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Phenotate: crowdsourcing phenotype annotations as exercises in undergraduate classes (vol 12, pg 631, 2020)

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GENETICS IN MEDICINE 2020年第8期22卷 1427-1427页

作者： Chang, Willie H. Mashouri, Pouria Lozano, Alexander X. Johnstone, Brittney Husic, Mia Olry, Annie Maiella, Sylvie Balci, Tugce B. Sawyer, Sarah L. Robinson, Peter N. Rath, Ana Brudno, Michael Centre for Computational Medicine The Hospital For Sick Children Toronto ON Canada Department of Computer Science Princeton University Princeton NJ USA Faculty of Medicine University of Toronto Toronto ON Canada Department of Materials Science & Engineering Stanford University Stanford CA USA Sunnybrook Health Sciences Centre Toronto ON Canada Orphanet Institut national de la santé et de la recherche médicale Paris France Medical Genetics Program of Southwestern Ontario London Health Sciences Centre London ON Canada Department of Genetics Children’s Hospital of Eastern Ontario and Children’s Hospital of Eastern Ontario Research Institute University of Ottawa Ottawa ON Canada The Jackson Laboratory for Genomic Medicine Farmington CT USA Institute for Systems Genomics University of Connecticut Farmington CT USA Department of Computer Science University of Toronto Toronto ON Canada Genetics and Genome Biology Program The Hospital for Sick Children Toronto ON Canada University Health Network Toronto ON Canada

PurposeComputational documentation of genetic disorders is highly reliant on structured data for differential diagnosis, pathogenic variant identification, and patient matchmaking. However, most information on rare diseases (RDs) exists in freeform text, such as academic literature. To increase availability of structured RD data, we developed a crowdsourcing approach for collecting phenotype information using student *** developed Phenotate, a web application for crowdsourcing disease phenotype annotations through assignments for undergraduate genetics students. Using student-collected data, we generated composite annotations for each disease through a machine learning approach. These annotations were compared with those from clinical practitioners and gold standard curated *** Phenotate in five undergraduate genetics courses, we collected annotations for 22 diseases. Student-sourced annotations showed strong similarity to gold standards, with F-measures ranging from 0.584 to 0.868. Furthermore, clinicians used Phenotate annotations to identify diseases with comparable accuracy to other annotation sources and gold standards. For six disorders, no gold standards were available, allowing us to create some of the first structured annotations for them, while students demonstrated ability to research *** enables crowdsourcing RD phenotypic annotations through educational assignments. Presented as an intuitive web-based tool, it offers pedagogical benefits and augments the computable RD knowledgebase.

关键词： rare diseases phenotype crowdsourcing medical education machine learning

The status of KAGRA underground cryogenic gravitational wave telescope 15

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The status of KAGRA underground cryogenic gravitational wave...

15th International Conference on Topics in Astroparticle and Underground Physics, TAUP 2017

作者： Akutsu, T. Ando, M. Araya, A. Aritomi, N. Asada, H. Aso, Y. Atsuta, S. Awai, K. Barton, M.A. Cannon, K. Craig, K. Creus, W. Doi, K. Eda, K. Enomoto, Y. Flaminio, R. Fujii, Y. Fujimoto, M.-K. Furuhata, T. Haino, S. Hasegawa, K. Hashino, K. Hayama, K. Hirobayashi, S. Hirose, E. Hsieh, A.H. Inoue, Y. Ioka, K. Itoh, Y. Kaji, T. Kajita, T. Kakizaki, M. Kamiizumi, M. Kambara, S. Kanda, N. Kanemura, S. Kaneyama, M. Kang, G. Kasuya, J. Kataoka, Y. Kawai, N. Kawamura, S. Kim, C. Kim, H. Kim, J. Kim, Y. Kimura, N. Kinugawa, T. Kirii, S. Kitaoka, Y. Kojima, Y. Kokeyama, K. Komori, K. Kotake, K. Kumar, R. Lee, H. Lee, H. Liu, Y. Luca, N. Majorana, E. Mano, S. Marchio, M. Matsui, T. Matsushima, F. Michimura, Y. Miyakawa, O. Miyamoto, T. Miyamoto, A. Miyo, K. Miyoki, S. Morii, W. Morisaki, S. Moriwaki, Y. Morozumi, T. Musha, M. Nagano, S. Nagano, K. Nakamura, K. Nakamura, T. Nakano, H. Nakano, M. Nakao, K. Narikawa, T. Quynh, L.Nguyen Ni, W.-T. Ochi, T. Oh, J. Oh, S. Ohashi, M. Ohishi, N. Ohkawa, M. Okutomi, K. Oohara, K. Alleano, F.E.P. Pinto, I. Sago, N. Saijo, M. Saito, Y. Sakai, K. Sakai, Y. Sasaki, Y. Sasaki, M. Sato, S. Sato, T. Sekiguchi, Y. Seto, N. Shibata, M. Shimoda, T. Shinkai, H. Shoda, A. Somiya, K. Son, E. Suemasa, A. Suzuki, T. Suzuki, T. Tagoshi, H. Takahashi, H. Takahashi, R. Takamori, A. Takeda, H. Tanaka, H. Tanaka, K. Tanaka, T. Tatsumi, D. Tomaru, T. Tomura, T. Travasso, F. Tsubono, K. Tsuchida, S. Uchikata, N. Uchiyama, T. Uehara, T. Ueki, S. Ueno, K. Ushiba, T. Van Putten, M.H.P.M. Vocca, H. Wada, S. Wakamatsu, T. Yamada, T. Yamamoto, S. Yamamoto, T. Yamamoto, K. Yamamoto, A. Yokoyama, J. Yokozawa, T. Yoon, T.H. Yuzurihara, H. Zeidler, S. Zhu, Z.-H. National Astronomical Observatory of Japan Mitaka Tokyo181-8588 Japan Department of Physics University of Tokyo Bunkyo Tokyo113-0033 Japan Earthquake Research Institute University of Tokyo Bunkyo Tokyo113-0032 Japan Department of Advanced Physics Hirosaki University Aomori Hirosaki036-8561 Japan National Astronomical Observatory of Japan Hida Gifu506-1205 Japan Department of Physics Tokyo Institute of Technology Meguro Tokyo152-8551 Japan Institute for Cosmic Ray Research University of Tokyo Hida Gifu506-1205 Japan Research Center for the Early Universe University of Tokyo Bunkyo Tokyo113-0033 Japan Institute for Cosmic Ray Research University of Tokyo Chiba Kashiwa277-8582 Japan Institute of Physics Academia Sinica Nankang Taipei11529 Taiwan Department of Physics University of Toyama Toyama Toyama930-8555 Japan Faculty of Engineering University of Toyama Toyama Toyama930-8555 Japan Yukawa Institute for Theoretical Physics Kyoto University Sakyo Kyoto606-8502 Japan Department of Physics Osaka City University Sumiyosi Osaka558-8585 Japan Department of Physics Osaka University Osaka Toyonaka560-0043 Japan Korea Institute of Science and Technology Information Yuseong Daejeon 34141 Korea Republic of Yuseong Daejeon34055 Korea Republic of National Institute for Mathematical Sciences Daejeon34047 Korea Republic of Department of Computer Simulation Inje University Gimhae Gyeongsangnam50834 Korea Republic of Department of Physics and Astronomy Seoul National University Seoul151-742 Korea Republic of High Energy Accelerator Research Organization Ibaraki Tsukuba305-0801 Japan Department of Physical Science Hiroshima University Higashihiroshima Hiroshima903-0213 Japan Department of Applied Physics Fukuoka University Jonan Fukuoka814-0180 Japan Department of Advanced Materials Science University of Tokyo Chiba Kashiwa277-8582 Japan Istituto Nazionale di Fisica Nucleare Sapienza University Roma00185 Italy Department o

KAGRA is a 3-km interferometric gravitational wave telescope located in the Kamioka mine in Japan. It is the first km-class gravitational wave telescope constructed underground to reduce seismic noise, and the first km-class telescope to use cryogenic cooling of test masses to reduce thermal noise. The construction of the infrastructure to house the interferometer in the tunnel, and the initial phase operation of the interferometer with a simple 3-km Michelson configuration have been completed. The first cryogenic operation is expected in 2018, and the observing runs with a full interferometer are expected in 2020s. The basic interferometer configuration and the current status of KAGRA are described. © Published under licence by IOP Publishing Ltd.

关键词： Interferometers

Reconfigurable all-dielectric metalens with diffraction-limited performance

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arXiv 2019年

作者： Shalaginov, Mikhail Y. An, Sensong Zhang, Yifei Yang, Fan Su, Peter Liberman, Vladimir Chou, Jeffrey B. Roberts, Christopher M. Kang, Myungkoo Rios, Carlos Du, Qingyang Fowler, Clayton Agarwal, Anuradha Richardson, Kathleen Rivero-Baleine, Clara Zhang, Hualiang Hu, Juejun Gu, Tian Department of Materials Science & Engineering Massachusetts Institute of Technology CambridgeMA United States Department of Electrical & Computer Engineering University of Massachusetts Lowell LowellMA United States Lincoln Laboratory Massachusetts Institute of Technology LexingtonMA United States The College of Optics & Photonics Department of Materials Science and Engineering University of Central Florida OrlandoFL United States Materials Research Laboratory Massachusetts Institute of Technology CambridgeMA United States Missiles and Fire Control Lockheed Martin Corporation OrlandoFL United States

Active metasurfaces, whose optical properties can be modulated post-fabrication, have emerged as an intensively explored field in recent years. The efforts to date, however, still face major performance limitations in tuning range, optical quality, and efficiency especially for non-mechanical actuation mechanisms. In this paper, we introduce an active metasurface platform combining phase tuning covering the full 2π range and diffraction-limited performance using an all-dielectric, low-loss architecture based on optical phase change materials (O-PCMs). We present a generic design principle enabling switching of metasurfaces between two arbitrary phase profiles and propose a new figure-of-merit (FOM) tailored for active meta-optics. We implement the approach to realize a high-performance varifocal metalens operating at 5.2 μm wavelength. The metalens is constructed using Ge2Sb2Se4Te1(GSST), an O-PCM with a large refractive index contrast (Δn > 1) and unique broadband low-loss characteristics in both amorphous and crystalline states. The reconfigurable metalens features focusing efficiencies above 20% at both states for linearly polarized light and a record large switching contrast ratio of 29.5 dB. We further validated aberration-free imaging using the metalens at both optical states, which represents the first experimental demonstration of a non-mechanical active metalens with diffraction-limited performance. Copyright © 2019, The Authors. All rights reserved.

关键词： Phase change materials

Some Remarks on Robust Gene Regulation in a Biomolecular Integral Controller

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Some Remarks on Robust Gene Regulation in a Biomolecular Int...

IEEE Annual Conference on Decision and Control

作者： Deepak K. Agrawal Ryan Marshall M. Ali Al-Radhawi Vincent Noireaux Eduardo D Sontag Department of Bioengineering and Department of Electrical and Computer Engineering Northeastern University Boston MA USA School of Physics and Astronomy University of Minnesota Minneapolis MN USA Laboratory of Systems Pharmacology Program in Therapeutic Science Harvard Medical School Boston MA USA

ISBN: (数字)9781728113982

ISBN: (纸本)9781728113999

Integral feedback can help achieve robust tracking independently of external disturbances. Motivated by this knowledge, biological engineers have proposed various designs of biomolecular integral feedback controllers to regulate biological processes. In this paper, we theoretically analyze the operation of a particular synthetic biomolecular integral controller, which we have recently proposed and implemented experimentally. Using a combination of methods, ranging from linearized analysis to sum-of-squares (SOS) Lyapunov functions, we demonstrate that, when the controller is operated in closed-loop, it is capable of providing integral corrections to the concentration of an output species in such a manner that the output tracks a reference signal linearly over a large dynamic range. We investigate the output dependency on the reaction parameters through sensitivity analysis, and quantify performance using control theory metrics to characterize response properties, thus providing clear selection guidelines for practical applications. We then demonstrate the stable operation of the closed-loop control system by constructing quartic Lyapunov functions using SOS optimization techniques, and establish global stability for a unique equilibrium. Our analysis suggests that by incorporating effective molecular sequestration, a biomolecular closed-loop integral controller that is capable of robustly regulating gene expression is feasible.

关键词： Steady-state Robustness Mathematical model Proteins Gene expression Kinetic theory Production

Triple reduction of threshold current for $1.3 \mu \mathrm{m}$ in as quantum dot lasers on patterned, on-axis (001) Si

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Triple reduction of threshold current for $1.3 \mu \mathrm{m...

Conference on Lasers and Electro-Optics (CLEO)

作者： Chen Shang Yating Wan Justin Norman Daehwan Jung Qiang Li Kei May Lau Arthur C. Gossard John E. Bowers Materials Department University of California Santa Barbara Santa Barbara California USA Institute for Energy Efficiency University of California Santa Barbara Santa Barbara California USA Department of Electronic and Computer Engineering Hong Kong University of Science & Technology Clear Water Bay Hong Kong Department of Electrical and Computer Engineering University of California Santa Barbara Santa Barbara California USA

Triple reduction of threshold current was achieved for 1.3 μm InAs quantum dot lasers on patterned, on-axis (001)Si. This was enabled by reducing the threading dislocation density, from 7×10 7 to 3×10 6 cm...

ISBN: (纸本)9781728137186

关键词：

engineering quantum interference in van der Waals heterostructures

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arXiv 2019年

作者： Nalabothula, Muralidhar Jha, Pankaj Low, Tony Kumar, Anshuman Physics Department Indian Institute of Technology Bombay Mumbai400076 India Department of Applied Physics and Materials Science California Institute of Technology PasadenaCA91125 United States Department of Electrical and Computer Engineering University of Minnesota MinneapolisMN55455 United States

In this paper, we present a novel route to tunable spontaneous valley coherence in heterostructures of two dimensional valleytronic materials with other layered materials hosting anisotropic polaritonic modes. We first discuss the dependence of this coherence on the conductivity tensor of the anisotropic part of a general heterostructure and on its geometrical configuration. Subsequently, we propose two implementations - one, using anisotropic plasmons in phosphorene and another with hyperbolic phonon polaritons in α−MoO3. In both these systems we show for the first time electrostatic tunability of the spontaneous valley coherence achieving unprecedented values of up to 80% in the near to mid infrared wavelengths at room temperature. The tunability of this valley coherence shown in these heterostructures will enable the realization of active valleytronic quantum circuitry. Copyright © 2019, The Authors. All rights reserved.

关键词： Anisotropy

Software-defined metasurface Paradigm: Concept, challenges, prospects

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arXiv 2019年

作者： Pitilakis, A. Tasolamprou, A.C. Liaskos, C. Liu, F. Tsilipakos, O. Wang, X. Mirmoosa, M.S. Kossifos, K. Georgiou, J. Pitsilides, A. Kantartzis, N.V. Ioannidis, S. Economou, E.N. Kafesaki, M. Tretyakov, S.A. Soukoulis, C.M. Foundation for Research and Technology Hellas Heraklion Crete71110 Greece Department of Electrical and Computer Engineering Aristotle University of Thessaloniki Thessaloniki Greece Department of Electronics and Nanoengineering Aalto University P.O. Box 15500 Espoo Finland Department of Electrical and Computer Engineering University of Cyprus Nicosia20537 Cyprus Department of Computer Science University of Cyprus Nicosia20537 Cyprus Department of Materials Science and Technology University of Crete Heraklion Crete71003 Greece Ames Laboratory Department of Physics and Astronomy Iowa State University AmesIA50011 United States

– HyperSurfaces (HSFs) are devices whose electromagnetic (EM) behavior is software-driven, i.e., it can be defined programmatically. The key components of this emerging technology are the metasurfaces, artificial layered materials whose EM properties depend on their internal subwavelength structuring. HSFs merge metasurfaces with a network of miniaturized custom electronic controllers, the nanonetwork, in an integrated scalable hardware platform. The nanonetwork receives external programmatic commands expressing the desired end-functionality and appropriately alters the metasurface configuration thus yielding the respective EM behavior for the HSF. In this work, we will present all the components of the HSF paradigm, as well as highlight the underlying challenges and future prospects. Copyright © 2019, The Authors. All rights reserved.

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Asymmetric Metal-dielectric Meta-cylinders and their Potential Applications from engineering Scattering Patterns to Spatial Optical Signal Processing

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arXiv 2019年

作者： Momeni, Ali Safari, Mahdi Abdolali, Ali Kherani, Nazir P. Fleury, Romain Applied Electromagnetic Laboratory School of Electrical Engineering Iran University of Science and Technology Narmak Tehran Iran Department of Electrical and Computer Engineering University of Toronto 10 Kings College Road TorontoM5S 3G4 Canada Department of Materials Science and Engineering University of Toronto 140 College Street TorontoONM5S 3E4 Canada LausanneCH-1015 Switzerland

We propose a novel type of bi-anisotropic hybrid metal-dielectric structure comprising dielectric and metallic cylindrical wedges wherein the composite meta-cylinder enables advanced control of electric, magnetic and magnetoelectric resonances. We establish a theoretical framework in which the electromagnetic response of this meta-atom is described through the electric and magneticmultipole moments. The complete dynamic polarizability tensor, expressed in a compact form, is derived as a function of the Mie scattering coefficients. Flexibility in the design makes the proposed meta-cylinder a viable candidate for various applications in the microscopic (single meta-atom) and macroscopic (metasurface) levels. We show that the highly versatile bi-anisotropic meta-atom is amenable to being designed for the desired electromagnetic response, such as electric dipole-free and zero/near-zero (backward and forward) scattering at the microscopic level. In addition, we show that the azimuthal asymmetry gives rise to normal polarizability components which are vital elements in synthesizing asymmetric Optical Transfer Function (OTF) at the macroscopic *** conduct a precise inspection, from the microscopic to the macroscopic level, of the metasurface synthesis for emphasizing on the role of normal polarizability components for spatial optical signal processing. It is shown that this simple two-dimensional asymmetric meta-atom can perform first-order differentiation and edge detection at normal *** results reported herein contribute toward improving the physical understanding of wave interaction with artificial materials composed of asymmetric elongated metal-dielectric inclusions and open the potential of its application in spatial signal and image processing. Copyright © 2019, The Authors. All rights reserved.

关键词： Polarization

Field-Free Spin-Orbit Torque Switching of Perpendicular Magnetization by the Rashba Interface

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ACS applied materials & interfaces 2019年第42期11卷 39369-39375页

作者： Baoshan Cui Hao Wu Dong Li Seyed Armin Razavi Di Wu Kin L Wong Meixia Chang Meizhen Gao Yalu Zuo Li Xi Kang L Wang Department of Electrical and Computer Engineering University of California Los Angeles California 90095 United States. Key Laboratory for Magnetism and Magnetic Materials of Ministry of Education & School of Physical Science and Technology Lanzhou University Lanzhou 730000 P. R. China. Research Institute of Materials Science Shanxi Normal University Linfen 041004 P. R. China.

Current-induced spin-orbit torques (SOTs) enable efficient electrical manipulation of the magnetization in heterostructures with a perpendicular magnetic anisotropy through the Rashba effect or spin-Hall effect. However, in conventional SOT-based heterostructures, an in-plane bias magnetic field along the current direction is required for the deterministic switching. Here, we report that the field-free SOT switching can be achieved by introducing a wedged oxide interface between a heavy metal and a ferromagnet. The results demonstrate that the field-free SOT switching is determined by a current-induced perpendicular effective field () originating from the interfacial Rashba effect due to the lateral structural symmetry-breaking introduced by the wedged oxide layer. Furthermore, we show that the sign and magnitude of exhibit a significant dependence on the interfacial oxygen content, which can be controlled by the inserted oxide thickness. Our findings provide a deeper insight into the field-free SOT switching by the interfacial Rashba effect.

关键词： Rashba effect field-free magnetization switching interfacial decoration interfacial oxygen content perpendicular magnetic anisotropy spin−orbit torque