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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

Ten simple rules for reproducible research in jupyter notebooks

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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

Mapping the Human Body at Cellular Resolution -- The NIH Common Fund Human BioMolecular Atlas program

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arXiv 2019年

作者： Snyder, Michael P. Lin, Shin Posgai, Amanda Atkinson, Mark Regev, Aviv Rood, Jennifer Rozenblatt-Rosen, Orit Gaffney, Leslie Hupalowska, Anna Satija, Rahul Gehlenborg, Nils Shendure, Jay Laskin, Julia Harbury, Pehr Nystrom, Nicholas A. Bar-Joseph, Ziv Zhang, Kun Börner, Katy Lin, Yiing Conroy, Richard Procaccini, Dena Roy, Ananda L. Pillai, Ajay Brown, Marishka Galis, Zorina S. Cai, Long Shendure, Jay Trapnell, Cole Lin, Shin Jackson, Dana Snyder, Michael P. Nolan, Garry Greenleaf, William James Lin, Yiing Plevritis, Sylvia Ahadi, Sara Lee, Hayan Nevins, Stephanie Esplin, Ed Horning, Aaron Bahmani, Amir Zhang, Kun Sun, Xin Jain, Sanjay Hagood, James Kharchenko, Peter Atkinson, Mark Bodenmiller, Bernd Brusko, Todd Clare-Salzler, Michael Nick, Harry Otto, Kevin Posgai, Amanda Wasserfall, Clive Maffioletti, Sergio Caprioli, Richard M. Spraggins, Jeffrey M. Gutierrez, Danielle Patterson, Nathan Heath Neumann, Elizabeth K. Harris, Raymond deCaestecker, Mark de Plas, Raf Van Lau, Ken Cai, Long Yuan, Guo-Cheng Zhu, Qian Dries, Ruben Yin, Peng Saka, Sinem K. Kishi, Jocelyn Y. Wang, Yu Goldaracena, Isabel Laskin, Julia Ye, DongHye Burnum-Johnson, Kristin E. Piehowski, Paul D. Ansong, Charles Zhu, Ying Harbury, Pehr Desai, Tushar Mulye, Jay Chou, Peter Nagendran, Monica Bar-Joseph, Ziv Teichmann, Sarah A. Paten, Benedict Murphy, Robert F. Ma, Jian Kiselev, Vladimir Yu Kingsford, Carl Ricarte, Allyson Ruffalo, Matthew Gehlenborg, Nils Kharchenko, Peter Vella, Margaret McCallum, Chuck Börner, Katy Cross, Leonard E. Friedman, Samuel H. Heiland, Randy Herr, Bruce Macklin, Paul Quardokus, Ellen M. Record, Lisel Sluka, James P. Weber, Griffin M. Nystrom, Nicholas A. Silverstein, Jonathan C. Blood, Philip D. Ropelewski, Alexander J. Shirey, William E. Mabee, Paula Lenhardt, W. Christopher Robasky, Kimberly Michailidis, Stavros Satija, Rahul Marioni, John Regev, Aviv Butler, Andrew Stuart, Tim Fisher, Eyal Ghazanfar, Shila Rood, Jennifer Gaffney, Leslie Ersalan, Gokcen Biancalani, Tommaso Conroy, Richard Procaccini, Dena Roy, Anan School of Medicine Stanford University 300 Pasteur Drive United States Department of Genetics Stanford School of Medicine StanfordCA94305 United States Department of Medicine University of Washington SeattleWA98195 United States Department of Pathology University of Florida Diabetes Institute GainesvilleFL32610 United States Klarman Cell Observatory Broad Institute of MIT and Harvard CambridgeMA02142 United States Howard Hughes Medical Institute Koch Institute of Integrative Cancer Research Department of Biology Massachusetts Institute of Technology CambridgeMA02140 United States New York Genome Center New York CityNY10013 United States New York University New YorkNY10012 United States Department of Biomedical Informatics Harvard Medical School BostonMA02115 United States Department of Genome Sciences University of Washington SeattleWA98105 United States Department of Chemistry Purdue University West LafayetteIN47907 United States Department of Biochemistry Stanford University School of Medicine StanfordCA94305 United States Pittsburgh Supercomputing Center Carnegie Mellon University PittsburghPA15213 United States Department of Computational Biology School of Computer Science Carnegie Mellon University PittsburghPA15213 United States Department of Bioengineering University of California San Diego La JollaCA92093 United States Department of Intelligent Systems Engineering School of Informatics Computing and Engineering Indiana University BloomingtonIN47408 United States Department of Surgery Washington University School of Medicine St LouisMO63110 United States Division of Program Coordination Planning and Strategic Initiatives National Institutes of Health BethesdaMD20892 United States National Human Genome Research Institute National Institutes of Health BethesdaMD20892 United States National Heart Lung and Blood Institute National Institutes of Health BethesdaMD20892 United States Caltech-UW TMC Departmen

Transformative technologies are enabling the construction of three dimensional (3D) maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible 3D molecular and cellular atlas of the human body, in health and various disease settings. Copyright © 2019, The Authors. All rights reserved.

关键词： Mapping

Author Correction: Open-access quantitative MRI data of the spinal cord and reproducibility across participants, sites and manufacturers

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Scientific data 2021年第1期8卷 242页

作者： Julien Cohen-Adad Eva Alonso-Ortiz Mihael Abramovic Carina Arneitz Nicole Atcheson Laura Barlow Robert L Barry Markus Barth Marco Battiston Christian Büchel Matthew Budde Virginie Callot Anna J E Combes Benjamin De Leener Maxime Descoteaux Paulo Loureiro de Sousa Marek Dostál Julien Doyon Adam Dvorak Falk Eippert Karla R Epperson Kevin S Epperson Patrick Freund Jürgen Finsterbusch Alexandru Foias Michela Fratini Issei Fukunaga Claudia A M Gandini Wheeler-Kingshott Giancarlo Germani Guillaume Gilbert Federico Giove Charley Gros Francesco Grussu Akifumi Hagiwara Pierre-Gilles Henry Tomáš Horák Masaaki Hori James Joers Kouhei Kamiya Haleh Karbasforoushan Miloš Keřkovský Ali Khatibi Joo-Won Kim Nawal Kinany Hagen H Kitzler Shannon Kolind Yazhuo Kong Petr Kudlička Paul Kuntke Nyoman D Kurniawan Slawomir Kusmia René Labounek Maria Marcella Laganà Cornelia Laule Christine S Law Christophe Lenglet Tobias Leutritz Yaou Liu Sara Llufriu Sean Mackey Eloy Martinez-Heras Loan Mattera Igor Nestrasil Kristin P O'Grady Nico Papinutto Daniel Papp Deborah Pareto Todd B Parrish Anna Pichiecchio Ferran Prados Àlex Rovira Marc J Ruitenberg Rebecca S Samson Giovanni Savini Maryam Seif Alan C Seifert Alex K Smith Seth A Smith Zachary A Smith Elisabeth Solana Y Suzuki George Tackley Alexandra Tinnermann Jan Valošek Dimitri Van De Ville Marios C Yiannakas Kenneth A Weber Ii Nikolaus Weiskopf Richard G Wise Patrik O Wyss Junqian Xu NeuroPoly Lab Institute of Biomedical Engineering Polytechnique Montreal Montreal QC Canada. jcohen@polymtl.ca. Functional Neuroimaging Unit CRIUGM Université de Montréal Montreal QC Canada. jcohen@polymtl.ca. Mila - Quebec AI Institute Montreal QC Canada. jcohen@polymtl.ca. NeuroPoly Lab Institute of Biomedical Engineering Polytechnique Montreal Montreal QC Canada. Department of Radiology Swiss Paraplegic Centre Nottwil Switzerland. Centre for Advanced Imaging The University of Queensland Brisbane Australia. Department of Radiology University of British Columbia Vancouver BC Canada. Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology Massachusetts General Hospital Charlestown MA USA. Department of Radiology Harvard Medical School Boston MA USA. Harvard-Massachusetts Institute of Technology Health Sciences & Technology Cambridge MA USA. School of Information Technology and Electrical Engineering The University of Queensland Brisbane Australia. NMR Research Unit Queen Square MS Centre UCL Queen Square Institute of Neurology Faculty of Brain Sciences University College London London UK. Department of Systems Neuroscience University Medical Center Hamburg-Eppendorf Hamburg Germany. Department of Neurosurgery Medical College of Wisconsin Milwaukee WI USA. Aix-Marseille Univ CNRS CRMBM Marseille France. APHM Hopital Universitaire Timone CEMEREM Marseille France. Vanderbilt University Institute of Imaging Science Vanderbilt University Medical Center Nashville TN USA. Department of Computer and Software Engineering Polytechnique Montreal Montreal Canada. CHU Sainte-Justine Research Centre Montreal QC Canada. Centre de Recherche CHUS CIMS Sherbrooke Canada. Sherbrooke Connectivity Imaging Lab (SCIL) Computer Science department Université de Sherbrooke Sherbrooke Canada. Université de Strasbourg CNRS ICube Strasbourg France. UHB - University Hospital Brno and Masaryk University Department of Radiology and Nuclear

Augmented Reality Based Brain Tumor 3D Visualization

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Procedia computer Science 2017年 113卷 400-407页

作者： Qian Shan Thomas E. Doyle Reza Samavi Mona Al-Rei Department of Computing and Software McMaster University 1280 Main St. W Hamilton ON L8S 4L8 Canada Department of Electrical and Computer Engineering School of Biomedical Engineering McMaster University 1280 Main St. W Hamilton ON L8S 4L8 Canada eHealth Graduate Program McMaster University 1280 Main St. W Hamilton ON L8S 4L8 Canada

In this paper we present an augmented reality system for mobile devices that facilitates 3D brain tumor visualization in real time. The system uses facial features to track the subject in the scene. The system performs camera calibration based on the face size of the subject, instead of the common approach of using a number of chessboard images to calibrate the camera every time the application is installed on a new device. Camera 3D pose estimation is performed by finding its position and orientation based on a set of 3D points and their corresponding 2D projections. According to the estimated camera pose, a reconstructed brain tumor model is displayed at the same location as the subject’s real anatomy. The results of our experiment show the system was successful in performing the brain tumor augmentation in real time with a reprojection accuracy of 97%.

关键词： Augmented reality 3D visualization Tumor visualization Markerless tracking Mobile device

Silicon waveguide modulator with embedded phase change material

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arXiv 2017年

作者： Miller, Kevin J. Hallman, Kent A. Haglund, Richard F. Weiss, Sharon M. Interdisciplinary Graduate Program in Materials Science Vanderbilt University NashvilleTN37235 United States Department of Physics and Astronomy Vanderbilt University NashvilleTN37235 United States Department of Electrical Engineering and Computer Science Vanderbilt University NashvilleTN37235 United States

Phase-change materials (PCMs) have emerged as promising active elements in silicon (Si) photonic systems. In this work, we design, fabricate, and characterize a hybrid Si-PCM optical modulator. By integrating vanadium dioxide (a PCM) within a Si photonic waveguide, in a non-resonant geometry, we demonstrate ~ 10 dB broadband modulation with a PCM length of 500 nm. Copyright © 2017, The Authors. All rights reserved.

关键词： Phase change materials

Retraction: Sylabus and Matrials Design for Vocational Student and Its Dissemination Using Website (J. Phys.: Conf. Ser. 1114 012023)

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

作者： Astro Julida Harahap Erianto Ongko Hotler Manurung Dian Kurnia H Hartono Dahlan Abdullah Cut Ita Erliana Hardianto Djanggih Kundharu Saddhono Dian Rianita Muhammad Ikhsan Setiawan Yuliyanto Budi Setiawan Rosida Tiurma Manurung S Sriadhi Mangasi Sinurat Aisyah Siregar Rapat Piter Soni Hutauruk Nico Benjamain Sibarani 1 Department of Informatics Akademi Teknologi Industri Immanuel Medan Indonesia Department of Computer Systems Universitas Pancabudi Medan Indonesia Department of Computer Science STMIK IBBI Medan Indonesia Department of Informatics Universitas Malikussaleh Aceh Indonesia Department of Industrial Engineering Universitas Malikussaleh Aceh Indonesia Graduate Program Universitas Sebelas Maret Surakarta Indonesia Department of Administration University of Lancang Kuning Pekanbaru Indonesia Department of Civil Engineering Narotama University Surabaya Indonesia Study Program of Communication Studies Universitas Semarang Indonesia Graduate Program in Scientific Psychology Universitas Kristen Maranatha Indonesia Department of Electrical Engineering Universitas Negeri Medan Indonesia STIE Bina Karya Tebing Tinggi 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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Author Correction: The interrelation of sleep and mental and physical health is anchored in grey-matter neuroanatomy and under genetic control

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Communications biology

Communications biology 2020年第1期3卷 290页

作者： Masoud Tahmasian Fateme Samea Habibolah Khazaie Mojtaba Zarei Shahrzad Kharabian Masouleh Felix Hoffstaedter Julia Camilleri Peter Kochunov B T Thomas Yeo Simon Bodo Eickhoff Sofie Louise Valk Institute of Medical Science and Technology Shahid Beheshti University Tehran Iran. Sleep Disorders Research Center Kermanshah University of Medical Sciences Kermanshah Iran. Institute of Neuroscience and Medicine (INM-7: Brain and Behaviour) Research Centre Jülich 52425 Jülich Germany. Institute of Systems Neuroscience Heinrich Heine University Düsseldorf 40225 Düsseldorf Germany. Maryland Psychiatric Research Center University of Maryland School of Medicine Baltimore MD 21201 USA. Department of Electrical and Computer Engineering Clinical Imaging Research Centre N.1 Institute for Health and Memory Networks Program National University of Singapore Singapore 119077 Singapore. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown MA 02114 USA. Centre for Sleep and Cognition National University of Singapore Singapore 119077 Singapore. NUS Graduate School for Integrative Sciences and Engineering National University of Singapore Singapore 119077 Singapore. Institute of Neuroscience and Medicine (INM-7: Brain and Behaviour) Research Centre Jülich 52425 Jülich Germany. svalk@fz-juelich.de. Institute of Systems Neuroscience Heinrich Heine University Düsseldorf 40225 Düsseldorf Germany. svalk@fz-juelich.de.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Signatures of Electronic Nematicity In (111) Laalo3/Srtio3 Interfaces

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arXiv 2017年

作者： Davis, S. Huang, Z. Han, K. Ariando Venkatesan, T. Chandrasekhar, V. Graduate Program in Applied Physics Department of Physics and Astronomy Northwestern University 2145 Sheridan Road EvanstonIL60208 United States NUSNNI-Nanocore National University of Singapore 117411 Singapore Department of Physics National University of Singapore 117551 Singapore NUS Graduate School for Integrative Sciences & Engineering National University of Singapore 117456 Singapore Department of Electrical and Computer Engineering National University of Singapore 117576 Singapore Department of Material Science and Engineering National University of Singapore 117575 Singapore

Symmetry breaking is a fundamental concept in condensed matter physics whose presence often heralds new phases of matter. For instance, the breaking of time reversal symmetry is traditionally linked to magnetic phases in a material, while the breaking of gauge symmetry can lead to superfluidity/superconductivity. Nematic phases are phases in which rotational symmetry is broken while maintaining translational symmetry, and are traditionally associated with liquid crystals. Electronic nematic states where the orthogonal in-plane crystal directions have different electronic properties have garnered a great deal of attention after their discovery in Sr3Ru2O7,1 multiple iron based superconductors,2,3 and in the superconducting state of CuBiSe.4,5 Here we demonstrate the existence of an electronic nematic phase in the two-dimensional carrier gas that forms at the (111) LaAlO3 (LAO)/SrTiO3 (STO) interface that onsets at low temperatures, and is tunable by an electric field. Copyright © 2017, The Authors. All rights reserved.

关键词： Electronic properties

Magnetoresistance in the superconducting state at the (111) LaAlO3/SrTiO3 interface

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arXiv 2017年

Condensed matter systems that simultaneously exhibit superconductivity and ferromagnetism are rare due the antagonistic relationship between conventional spin-singlet superconductivity and ferromagnetic order. In materials in which superconductivity and magnetic order is known to coexist (such as some heavy-fermion materials), the superconductivity is thought to be of an unconventional nature. Recently, the conducting gas that lives at the interface between the perovskite band insulators LaAlO3 (LAO) and SrTiO3 (STO) has also been shown to host both superconductivity and magnetism. Most previous research has focused on LAO/STO samples in which the interface is in the (001) crystal plane. Relatively little work has focused on the (111) crystal orientation, which has hexagonal symmetry at the interface, and has been predicted to have potentially interesting topological properties, including unconventional superconducting pairing states. Here we report measurements of the magnetoresistance of (111) LAO/STO heterostructures at temperatures at which they are also superconducting. As with the (001) structures, the magnetoresistance is hysteretic, indicating the coexistence of magnetism and superconductivity, but in addition, we find that this magnetoresistance is anisotropic. Such an anisotropic response is completely unexpected in the superconducting state, and suggests that (111) LAO/STO heterostructures may support unconventional superconductivity. Copyright © 2017, The Authors. All rights reserved.

关键词： Strontium titanates