检索结果-内蒙古大学图书馆

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

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.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Graph Laplacian Learning with Exponential Family Noise

引用

IEEE Transactions on Signal and Information Processing over Networks 2025年

作者： Shi, Changhao Mishne, Gal UC San Diego Electrical and Computer Engineering Department CA92093 United States UC San Diego Hal.c.o.glu Data Science Institute and the Neurosciences Graduate Program CA92093 United States

Graph signal processing (GSP) is a prominent framework for analyzing signals on non-Euclidean domains. The graph Fourier transform (GFT) uses the combinatorial graph Laplacian matrix to reveal the spectral decomposition of signals in the graph frequency domain. However, a common challenge in applying GSP methods is that in many scenarios the underlying graph of a system is unknown. A solution in such cases is to construct the unobserved graph from available data, which is commonly referred to as graph or network inference. Although different graph inference methods exist, they are restricted to learning from either smooth graph signals or simple additive Gaussian noise. Other types of noisy data, such as discrete counts or binary digits, are rather common in real-world applications, yet are underexplored in graph inference. In this paper, we propose a versatile graph inference framework for learning from graph signals corrupted by exponential family noise. Our framework generalizes previous methods from continuous smooth graph signals to various data types. We propose an alternating algorithm that jointly estimates the graph Laplacian and the unobserved smooth representation from the noisy signals. We also extend our approach to include an offset variable which models different levels of variation of the nodes. Since real-world graph signals are frequently non-independent and temporally correlated, we further adapt our original setting to a timevertex formulation. We demonstrate on synthetic and real-world data that our new algorithms outperform competing Laplacian estimation methods that suffer from noise model mismatch. © 2025 IEEE.

关键词： Laplace transforms

来源：评论

学校读者我要写书评

暂无评论

Structural, optical, and thermal properties of BN thin films grown on diamond via pulsed laser deposition

arXiv

引用

arXiv 2023年

作者： Biswas, Abhijit Alvarez, Gustavo A. Li, Tao Christiansen-Salameh, Joyce Jeong, Eugene Puthirath, Anand B. Iyengar, Sathvik Ajay Li, Chenxi Gray, Tia Zhang, Xiang Pieshkov, Tymofii S. Kannan, Harikishan Elkins, Jacob Vajtai, Robert Birdwell, A. Glen Neupane, Mahesh R. Garratt, Elias J. Pate, Bradford B. Ivanov, Tony G. Zhao, Yuji Tian, Zhiting Ajayan, Pulickel M. Department of Materials Science and Nanoengineering Rice University HoustonTX77005 United States Sibley School of Mechanical and Aerospace Engineering Cornell University IthacaNY14853 United States Department of Electrical and Computer Engineering Rice University HoustonTX77005 United States Applied Physics Graduate Program Smalley-Curl Institute Rice University HoustonTX77005 United States DEVCOM Army Research Laboratory RF Devices and Circuits AdelphiMD20783 United States Naval Research Laboratory Chemistry Division WashingtonDC20375 United States

Heterostructures based on ultrawide-bandgap (UWBG) semiconductors (bandgap >4.0 eV), such as boron nitride (BN) and diamond, hold significant importance for the development of high-power electronics in the next generation. However, achieving in-situ hetero-epitaxy of BN/diamond or vice versa remains exceptionally challenging due to the complex growth kinetics involved. In this study, we have grown BN thin film on (100) single crystal diamonds using pulsed laser deposition and investigated its structural, magnetic, optical, and thermal properties. The structural analyses confirmed the growth of BN films, which exhibited diamagnetic behavior at room temperature. Notably, the film demonstrated anisotropic refractive index characteristics within the visible-to-near-infrared wavelength range. The room temperature cross-plane thermal conductivity of BN is 1.53 (± 0.77) W/mK, while the thermal conductance of the BN/diamond interface is 20 (± 2) MW/m2K. These findings have significant implications for a range of device applications based on UWBG BN/diamond heterostructures. © 2023, CC BY.

关键词： Diamonds

来源：评论

学校读者我要写书评

暂无评论

Ferroelectric transistors based on shear-transformation-mediated rhombohedral-stacked molybdenum disulfide

引用

Nature Electronics 2024年第1期7卷 29-38页

作者： Yang, Tilo H. Liang, Bor-Wei Hu, Hsiang-Chi Chen, Fu-Xiang Ho, Sheng-Zhu Chang, Wen-Hao Yang, Liu Lo, Han-Chieh Kuo, Tzu-Hao Chen, Jyun-Hong Lin, Po-Yen Simbulan, Kristan Bryan Luo, Zhao-Feng Chang, Alice Chinghsuan Kuo, Yi-Hao Ku, Yu-Seng Chen, Yi-Cheng Huang, You-Jia Chang, Yu-Chen Chiang, Yu-Fan Lu, Ting-Hua Lee, Min-Hung Li, Kai-Shin Wu, Menghao Chen, Yi-Chun Lin, Chun-Liang Lan, Yann-Wen Department of Physics National Taiwan Normal University Taipei Taiwan Taiwan Semiconductor Research Institute National Applied Research Laboratories Hsinchu Taiwan Department of Electrophysics National Yang Ming Chiao Tung University Hsinchu Taiwan Department of Physics National Cheng Kung University Tainan Taiwan School of Physics Huazhong University of Science and Technology Wuhan China Institute of Cellular and Organismic Biology Academia Sinica Taipei Taiwan Department of Mathematics and Physics University of Santo Tomas Manila Philippines Program for Semiconductor Devices Materials and Hetero-integration Graduate School of Advanced Technology National Taiwan University Taipei Taiwan Hsinchu Taiwan Department of Physics National Taiwan University Taipei Taiwan Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA United States

To develop low-power, non-volatile computing-in-memory device using ferroelectric transistor technologies, ferroelectric channel materials with scaled thicknesses are required. Two-dimensional semiconductors, such as molybdenum disulfide (MoS2), equipped with sliding ferroelectricity could provide an answer. However, achieving switchable electric polarization in epitaxial MoS2 remains challenging due to the absence of mobile domain boundaries. Here we show that polarity-switchable epitaxial rhombohedral-stacked (3R) MoS2 can be used as a ferroelectric channel in ferroelectric memory transistors. We show that a shear transformation can spontaneously occur in 3R MoS2 epilayers, producing heterostructures with stable ferroelectric domains embedded in a highly dislocated and unstable non-ferroelectric matrix. This diffusionless phase transformation process produces mobile screw dislocations that enable collective polarity control of 3R MoS2 via an electric field. Polarization–electric-field measurements reveal a switching field of 0.036 V nm−1 for shear-transformed 3R MoS2. Our sliding ferroelectric transistors are non-volatile memory units with thicknesses of only two atomic layers and exhibit an average memory window of 7 V with an applied voltage of 10 V, retention times greater than 104 seconds and endurance greater than 104 cycles. © 2023, The Author(s), under exclusive licence to Springer Nature Limited.

关键词： Molybdenum disulfide

来源：评论

学校读者我要写书评

暂无评论

Enhanced Superconducting Qubit Performance Through Ammonium Fluoride Etch

arXiv

引用

arXiv 2024年

作者： Kopas, Cameron J. Goronzy, Dominic P. Pham, Thang Torres Castanedo, Carlos G. Cheng, Matthew Cochrane, Rory Nast, Patrick Lachman, Ella Zhelev, Nikolay Z. Vallières, André Murthy, Akshay A. Oh, Jin-Su Zhou, Lin Kramer, Matthew J. Cansizoglu, Hilal Bedzyk, Michael J. Dravid, Vinayak P. Romanenko, Alexander Grassellino, Anna Mutus, Josh Y. Hersam, Mark C. Yadavalli, Kameshwar Rigetti Computing BerkeleyCA United States Department of Materials Science and Engineering Northwestern University EvanstonIL United States Center for Applied Physics and Superconducting Technologies Northwestern University EvanstonIL United States Department of Physics and Astronomy Northwestern University EvanstonIL United States Department of Physics University of Oregon EugeneOR United States Graduate Program in Applied Physics Northwestern University EvanstonIL60208 United States Fermi National Accelerator Laboratory BataviaIL United States Ames Laboratory U.S. Department of Energy AmesIA United States Northwestern University EvanstonIL United States Department of Chemistry Northwestern University EvanstonIL United States Department of Electrical and Computer Engineering Northwestern University EvanstonIL United States

The performance of superconducting qubits is often limited by dissipation and two-level systems (TLS) losses. The dominant sources of these losses are believed to originate from amorphous materials and defects at interfaces and surfaces, likely as a result of fabrication processes or ambient exposure. Here, we explore a novel wet chemical surface treatment at the Josephson junction-substrate and the substrate-air interfaces by replacing a buffered oxide etch (BOE) cleaning process with one that uses hydrofluoric acid followed by aqueous ammonium fluoride. We show that the ammonium fluoride etch process results in a statistically significant improvement in median T1 by ∼ 22% (p = 0.002), and a reduction in the number of strongly-coupled TLS in the tunable frequency range. Microwave resonator measurements on samples treated with the ammonium fluoride etch prior to niobium deposition also show ∼ 33% lower TLS-induced loss tangent compared to the BOE treated samples. As the chemical treatment primarily modifies the Josephson junction-substrate interface and substrate-air interface, we perform targeted chemical and structural characterizations to examine materials’ differences at these interfaces and identify multiple microscopic changes that could contribute to decreased TLS. © 2024, CC BY-NC-ND.

关键词： Fluorine compounds

来源：评论

学校读者我要写书评

暂无评论

Ultrastrong Spin-Photon Coupling in Gadolinium Gallium Garnet

Ultrastrong Spin-Photon Coupling in Gadolinium Gallium Garne...

引用

Conference on Lasers and Electro-Optics (CLEO)

作者： T. Elijah Kritzell Junzhe Bao Jacques Doumani Jae Joon Lee Hongjing Xu Fuyang Tay Hiroyuki Nojiri Motoaki Bamba Andrey Baydin Junichiro Kono Department of Electrical and Computer Engineering Rice University Houston Texas USA Applied Physics Graduate Program Smalley-Curl Institute Rice University Houston Texas USA Department of Physics and Astronomy Rice University Houston Texas USA Institute for Materials Research Tohoku University Senai Japan The Hakubi Center for Advanced Research Kyoto University Kyoto Japan Department of Physics I Kyoto University Kyoto Japan Smalley-Curl Institute Rice University Houston Texas USA Department of Material Science and NanoEngineering Rice University Houston Texas USA

We examine ultrastrong coupling of an ensemble of paramagnetic spins in Gd 3 Ga 5 O 12 with terahertz photons in the presence of a high external magnetic field both in the bulk and thin-film limits.

ISBN: (纸本)9781957171258

We examine ultrastrong coupling of an ensemble of paramagnetic spins in Gd 3 Ga 5 O 12 with terahertz photons in the presence of a high external magnetic field both in the bulk and thin-film limits.

关键词： CCD cameras Condensed matter Magnetic fields Photons Quantum optics Terahertz spectroscopy

来源：评论

学校读者我要写书评

暂无评论

Compressibility-Near-Zero Acoustic Radiation

引用

Physical Review Applied 2021年第2期15卷 024022-024022页

作者： Curtis Rasmussen Andrea Alù Department of Mechanical Engineering The University of Texas at Austin Austin Texas 78712 USA Department of Electrical and Computer Engineering The University of Texas at Austin Austin Texas 78712 USA Photonics Initiative CUNY Advanced Science Research Center New York New York 10031 USA Physics Program Graduate Center City University of New York New York New York 10026 USA

A hallmark of near-zero-index materials is the uniform phase profile that the waves experience as they propagate with staticlike properties in these media. This feature is exploited in electromagnetics for several applications, including for the realization of compact highly directive antennas illuminated by a single source. Here, we discuss the promise of near-zero metamaterials for acoustic radiation, based on the cutoff of a higher-order mode in a waveguide with small holes. We show that the near-zero nature of this phenomenon ensures unusual robustness to disorder, which is analyzed using a statistical description of the radiation patterns for randomly generated location of the holes. The radiation pattern can be made more directive by simply increasing the overall radiating aperture, without having to worry about the specific location of individual holes and their relative distance. The proposed zero-compressibility material offers a promising alternative to traditional acoustic directive sources due to its design simplicity, inherent robustness, and compact profile.

关键词： Acoustic metamaterials Acoustic wave phenomena Disordered systems Acoustic techniques Cavity resonators Green's function methods

来源：评论

学校读者我要写书评

暂无评论

FaNDOM: Fast Nested Distance-Based Seeding of Optical Maps

SSRN

引用

SSRN 2021年

作者： Dehkordi, Siavash Raeisi Luebeck, Jens Bafna, Vineet Department of Computer Science & Engineering University of California San Diego San diegoCA92093 United States Bioinformatics & Systems Biology Graduate Program University of California San Diego San diegoCA92093 United States

Optical mapping provides single-molecule readouts of the locations of fluorescently labeled sequence motifs on long fragments of DNA, resolved to nucleotide-level coordinates. With the advent of microfluidic technologies for manipulating large numbers of individual molecules, and advances in the imaging of fluorescent DNA tags, it is possible to inexpensively generate high coverage and long OM molecules (>150Kbp). In addition to its use in scaffolding for de novo assembly, optical map data can also be mapped to a reference for identifying genetic structural variants implicated in Mendelian diseases and cancer. To address the computational challenge, we introduce FaNDOM (Fast Nested Distance seeding of Optical Maps) - an optical map alignment tool which greatly reduces the search space of the alignment process. On 4 benchmark human data-sets, FaNDOM was significantly (4-14X) faster than competing tools while maintaining comparable sensitivity and specificity. We used FaNDOM to map variants in 3 cancer cell-lines and identified many structural variations, including deletion of tumor-suppressor genes, duplications, gene fusions and gene-disrupting rearrangements. FaNDOM is publicly available at (https://***/jluebeck/FaNDOM). © 2021, The Authors. All rights reserved.

关键词： Genes

来源：评论

学校读者我要写书评

暂无评论

Progress in wearable electronics/photonics—Moving toward the era of artificial intelligence and internet of things

引用

InfoMat 2020年第6期2卷 1131-1162页

作者： Qiongfeng Shi Bowei Dong Tianyiyi He Zhongda Sun Jianxiong Zhu Zixuan Zhang Chengkuo Lee Department of Electrical and Computer Engineering National University of SingaporeSingapore117576Singapore Center for Intelligent Sensors and MEMS National University of SingaporeSingapore117608Singapore Hybrid-Integrated Flexible(Stretchable)Electronic Systems Program National University of SingaporeSingapore117608Singapore NUS Suzhou Research Institute(NUSRI) Suzhou215123China NUS Graduate School for Integrative Science and Engineering National University of SingaporeSingapore117456Singapore

The past few years have witnessed the significant impacts of wearable electronics/photonics on various aspects of our daily life,for example,healthcare monitoring and treatment,ambient monitoring,soft robotics,prosthetics,flexible display,communication,human-machine interactions,and so *** to the development in recent years,the next-generation wearable electronics and photonics are advancing rapidly toward the era of artificial intelligence(AI)and internet of things(IoT),to achieve a higher level of comfort,convenience,connection,and ***,this review provides an opportune overview of the recent progress in wearable electronics,photonics,and systems,in terms of emerging materials,transducing mechanisms,structural configurations,applications,and their further integration with other ***,development of general wearable electronics and photonics is summarized for the applications of physical sensing,chemical sensing,humanmachine interaction,display,communication,and so *** self-sustainable wearable electronics/photonics and systems are discussed based on system integration with energy harvesting and storage ***,technology fusion of wearable systems and AI is reviewed,showing the emergence and rapid development of intelligent/smart *** the last section of this review,perspectives about the future development trends of the next-generation wearable electronics/photonics are provided,that is,toward multifunctional,self-sustainable,and intelligent wearable systems in the AI/IoT era.

关键词： artificial intelligence energy harvesting human-machine interface internet of things wearable electronics wearable photonics

来源：评论

学校读者我要写书评

暂无评论

Riemann-Encircling Exceptional Points for Efficient Asymmetric Polarization-Locked Devices

引用

Physical Review Letters 2022年第12期129卷 127401-127401页

作者： Aodong Li Weijin Chen Heng Wei Guowei Lu Andrea Alù Cheng-Wei Qiu Lin Chen Wuhan National Laboratory for Optoelectronics and School of Optical and Electronic Information Huazhong University of Science and Technology Wuhan 430074 China Department of Electrical and Computer Engineering National University of Singapore Singapore 117583 Singapore State Key Laboratory for Mesoscopic Physics School of Physics Peking University Beijing 100871 China Photonics Initiative Advanced Science Research Center City University of New York New York New York 10031 USA Physics Program Graduate Center City University of New York New York New York 10016 USA

Dynamically encircling exceptional points (EPs) have unveiled intriguing chiral dynamics in photonics. However, the traditional approach based on an open manifold of Hamiltonian parameter space fails to explore trajectories that pass through an infinite boundary. Here, by mapping the full parameter space onto a closed manifold of the Riemann sphere, we introduce a framework to describe encircling-EP loops. We demonstrate that an encircling trajectory crossing the north vertex can realize near-unity asymmetric transmission. An efficient gain-free, broadband asymmetric polarization-locked device is realized by mapping the encircling path onto L-shaped silicon waveguides.

关键词： PT-symmetric quantum mechanics Photonics

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：