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Automatic Extraction of Medication Mentions from Tweets-Overview of the BioCreative VII Shared Task 3 Competition

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Database : the journal of biological databases and curation 2023年第2023期2023卷 baac108页

作者： Davy Weissenbacher Karen O'Connor Siddharth Rawal Yu Zhang Richard Tzong-Han Tsai Timothy Miller Dongfang Xu Carol Anderson Bo Liu Qing Han Jinfeng Zhang Igor Kulev Berkay Köprü Raul Rodriguez-Esteban Elif Ozkirimli Ammer Ayach Roland Roller Stephen Piccolo Peijin Han V G Vinod Vydiswaran Ramya Tekumalla Juan M Banda Parsa Bagherzadeh Sabine Bergler João F Silva Tiago Almeida Paloma Martinez Renzo Rivera-Zavala Chen-Kai Wang Hong-Jie Dai Luis Alberto Robles Hernandez Graciela Gonzalez-Hernandez Department of Computational Biomedicine Cedars-Sinai Medical Center Los Angeles CA USA. DBEI The Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Computer Science and Information Engineering National Central University No. 300 Zhongda Rd Zhongli District Taoyuan 320 Taiwan. IoX Center National Taiwan University Da'an District Section 4 Roosevelt Rd No. 1 Barry Lam Hall Taipei 106 Taiwan. Research Center for Humanities and Social Sciences Academia Sinica No. 128 Section 2 Academia Rd Nangang District Taipei 115 Taiwan. Computational Health Informatics Program Boston Children's Hospital Boston MA USA. Department of Pediatrics Harvard Medical School Boston MA USA. NVIDIA Santa Clara CA USA. Department of Statistics Florida State University Tallahassee FL USA. Data and Analytics Chapter F. Hoffmann-La Roche Ltd Switzerland. Pharmaceutical Research and Early Development Roche Innovation Center Basel Switzerland. Speech and Language Technology Lab DFKI Berlin Germany. Department of Biology Brigham Young University Provo UT USA. Department of Computational Medicine and Bioinformatics Medical School University of Michigan Ann Arbor MI USA. Department of Learning Health Sciences Medical School University of Michigan Ann Arbor MI USA. School of Information University of Michigan Ann Arbor MI USA. Department of Computer Science Georgia State University Atlanta GA USA. CLaC Labs Concordia University Montreal Canada. DETI Institute of Electronics and Informatics Engineering of Aveiro University of Aveiro Portugal. Department of Computation University of A Coruña Spain. Computer Science and Engineering Department Universidad Carlos III de Madrid Madrid Spain. Big Data Laboratory Chunghwa Telecom Laboratories Taoyuan Taiwan. Department of Computer Science National Yang Ming Chiao Tung University Hsinchu Taiwan. Department of Electrical Engineering College of Electrical Engineering and Computer Sci

This study presents the outcomes of the shared task competition BioCreative VII (Task 3) focusing on the extraction of medication names from a Twitter user's publicly available tweets (the user's 'timeline'). In general, detecting health-related tweets is notoriously challenging for natural language processing tools. The main challenge, aside from the informality of the language used, is that people tweet about any and all topics, and most of their tweets are not related to health. Thus, finding those tweets in a user's timeline that mention specific health-related concepts such as medications requires addressing extreme imbalance. Task 3 called for detecting tweets in a user's timeline that mentions a medication name and, for each detected mention, extracting its span. The organizers made available a corpus consisting of 182 049 tweets publicly posted by 212 Twitter users with all medication mentions manually annotated. The corpus exhibits the natural distribution of positive tweets, with only 442 tweets (0.2%) mentioning a medication. This task was an opportunity for participants to evaluate methods that are robust to class imbalance beyond the simple lexical match. A total of 65 teams registered, and 16 teams submitted a system run. This study summarizes the corpus created by the organizers and the approaches taken by the participating teams for this challenge. The corpus is freely available at https://***/tasks/biocreative-vii/track-3/. The methods and the results of the competing systems are analyzed with a focus on the approaches taken for learning from class-imbalanced data.

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Erratum: “Two-dimensional porous graphitic carbon nitride C6N7 monolayer: First-principles calculations” [Appl. Phys. Lett. 119, 142102 (2021)]

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Applied Physics Letters 2022年第18期120卷

作者： A. Bafekry M. Faraji M. M. Fadlallah I. Abdolhosseini Sarsari H. R. Jappor S. Fazeli M. Ghergherehchi 1Department of Radiation Application Shahid Beheshti University Tehran Iran 2Micro and Nanotechnology Graduate Program TOBB University of Economics and Technology Sogutozu Caddesi No 43 Sogutozu 06560 Ankara Turkey 3Department of Physics Faculty of Science Benha University 13518 Benha Egypt 4Department of Physics Isfahan University of Technology Isfahan 84156-83111 Iran 5Department of Physics College of Education for Pure Sciences University of Babylon Hilla Iraq 6Department of Material Science and Engineering Sharif University of Technology PO Box 11155-9466 Tehran Iran 7Department of Electrical and Computer Engineering Sungkyunkwan University 16419 Suwon South Korea

The original article1 contains misprints in the values of the elastic parameters. The values of C11 = 258.6 GPa, C22 = 290.8 GPa, and C12 = 70.73 GPa and C13 =

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Atomic-Scale Defect Detection by Nonlinear Light Scattering and Localization

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arXiv 2020年

作者： Shafiei, Farbod Orzali, Tommaso Vert, Alexey Miri, Mohammad-Ali Hung, P.Y. Wong, Man Hoi Alù, Andrea Bersuker, Gennadi Downer, Michael C. Department of Physics University of Texas at Austin AustinTX United States SEMATECH AlbanyNY United States Sunny Polytechnic Institute AlbanyNY United States Department of Electrical and Computer Engineering University of Texas at Austin AustinTX United States Department of Physics Queens College of the CUNY QueensNY United States Photonics Initiative Advanced Science Research Center CUNY New YorkNY United States Physics Program Graduate Center CUNY New YorkNY United States Aerospace Corporation Los AngelesCA United States

Hetero-epitaxial crystalline films underlie many electronic and optical technologies but are prone to forming defects at their hetero-interfaces. Atomic-scale defects such as threading dislocations that propagate into a film impede the flow of charge carriers and light degrading electrical/optical performance of devices. Diagnosis of sub-surface defects traditionally requires time-consuming invasive techniques such as cross–sectional transmission electron microscopy. Using III-V films grown on Si, we have demonstrated noninvasive, bench-top diagnosis of sub-surface defects by optical second-harmonic scanning probe microscope. We observed a high-contrast pattern of sub-wavelength "hot spots" caused by scattering and localization of fundamental light by defect scattering sites. Size of these observed hotspots are strongly correlated to the density of dislocation defects. Our results not only demonstrate a global and versatile method for diagnosing sub-surface scattering sites but uniquely elucidate optical properties of disordered media. An extension to third harmonics would enable irregularities detection in non-χ(2) materials making the technique universally applicable. Copyright © 2020, The Authors. All rights reserved.

关键词： High resolution transmission electron microscopy

Spoof-Fluid-Spoof Acoustic Waveguide and its Applications for Sound Manipulation

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Physical Review Applied 2019年第5期12卷 054014-054014页

作者： Norbert Cselyuszka Andrea Alù Nikolina Janković BioSense Institute University of Novi Sad Novi Sad Serbia Silicon Austria Labs Sensor System Microsystem Technologies Villach Austria Department of Electrical and Computer Engineering The University of Texas at Austin Austin Texas 78712 USA Photonics Initiative Advanced Science Research Center City University of New York New York New York 10031 USA Physics Program Graduate Center City University of New York New York New York 10026 USA Department of Electrical Engineering City College of New York New York New York 10031 USA

We explore the implementation of a spoof–fluid-spoof (SFS) acoustic waveguide, which is the acoustic analogue of a metal-insulator–metal waveguide in plasmonics. The proposed structure consists of two corrugated rigid surfaces separated by a fluid layer. The properties of the guided acoustic modes between corrugated rigid parallel plates are analytically and numerically studied by deriving their dispersion relation and through a careful analysis of symmetric and antisymmetric modes supported by this structure. Similar to plasmonic waveguides, it is shown that the dispersion relation of the proposed SFS acoustic waveguide, and the supported group and phase velocities, can be largely controlled by changes in the geometrical parameters of the waveguide, opening the possibility for application of this technology for acoustic delay lines, modulators, and sensors. The analytical and numerical results are validated through experiments in a controlled environment.

关键词： Acoustic measurements Acoustic metamaterials Acoustic modeling Acoustic wave phenomena Plasmonics Surface plasmon polariton Waveguides Surface acoustic wave

Correction to: Pharmacological Rescue With SR8278, A Circadian Nuclear Receptor REV-ERBα Antagonist As A Therapy for Mood Disorders In Parkinson's Disease

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Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics 2022年第4期19卷 1432页

作者： Jeongah Kim Inah Park Sangwon Jang Mijung Choi Doyeon Kim Woong Sun Youngshik Choe Ji-Woong Choi Cheil Moon Sung Ho Park Han Kyoung Choe Kyungjin Kim Department of Brain Sciences Daegu Gyeongbuk Institute of Science and Technology (DGIST) Daegu 42988 Korea. Department of Anatomy College of Medicine Korea University Seoul Korea. Program in Neurosciences & Mental Health The Hospital for Sick Children Toronto ON Canada. Korea Brain Research Institute (KBRI) Daegu Korea. Department of Electrical Engineering and Computer Science DGIST Daegu Korea. Convergence Research Advanced Centre for Olfaction DGIST Daegu Korea. Department of Biological Sciences Ulsan National Institute of Science and Technology (UNIST) Ulsan 44919 Korea. Department of Brain Sciences Daegu Gyeongbuk Institute of Science and Technology (DGIST) Daegu 42988 Korea. kyungjin@dgist.ac.kr. Convergence Research Advanced Centre for Olfaction DGIST Daegu Korea. kyungjin@dgist.ac.kr.

Lithium-Ion Batteries: Operando Magnetometry Probing the Charge Storage Mechanism of CoO Lithium-Ion Batteries (Adv. Mater. 12/2021)

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Advanced Materials 2021年第12期33卷

作者： Hongsen Li Zhengqiang Hu Qingtao Xia Hao Zhang Zhaohui Li Huaizhi Wang Xiangkun Li Fengkai Zuo Fengling Zhang Xiaoxiong Wang Wanneng Ye Qinghao Li Yunze Long Qiang Li Shishen Yan Xiaosong Liu Xiaogang Zhang Guihua Yu Guo-Xing Miao College of Physics Center for Marine Observation and Communications Qingdao University Qingdao 266071 China School of Physics State Key Laboratory of Crystal Materials Shandong University Jinan 250100 China State Key Laboratory of Functional Materials for Informatics Shanghai Institute of Microsystem and Information Technology (SIMIT) Chinese Academy of Sciences Shanghai 200050 China College of Material Science and Engineering Nanjing University of Aeronautics and Astronautics Nanjing 210016 China Materials Science and Engineering Program and Department of Mechanical Engineering The University of Texas at Austin Austin TX 78712 USA Department of Electrical and Computer Engineering & Institute for Quantum Computing University of Waterloo Waterloo ON N2L 3G1 Canada

Optomechanically Induced Birefringence and Faraday Effect

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arXiv 2019年

作者： Duggan, Robert del Pino, Javier Verhagen, Ewold Alù, Andrea Department of Electrical and Computer Engineering University of Texas at Austin AustinTX78712 United States Center for Nanophotonics AMOLF Science Park 104 Amsterdam1098 XG Netherlands Photonics Initiative Advanced Science Research Center City University of New York NY10031 United States Physics Program Graduate Center City University of New York NY10016 United States Department of Electrical Engineering City College of The City University of New York NY10031 United States

We demonstrate an optomechanical platform where optical mode conversion mediated by mechanical motion enables arbitrary tailoring of polarization states of propagating light fields. Optomechanical interactions are realized in a Fabry-Perót resonator, which naturally supports two polarization-degenerate states while an optical control field induces rotational symmetry breaking. Applying such principles, the entire Poincaré sphere is spanned by just optical control of the driving field, realizing reciprocal and non-reciprocal optomechanically-induced birefringence for linearly polarized and circularly polarized control driving. A straightforward extension of this setup also enables all-optical tunable isolation and circulation. Our findings open new avenues to exploit optomechanics for arbitrary manipulation of light polarization. Copyright © 2019, The Authors. All rights reserved.

关键词： Birefringence

Unifying femtosecond and picosecond single-pulse magnetic switching in GdFeCo

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arXiv 2020年

作者： Jakobs, F. Ostler, T.A. Lambert, C.-H. Yang, Y. Salahuddin, S. Wilson, R.B. Gorchon, J. Bokor, J. Atxitia, U. Dahlem Center for Complex Quantum Systems and Fachbereich Physik Freie Universität Berlin Berlin14195 Germany LiégeB-4000 Belgium College of Business Technology and Engineering Sheffield Hallam University Howard Street SheffieldS1 1WB United Kingdom Department of Electrical Engineering and Computer Sciences University of California BerkeleyCA94720 United States Department of Materials Science and Engineering University of California BerkeleyCA94720 United States Lawrence Berkeley National Laboratory 1 Cyclotron Road BerkeleyCA94720 United States Department of Mechanical Engineering and Materials Science and Engineering Program University of California RiversideCA92521 United States ETH Zurich Hönggerbergring 64 Zürich8093 Switzerland Portland Technology Development Department Intel Corp. HillsboroOR97006 United States Universite de Lorraine CNRS IJL NancyF-54000 France

Many questions are still open regarding the physical mechanisms behind the magnetic switching in GdFeCo alloys by single optical pulses. Phenomenological models suggest a femtosecond scale exchange relaxation between sublattice magnetization as the driving mechanism for switching. The recent observation of thermally induced switching in GdFeCo by using both several picosecond optical laser pulse as well as electric current pulses has questioned this previous understanding. This has raised the question of whether or not the same switching mechanics are acting at the femoand picosecond scales. In this work, we aim at filling this gap in the understanding of the switching mechanisms behind thermal single-pulse switching. To that end, we have studied experimentally thermal single-pulse switching in GdFeCo alloys, for a wide range of system parameters, such as composition, laser power and pulse duration. We provide a quantitative description of the switching dynamics using atomistic spin dynamics methods with excellent agreement between the model and our experiments across a wide range of parameters and timescales, ranging from femtoseconds to picoseconds. Furthermore, we find distinct element-specific damping parameters as a key ingredient for switching with long picosecond pulses and argue, that switching with pulse durations as long as 15 picoseconds is possible due to a low damping constant of Gd. Our findings can be easily extended to speed up dynamics in other contexts where ferrimagnetic GdFeCo alloys have been already demonstrated to show fast and energy-efficient processes, e.g. domain-wall motion in a track and spin-orbit torque switching in spintronics devices. Copyright © 2020, The Authors. All rights reserved.

关键词： Ternary alloys

One-way hyperbolic metasurfaces based on synthetic motion

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arXiv 2019年

作者： Mazor, Yarden Alù, Andrea Department of Electrical and Computer Engineering University of Texas Austin AustinTX78712 United States Physics Program Graduate Center City University of New York New YorkNY10026 United States Photonics Initiative Advanced Science Research Center City University New York New YorkNY10031 United States Department of Electrical Engineering City College New York New YorkNY10031 United States

Moving metasurfaces support guided waves exhibiting unusual optical properties, including strong anisotropy, nonreciprocity and hyperbolic dispersion. However, for these phenomena to be noticeable, high speeds are typically required, challenging their practical implementation. Here, we show a viable route towards the realization of one-way hyperbolic propagation in metasurfaces placed synthetically in motion through traveling-wave space-time modulation. In addition to non-reciprocal hyperbolic propagation, the proposed time-modulation scheme induces additional exotic opportunities for nanophotonic systems, such as efficient nonreciprocal frequency conversion and mode transfer. Copyright © 2019, The Authors. All rights reserved.

关键词： Guided electromagnetic wave propagation