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Author Correction: Proteogenomic landscape of human pancreatic ductal adenocarcinoma in an Asian population reveals tumor cell-enriched and immune-rich subtypes

Nature cancer

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Nature cancer 2023年 2023 May 19页

作者： Do Young Hyeon Dowoon Nam Youngmin Han Duk Ki Kim Gibeom Kim Daeun Kim Jingi Bae Seunghoon Back Dong-Gi Mun Inamul Hasan Madar Hangyeore Lee Su-Jin Kim Hokeun Kim Sangyeop Hyun Chang Rok Kim Seon Ah Choi Yong Ryoul Kim Juhee Jeong Suwan Jeon Yeon Woong Choo Kyung Bun Lee Wooil Kwon Seunghyuk Choi Taewan Goo Taesung Park Young-Ah Suh Hongbeom Kim Ja-Lok Ku Min-Sik Kim Eunok Paek Daechan Park Keehoon Jung Sung Hee Baek Jin-Young Jang Daehee Hwang Sang-Won Lee School of Biological Sciences Seoul National University Seoul Republic of Korea. Department of Chemistry and Center for Proteogenome Research Korea University Seoul Republic of Korea. Department of Surgery and Cancer Research Institute Seoul National University College of Medicine Seoul Republic of Korea. Department of Anatomy and Cell Biology and Department of Biomedical Sciences Seoul National University College of Medicine Seoul Republic of Korea. Graduate School of Medical Science and Engineering Korea Advanced Institute of Science and Technology (KAIST) Seoul Republic of Korea. Creative Research Initiatives Center for Epigenetic Code and Diseases Seoul National University Seoul Republic of Korea. Department of Biological Sciences College of Natural Sciences and Department of Molecular Science and Technology Ajou University Suwon Republic of Korea. Department of Pathology Seoul National University College of Medicine Seoul Korea. Department of Computer Science Hanyang University Seoul Republic of Korea. Interdisciplinary Program in Bioinformatics Seoul National University Seoul Republic of Korea. Department of Statistics Seoul National University Seoul Republic of Korea. Korean Cell Line Bank Laboratory of Cell Biology Cancer Research Institute Seoul National University College of Medicine Seoul Korea. Department of New Biology Daegu Gyeongbuk Institute of Science and Technology Daegu Republic of Korea. Department of Biological Sciences College of Natural Sciences and Department of Molecular Science and Technology Ajou University Suwon Republic of Korea. dpark@ajou.ac.kr. Department of Anatomy and Cell Biology and Department of Biomedical Sciences Seoul National University College of Medicine Seoul Republic of Korea. keehoon.jung@snu.ac.kr. Institute of Allergy and Clinical Immunology Seoul National University Medical Research Center Seoul Republic of Korea. keehoon.jung@snu.ac.kr. School of Biological Sciences Seoul National University Seoul Republic of

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Total variation superiorized conjugate gradient method for image reconstruction

arXiv

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arXiv 2017年

作者： Zibetti, Marcelo V. W. Lin, Chuan Herman, Gabor T. Graduate Program in Electrical Engineering and Computer Science Federal University of Technology - Paraná Curitiba80230-901 Brazil School of Electrical Engineering Southwest Jiaotong University Chengdu Sichuan610031 China Department of Computer Science Graduate Center City University of New York New YorkNY10016 United States

The conjugate gradient (CG) method is commonly used for the relatively-rapid solution of least squares problems. In image reconstruction, the problem can be ill-posed and also contaminated by noise;due to this, approaches such as regularization should be utilized. Total variation (TV) is a useful regularization penalty, frequently utilized in image reconstruction for generating images with sharp edges. When a non-quadratic norm is selected for regularization, as is the case for TV, then it is no longer possible to use CG. Nonlinear CG is an alternative, but it does not share the efficiency that CG shows with least squares and methods such as fast iterative shrinkage-thresholding algorithms (FISTA) are preferred for problems with TV norm. A different approach to including prior information is superiorization. In this paper it is shown that the conjugate gradient method can be superiorized. Five different CG variants are proposed, including preconditioned CG. The CG methods superiorized by the total variation norm are presented and their performance in image reconstruction is demonstrated. It is illustrated that some of the proposed variants of the superiorized CG method can produce reconstructions of superior quality to those produced by FISTA and in less computational time, due to the speed of the original CG for least squares problems. In the Appendix we examine the behavior of one of the superiorized CG methods (we call it S-CG);one of its input parameters is a positive number ". It is proved that, for any given " that is greater than the half-squared-residual for the least squares solution, S-CG terminates in a finite number of steps with an output for which the half-squared-residual is less than or equal to ". Importantly, it is also the case that the output will have a lower value of TV than what would be provided by unsuperiorized CG for the same value " of the half-squared residual. Copyright © 2017, The Authors. All rights reserved.

关键词： Conjugate gradient method

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Improved Combinatorial Benders Decomposition for a Scheduling Problem with Unrelated Parallel Machines

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Journal of Applied Mathematics 2017年第1期2017卷

作者： Gomes, Francisco Regis Abreu Mateus, Geraldo Robson Graduate Program in Production Engineering Federal University of Minas Gerais and Federal Institute of Education Science and Technology of Ceará Belo Horizonte MG Brazil Computer Science Department Federal University of Minas Gerais Belo Horizonte MG Brazil

This paper addresses the unrelated parallel machines scheduling problem with sequence and machine dependent setup times. Its goal is to minimize the makespan. The problem is solved by a combinatorial Benders decomposition. This method can be slow to converge. Therefore, three procedures are introduced to accelerate its convergence. The first procedure is a new method that consists of terminating the execution of the master problem when a repeated optimal solution is found. The second procedure is based on the multicut technique. The third procedure is based on the warm-start. The improved Benders decomposition scheme is compared to a mathematical formulation and a standard implementation of Benders decomposition algorithm. In the experiments, two test sets from the literature are used, with 240 and 600 instances with up to 60 jobs and 5 machines. For the first set the proposed method performs 21.85% on average faster than the standard implementation of the Benders algorithm. For the second set the proposed method failed to find an optimal solution in only 31 in 600 instances, obtained an average gap of 0.07%, and took an average computational time of 377.86 s, while the best results of the other methods were 57, 0.17%, and 573.89 s, respectively. © 2017 Francisco Regis Abreu Gomes and Geraldo Robson Mateus.

关键词： Optimal systems

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Functional annotation of chemical libraries across diverse biological processes (vol 13, pg 982, 2017)

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NATURE CHEMICAL BIOLOGY 2017年第12期13卷 1286-1286页

作者： Piotrowski, Jeff S. Li, Sheena C. Deshpande, Raamesh Simpkins, Scott W. Nelson, Justin Yashiroda, Yoko Barber, Jacqueline M. Safizadeh, Hamid Wilson, Erin Okada, Hiroki Gebre, Abraham A. Kubo, Karen Torres, Nikko P. LeBlanc, Marissa A. Andrusiak, Kerry Okamoto, Reika Yoshimura, Mami DeRango-Adem, Eva van Leeuwen, Jolanda Shirahige, Katsuhiko Baryshnikova, Anastasia Brown, Grant W. Hirano, Hiroyuki Costanzo, Michael Andrews, Brenda Ohya, Yoshikazu Osada, Hiroyuki Yoshida, Minoru Myers, Chad L. Boone, Charles RIKEN Center for Sustainable Resource Science Wako Saitama Japan Department of Computer Science and Engineering University of Minnesota-Twin Cities Minneapolis Minnesota USA Bioinformatics and Computational Biology Program University of Minnesota-Twin Cities Minneapolis Minnesota USA Department of Electrical and Computer Engineering University of Minnesota-Twin Cities Minneapolis Minnesota USA Department of Integrated Biosciences Graduate School of Frontier Sciences University of Tokyo Kashiwa Chiba Japan Donnelly Centre University of Toronto Toronto Ontario Canada Institute of Molecular and Cellular Biosciences Center for Epigenetic Disease University of Tokyo Bunkyo-ku Tokyo Japan Lewis-Sigler Institute for Integrative Genomics Princeton University Princeton New Jersey USA Department of Biochemistry University of Toronto Toronto Ontario Canada.

Chemical-genetic approaches offer the potential for unbiased functional annotation of chemical libraries. Mutations can alter the response of cells in the presence of a compound, revealing chemical-genetic interactions that can elucidate a compound’s mode of action. We developed a highly parallel, unbiased yeast chemical-genetic screening system involving three key components. First, in a drug-sensitive genetic background, we constructed an optimized diagnostic mutant collection that is predictive for all major yeast biological processes. Second, we implemented a multiplexed (768-plex) barcode-sequencing protocol, enabling the assembly of thousands of chemical-genetic profiles. Finally, based on comparison of the chemical-genetic profiles with a compendium of genome-wide genetic interaction profiles, we predicted compound functionality. Applying this high-throughput approach, we screened seven different compound libraries and annotated their functional diversity. We further validated biological process predictions, prioritized a diverse set of compounds, and identified compounds that appear to have dual modes of action.

关键词： Chemical genetics High-throughput screening Networks and systems biology Target identification

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Magnetic-free nonreciprocal photonic platform based on time-modulated graphene capacitors

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Physical Review B 2018年第16期98卷 165428-165428页

作者： D. Correas-Serrano A. Alù J. S. Gomez-Diaz Department of Electrical and Computer Engineering University of California Davis One Shields Avenue Kemper Hall 2039 Davis California 95616 USA Photonics Initiative Advanced Science Research Center City University of New York 85 St. Nicholas Terrace New York City New York 10031 USA Physics Program Graduate Center City University of New York New York New York 10016 USA and Department of Electrical Engineering City College of the City University of New York New York New York 10031 USA

We propose a paradigm for the realization of nonreciprocal photonic devices based on time-modulated graphene capacitors coupled to photonic waveguides, without relying on magneto-optic effects. The resulting hybrid graphene-dielectric platform is low loss, silicon compatible, robust against graphene imperfections, scalable from terahertz to near-infrared frequencies, and it exhibits large nonreciprocal responses using realistic biasing schemes. We introduce an analytical framework based on solving the eigenstates of the modulated structure and on spatial coupled mode theory, unveiling the physical mechanisms that enable nonreciprocity and enabling a quick analysis and design of optimal isolator geometries based on synthetic linear and angular momentum bias. Our results, validated through harmonic-balance full-wave simulations, confirm the feasibility of the introduced low-loss (<3 dB) platform to realize large photonic isolation through various mechanisms, such as narrow-band asymmetric band gaps and interband photonic transitions that allow multiple isolation frequencies and large bandwidths. We envision that this technology may pave the wave to magnetic-free, fully integrated, and CMOS–compatible nonreciprocal components with wide applications in photonic networks and thermal management.

关键词： Photonics Plasmonics Graphene Waveguides Lorentz symmetry

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Ten simple rules for reproducible research in jupyter notebooks

arXiv

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arXiv 2018年

作者： Rule, Adam Birmingham, Amanda Zuniga, Cristal Altintas, Ilkay Huang, Shih-Cheng Knight, Rob Moshiri, Niema Nguyen, Mai H. Rosenthal, Sara Brin Pérez, Fernando Rose, Peter W. Design Lab UC San Diego San DiegoCA United States Center for Computational Biology and Bioinformatics UC San Diego San DiegoCA United States Department of Pediatrics UC San Diego San DiegoCA United States Data Science Hub San Diego Supercomputer Center UC San Diego San DiegoCA United States Departments of Bioengineering and Computer Science and Engineering Center for Microbiome Innovation UC San Diego San DiegoCA United States Bioinformatics and Systems Biology Graduate Program UC San Diego San DiegoCA United States Department of Statistics Berkeley Institute for Data Science UC Berkeley Lawrence Berkeley National Laboratory BerkeleyCA United States Biomedical Informatics Graduate Program Stanford University StanfordCA United States

Reproducibility of computational studies is a hallmark of scientific methodology. It enables researchers to build with confidence on the methods and findings of others, reuse and extend computational pipelines, and thereby drive scientific progress. Since many experimental studies rely on computational analyses, biologists need guidance on how to set up and document reproducible data analyses or simulations. In this paper, we address several questions about reproducibility. For example, what are the technical and non-technical barriers to reproducible computational studies? What opportunities and challenges do computational notebooks offer to overcome some of these barriers? What tools are available and how can they be used effectively? We have developed a set of rules to serve as a guide to scientists with a specific focus on computational notebook systems, such as Jupyter Notebooks, which have become a tool of choice for many applications. Notebooks combine detailed workflows with narrative text and visualization of results. Combined with software repositories and open source licensing, notebooks are powerful tools for transparent, collaborative, reproducible, and reusable data analyses. Copyright © 2018, The Authors. All rights reserved.

关键词： Digital storage

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Application of Message Security Application Using Vigenere Cipher Algorithm Utilizing One Time Pad (OTP) Algorithm as a Key Generator

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Journal of Physics: Conference Series 2019年第1期1363卷 012080-012080页

作者： Pardede, A M H Lorena Perbina Br Sitepu Zarlis, Muhammad Tulus Iskandar, Akbar Sriadhi, S Manurung, Rosida Tiurma Nurintan Asyiah Siregar Sari, Ayu Esteka Yunawati, Sri Mursyidah, M Mursalin, M Kurniasih, Nuning Kurniawan, Citra Winarno, Edy STMIK Kaputama Binjai Sumatera Utara Indonesia Department of Computer Science Universitas Sumatera Utara Medan Indonesia Department of Mathematics Universitas Sumatera Utara Medan Indonesia Department of Electrical Engineering Universitas Negeri Medan Indonesia Graduate Program in Scientific Psychology Universitas Kristen Maranatha Indonesia Department of Management STIE Labuhanbatu Sumatera Utara Indonesia Department of Management STIE Sakti Alam Kerinci Jambi Indonesia Program Study of Accounting Pasir Pengaraian University Riau Indonesia Departement of Information Technology and Computer Politeknik Negeri Lhokseumawe Aceh Indonesia Department of Mathematics Education Universitas Malikussaleh Aceh Indonesia Faculty of Communication Sciences Library and Information Science Program Universitas Padjadjaran Bandung Indonesia Department of Electrical Engineering Sekolah Tinggi Teknik Malang Indonesia Faculty of Information Technology Universitas Stikubank Semarang Indonesia

Cryptography is the science and art of maintaining the security of messages when messages are sent from one place to another. One of the ways securing the form of text message information is by the encryption process using the Vigenere Cipher algorithm and utilizing the One Time Pad (OTP) algorithm as a key generator, where the message will be random when it is opened. The message encryption process used the vigenere cipher algorithm while OTP is used to secure the key with the same formula. After this research has been done, an application was designed to secure text messages by converting the text message into a random message so that the message was unreadable due to a secret message that could not be known by others. The results achieved can secure an encrypted message that cannot be reopened and if those messages were reopened, they must be decrypted.

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Intrinsic Raman signatures of pristine hybrid perovskite CH3NH3PbI3 and its multiple stages of structure transformation 44

Intrinsic Raman signatures of pristine hybrid perovskite CH3...

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44th IEEE Photovoltaic Specialist Conference, PVSC 2017

作者： Chen, Qiong Liu, Henan Kim, Hui-Seon Liu, Yucheng Yang, Mengjin Yue, Naili Ren, Gang Zhu, Kai Liu, Shengzhong Frank Park, Nam-Gyu Zhang, Yong Department of Electrical and Computer Engineering Korea Republic of Optical Science and Engineering Graduate Program University of North Carolina at Charlotte CharlotteNC28223 United States School of Chemical Engineering and Department of Energy Science Sungkyunkwan University Suwon440-746 Korea Republic of Key Laboratory of Applied Surface and Colloid Chemistry National Ministry of EducationInstitute for Advanced Energy Materials School of Materials Science and Engineering Shaanxi Normal University Xi'an710062 China Chemical and Materials Science Center National Renewable Energy Laboratory GoldenCO80401 United States Molecular Foundry Lawrence Berkeley National Laboratory BerkeleyCA94720 United States

ISBN: (纸本)9781509056057

By performing spatially resolved Raman and photoluminescence spectroscopy with different illumination conditions, we have achieved a unified understanding towards the spectroscopy signatures of the organic-inorganic hybrid perovskite, transforming from the pristine state (CH3NH3PbI3 or MAPbI3) to fully degraded state (i.e., PbI2), for samples with varying crystalline domain size from mesoscopic scale to macroscopic size, synthesized by three different techniques. © 2017 IEEE.

关键词： Perovskite

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MATLAB-based analysis of labor dispatch and work distribution: An example involving caseworkers in central Taiwan

MATLAB-based analysis of labor dispatch and work distributio...

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2017 IEEE International Conference on Applied System Innovation, ICASI 2017

作者： Oh, Chin-Yu Hsu, Meng-Chueh Tsai, Chang-Ming Jhang, Jyun-Yao Chen, Yu-Ren Chen, Bo-Xiang Chen, Yi-Chung Teng, Chun-Wen Chen, Shu-Hui Department of Information Engineering and Computer Science Feng Chia University Taichung40724 Taiwan Ph. D. Program of Business Feng Chia University Taichung40724 Taiwan Graduate Institute of Public Policy and social innovation Feng Chia University Taichung40724 Taiwan General Education Center Feng Chia University Taichung40724 Taiwan

ISBN: (纸本)9781509048977

The dispatching of labor and distribution of tasks among workers are important aspects of corporate operations. Labor dispatch refers to the dispatching of employees to meet with clients;however, dispatches commonly vary with time. This means that any analysis pertaining to labor dispatch and work distribution should also vary with time. In this study, MATLAB was used to analyze data from anonymous caseworkers in central Taiwan in order to identify relationships between the location of their offices and the homes of their clients. Our aim was to determine the rationality behind labor dispatch and work distribution. This led us to develop a novel method by which to dispatch labor in order to achieve a more equitable distribution of work. Simulations demonstrate the efficacy of the proposed scheme in improving labor dispatch and work distribution. © 2017 IEEE.

关键词： MATLAB

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Coherently Enhanced Wireless Power Transfer

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Physical Review Letters 2018年第14期120卷 143901-143901页

作者： Alex Krasnok Denis G. Baranov Andrey Generalov Sergey Li Andrea Alù Department of Electrical and Computer Engineering The University of Texas at Austin Austin Texas 78712 USA Department of Physics Chalmers University of Technology 412 96 Gothenburg Sweden Moscow Institute of Physics and Technology Dolgoprudny 141700 Russia Department of Electronics and Nanoengineering Aalto University 02150 Espoo Finland ITMO University St. Petersburg 197101 Russia Photonics Initiative Advanced Science Research Center City University of New York New York 10031 USA Physics Program Graduate Center City University of New York New York 10016 USA Department of Electrical Engineering City College of The City University of New York New York 10031 USA

Extraction of electromagnetic energy by an antenna from impinging external radiation is at the basis of wireless communications and wireless power transfer (WPT). The maximum of transferred energy is ensured when the antenna is conjugately matched, i.e., when it is resonant and it has an equal coupling with free space and its load. This condition, however, can be easily affected by changes in the environment, preventing optimal operation of a WPT system. Here, we introduce the concept of coherently enhanced WPT that allows us to bypass this difficulty and achieve dynamic control of power transfer. The approach relies on coherent excitation of the waveguide connected to the antenna load with a backward propagating signal of specific amplitude and phase. This signal creates a suitable interference pattern at the load resulting in a modification of the local wave impedance, which in turn enables conjugate matching and a largely increased amount of extracted energy. We develop a simple theoretical model describing this concept, demonstrate it with full-wave numerical simulations for the canonical example of a dipole antenna, and verify experimentally in both near-field and far-field regimes.

关键词： Electromagnetism engineering Light propagation, transmission & absorption Photonics

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