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

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

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Corrigendum to “Using remote sensing to calculate floating photovoltaic technical potential of a dam’s surface” [Sustain. Energy Technol. Assess. 41 (2020) 100799]

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Sustainable Energy Technologies and Assessments 2021年 43卷

作者： Ali Murat Ates Osman Salih Yilmaz Fatih Gulgen Manisa Celal Bayar University Faculty of Education Computer and Instructional Technologies Department Turkey Manisa Celal Bayar University Demirci Vocational School Geographical Information Systems Program Turkey Yildiz Technical University Faculty of Civil Engineering Geomatic Engineering Department Turkey

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Valley-polarized Exitonic Mott Insulator in WS2/WSe2 Moiré Superlattice

arXiv

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arXiv 2023年

作者： Lian, Zhen Meng, Yuze Ma, Lei Maity, Indrajit Yan, Li Wu, Qiran Huang, Xiong Chen, Dongxue Chen, Xiaotong Chen, Xinyue Blei, Mark Taniguchi, Takashi Watanabe, Kenji Tongay, Sefaattin Lischner, Johannes Cui, Yong-Tao Shi, Su-Fei Department of Chemical and Biological Engineering Rensselaer Polytechnic Institute TroyNY12180 United States Departments of Materials The Thomas Young Centre for Theory and Simulation of Materials Imperial College London United Kingdom Department of Physics and Astronomy University of California RiversideCA92521 United States Department of Materials Science and Engineering University of California RiversideCA92521 United States Materials Science and Engineering Program School for Engineering of Matter Transport and Energy Arizona State University TempeAZ85287 United States International Center for Materials Nanoarchitectonics National Institute for Materials Science 1-1 Namiki Tsukuba305-0044 Japan Research Center for Functional Materials National Institute for Materials Science 1-1 Namiki Tsukuba305-0044 Japan Department of Electrical Computer & Systems Engineering Rensselaer Polytechnic Institute TroyNY12180 United States

Strongly enhanced electron-electron interaction in semiconducting moiré superlattices formed by transition metal dichalcogenides (TMDCs) heterobilayers has led to a plethora of intriguing fermionic correlated states1–7. Meanwhile, interlayer excitons in a type-II aligned TMDC heterobilayer moiré superlattice, with electrons and holes separated in different layers8,9, inherit this enhanced interaction and strongly interact with each other, promising for realizing tunable correlated bosonic quasiparticles10,11 with valley degree of freedom. We employ photoluminescence spectroscopy to investigate the strong repulsion between interlayer excitons and correlated electrons in a WS2/WSe2 moiré superlattice and combine with theoretical calculations to reveal the spatial extent of interlayer excitons and the band hierarchy of correlated states. We further find that an excitonic Mott insulator state emerges when one interlayer exciton occupies one moiré cell, evidenced by emerging photoluminescence peaks under increased optical excitation power. Double occupancy of excitons in one unit cell requires overcoming the energy cost of exciton-exciton repulsion of about 30-40 meV, depending on the stacking configuration of the WS2/WSe2 heterobilayer. Further, the valley polarization of the excitonic Mott insulator state is enhanced by nearly one order of magnitude. Our study demonstrates the WS2/WSe2 moiré superlattice as a promising platform for engineering and exploring new correlated states of fermion, bosons, and a mixture of both12 © 2023, CC BY.

关键词： Excitons

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Scalable Crystal Structure Relaxation Using an Iteration-Free Deep Generative Model with Uncertainty Quantification

arXiv

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arXiv 2024年

作者： Yang, Ziduo Zhao, Yi-Ming Wang, Xian Liu, Xiaoqing Zhang, Xiuying Li, Yifan Lv, Qiujie Chen, Calvin Yu-Chian Shen, Lei Department of Mechanical Engineering National University of Singapore Singapore117575 Singapore Artificial Intelligence Medical Research Center School of Intelligent Systems Engineering Shenzhen Campus of Sun Yat-sen University Shenzhen518107 China Department of Physics National University of Singapore Singapore117551 Singapore -Preferred Program School of Electronic and Computer Engineering Peking University Shenzhen Graduate School Shenzhen518055 China State Key Laboratory of Chemical Oncogenomics School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School Shenzhen518055 China Department of Medical Research China Medical University Hospital Taichung40447 Taiwan Department of Bioinformatics and Medical Engineering Asia University Taichung41354 Taiwan Guangdong L-Med Biotechnology Co. Ltd. Guangdong Meizhou514699 China Research Institute Chongqing401123 China

In computational molecular and materials science, determining equilibrium structures is the crucial first step for accurate subsequent property calculations. However, the recent discovery of millions of new crystals and complex twisted structures has challenged traditional computational methods, both ab initio and machine-learning-based, due to their computationally intensive iterative processes. To address these scalability issues, here we introduce DeepRelax, a deep generative model capable of performing geometric crystal structure relaxation rapidly and without iterations. DeepRelax learns the equilibrium structural distribution, enabling it to predict relaxed structures directly from their unrelaxed ones. The ability to perform structural relaxation at the millisecond level per structure, combined with the scalability of parallel processing, makes DeepRelax particularly useful for large-scale virtual screening. We demonstrate DeepRelax's reliability and robustness by applying it to five diverse databases, including oxides, Materials Project, two-dimensional materials, van der Waals crystals, and crystals with point defects. DeepRelax consistently shows high accuracy and efficiency, validated by density functional theory calculations. Finally, we enhance its trustworthiness by integrating uncertainty quantification. This work significantly accelerates computational workflows, offering a robust and trustworthy machine-learning method for material discovery and advancing the application of AI for science. Code for DeepRelax is available at https://***/Shen-Group/DeepRelax. Copyright © 2024, The Authors. All rights reserved.

关键词： Point defects

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Resource allocation decision making in the military health system

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IIE Transactions on Healthcare systems engineering 2014年第2期4卷 80-87页

作者： Bastian, Nathaniel D. Fulton, Lawrence V. Shah, Vivek P. Ekin, Tahir The Pennsylvania State University Center for Integrated Healthcare Delivery Systems Department of Industrial and Manufacturing Engineering University Park PA 16802 355 Leonhard Building United States U.S. Army - Baylor University Graduate Program in Health and Business Administration U.S. Army Medical Department Center and School Fort Sam Houston TX 78234-6100 3630 Stanley Road United States Texas State University McCoy College of Business Administration Department of Computer Information Systems and Quantitative Methods San Marcos TX 78666 611 University Drive United States

The necessity to efficiently balance and re-allocate system resources among hospitals in a hospital network is paramount, especially as health systems experience increasing demand and costs for health services. In this paper, we proffer a resource allocation-based optimization model that adjusts resources (system inputs) automatically, which provides decision makers (such as health care managers and policy-makers) with a decision-support tool for re-allocating resources in large health systems that are centrally controlled and funded, such as the Military Health System. In these systems, inputs are fixed at certain levels and may only be adjusted within medical treatment facilities, while outputs must be maintained. We provide a mathematical formulation and example solutions from a case study using real-world data from sixteen U.S. Army hospitals. We also find utility in the use of multi-start evolutionary algorithms to store multiple optimal solutions for consideration by decision makers. © 2014 "IIE".

关键词： decision analysis healthcare management military medicine multi-criteria optimization Resource allocation

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Experimental Investigation of Lord Kelvin’s Isentropic Cooling and Heating Expression in Tensile Bars for Two engineering Alloys

arXiv

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arXiv 2023年

作者： Burns, S.J. Pratt, Christine E. Carrock, Joseph Gagnon, Jean-Philippe Sefkow, A.B. Materials Science Program College of Arts Science and Engineering University of Rochester RochesterNY14627 United States Department of Mechanical Engineering University of Rochester 236 Hopeman Hall RochesterNY14627 United States Field Application Engineering Telops GenevaNY14456 United States Systems Engineering Telops 100-2600 St-Jean-Baptiste Ave. QuébecQCG2E 6J5 Canada Laboratory for Laser Energetics University of Rochester 250 E. River Rd. RochesterNY14623 United States Department of Physics and Astronomy University of Rochester 206 Bausch and Lomb Hall RochesterNY14627 United States Department of Computer Science University of Rochester 2513 Wegmans Hall RochesterNY14627 United States

Solids when rapidly and elastically stressed change temperature, the effect proposed by Lord Kelvin is adiabatic thermo-elastic cooling or heating depending on the sign of the stress. A fast sensitive IR camera has measured temperature both decreasing and increasing. Temperature measurements made from the reversible, elastic part of the stress-strain curve during fast uniaxial tensile loading have been investigated. The isentropic temperature cooling from the loading curve is recovered by heating after the specimen fractures when the load is released. These measurements establish for the first time isentropic thermal recovery in two engineering alloys. The materials tested are an AISI 4340 steel and an aluminum 2024 alloy. Measurements of the isentropic thermo-elastic stress cooling are -0.61 K/GPa for steel and -1.7 K/GPa for aluminum alloy. The isentropic thermo-elastic stress heating is -1.16 K/GPa for steel and -1.6 K/GPa for aluminum alloy. These values are compared to Lord Kelvin’s theoretical thermodynamic prediction. Comparisons are also to equations of state tables. The experimental values are slightly below theoretical predictions. The isentropic, elastic part of the temperature is fully recoverable even after extensive plastic deformation upon fracture. Copyright © 2023, The Authors. All rights reserved.

关键词： Cooling

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Photonic Terahertz Phased Array

arXiv

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arXiv 2024年

作者： Niu, Li Feng, Xi Zhang, Xueqian Lu, Yongchang Wang, Qingwei Xu, Quan Chen, Xieyu Ma, Jiajun Qiu, Haidi Sha, Wei E.I. Zhang, Shuang Alù, Andrea Zhang, Weili Han, Jiaguang Center for Terahertz Waves College of Precision Instrument and Optoelectronics Engineering The Key Laboratory of Optoelectronics Information and Technology Tianjin University Tianjin300072 China Key Laboratory of Micro-nano Electronic Devices and Smart Systems of Zhejiang Province College of Information Science & Electronic Engineering Zhejiang University Hangzhou310027 China Department of Electrical & Electronic Engineering University of Hong Kong 999077 Hong Kong Photonics Initiative Advanced Science Research Center City University of New York New York10031 United States Physics Program Graduate Center City University of New York New York10016 United States School of Electrical and Computer Engineering Oklahoma State University StillwaterOK74078 United States Guangxi Key Laboratory of Optoelectronic Information Processing School of Optoelectronic Engineering Guilin University of Electronic Technology Guilin541004 China

Phased arrays are crucial in various technologies, such as radar and wireless communications, due to their ability to precisely control and steer electromagnetic waves. This precise control improves signal processing and enhances imaging performance. However, extending phased arrays to the terahertz (THz) frequency range has proven challenging, especially for high-frequency operation, broadband performance, two-dimensional (2D) phase control with large antenna arrays, and strong phase modulation. Here, we introduce a photonic platform to realize a THz phased array that bypasses the above challenges. Our method employs 2D phase coding with 2-bit across a broad THz frequency range from 0.8 to 1.4 THz. The core of our design is a pixelated nonlinear Pancharatnam-Berry metasurface driven by a spatially modulated femtosecond laser, allowing precise phase control of THz signals. We showcase the effectiveness of our method through four proof-of-concept applications: single beamforming, dual beamforming, imaging and vortex beam generation. The realized photonic platform provides a promising pathway for developing broadband phased arrays in the THz regime. Copyright © 2024, The Authors. All rights reserved.

关键词： Terahertz waves

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Spatio-temporal assessment of whole-body center of mass coordination on standard maximum vertical jump

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Gait & Posture 2022年 97卷 S208-S209页

作者： Rodrigues, C. Correia, M. Abrantes, J. Rodrigues, B. Nadal, J. Faculty of Engineering- University of Porto Biomedical Engineering Program Porto Portugal INESC TEC - Institute for Systems and Computer Engineering- Technology and Science C-BER - Centre for Biomedical Engineering Research Porto Portugal University of Porto Faculty of Engineering Porto Portugal Lusófona University- CICANT - Centre for Research in Applied Communication- Culture and New Technologies MovLab Laboratory of Technologies for Interactions and Interfaces Lisbon Portugal Federal University of Pernambuco Department of Electronic and Systems Recife Brazil Federal University of Rio de Janeiro Biomedical Engineering Program Rio de Janeiro Brazil

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IMPROVING THE SHIP DESIGN, ACQUISITION AND CONSTRUCTION PROCESS

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NAVAL ENGINEERS JOURNAL 1992年第2期104卷 39-57页

作者： RYAN, JC JONS, OP J. Christopher Ryan:earned his bachelor's and master's degrees in Naval Architecture from Webb Institute and MIT respectively. He spent three years at the Advanced Marine Technology Division of Litton Industries working on the DD-963 class ship design and related computer aided design projects. he subsequently went to the Navy Department concentrating on early stage design of surface combatants for 12 years including work on the FFG-7 Sea Control Ship CSGN and CVV aircraft carrier projects. He then shifted focus and became the technical director for the Computer Supported Design Program in NavSea for five years. Mr. Ryan has served in several supervisory positions within the Ship Design Group in NavSea since that time. He is currently the project manager for the Ship Design Acquisition and Construction Process Improvement Project. Otto P. Jons:received a Diplom Ing. in shipbuilding from the Technical University of Hannover W. Germany and an M.S. in naval architecture and marine engineering from the Massachusetts Institute of Technology in 1967. He then joined Litton Ship Systems where he was responsible for the preliminary design of the DD-963 hull structure and then for ship systems as manager LHA Ship Systems Engineering Department. From 1972 to 1974 he was principal research scientist at Hydronautics. In 1976 as technical director he helped establish the local office of Designers and Planners. Otto Jons was one of the co-founders of Advanced Marine Enterprises Inc. in 1976 where he is corporate vice president engineering.

In the spring of 1990, the NavSea Chief Engineer initiated a project to improve the design, acquisition and construction (DAC) of U.S. Navy ships. The project's objectives are to reduce the time and cost of acquiring and operating Navy ships while improving their quality, unlike previous studies on the subject, the project utilizes a rigorous process analysis approach and attempts to use quantitative measures as the basis for recommending improvements. The paper is, of necessity, a status report on the progress of this project. Topics covered include: the DAC process;a look at the current state of ship acquisition time, cost, and quality;the methodology for process improvements;and early findings.

关键词： Naval Vessels

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TECHNICAL DOCUMENTATION MANAGEMENT IN THE ERA OF THE PAPERLESS SHIP

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NAVAL ENGINEERS JOURNAL 1989年第3期101卷 61-72页

作者： CHICKERING, JE QUALLS, WB John E. Chickering:is a systems analyst with American Management Systems Inc. in Arlington Virginia. Mr. Chickering received his BS degree in marine engineering from the U.S. Merchant Marine Academy in Kings Point New York in 1981 and his MBA degree in operations research and statistics from the University of Maryland in 1985. He is a licensed third assistant engineer of steam and motor vessels and a member of the Naval Reserve. Mr. Chickering's work includes the design and specification of several management information systems for the U.S. Navy including one that will automate the Navy's engineering drawing management system. Most recently Mr. Chickering has helped develop a workstation for the Navy's Paperless Ship Initiative. William B. Quails:is a management consultant with American Management Systems Inc. in Arlington Virginia. Mr. Quails received his BA degree in English from the Tulane University in New Orleans Louisiana in 1977 and his MPA degree in management science from the University of Georgia in 1982. Mr. Quails participated in the design and development of the U.S. Navy's Shipboard Non-tactical ADP Program II (SNAP II). Recently Mr. Quails has participated in the design and development of several knowledge-based computer systems using artificial intelligence programming technologies. Mr. Quails is a member of Pi Alpha Alpha an honorary public affairs and administration society.

The U.S. Navy relies heavily on advanced technology to carry out its missions. As a consequence, today's sailors are spending increasing amounts of time maintaining and repairing complex systems and equipment. In performing these duties, sailors depend on supporting technical documentation. As the complexity of systems and equipment grow, the volume and complexity of this technical documentation also increases. As a result, technical information, one of the Navy's critical resources, is simultaneously becoming more vital and more difficult to use. The Navy is meeting this challenge by exploring innovative approaches to the management of technical documentation. One example is the Paperless Ship Initiative, which employs optical disk technology as the primary means for document storage. Optical disks can store large volumes of technical information in a small space. One way to take advantage of this auto mated access is to make technical information more readily accessible and easier to use. As an example, a technical manual can be organized on an optical disk into discrete segments of text and indexed for fast retrieval by section, subsection, or paragraph. Furthermore, mechanisms can be developed which allow computer-supported links between logically related segments of the text. This style of interface allows a user to interact directly with the textual passages and to establish new organizational and referential links between them. This style of interface falls under the general category of hypertext (also known as linked text ). The combination of optical disk storage and hypertext offers new possibilities for improving access to large volumes of technical documentation while maintaining all of the advantages of traditional paper-based documentation. This paper begins with a discussion of the need for better technical documentation support. Alternatives that can fulfill this need are reviewed and the role of hypertext is described. The paper illustrates a sample

关键词： Information Retrieval systems

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