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Author Correction: Predicting the efficiency of prime editing guide RNAs in human cells

Nature biotechnology 2024年第3期42卷 529页

作者： Hui Kwon Kim Goosang Yu Jinman Park Seonwoo Min Sungtae Lee Sungroh Yoon Hyongbum Henry Kim Department of Pharmacology Yonsei University College of Medicine Seoul Republic of Korea. Brain Korea 21 Plus Project for Medical Sciences Yonsei University College of Medicine Seoul Republic of Korea. Center for Nanomedicine Institute for Basic Science (IBS) Seoul Republic of Korea. Graduate Program of Nano Biomedical Engineering (NanoBME) Advanced Science Institute Yonsei University Seoul Republic of Korea. Electrical and Computer Engineering Seoul National University Seoul Republic of Korea. Interdisciplinary Program in Bioinformatics Seoul National University Seoul Republic of Korea. Graduate School of Data Science Seoul National University Seoul Republic of Korea. Department of Pharmacology Yonsei University College of Medicine Seoul Republic of Korea. hkim1@yuhs.ac. Brain Korea 21 Plus Project for Medical Sciences Yonsei University College of Medicine Seoul Republic of Korea. hkim1@yuhs.ac. Center for Nanomedicine Institute for Basic Science (IBS) Seoul Republic of Korea. hkim1@yuhs.ac. Graduate Program of Nano Biomedical Engineering (NanoBME) Advanced Science Institute Yonsei University Seoul Republic of Korea. hkim1@yuhs.ac. Severance Biomedical Science Institute Yonsei University College of Medicine Seoul Republic of Korea. hkim1@yuhs.ac. Graduate Program of NanoScience and Technology Yonsei University Seoul Republic of Korea. hkim1@yuhs.ac.

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Breast cancer histopathology using infrared spectroscopic imaging: The impact of instrumental configurations

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Clinical Spectroscopy 2021年 3卷

作者： Shachi Mittal Tomasz P. Wrobel Michael Walsh Andre Kajdacsy-Balla Rohit Bhargava Department of Bioengineering and Beckman Institute for Advanced Science and Technology University of Illinois at Urbana−Champaign Urbana IL United States Department of Materials Science and Biomedical Engineering University of Wisconsin – Eau Claire WI United States Department of Pathology University of Illinois at Chicago IL United States Departments of Mechanical Science and Engineering Electrical and Computer Engineering Chemical and Biomolecular Engineering and Chemistry University of Illinois at Urbana−Champaign Urbana IL United States Cancer Center at Illinois University of Illinois at Urbana−Champaign Urbana IL United States

Digital analysis of cancer specimens using spectroscopic imaging coupled to machine learning is an emerging area that links spatially localized spectral signatures to tissue structure and disease. In this study, we examine the role of spatial-spectral tradeoffs in infrared spectroscopic imaging configurations for probing tumors and the associated microenvironment profiles at different levels of model complexity. We image breast tissue using standard and high-definition Fourier Transform Infrared (FT-IR) imaging and systematically examine the localization, spectral origins, and utility of data for classification. Results demonstrate that higher spatial detail provides high sensitivity and specificity of tissue segmentation, despite the increased subcellular variability. High definition imaging also allows accurate analysis of complex, multiclass models of breast tissue without compromising accuracy. A comparison of results also highlights the key differences in the data distributions and classification performance across modalities to better guide decision making for acquiring and analyzing IR imaging data for specific histopathological models.

关键词： High definition imaging Standard definition Breast pathology Machine learning Tissue segmentation

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Assessing the Potential of GPT-4 to Annotate Medical Notes Across Different Languages and Countries: A Model Evaluation Study

SSRN

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SSRN 2024年

作者： Saad Menezes, Maria Clara Hoffman, Alexander F. Tan, Amelia L.M. Nalbandyan, Mariné Omenn, Gilbert S. Mazzotti, Diego R. Hernández-Arango, Alejandro Visweswaran, Shyam Venkatesh, Shruthi Mandl, Kenneth D. Bourgeois, Florence T. Lee, James W.K. Makmur, Andrew Hanauer, David A. Semanik, Michael G. Kerivan, Lauren T. Hill, Terra Forero, Julian Restrepo Castro, Carlos Andrés C.R. Vigna, Matteo Ceriana, Piero Abu-El-rub, Noor Avillach, Paul Bellazzi, Riccardo Callaci, Thomas Gutiérrez-Sacristán, Alba Malovini, Alberto Mathew, Jomol P. Morris, Michele Murthy, Venkatesh Parimbelli, Enea Patel, Lav P. Sáez, Carlos Samayamuthu, Malarkodi Jebathilagam Thompson, Jeffrey A. Tibollo, Valentina Xia, Zongqi Kohane, Isaac S. Harvard Medical School Department of Biomedical Informatics 10 Shattuck Street BostonMA02115 United States School of Medicine and Public Health University of Wisconsin-Madison Office of Informatics and Information Technology 750 Highland Ave MadisonWI53705 United States University of Michigan Department of Computational Medicine & Bioinformatics Internal Medicine Human Genetics Environmental Health 100 Washtenaw Avenue Ann ArborMI48109 United States University of Kansas Medical Center Division of Medical Informatics Division of Pulmonary Critical Care and Sleep Medicine Department of Internal Medicine 3901 Rainbow Blvd Kansas CityKS66160 United States University of Antioquia Hospital Alma Máter de Antioquia Department of Internal Medicine Calle 64 N°51 D - 154 Medellín Colombia University of Pittsburgh Department of Biomedical Informatics 5607 Baum Blvd PittsburghPA15206 United States University of Pittsburgh Department of Neurology 3501 5th Avenue PittsburghPA15206 United States Boston Children's Hospital Computational Health Informatics Program 300 Longwood Avenue BostonMA02115 United States Boston Children's Hospital Department of Pediatrics 300 Longwood Avenue BostonMA02115 United States National University Health System Department of Surgery 1E Kent Ridge Rd Singapore119228 Singapore National University Health System Department of Diagnostic Imaging 1E Kent Ridge Rd Singapore119228 Singapore University of Michigan Department of Learning Health Sciences NCRC 100 2800 Plymouth Road Ann ArborMI48109 United States University of Kansas Medical Center Department of Surgery 3901 Rainbow Blvd Kansas CityKS66160 United States Istituti Clinici Scientifici Maugeri IRCCS Respiratory rehabilitation unit Via Maugeri 10 Pavia27100 Italy University of Kansas Medical Center 3901 Rainbow Blvd Kansas CityKS66160 United States University of Pavia Department of Electrical Computer and Biomedical Engineering via Ferrata 5 Pavia2710

Background: Physicians invest hours creating patient notes, which are rich in information but difficult for computers to analyze due to their unstructured format. GPT-4 reshaped our ability to process text, yet it is unknown how well this model can handle medical notes. This project aims to compare GPT-4’s ability to annotate medical notes against experienced physicians across three different languages at multiple institutions and countries. Methods: This study included eight sites from four countries - the United States, Colombia, Singapore, and Italy. Each site contributed seven de-identified notes (admission, progress, or consult) from hospitalized patients. GPT-4 assessed each note by answering 14 questions, including demographic information, clinical judgments, data quality, and patients’ eligibility for a hypothetical study enrollment. For validation, two physicians from each site independently evaluated GPT-4's responses. Findings: Overall, 56 medical notes, written in English, Italian, and Spanish, were analyzed. A total of 784 responses from GPT-4 were generated. Both physicians agreed with GPT-4’s response 79% of the time (622/784, 95%CI 76-82%). Only one of the two physicians agreed with GPT-4’s response 10% of the time (82/784, 95%CI 8-13%). Neither physician agreed with GPT-4’s response 10% of the time (80/784, 95%CI 8-13%). Both physicians agreed with GPT-4 more often in notes written in Spanish and Italian than in English, with agreement rates of 88% (86/98, 95%CI 79-93%), 84% (82/98, 95%CI 75-90%), and 77% (454/588, 95%CI 74-80%), respectively. Hallucinations were rare (10/784, 95%CI 0-2%). GPT-4 correctly selected patients for a hypothetical study enrollment based on three criteria 90% of the time (95%CI 81-98%). Interpretation: The findings indicate that GPT-4 annotations demonstrated a high agreement rate with physicians across all languages. We also demonstrate GPT-4's potential to assist in patient selection for studies. Funding: None. Declarati

关键词： Medical computing

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Hybrid Cryptography on Wireless Sensor Network: A Systematic Literature Review 3

Hybrid Cryptography on Wireless Sensor Network: A Systematic...

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3rd International Conference on Information Management and Technology, ICIMTech 2018

作者： Gandara, R. Benny Wang, Gunawan Utama, Ditdit Nugeraha Mereu Buana University Master Program of Electrical Engineering Jakarta Indonesia Information Systems Management Department Bina Nusantara University BINUS Graduate Program-Master of Information Systems Management Jakarta11480 Indonesia Computer Science Department Bina Nusantara University BINUS Graduate Program-Master of Computer Science Jakarta11480 Indonesia

ISBN: (纸本)9781538658215

Wireless technology gradual growth in the latest years has facilitated it to bridge its applications operated extensively in many types of industry. Wireless sensor network (WSN) technology brings several benefits over traditional wired technology by reason of the lower cost, immense flexibility escalation, and scalability which is able to be obtained from the old-style one. However, in its application WSN still experience some constraints on resource limitations in the form: processor, memory and energy, and any more challenges that related to availability, reliability and security. Based on its benefits, limitation, and challenges, and also three systematic stages, the review study was performed. The result of study was portrayed in this paper. It is regarding investigation result of hybrid cryptography (HC, as one of defense methods) realized for WSN to methodically increase the security level and decrease the resources usage. The result concluded that HC was proven in escalating the security defense level and downgrading the resources use on WSN compared to symmetric and asymmetric algorithms. © 2018 IEEE.

关键词： Wireless sensor networks

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Author Correction: Disrupting cellular memory to overcome drug resistance

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Nature communications 2024年第1期15卷 4264页

作者： Guillaume Harmange Raúl A Reyes Hueros Dylan L Schaff Benjamin Emert Michael Saint-Antoine Laura C Kim Zijian Niu Shivani Nellore Mitchell E Fane Gretchen M Alicea Ashani T Weeraratna M Celeste Simon Abhyudai Singh Sydney M Shaffer Cellular and Molecular Biology Graduate Group Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Biochemistry and Molecular Biophysics Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Bioengineering School of Engineering and Applied Sciences University of Pennsylvania Philadelphia PA USA. Division of Biology and Biological Engineering California Institute of Technology Pasadena CA 91125 USA. Department of Electrical and Computer Engineering University of Delaware Newark DE 19716 USA. Abramson Family Cancer Research Institute Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Chemistry College of the Arts and Sciences University of Pennsylvania Philadelphia PA USA. Department of Physics College of the Arts and Sciences University of Pennsylvania Philadelphia PA USA. Department of Biology College of the Arts and Sciences University of Pennsylvania Philadelphia PA USA. The Wharton School University of Pennsylvania Philadelphia PA USA. Cancer Signaling and Microenvironment Research Program Fox Chase Cancer Center Philadelphia PA USA. Department of Biochemistry and Molecular Biology Johns Hopkins School of Public Health Baltimore MD USA. Sidney Kimmel Cancer Center Johns Hopkins School of Medicine Baltimore MD USA. Department of Cell and Developmental Biology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Bioengineering School of Engineering and Applied Sciences University of Pennsylvania Philadelphia PA USA. sydshaffer@***. Department of Pathology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. sydshaffer@***.

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Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors

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Physical Review B 2020年第2期101卷 020504(R)-020504(R)页

作者： Areg Ghazaryan P. L. S. Lopes Pavan Hosur Matthew J. Gilbert Pouyan Ghaemi IST Austria (Institute of Science and Technology Austria) Am Campus 1 3400 Klosterneuburg Austria Stewart Blusson Quantum Matter Institute University of British Columbia Vancouver British Columbia Canada V6T 1Z4 Department of Physics University of Houston Houston Texas 77204 USA Micro and Nanotechnology Laboratory University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA Department of Electrical and Computer Engineering University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA Department of Electrical Engineering Stanford University Stanford California 94305 USA Physics Department City College of the City University of New York New York New York 10031 USA Physics Program Graduate Center of the City University of New York New York 10031 USA

In the superconducting regime of FeTe(1−x)Sex, there exist two types of vortices which are distinguished by the presence or absence of zero-energy states in their core. To understand their origin, we examine the interplay of Zeeman coupling and superconducting pairings in three-dimensional metals with band inversion. Weak Zeeman fields are found to suppress intraorbital spin-singlet pairing, known to localize the states at the ends of the vortices on the surface. On the other hand, an orbital-triplet pairing is shown to be stable against Zeeman interactions, but leads to delocalized zero-energy Majorana modes which extend through the vortex. In contrast, the finite-energy vortex modes remain localized at the vortex ends even when the pairing is of orbital-triplet form. Phenomenologically, this manifests as an observed disappearance of zero-bias peaks within the cores of topological vortices upon an increase of the applied magnetic field. The presence of magnetic impurities in FeTe(1−x)Sex, which are attracted to the vortices, would lead to such Zeeman-induced delocalization of Majorana modes in a fraction of vortices that capture a large enough number of magnetic impurities. Our results provide an explanation for the dichotomy between topological and nontopological vortices recently observed in FeTe(1−x)Sex.

关键词： Majorana bound states Topological superconductors Iron-based superconductors

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Broadband Scanning Microwave Microscopy of a Biological Cell with Unprecedented Image Quality and Signal-to-Noise Ratio

Broadband Scanning Microwave Microscopy of a Biological Cell...

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Microwave, MTT-S International Symposium

作者： Xin Jin Marco Farina Xiaopeng Wang Gianluca Fabi Xuanhong Cheng James C. M. Hwang Department of Electrical and Computer Engineering Lehigh University Bethlehem PA USA Dipartimento di Ingegneria dell’Informazione Università Politecnica delle Marche Ancona Italy Dept. of Materials Science and Engineering and Dept. of Bioengineering Lehigh University PA USA

A broadband scanning microwave microscope (SMM) was developed by modifying both the hardware and software of a narrowband commercial SMM. Using the broadband SMM, images of a Jurkat human lymphocyte cell were acquired over 128 × 128 pixels at 201 frequencies from 1 GHz to 9 GHz, all in 20 min. The acquired broadband signals allowed Fourier transformation for time-gated postprocessing of the SMM data with unprecedented image quality and signal-to-noise ratio. The broadband SMM can enable microwave spectroscopy and 3D tomography of intracellular structures in a live cell.

关键词： Broadband communication Signal to noise ratio Narrowband Probes Microwave imaging Microwave circuits

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scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs

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Cell systems 2023年第4期14卷 302-311.e4页

作者： Yongjian Yang Guanxun Li Yan Zhong Qian Xu Yu-Te Lin Cristhian Roman-Vicharra 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 Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan. Department of Nutrition and the Program in Integrative Nutrition & Complex Diseases Texas A&M University College Station TX 77843 USA. Electronic address: r-chapkin@tamu.edu. Department of Electrical and Computer Engineering Texas A&M University College Station TX 77843 USA Department of Veterinary Integrative Biosciences Texas A&M University College Station TX 77843 USA Interdisciplinary Program of Genetics Texas A&M University College Station TX 77843 USA. Electronic address: jcai@tamu.edu.

We present scTenifoldXct, a semi-supervised computational tool for detecting ligand-receptor (LR)-mediated cell-cell interactions and mapping cellular communication graphs. Our method is based on manifold alignment, using LR pairs as inter-data correspondences to embed ligand and receptor genes expressed in interacting cells into a unified latent space. Neural networks are employed to minimize the distance between corresponding genes while preserving the structure of gene regression networks. We apply scTenifoldXct to real datasets for testing and demonstrate that our method detects interactions with high consistency compared with other methods. More importantly, scTenifoldXct uncovers weak but biologically relevant interactions overlooked by other methods. We also demonstrate how scTenifoldXct can be used to compare different samples, such as healthy vs. diseased and wild type vs. knockout, to identify differential interactions, thereby revealing functional implications associated with changes in cellular communication status.

关键词： cell-cell interaction cellular communication gene regression network machine learning manifold alignment neural networks scRNA-seq single-cell RNA sequencing

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Reconfigurable Hyperbolic Polaritonics with Correlated Oxide Metasurfaces

Research Square

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Research Square 2021年

作者： Aghamiri, Neda Alsadat Hu, Guangwei Fali, Alireza Zhang, Zhen Li, Jiahan Balendhran, Sivacarendran Walia, Sumeet Sriram, Sharath Edgar, James H. Ramanathan, Shriram Alù, Andrea Abate, Yohannes Department of Physics and Astronomy University of Georgia AthensGA30602 United States Photonics Initiative Advanced Science Research Center City University of New York New YorkNY10031 United States Department of Electrical and Computer Engineering National University of Singapore Kent Ridge Singapore117583 Singapore School of Materials Engineering Purdue University West LafayetteIN47907 United States Tim Taylor Department of Chemical Engineering Kansas State University ManhattanKN 66506 United States School of Physics University of Melbourne ParkvilleVIC3010 Australia School of Engineering RMIT University MelbourneVIC Australia Functional Materials and Microsystems Research Group Micro Nano Research Facility RMIT University MelbourneVIC Australia ARC Centre of Excellence for Transformative Meta-Optical Systems RMIT University MelbourneVIC Australia Physics Program Graduate Center City University of New York New YorkNY10016 United States

Polaritons enable subwavelength confinement and highly anisotropic flows of light over a wide spectral range, holding the promise for applications in modern nanophotonic and optoelectronic devices. However, to fully realize their practical application potential, facile methods enabling nanoscale active control of polaritons are needed. Here, we introduce a hybrid polaritonic-oxide heterostructure platform consisting of van der Waals crystals, such as hexagonal boron nitride (hBN) or alpha-phase molybdenum trioxide (α-MoO3), transferred on nanoscale oxygen vacancy patterns on the surface of prototypical correlated perovskite oxide SmNiO3 (SNO). Using a combination of scanning probe microscopy and infrared nanoimaging techniques, we demonstrate nanoscale real-time reconfigurability of complex hyperbolic phonon polaritons patterned at the nanoscale with unmatched resolution. Hydrogenation and temperature modulation allow spatially localized conductivity modulation of SNO nanoscale patterns, enabling robust real-time modulation and nanoscale reconfiguration of hyperbolic polaritons. Our work paves the way towards nanoscale programmable metasurface engineering as a new paradigm for reconfigurable nanophotonic applications facilitated by a hybrid material platform exploiting extreme light-matter interactions in polaritonic systems. © 2021, CC BY.

关键词： Polariton

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Augmented Reality for Presenting Local Wisdom: Sumatera Utara Traditional House 3

Augmented Reality for Presenting Local Wisdom: Sumatera Utar...

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3rd International Conference on Computing and Applied Informatics 2018, ICCAI 2018

作者： Syahputra, M.F. Aulia, R. Sitompul, O.S. Andayani, U. Abdullah, D. Sriadhi, S. Nanuru, R.F. Utama, M.D. Manurung, R.T. Djanggih, H. Mouw, E. Department of Information Technology Faculty of Computer Science and Information Technology Universitas Sumatera Utara Medan Indonesia Department of Informatics Universitas Malikussaleh Aceh Utara Indonesia Department of Electrical Engineering Universitas Negeri Medan Indonesia Universitas Kristen Indonesia Maluku Ambon Indonesia Graduate Program in Scientific Psychology Universitas Kristen Maranatha Indonesia Faculty of Law Universitas Tompotika Luwuk Banggai Indonesia Faculty of Social and Human Sciences Universitas Halmahera Indonesia

Augmented Reality is a technology that allows users to see the real world, with virtual objects placed on it or combined with the real world. Augmented Reality itself can be applied to various things, including as an educational media. In the field of education, technology can be used a culture introduction to society. One part of Indonesian culture is traditional houses. Traditional house is a building that symbolizes the culture of the local community. In North Sumatra itself, there are several traditional houses that have different forms. The use of Vuforia SDK in the construction of this application can display augmented objects in the form of 3-dimentional objects and also provide information on the house. This application will run on the Android mobile platform to make it easier for users to access it. In addition, users can choose their own objects to be used as markers to make the application use much easier. © 2019 Published under licence by IOP Publishing Ltd.

关键词： Augmented reality

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