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Biomedical Text Mining: a Survey of Recent Progress
Chapter 14 BIOMEDICAL TEXT MINING: A SURVEY OF RECENT PROGRESS Matthew S. Simpson Lister Hill National Center for Biomedical Communications United States National Library of Medicine, National Institutes of Health [email protected] Dina Demner-Fushman Lister Hill National Center for Biomedical Communications United States National Library of Medicine, National Institutes of Health [email protected] Abstract The biomedical community makes extensive use of text mining tech- nology. In the past several years, enormous progress has been made in developing tools and methods, and the community has been witness to some exciting developments. Although the state of the community is regularly reviewed, the sheer volume of work related to biomedical text mining and the rapid pace in which progress continues to be made make this a worthwhile, if not necessary, endeavor. This chapter pro- vides a brief overview of the current state of text mining in the biomed- ical domain. Emphasis is placed on the resources and tools available to biomedical researchers and practitioners, as well as the major text mining tasks of interest to the community. These tasks include the recognition of explicit facts from biomedical literature, the discovery of previously unknown or implicit facts, document summarization, and question answering. For each topic, its basic challenges and methods are outlined and recent and influential work is reviewed. Keywords: Biomedical information extraction, named entity recognition, relations, events, summarization, question answering, literature-based discovery C.C. Aggarwal and C.X. Zhai (eds.), Mining Text Data, DOI 10.1007/978-1-4614-3223-4_14, 465 © Springer Science+Business Media, LLC 2012 466 MINING TEXT DATA 1. -
MEDLINE® Comprehensive Biomedical and Health Sciences Information
ValuaBLE CONTENT; HIGhly FOCUSED seaRCH capaBILITIES MEDLINE® COMPREHENSIVE BIOmedical AND health SCIENCES INFORmatiON WHAT YOU’LL FIND WHAT YOU CAN DO • Content from over 5,300 journals in • Keep abreast of vital life sciences information 30 languages, plus a select number of • Uncover relevant results in related fields relevant items from newspapers, magazines, and newsletters • Identify potential collaborators with significant citation records • Over 17 million records from publications worldwide • Discover emerging trends that help you pursue successful research and grant acquisition • Approximately 600,000 records added annually • Target high-impact journals for publishing • Links from MEDLINE records to the valuable your manuscript NCBI protein and DNA sequence databases, and to PubMed Related Articles • Integrate searching, writing, and bibliography creation into one streamlined process • Direct links to your full-text collections • Fully searchable and indexed backfiles to 1950 • Full integration with ISI Web of Knowledge content and capabilities GLOBAL COVERAGE AND SPECIALIZED INDEXING ACCESS THE MOST RECENT INFORMAtion — AS MEDLINE is the U.S. National Library of Medicine® WELL AS BACKFILES TO 1950 (NLM®) premier bibliographic database, covering Discover the most recent information by viewing biomedicine and life sciences topics vital to biomedical MEDLINE In-Process records, recently added records practitioners, educators, and researchers. You’ll find that haven’t yet been fully indexed. And track nearly 60 coverage of the full range of disciplines, such as years of vital backfile data to find the supporting — or medicine, life sciences, behavioral sciences, chemical refuting — data you need. More backfiles give you the sciences, and bioengineering, as well as nursing, power to conduct deeper, more comprehensive searches dentistry, veterinary medicine, the health care system, and track trends through time. -
Experimental Photonics Multiple Post-Doctoral Positions Experimental Expertise in Any One of the Following Topics/Areas Is Highly Desired
Experimental Photonics Multiple Post-Doctoral Positions Experimental Expertise in any one of the following topics/areas is highly desired . Single photon level measurements , quantum communications . Computational imaging, super-resolution imaging, biomedical imaging . Quantum dots, 2D materials, quantum devices, quantum transport . Single molecule spectroscopy/imaging . Fluorescence microscopy . Optical manipulation of spin , ODMR, Magnetometry, NV centers . Nanofabication (Metasurfaces, plasmonics,silicon photonics) . Streak camera or time-correlated single photon counting experiments . Ultrafast spectroscopy, pump-probe measurements . Single nanoparticle/nanoantenna experiments . Coupling of single quantum emitters to nanophotonic structures . Cold atoms and quantum optics . Infrared spectroscopy, thermal emission measurements Please send your full CV and three representative publications to: [email protected] Prof. Zubin Jacob Birck Nanotechnology Center School of Electrical and Computer Engineering Purdue University, U.S.A. www.electrodynamics.org Zubin Jacob Research Group: Purdue University www.electrodynamics.org About the group Google Scholar Page: https://scholar.google.ca/citations?user=8FXvN_EAAAAJ&hl=en Main Research Areas: Casimir forces, quantum nanophotonics, plasmonics, metamaterials, Vacuum fluctuations, open quantum systems Weblink: www.electrodynamics.org Theory and Experiment Twitter: twitter.com/zjacob_group • Opportunity to closely interact with theorists and experimentalists within the group • Opportunity to travel -
Quantum Optics in Nanostructures
nanomaterials Review Quantum Optics in Nanostructures Yulia V. Vladimirova 1,2,*,† and Victor N. Zadkov 2,3,† 1 Department of Physics and Quantum Technology Centre, Lomonosov Moscow State University, 119991 Moscow, Russia 2 Faculty of Physics, Higher School of Economics, Old Basmannya 21/4, 105066 Moscow, Russia; [email protected] 3 Institute of Spectroscopy of the Russian Academy of Sciences, Fizicheskaya Str. 5, Troitsk, 108840 Moscow, Russia * Correspondence: [email protected] † These authors contributed equally to this work. Abstract: This review is devoted to the study of effects of quantum optics in nanostructures. The mechanisms by which the rates of radiative and nonradiative decay are modified are considered in the model of a two-level quantum emitter (QE) near a plasmonic nanoparticle (NP). The distributions of the intensity and polarization of the near field around an NP are analyzed, which substantially depend on the polarization of the external field and parameters of plasmon resonances of the NP. The effects of quantum optics in the system NP + QE plus external laser field are analyzed—modification of the resonance fluorescence spectrum of a QE in the near field, bunching/antibunching phenomena, quantum statistics of photons in the spectrum, formation of squeezed states of light, and quantum entangled states in these systems. Keywords: nanophotonics; nanoplasmonics; nanostructure; quantum emitter; two-level system; quantum optics; resonance fluorescence; antibunching and quantum statistics of photons; squeezed -
Recent Advances in Vertically Aligned Nanowires for Photonics Applications
micromachines Review Recent Advances in Vertically Aligned Nanowires for Photonics Applications Sehui Chang, Gil Ju Lee and Young Min Song * School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Korea; [email protected] (S.C.); [email protected] (G.J.L.) * Correspondence: [email protected]; Tel.: +82-62-715-2655 Received: 29 June 2020; Accepted: 25 July 2020; Published: 26 July 2020 Abstract: Over the past few decades, nanowires have arisen as a centerpiece in various fields of application from electronics to photonics, and, recently, even in bio-devices. Vertically aligned nanowires are a particularly decent example of commercially manufacturable nanostructures with regard to its packing fraction and matured fabrication techniques, which is promising for mass-production and low fabrication cost. Here, we track recent advances in vertically aligned nanowires focused in the area of photonics applications. Begin with the core optical properties in nanowires, this review mainly highlights the photonics applications such as light-emitting diodes, lasers, spectral filters, structural coloration and artificial retina using vertically aligned nanowires with the essential fabrication methods based on top-down and bottom-up approaches. Finally, the remaining challenges will be briefly discussed to provide future directions. Keywords: nanowires; photonics; LED; nanowire laser; spectral filter; coloration; artificial retina 1. Introduction In recent years, nanowires originated from a wide variety of materials have arisen as a centerpiece for optoelectronic applications such as sensors, solar cells, optical filters, displays, light-emitting diodes and photodetectors [1–12]. Tractable but outstanding, optical features of nanowire arrays achieved by modulating its physical properties (e.g., diameter, height and pitch) allow to confine and absorb the incident light considerably, albeit its compact configuration. -
Information-Seeking Behavior in Complementary and Alternative Medicine (CAM): an Online Survey of Faculty at a Health Sciences Campus*
Information-seeking behavior in complementary and alternative medicine (CAM): an online survey of faculty at a health sciences campus* By David J. Owen, M.L.S., Ph.D. [email protected] Education Coordinator, Basic Sciences Min-Lin E. Fang, M.L.I.S. [email protected] Information Services Librarian Kalmanovitz Library and Center for Knowledge Management University of California, San Francisco San Francisco, California 94143-0840 Background: The amount of reliable information available for complementary and alternative medicine (CAM) is limited, and few authoritative resources are available. Objective: The objective is to investigate the information-seeking behavior of health professionals seeking CAM information. Methods: Data were gathered using a Web-based questionnaire made available to health sciences faculty af®liated with the University of California, San Francisco. Results: The areas of greatest interest were herbal medicine (67%), relaxation exercises (53%), and acupuncture (52%). About half the respondents perceived their CAM searches as being only partially successful. Eighty-two percent rated MEDLINE as a useful resource, 46% personal contacts with colleagues, 46% the Web, 40% journals, and 20% textbooks. Books and databases most frequently cited as useful had information about herbs. The largest group of respondents was in internal medicine (26%), though 15% identi®ed their specialties as psychiatry, psychology, behavioral medicine, or addiction medicine. There was no correlation between specialty and patterns of information- seeking behavior. Sixty-six percent expressed an interest in learning more about CAM resources. Conclusions: Health professionals are frequently unable to locate the CAM information they need, and the majority have little knowledge of existing CAM resources, relying instead on MEDLINE. -
Exploring Biomedical Records Through Text Mining-Driven Complex Data Visualisation
medRxiv preprint doi: https://doi.org/10.1101/2021.03.27.21250248; this version posted March 29, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Exploring biomedical records through text mining-driven complex data visualisation Joao Pita Costa Luka Stopar Luis Rei Institute Jozef Stefan Institute Jozef Stefan Institute Jozef Stefan Ljubljana, Slovenia Ljubljana, Slovenia Ljubljana, Slovenia [email protected] [email protected] [email protected] Besher Massri Marko Grobelnik Institute Jozef Stefan Institute Jozef Stefan Ljubljana, Slovenia Ljubljana, Slovenia [email protected] [email protected] ABSTRACT learning technologies that have been entering the health domain The recent events in health call for the prioritization of insightful at a slow and cautious pace. The emergencies caused by the recent and meaningful information retrieval from the fastly growing pool pandemics and the need to act fast and accurate were a motivation of biomedical knowledge. This information has its own challenges to fast forward some of the modernization of public health and both in the data itself and in its appropriate representation, enhanc- healthcare information systems. Though, the amount of available ing its usability by health professionals. In this paper we present information and its heterogeneity creates obstacles in its usage in a framework leveraging the MEDLINE dataset and its controlled meaningful ways. vocabulary, the MeSH Headings, to annotate and explore health- related documents. The MEDijs system ingests and automatically annotates text documents, extending their legacy metadata with MeSH Headings. -
Fall-2020-Print-Axia
INSIDE THIS SPECIAL FALL 2020 Contents EDITION OF ACS AXIAL axial.acs.org deeper ACS PUBLICATIONS SHANGHAITECH UNIVERSITY NEW ENVIRONMENTAL SCIENCE & WHAT CHEMISTS NEED LAUNCHESdive NEW JOURNALS PARTNERS WITH ACS PUBLICATIONS TO TECHNOLOGY JOURNALS TO KNOW ABOUT Explore the ResearchFOCUSED behind ON theFOOD 2020 AND Journal Citation Reports® LAUNCH ACCOUNTS OF MATERIALS NAME EDITORS AND MACHINE LEARNING AGRICULTURAL CHEMISTRY RESEARCH OPEN FOR SUBMISSIONS The 2020 Journal Citation Reports® (JCR) show the vital role ACS Publications journals play in publishing important, highly cited research. Thanks to the dedication and brilliance of our authors and reviewers, 89% of ACS journals have an Impact Factor greater than 3 this year. Browse this year’s JCR figures, which are based on citations from 2018 to 2019: EXPLORE THE RESEARCH HOW ACS IS SUPPORTING THE LEARN HOW ACS SUPPORTS SCIMEETINGS: PRESENT YOUR RESEARCH BEHIND THE 2020 JOURNAL CHEMISTRY COMMUNITY DURING THE OPEN SCIENCE BEYOND THE ACS FALL 2020 VIRTUAL CITATION REPORTS® COVID-19 PANDEMIC MEETING & EXPO Impact Factor 20.832 Impact Factor 4.473 Impact Factor Impact Factor 4.152 8.758 Impact Factor Impact Factor 4.486 Impact Factor 12.685 12.350 Impact Factor 4.434 Impact Factor Impact Factor 3.381 19.003 Impact Factor 3.418 Impact Factor Impact Factor 3.975 Impact Factor 4.614 6.042 Impact Factor Impact Factor Impact Factor 7.333 14.588 6.864 Impact Factor 2.870 Impact Factor Impact Factor 6.785 4.411 Impact Factor 7.632 Impact Factor 6.092 Impact Factor 2.865 Impact Factor 4.031 pubs.acs.org/acsagscitech ACS PUBLICATIONS LAUNCHES NEW JOURNALS FOCUSED ON FOOD AND AGRICULTURAL CHEMISTRY ournal of Agricultural and Food Chemistry Technical University of Munich and the chair of is growing into a family of journals with the Food Chemistry and Molecular Sensors. -
Marnix Medema Curriculum Vitae
Page 1 of 10 Curriculum vitae Personal Information FIRST NAME / SURNAME Marnix Medema ADDRESS (PRIVATE) Soetendaalseweg 16A, 6721XB Bennekom, NL ADDRESS (WORK) Droevendaalsesteeg 1, 6708PB Wageningen, NL TEL +31317484706 / +31654758321 (cell) EMAIL [email protected] WEB http://www.marnixmedema.nl NATIONALITY Dutch DATE OF BIRTH 24.01.1986 GENDER Male Work Experience & Education DATES March 2015 - present EMPLOYER Wageningen University, Wageningen, The Netherlands POSITION Assistant Professor DATES August 2013 - February 2015 EMPLOYER MPI for Marine Microbiology, Bremen, Germany POSITION Postdoctoral Researcher DATES September 2010 - March 2011 EMPLOYER University of California, San Francisco, USA POSITION Visiting Research Scholar DATES September 2009 - August 2013 EMPLOYER University of Groningen, The Netherlands POSITION PhD Student DATE / DISTINCTION 27.09.2013, cum laude ** DATES September 2006 - August 2008 QUALIFICATION AWARDED Master of Science Biomolecular Science, cum laude ** INSTITUTION University of Groningen, The Netherlands DATES September 2003 - August 2006 QUALIFICATION AWARDED Bachelor of Science Biology, cum laude ** INSTITUTION Radboud University Nijmegen, The Netherlands ** In the Netherlands, only two classes of honors are used: eervolle vermelding ("honorable mention") and cum laude, typically only to mark exceptional achievement. [...] Generally, less than 20% receive the "honorable mention" distinction, and "cum laude" is even harder to attain (less than 1%-5% depending on the university and study program). -
Accelerating the Translation of Nanomaterials in Biomedicine
Accelerating the Translation of Nanomaterials in Biomedicine The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Mitragotri, Samir; Anderson, Daniel G.; Chen, Xiaoyuan; Chow, Edward K.; Ho, Dean; Kabanov, Alexander V.; Karp, Jeffrey M. et al. “Accelerating the Translation of Nanomaterials in Biomedicine.” ACS Nano 9, no. 7 (July 2015): 6644–6654. © 2015 American Chemical Society As Published http://dx.doi.org/10.1021/acsnano.5b03569 Publisher American Chemical Society (ACS) Version Author's final manuscript Citable link http://hdl.handle.net/1721.1/108653 Terms of Use Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author ACS Nano Manuscript Author . Author manuscript; Manuscript Author available in PMC 2017 January 12. Published in final edited form as: ACS Nano. 2015 July 28; 9(7): 6644–6654. doi:10.1021/acsnano.5b03569. Accelerating the Translation of Nanomaterials in Biomedicine Samir Mitragotri†,*, Daniel G. Anderson‡, Xiaoyuan Chen§, Edward K. Chow||, Dean Ho⊥, Alexander V. Kabanov#, Jeffrey M. Karp¶, Kazunori Kataoka□, Chad A. Mirkin■, Sarah Hurst Petrosko■, Jinjun Shi○, Molly M. Stevens●, Shouheng Sun△, Sweehin Teoh▽, Subbu S. Venkatraman▲, Younan Xia▼, Shutao Wang , Zhen Gu⬢,††,‡‡,*, and Chenjie Xu▽,* †Center for Bioengineering, Department of Chemical Engineering, University -
Updated for 2014
Information for Authors (Revised May 2014) Contents (click on the topic) Journal Scope | Types of Content | Submission Procedure | Editorial Process and Peer- Review | Submission Policies | Additional Journal Information Journal Scope ACS Photonics is dedicated to publishing high-impact research in the rapidly evolving field of photonics. The journal seeks to be the primary publication avenue for work in the areas where photonics and optoelectronics are key enabling technologies. Interdisciplinary research and research addressing emerging issues in photonics are of particular interest. Areas of interest to the journal include: • Molecular and nano-photonics • Solid state inorganic materials for optoelectronics • Polymer and organic optoelectronic materials • Plasmonics and optical metamaterials • Photonic crystals • Mesoscale photonics and optoelectronics • Nonlinear optics and materials • Quantum optics and single-photon processes • Flexible electronics and displays • Silicon photonics • Optical switching, memory, and data storage • Lasers, quantum electronics, and optical amplifiers • LEDs and solid-state lighting • Photonics for energy materials • Biophotonics • Micro- and nano-optoelectromechanical systems • Modeling and simulation of photonic processes Types of Content ACS Photonics publishes original Articles, Letters, Perspectives, and Reviews that highlight recent developments and that further the understanding of photonics. Articles. Concise, yet comprehensive, original research presenting an advance of immediate, broad, - 1 - and lasting impact. Articles are not intended to be follow-up manuscripts, unless they contain new and extensive information that will advance the understanding of the system. Articles are peer-reviewed and contain an unreferenced abstract of 250 words or less. Abstracts should not contain abbreviations or acronyms unless essential. A referenced introduction should expand on the background of the work. In general, Articles include 8–10 display items (figures/tables/schemes) and ~50 references. -
Nanoplatforms for Imaging, Targeting, and Image-Guided Drug Delivery
LXIV JCET LECTURE, 25.05.2015, 9.00 Nanoplatforms for Imaging, Targeting, and Image-Guided Drug Delivery Prof. Weibo Cai The Molecular Imaging and Nanotechnology Laboratory Departments of Radiology and Medical Physics School of Medicine and Public Health University of Wisconsin – Madison, USA 1111 Highland Ave, Room 7137 Madison, WI 53705-2275 Tel: (608) 262-1749 Fax: (608) 265-0614 Email: [email protected] OR [email protected] Group website: http://mi.wisc.edu The Molecular Imaging and Nanotechnology Laboratory at the University of Wisconsin - Madison (http://mi.wisc.edu/) is mainly focused on three areas: 1) development of multimodality molecular imaging agents; 2) nanotechnology and its biomedical applications; and 3) molecular therapy of cancer. In this talk, I will present our recent work on molecular imaging and image-guided drug delivery of cancer and some cardiovascular diseases with peptides, proteins, and a variety of nanomaterials. The primary imaging techniques used in these studies are positron emission tomography (PET), photoacoustic tomography (PAT), optical imaging, and magnetic resonance imaging (MRI). Three of the major molecular targets that we are investigating are CD105 (i.e. endoglin), VEGFR, and integrin αvβ3. The nanomaterials that will be discussed in this presentation include nano-graphene oxide, zinc oxide nanomaterials, micelles, silica-based nanoparticles, magnetic nanoparticles, among many others. A few representative side projects will also be presented, such as the facile synthesis of PET/MRI and PET/PAT dual-modality agents. CURRICULUM VITAE Dr. Weibo Cai is an Associate Professor of Radiology and Medical Physics (with Tenure) at the University of Wisconsin - Madison. He received his Ph.D.