXiv

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arXiv 2020年

作者： Rego, Brenner S. Raimondo, Davide M. Raffo, Guilherme V. Graduate Program in Electrical Engineering Federal University of Minas Gerais Belo Horizonte Brazil Department of Electrical Computer and Biomedical Engineering University of Pavia Pavia Italy Department of Electronics Engineering Federal University of Minas Gerais Belo Horizonte Brazil

This paper presents new methods for set-valued state estimation and active fault diagnosis of linear descriptor systems. The algorithms are based on constrained zonotopes, a generalization of zonotopes capable of describing strongly asymmetric convex sets, while retaining the computational advantages of zonotopes. Additionally, unlike other set representations like intervals, zonotopes, ellipsoids, paralletopes, among others, linear static constraints on the state variables, typical of descriptor systems, can be directly incorporated in the mathematical description of constrained zonotopes. Therefore, the proposed methods lead to more accurate results in state estimation in comparison to existing methods based on the previous sets without requiring rank assumptions on the structure of the descriptor system and with a fair trade-off between accuracy and efficiency. These advantages are highlighted in two numerical examples. Copyright © 2020, The Authors. All rights reserved.

关键词： Failure analysis

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Deep inference of latent dynamics with spatio-temporal super-resolution using selective backpropagation through time

arXiv

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arXiv 2021年

作者： Zhu, Feng Sedler, Andrew R. Grier, Harrison A. Ahad, Nauman Davenport, Mark A. Kaufman, Matthew T. Giovannucci, Andrea Pandarinath, Chethan Neuroscience Graduate Program Emory University Center for Machine Learning Georgia Tech Computational Neuroscience Graduate Program The University of Chicago School of Electrical and Computer Engineering Georgia Tech Dept. of Organismal Biology and Anatomy The University of Chicago Neuroscience Institute The University of Chicago Joint Dept. of Biomedical Engineering UNC Chapel Hill NC State University UNC Chapel Hill Neuroscience Center Coulter Dept. of Biomedical Engineering Emory University Georgia Tech Dept. of Neurosurgery Emory University

Modern neural interfaces allow access to the activity of up to a million neurons within brain circuits. However, bandwidth limits often create a trade-off between greater spatial sampling (more channels or pixels) and the temporal frequency of sampling. Here we demonstrate that it is possible to obtain spatio-temporal super-resolution in neuronal time series by exploiting relationships among neurons, embedded in latent low-dimensional population dynamics. Our novel neural network training strategy, selective backpropagation through time (SBTT), enables learning of deep generative models of latent dynamics from data in which the set of observed variables changes at each time step. The resulting models are able to infer activity for missing samples by combining observations with learned latent dynamics. We test SBTT applied to sequential autoencoders and demonstrate more efficient and higher-fidelity characterization of neural population dynamics in electrophysiological and calcium imaging data. In electrophysiology, SBTT enables accurate inference of neuronal population dynamics with lower interface bandwidths, providing an avenue to significant power savings for implanted neuroelectronic interfaces. In applications to two-photon calcium imaging, SBTT accurately uncovers high-frequency temporal structure underlying neural population activity, substantially outperforming the current state-of-the-art. Finally, we demonstrate that performance could be further improved by using limited, high-bandwidth sampling to pretrain dynamics models, and then using SBTT to adapt these models for sparsely-sampled data. © 2021, CC BY-NC-SA.

关键词： Neurons

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Spinal functional Magnetic Resonance Imaging (fMRI) on Human Studies: A Literature Review

Spinal functional Magnetic Resonance Imaging (fMRI) on Human...

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2019 Advances in Science and engineering Technology International Conferences, ASET 2019

作者： Al-Momani, Sajedah Dhou, Salam Biomedical Engineering Graduate Program American University of Sharjah Sharjah United Arab Emirates Department of Computer Science and Engineering Biomedical Engineering Graduate Program Biosciences and Bioengineering Research Institute American University of Sharjah Sharjah United Arab Emirates

ISBN: (纸本)9781538682715

Spinal functional Magnetic Resonance Imaging (fMRI) is a newly emerging non-invasive imaging technique that has been introduced to study the Blood Oxygenation Level Dependent (BOLD) changes in the spinal cord associated with a certain activity or even at rest. Spinal fMRI is also used to assess the treatment of many dysfunctions affect the spinal cord such as spinal cord injury (SCI) and Multiple sclerosis (MS). The purpose of this paper is to propose a literature review of spinal fMRI studies performed on healthy human volunteers. The studies reviewed are divided based on the paradigm being performed during image acquisition into (1) studies under activities and stimulus which are further classified according to the type of the stimuli, and (2) studies at resting state. Moreover, the limitations of spinal fMRI and how to tackle them are discussed. © 2019 IEEE.

关键词： Magnetic resonance imaging

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Review of Image-Guided Percutaneous Coronary Interventions

Review of Image-Guided Percutaneous Coronary Interventions

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2019 Advances in Science and engineering Technology International Conferences, ASET 2019

作者： Alatoom, Aseel Farhat, Jumana Dhou, Salam Biomedical Engineering Graduate Program American University of Sharjah Sharjah United Arab Emirates Department of Computer Science and Engineering Biomedical Engineering Graduate Program Biosciences and Bioengineering Research Institute American University of Sharjah Sharjah United Arab Emirates

ISBN: (纸本)9781538682715

Image-guided surgery (IGS) involves using surgical instruments tracking system to guide the surgeon during invasive surgical procedures. The use of preoperative or intraoperative images is very essential in providing navigation for different medical applications. In this paper, a literature review of different imaging modalities that aid in the diagnosis and treatment of coronary artery disease (CAD) is proposed. The imaging modalities discussed include x-ray fluoroscopy, coronary computed tomography angiography (CCTA), fractional flow reserve (FFR), cardiac single-photon emission computed tomography (SPECT), cardiovascular magnetic resonance imaging (CMRI) and ultrasound. Additionally, pseudoaneurysms, which can result from percutaneous coronary interventions (PCI) procedure, are reviewed as well as the treatment procedure. Finally, a comparison between the different imaging modalities is carried out, based on the number of papers that have been published, in addition to the sensitivity and specificity for each modality according to PubMed and Web of Science databases. © 2019 IEEE.

关键词： Ultrasonics

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Machine Learning for Improved Current Density Reconstruction from 2D Vector Magnetic Images

arXiv

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arXiv 2024年

作者： Reed, Niko R. Bhutto, Danyal Turner, Matthew J. Daly, Declan M. Oliver, Sean M. Tang, Jiashen Olsson, Kevin S. Langellier, Nicholas Ku, Mark J.H. Rosen, Matthew S. Walsworth, Ronald L. Department of Physics University of Maryland College ParkMD United States Quantum Technology Center University of Maryland College ParkMD United States Joint Quantum Institute University of Maryland College ParkMD United States Department of Biomedical Engineering Boston University BostonMA United States A. A. Martinos Center for Biomedical Imaging Massachusetts General Hospital CharlestownMA United States Department of Electrical and Computer Engineering University of Maryland College ParkMD United States The MITRE Corporation McLeanVA22102 United States Intelligence Community Postdoctoral Research Fellowship Program University of Maryland College ParkMD20742 United States Department of Physics Harvard University CambridgeMA United States Department of Materials Science and Engineering University of Delaware NewarkDE19716 United States Department of Physics and Astronomy University of Delaware NewarkDE19716 United States Harvard Medical School 25 Shattuck St. BostonMA United States

The reconstruction of electrical current densities from magnetic field measurements is an important technique with applications in materials science, circuit design, quality control, plasma physics, and biology. Analytic reconstruction methods exist for planar currents, but break down in the presence of high spatial frequency noise or large standoff distance, restricting the types of systems that can be studied. Here, we demonstrate the use of a deep convolutional neural network for current density reconstruction from two-dimensional (2D) images of vector magnetic fields acquired by a quantum diamond microscope (QDM). Trained network performance significantly exceeds analytic reconstruction for data with high noise or large standoff distances. This machine learning technique can perform quality inversions on lower SNR data, significantly reducing the data collection time and permitting reconstructions of weaker and three-dimensional current sources. © 2024, CC BY.

关键词： Magnetic fields

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Two-step electronic response to magnetic ordering in a van der Waals ferromagnet

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Physical Review B 2024年第4期109卷 045416-045416页

作者： Han Wu Jian-Xin Zhu Lebing Chen Matthew W. Butcher Ziqin Yue Dongsheng Yuan Yu He Ji Seop Oh Bin Gao Jianwei Huang Shan Wu Cheng Gong Yucheng Guo Sung-Kwan Mo Jonathan Denlinger Donghui Lu Makoto Hashimoto Matthew B. Stone Alexander I. Kolesnikov Songxue Chi Junichiro Kono Andriy H. Nevidomskyy Robert J. Birgeneau Pengcheng Dai Ming Yi Department of Physics and Astronomy and Rice Center for Quantum Materials Rice University Houston Texas 77005 USA Theoretical Division Los Alamos National Laboratory Los Alamos New Mexico 87545 USA Center for Integrated Nanotechnologies Los Alamos National Laboratory Los Alamos New Mexico 87545 USA Department of Physics University of California at Berkeley Berkeley California 94720 USA Applied Physics Graduate Program Smalley-Curl Institute Rice University Houston Texas 77005 USA Materials Sciences Division Lawrence Berkeley National Laboratory Berkeley California 94720 USA National Institute for Materials Science 1-1 Namiki Tsukuba Ibaraki 305-0044 Japan Department of Applied Physics Yale University New Haven Connecticut 06511 USA Department of Electrical and Computer Engineering and Quantum Technology Center University of Maryland College Park Maryland 20742 USA Advanced Light Source Lawrence Berkeley National Laboratory Berkeley California 94720 USA Stanford Synchrotron Radiation Lightsource SLAC National Accelerator Laboratory Menlo Park California 94025 USA Neutron Scattering Division Oak Ridge National Laboratory Oak Ridge Tennessee 37831 USA Department of Electrical and Computer Engineering Rice University Houston Texas 77005 USA Smalley-Curl Institute Rice University Houston Texas 77005 USA Department of Material Science and Nanoengineering Rice University Houston Texas 77005 USA Department of Materials Science and Engineering University of California Berkeley California 94720 USA

The two-dimensional material Cr2Ge2Te6 is a member of the class of insulating van der Waals (vdW) magnets. Here, using high resolution angle-resolved photoemission spectroscopy in a detailed temperature dependence study, we identify a clear response of the electronic structure to a dimensional crossover in the form of two distinct temperature scales marking onsets of modifications in the electronic structure. Specifically, we observe Te p-orbital-dominated bands to undergo changes at the Curie transition temperature TC while the Cr d-orbital-dominated bands begin evolving at a higher temperature scale. Combined with neutron scattering, density functional theory calculations, and Monte Carlo simulations, we find that the electronic system can be consistently understood to respond sequentially to the distinct temperatures at which in-plane and out-of-plane spin correlations exceed a characteristic length scale. Our findings reveal the sensitivity of the orbital-selective electronic structure for probing the dynamical evolution of local moment correlations in vdW insulating magnets.

关键词： Electronic structure Magnetic order Magnetic phase transitions Van der Waals systems Angle-resolved photoemission spectroscopy

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