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The Brain Tumor Sequence Registration (BraTS-Reg) Challenge: Establishing Correspondence Between Pre-Operative and Follow-up MRI Scans of Diffuse Glioma Patients

arXiv

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arXiv 2021年

作者： Baheti, Bhakti Chakrabarty, Satrajit Akbari, Hamed Bilello, Michel Wiestler, Benedikt Schwarting, Julian Calabrese, Evan Rudie, Jeffrey Abidi, Syed Mousa, Mina Villanueva-Meyer, Javier Fields, Brandon K.K. Kofler, Florian Shinohara, Russell Takeshi Iglesias, Juan Eugenio Mok, Tony C.W. Chung, Albert C.S. Wodzinski, Marek Jurgas, Artur Marini, Niccolò Atzori, Manfredo Müller, Henning Grosbröhmer, Christoph Siebert, Hanna Hansen, Lasse Heinrich, Mattias P. Canalini, Luca Klein, Jan Gerken, Annika Heldmann, Stefan Hering, Alessa Hahn, Horst K. Meng, Mingyuan Bi, Lei Feng, Dagan Kim, Jinman Zeineldinal, Ramy A. Karar, Mohamed E. Mathis-Ullrich, Franziska Burgert, Oliver Abderezaei, Javid Pionteck, Aymeric Chopra, Agamdeep Kurt, Mehmet Yan, Kewei Yan, Yonghong Tang, Zhe Ma, Jianqiang Nasser, Sahar Almahfouz Kurian, Nikhil Cherian Meena, Mohit Shamsi, Saqib Sethi, Amit Tustison, Nicholas J. Avants, Brian B. Cook, Philip Gee, James C. Tian, Lin Greer, Hastings Niethammer, Marc Hoopesar, Andrew Hoffmannas, Malte Dalcaar, Adrian V. Christodoulidis, Stergios Estiene, Théo Vakalopoulou, Maria Paragios, Nikos Marcus, Daniel S. Davatzikos, Christos Sotiras, Aristeidis Menze, Bjoern Bakas, Spyridon Waldmannstetter, Diana Division of Computational Pathology Department of Pathology and Laboratory Medicine Indiana University School of Medicine IndianapolisIN United States Department of Electrical and Systems Engineering Washington University in St. Louis St. LouisMO United States GE HealthCare San RamonCA United States University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Mallinckrodt Institute of Radiology Washington University School of Medicine St. LouisMO United States Institute for Informatics Data Science & Biostatistics Washington University School of Medicine St. LouisMO United States Department of Bioengineering Santa Clara University Santa ClaraCA United States Department of Quantitative Biomedicine University of Zurich Zurich Switzerland Department of Computer Science TUM School of Computation Information and Technology Technical University of Munich Munich Germany Department of Diagnostic and Interventional Neuroradiology School of Medicine Klinikum rechts der Isar Technical University of Munich Munich Germany Department of Nuclear Medicine University Hospital Regensburg Regensburg Germany University Hospital Regensburg Regensburg Germany Department of Radiology & Biomedical Imaging University of California San FranciscoCA United States Department of Radiology Duke University Medical Center DurhamNC United States Department of Radiology University of California San DiegoCA United States Helmholtz AI Helmholtz Munich Neuherberg Germany Penn Statistics in Imaging and Visualization Center Department of Biostatistics Epidemiology and Informatics University of Pennsylvania Philadelphia United States Massachusetts General Hospital Harvard Medical School United States Centre for Medical Imaging Computing University College London United Kingdom The Hong Kong University of Science and Technology Hong Kong University of Applied Sciences West

Registration of longitudinal brain Magnetic Resonance Imaging (MRI) scans containing pathologies is challenging due to dramatic changes in tissue appearance. Although there has been considerable progress in developing general-purpose medical image registration techniques, they have not yet attained the requisite precision and reliability for this task, highlighting its inherent complexity. Here we describe the Brain Tumor Sequence Registration (BraTS-Reg) challenge, as the first public benchmark environment for deformable registration algorithms focusing on estimating correspondences between pre-operative and follow-up scans of the same patient diagnosed with a diffuse brain glioma. The challenge was conducted in conjunction with both the IEEE International Symposium on Biomedical Imaging (ISBI) 2022 and the International Conference on Medical Image Computing and computer-Assisted Intervention (MICCAI) 2022. The BraTS-Reg data comprise de-identified multi-institutional multi-parametric MRI (mpMRI) scans, curated for size and resolution according to a canonical anatomical template, and divided into training, validation, and testing sets. Clinical experts annotated ground truth (GT) landmark points of anatomical locations distinct across the temporal domain. The training data with their GT annotations, were publicly released to enable the development of registration algorithms. The validation data, without their GT annotations, were also released to allow for algorithmic evaluation prior to the testing phase, which only allowed submission of containerized algorithms for evaluation on hidden hold-out testing data. Quantitative evaluation and ranking was based on the Median Euclidean Error (MEE), Robustness, and the determinant of the Jacobian of the displacement field. The top-ranked methodologies yielded similar performance across all evaluation metrics and shared several methodological commonalities, including pre-alignment, deep neural networks, inverse consistency

关键词： Magnetic resonance imaging

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THE AEGIS DATA BUS EXPERIMENT

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NAVAL ENGINEERS JOURNAL 1989年第5期101卷 53-58页

作者： FRINK, JG VERVEN, DM John G. Frink is an assistant group supervisor in the Fleet Systems Department of The Johns Hopkins University Applied Physics Laboratory. He received his B.S. degree in physics from Michigan State University in 1968 and the M.S. degree in computer science from the University of Maryland in 1971. Mr. Frink worked at the Naval Surface Weapons Center White Oak Laboratory on a variety of weapons systems before joining the Applied Physics Laboratory in 1978. Mr. Frink has supervised the development of a large scale battle group simulation that successfully employs the receiver selection paradigm described herein on a hardware suite composed of an extensible number of (currently 15) processors. David M. Verven is a senior electrical engineer in the Fleet Systems Department of The Johns Hopkins University Applied Physics Laboratory. He received the B.S. degree in electrical engineering from the University of Maryland College Park in 1979 and the M. S. degree in the same discipline from The Johns Hopkins University in 1984. Mr. Verven joined the Applied Physics Laboratory in 1979 and initially worked on analysis of Navy sensor systems. In 1981 he was the AN/SPS-49 test team leader for the New Threat Upgrade (NTU) combat system land-based test. In 1982 he became involved in the development of the BBWRS system. Currently he is involved in real-time computer program development for the CEP project.

This paper documents an experiment performed by The Johns Hopkins University Applied Physics Laboratory to measure the effect of inserting a data bus into a combat system. The experiment was conducted at the Aegis computer Center located at the Naval Surface Weapons Center in Dahlgren, Virginia (NSWC/DL). The purpose of the experiment was to determine whether or not the Aegis Weapon System (the core of the Aegis Combat System) could be operated with a portion of its point-to-point interelement cables replaced by a data bus. The data bus chosen for the experiment employs message broadcasting with receiver selection. A primary goal of the experiment was to minimize the amount of Aegis computer program changes required to accommodate the data bus. The results presented in this paper will show that the experiment was a success. Key certification tests were passed with no computer program changes to the tactical elements and minimal changes in the Aegis tactical executive (ATES) program (less than 110 words changed).

关键词： Data Transmission Equipment

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Fano Resonances: Tunable Fano Resonance and Plasmon–Exciton Coupling in Single Au Nanotriangles on Monolayer WS2at Room Temperature (Adv. Mater. 22/2018)

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Advanced Materials 2018年第22期30卷

作者： Mingsong Wang Alex Krasnok Tianyi Zhang Leonardo Scarabelli He Liu Zilong Wu Luis M. Liz‐Marzán Mauricio Terrones Andrea Alù Yuebing Zheng Department of Mechanical Engineering Materials Science and Engineering Program Texas Materials Institute The University of Texas at Austin Austin TX 78712 USA Department of Electrical and Computer Engineering The University of Texas at Austin Austin TX 78712 USA Department of Materials Science and Engineering The Pennsylvania State University University Park PA 16802 USA Bionanoplasmonics Laboratory CIC biomaGUNE Paseo de Miramón 182 20014 Donostia‐San Sebastián Spain Department of Chemistry and Biochemistry California NanoSystems Institute University of California Los Angeles Los Angeles CA 90095 USA Department of Chemistry The Pennsylvania State University University Park PA 16802 USA Ikerbasque Basque Foundation for Science 48013 Bilbao Spain Biomedical Research Networking Center in Bioengineering Biomaterials and Nanomedicine CIBER‐BBN 20014 Donostia‐San Sebastián Spain Department of Physics and Center for 2‐Dimensional and Layered Materials The Pennsylvania State University University Park PA 16802 USA Department of Materials Science and Engineering & Chemical Engineering Carlos III University of Madrid Avenida Universidad 30 28911 Leganés Madrid Spain IMDEA Materials Institute Eric Kandel 2 Getafe Madrid 28005 Spain

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Retraction: Design of Decision Support System Determination of Inventory Inventory Using Single Exponential Smoothing Forecasting Method (J. Phys.: Conf. Ser. 1114 012082)

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Journal of Physics: Conference Series 2018年第1期1114卷

作者： Muhammad Iqbal Dahlan Abdullah H Hartono Cut Ita Erliana S Sriadhi Nurmawati M Adhi Prasnowo Abdurrozzaq Hasibuan Akbar Iskandar Kundharu Saddhono Abdussakir Hastuti Musa Muhammad Ikhsan Setiawan Youmeni Sagala Rumiris Siahaan Eka Mayastika Sinaga Anggraini Syahputri Feby Milanie Henry Aspan Muammar Khaddafi Department of Computer System Universitas Pembangunan Panca Budi Medan Indonesia Department of Informatics Universitas Malikussaleh Aceh Indonesia Department of Computer Science STMIK IBBI Medan Indonesia Department of Industrial Engineering Universitas Malikussaleh Aceh Indonesia Department of Electrical Engineering Universitas Negeri Medan Indonesia Faculty of Industry Technique University of 45 Surabaya Indonesia Department of Industrial Engineering Universitas Maarif Hasyim Latif Sidoarjo Indonesia Faculty of Engineering Universitas Islam Sumatera UtaraMedan-Indonesia Informatics Engineering STMIK AKBA Makassar Indonesia Graduate Program Universitas Sebelas Maret Surakarta Indonesia Department of Mathematics Education State Islamic University of Malang Malang Indonesia Department of Mathematics Universitas Muhammadiyah Parepare Indonesia Department of Civil Engineering Narotama University Surabaya Indonesia STIE Bina Karya Tebing Tinggi Indonesia Universitas Pembangunan Panca Budi Medan Indonesia Department of Accounting Universitas Malikussaleh Aceh Indonesia

This paper was retracted by IOP Publishing on 12 December 2018. This paper was published due to a technical error and was not intended to be included in this journal. Retraction published: 8 February 2019

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Bird's-eye view on noise-based logic

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International journal of modern physics. Conference series 2014年第33期33卷 1460363页

作者： Laszlo B Kish Claes G Granqvist Tamas Horvath Andreas Klappenecker He Wen Sergey M Bezrukov Department of Electrical and Computer Engineering Texas A&M University College Station Texas 77843-2128 USA laszlo.kish@ece.tamu.edu. Department of Engineering Sciences The Ångström Laboratory Uppsala University P.O. Box 534 SE-75121 Uppsala Sweden claes-goran.granqvist@angstrom.uu.se. Department of Computer Science University of Bonn Germany Fraunhofer IAIS Schloss Birlinghoven D-53754 Sankt Augustin Germany tamas.horvath@iais.fraunhofer.de. Department of Computer Science Texas A&M University College Station Texas 77843-2128 USA klappi@cse.tamu.edu. College of Electrical and Information Engineering Hunan University Changsha China he_wen82@***. Laboratory of Physical and Structural Biology Program in Physical Biology NICHD National Institutes of Health Bethesda MD 20892 USA.

Noise-based logic is a practically deterministic logic scheme inspired by the randomness of neural spikes and uses a system of uncorrelated stochastic processes and their superposition to represent the logic state. We briefly discuss various questions such as () What does practical determinism mean? () Is noise-based logic a Turing machine? () Is there hope to beat (the dreams of) quantum computation by a classical physical noise-based processor, and what are the minimum hardware requirements for that? Finally, () we address the problem of random number generators and show that the common belief that quantum number generators are superior to classical (thermal) noise-based generators is nothing but a myth.

关键词： Brain Classical versus quantum random number generators Computational complexity Probabilistic Turing machine

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Cover Picture: Proteolytic Actuation of Nanoparticle Self-Assembly (Angew. Chem. Int. Ed. 19/2006)

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Angewandte Chemie International Edition 2006年第19期45卷

作者： Todd J. Harris Geoffrey von Maltzahn Austin M. Derfus Erkki Ruoslahti Sangeeta N. Bhatia Prof. Harvard-MIT Division of Health Sciences and Technology Massachusetts Institute of Technology E19-502D Cambridge MA 02139 USA Fax: (+1) 617-324-0710 These authors contributed equally Department of Bioengineering University of California San Diego La Jolla CA USA Burnham Institute La Jolla CA USA Electrical Engineering and Computer Science/MIT Brigham & Women's Hospital Boston MA USA

Sterically shielded …︁ …︁ nanoparticles diffuse freely in solution and biological fluids until proteases expressed by cancer cells trigger them to self-assemble. In their Communication on page 3161ff., S. N. Bhatia and co-workers show that complimentary Fe 3 O 4 nanoparticle binding is inhibited by the attachment of protease-cleavable polymers. Cleavage of these polymers triggers “latent” nanoparticles to form multimeric assemblies with emergent properties.

关键词： magnetic properties nanostructures proteases self-assembly triggered assembly

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Correction: Liquid-capped encoded microcapsules for multiplex assays

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Lab on a chip 2017年第4期17卷 738页

作者： Younghoon Song Yunjin Jeong Taehong Kwon Daewon Lee Dong Yoon Oh Tae-Joon Park Junhoi Kim Jiyun Kim Sunghoon Kwon Institutes of Entrepreneurial BioConvergence Seoul National University Seoul 151-742 Republic of Korea. skwon@snu.ac.kr and Department of Electrical and Computer Science Seoul National University Seoul 151-742 Republic of Korea. Institutes of Entrepreneurial BioConvergence Seoul National University Seoul 151-742 Republic of Korea. skwon@snu.ac.kr and Interdisciplinary Program of Bioengineering Seoul National University Seoul 151-742 Republic of Korea. Nano Systems Institute Seoul National University Seoul 151-742 Republic of Korea. Department of Materials Science and Engineering Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea. Institutes of Entrepreneurial BioConvergence Seoul National University Seoul 151-742 Republic of Korea. skwon@snu.ac.kr and Department of Electrical and Computer Science Seoul National University Seoul 151-742 Republic of Korea and Interdisciplinary Program of Bioengineering Seoul National University Seoul 151-742 Republic of Korea and Nano Systems Institute Seoul National University Seoul 151-742 Republic of Korea and Seoul National University Hospital Biomedical Research Institute Seoul National University Hospital Seoul 151-742 Republic of Korea and Quantamatrix Inc. Seoul 151-742 Republic of Korea.

Correction for 'Liquid-capped encoded microcapsules for multiplex assays' by Younghoon Song et al., Lab Chip, 2017, DOI: .

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Erratum: Extended Drude Model for Intraband-Transition-Induced Optical Nonlinearity [Phys. Rev. Applied 11, 064062 (2019)]

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Physical Review Applied 2020年第3期14卷 039901-039901页

作者： Heng Wang Kang Du Chuhao Jiang Zhiqiang Yang Lixia Ren Wending Zhang Soo Jin Chua Ting Mei MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions and Shaanxi Key Laboratory of Optical Information Technology School of Physical Science and Technology Northwestern Polytechnical University Xi’an 710129 China Department of Electrical and Computer Engineering National University of Singapore 4 Engineering Drive 3 Singapore 117583 LEES Program Singapore-MIT Alliance for Research & Technology (SMART) 1 CREATE Way #10-01 CREATE Tower Singapore 138602

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Dark Excitons: Dark-Exciton-Mediated Fano Resonance from a Single Gold Nanostructure on Monolayer WS2at Room Temperature (Small 31/2019)

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Small 2019年第31期15卷

作者： Mingsong Wang Zilong Wu Alex Krasnok Tianyi Zhang Mingzu Liu He Liu Leonardo Scarabelli Jie Fang Luis M. Liz-Marzán Mauricio Terrones Andrea Alù Yuebing Zheng Department of Mechanical Engineering Texas Materials Institute The University of Texas at Austin Austin TX 78712 USA Photonics Initiative Advanced Science Research Center Physics Program Graduate Center Department of Electrical Engineering City College of the City University of New York New York NY 10031 USA Department of Materials Science and Engineering Department of Physics Department of Chemistry Center for 2-Dimensional and Layered Materials The Pennsylvania State University University Park PA 16802 USA Department of Chemistry and Biochemistry California NanoSystems Institute University of California Los Angeles Los Angeles CA 90095 USA Bionanoplasmonics Laboratory CIC biomaGUNE Paseo de Miramón 182 20014 Donostia-San Sebastián Spain Ikerbasque Basque Foundation for Science 48013 Bilbao Spain Biomedical Research Networking Center in Bioengineering Biomaterials and Nanomedicine CIBER-BBN 20014 Donostia-San Sebastián Spain

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Historical growth of concept networks in Wikipedia

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Collective Intelligence 2022年第2期1卷 26339137221109839页

作者： Harang Ju Dale Zhou Ann S Blevins David M Lydon-Staley Judith Kaplan Julio R Tuma Dani S Bassett Neuroscience Graduate Group University of Pennsylvania Philadelphia PA USA Department of Bioengineering School of Engineering & Applied Science University of Pennsylvania Philadelphia PA USA Annenberg School for Communication University of Pennsylvania Philadelphia PA USA Department of History and Sociology of Science College of Arts and Sciences University of Pennsylvania Philadelphia PA USA Integrated Studies Program College of Arts and Sciences University of Pennsylvania Philadelphia PA USA Integrated Studies Program College of Arts and Sciences University of Pennsylvania Philadelphia PA USA Department of Philosophy College of Arts and Sciences University of Pennsylvania Philadelphia PA USA Department of Electrical & Systems Engineering School of Engineering & Applied Science University of Pennsylvania Philadelphia PA USA Department of Physics & Astronomy College of Arts & Sciences University of Pennsylvania Philadelphia PA USA Department of Neurology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Psychiatry Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Santa Fe Institute Santa Fe NM USA

Philosophers of science have long questioned how collective scientific knowledge grows. Although disparate answers have been posited, empirical validation has been challenging due to limitations in collecting and systematizing large historical records. Here, we introduce new methods to analyze scientific knowledge formulated as a growing network of articles on Wikipedia and their hyperlinks. We demonstrate that in Wikipedia, concept networks in subdisciplines of science do not grow by expanding from their central core to reach an ancillary periphery. Instead, science concept networks in Wikipedia grow by creating and filling knowledge gaps. Notably, the process of gap formation and closure may be valued by the scientific community, as evidenced by the fact that it produces discoveries that are more frequently awarded Nobel prizes than other processes. To determine whether and how the gap process is interrupted by paradigm shifts, we operationalize a paradigm as a particular subdivision of scientific concepts into network modules. Hence, paradigm shifts are reconfigurations of those modules. The approach allows us to identify a temporal signature in structural stability across scientific subjects in Wikipedia. In a network formulation of scientific discovery, our findings suggest that data-driven conditions underlying scientific breakthroughs depend as much on exploring uncharted gaps as on exploiting existing disciplines and support policies that encourage new interdisciplinary research.

关键词： science of science networks philosophy of science Wikipedia cavity

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