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arXiv 2021年

作者： Lee, Benjamin D. Gitter, Anthony Greene, Casey S. Raschka, Sebastian Maguire, Finlay Titus, Alexander J. Kessler, Michael D. Lee, Alexandra J. Chevrette, Marc G. Stewart, Paul Allen Britto-Borges, Thiago Cofer, Evan M. Yu, Kun-Hsing Carmona, Juan Jose Fertig, Elana J. Kalinin, Alexandr A. Signal, Beth Lengerich, Benjamin J. Triche, Timothy J. Boca, Simina M. In-Q-Tel Labs School of Engineering and Applied Sciences Harvard University Department of Genetics Harvard Medical School United States Department of Biostatistics and Medical Informatics University of Wisconsin-Madison MadisonWI United States Morgridge Institute for Research MadisonWI United States Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Biochemistry and Molecular Genetics University of Colorado School of Medicine AuroraCO United States Center for Health AI University of Colorado School of Medicine AuroraCO United States Department of Statistics University of Wisconsin Madison United States Faculty of Computer Science Dalhousie University Canada University of New Hampshire Bioeconomy.XYZ United States Department of Oncology Johns Hopkins University United States Institute for Genome Sciences University of Maryland School of Medicine United States Genomics and Computational Biology Graduate Program University of Pennsylvania United States Department of Systems Pharmacology and Translational Therapeutics University of Pennsylvania United States Wisconsin Institute for Discovery Department of Plant Pathology University of Wisconsin-Madison United States Department of Biostatistics and Bioinformatics Moffitt Cancer Center TampaFL United States Section of Bioinformatics and Systems Cardiology Klaus Tschira Institute for Integrative Computational Cardiology University Hospital Heidelberg Germany University Hospital Heidelberg Germany Lewis-Sigler Institute for Integrative Genomics Princeton University PrincetonNJ United States Graduate Program in Quantitative and Computational Biology Princeton University PrincetonNJ United States Department of Biomedical Informatics Harvard Medical School United States Department of Pathology Brigham and Women's Hospital United States Philips Healthcare CambridgeMA United States Philips Research

Machine learning is a modern approach to problem-solving and task automation. In particular, machine learning is concerned with the development and applications of algorithms that can recognize patterns in data and use them for predictive modeling. Artificial neural networks are a particular class of machine learning algorithms and models that evolved into what is now described as deep learning. Given the computational advances made in the last decade, deep learning can now be applied to massive data sets and in innumerable contexts. Therefore, deep learning has become its own subfield of machine learning. In the context of biological research, it has been increasingly used to derive novel insights from high-dimensional biological data. To make the biological applications of deep learning more accessible to scientists who have some experience with machine learning, we solicited input from a community of researchers with varied biological and deep learning interests. These individuals collaboratively contributed to this manuscript's writing using the GitHub version control platform and the Manubot manuscript generation toolset. The goal was to articulate a practical, accessible, and concise set of guidelines and suggestions to follow when using deep learning. In the course of our discussions, several themes became clear: the importance of understanding and applying machine learning fundamentals as a baseline for utilizing deep learning, the necessity for extensive model comparisons with careful evaluation, and the need for critical thought in interpreting results generated by deep learning, among others. © 2021, CC BY.

关键词： Learning algorithms

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Label-free GR5 DNAzyme-based colorimetric sensing for lead ions (Pb2+) detection

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AIP Conference Proceedings 2023年第1期2720卷

作者： Muhammad Nur Hasan Patsamon Rijiravanich Werasak Surareungchai Nanoscience and Nanotechnology Graduate Program Faculty of Science King Mongkut’s University of Technology Thonburi Bang Mod Thung Khru Bangkok 10140 Thailand Biosciences and Systems Biology Research Team National Center for Genetic Engineering and Biotechnology National Sciences and Technology Development Agency at King Mongkut’s University of Technology Thonburi Bang Khun Thian Bangkok 10150 Thailand School of Bioresources and Technology King Mongkut’s University of Technology Thonburi Bang Khun Thian Bangkok 10150 Thailand

Lead (Pb2+) contamination in blood can trigger the developmental of disabilities in children and some serious problems of chronic illnesses. In this work, a simple label-free GR5 DNAzyme and gold nanoparticles were applied in a colorimetric assay for Pb2+ detection. Using this method, the reaction and cleaving process between DNAzyme and lead were perfect. The experiment was successfully tested for the detection of Pb2+ in the buffer. The visual detection limit of this colorimetric assay obtained was 10 nM. The biosensor showed excellent specificity for Pb2+ compared to other metal ions.

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A NOTE ON ANTI-SHIP MISSILES AND FUTURE SHIP DESIGN

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NAVAL ENGINEERS JOURNAL 1980年第4期92卷 84-86页

作者： RUHE, WJ USN (RET.) THE AUTHOR: is a graduate of the U.S. Naval Academy Class of 1939 who served in Submarines during World War II and much of his naval career. Later he commanded Destroyers and Missile-Armed Destroyer Units his major command being the TERRIER-Armed Guided Missile Cruiser USS Topeka. Much of his shore duty career involved conceptual planning for new Navy systems as well as operational research involving sea wars of the future and he directed the study effort for the ocean wars in the first General Purpose Forces Studies conducted by the Joint Chiefs of Staff. On retirement in 1967 he joined the Staff of the President's Commission on Ocean Engineering and Research and upon completing his Commission work joined General Dynamics' Corporate Director of Marine Program Development presently serving in General Dynamics' Washington Office as Manager of Warfare Analysis and Energy Programs. His numerous articles in national magazines stress the great changes which he feels we must be aware of if we are to meet the challenge which the missile-dependent Soviet Navy now poses.

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ARCTIC TRAFFICABILITY program - A REVIEW

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NAVAL ENGINEERS JOURNAL 1984年第3期96卷 169-175页

作者： VOELKER, R GLEN, IF SEIBOLD, F BAYLY, I Richard Voelker:is Vice President of ARCTEC Incorporated a firm specializing in cold regions technology. He has been responsible for the management of thePolarClass Traffic-ability Program since its inception and annually participates in the field data collection in the Arctic. His prior experience includes positions with the U.S. Coast Guard in the icebreaker design project the Military Sealift Command and at Newport News Shipbuilding. He is a graduate of N. Y.S. Maritime College and has a MS degree from the University of Michigan. I.F. Glen:received his professional degrees in naval architecture from the Royal Naval Engineering College Manadon Plymouth and RN College Greenwich London entering the Royal Corps of Naval Constructors in 1967. After serving as a Constructor Lieutenant in the Royal Navy's Far East Fleet for a short period he joined the Polaris submarine project team in Bath England in 1968. In 1971 he was seconded to the Canadian Department of National Defense in Ottawa as a Constructor Lieutenant Commander under NATO exchange arrangements where he had responsibilities initially for conventional submarines and latterly for computer aided conceptual design. He ventured to Bath England in 1974 and joined Forward Design Group. In 1975 he took a position as a civilian engineer in the Canadian Defense Department and was Head of Hull Systems Engineering from 1977 to 1979. He joined ARCTEC CANADA LIMITED in 1980 and in addition to managing ice model testing projects and full scale trials has specialized in structural response of ships to ice impact. He headed ARCTEC's Kanata Laboratory from 1981 to 1983 when he was promoted to president. Frederick Seibold:is a research program manager with the Maritime Administration's Office of Advanced Ship Development and Technology. He is responsible for the marine science program which includes research in the areas of ship powering structures and propeller performance and Arctic technology. Mr. Seibold has been employed by Mar Ad since 1961 having hel

This paper describes a multiyear program to make an operational assessment on the feasibility of a year-round Arctic marine transportation system to serve Alaska. Specifically, the three objectives were to: collect meteorological and ice data along potential marine routes; instrument the hull and propulsion machinery to improve design critera for ice-worthy ships; and demonstrate that ships can operate in midwinter Alaskan Arctic ice conditions. The U.S. Coast Guard's Polar class icebreakers were used to make the operational assessment by annually extending the route northward and by operating throughout the winter season. This paper reviews some of the operational and technical achievements to date, as well as plans for future Arctic deployments.

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THE INTRODUCTION OF HEAT RECOVERABLE COUPLINGS TO SHIP REPAIR AND MAINTENANCE

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NAVAL ENGINEERS JOURNAL 1982年第6期94卷 63-71页

作者： LIBERATORE, DJ BASKERVILLE, JE LCdr. Donald J. Liberatore USN: began his career in the U.S. Navy in 1965. He has had many diverse assignments involving surface ships and submarines during the past seventeen years. During his tour at Naval Shipyard Portsmouth (N.H.) he was Assistant Design Superintendent and responsible for the introduction of Heat Recoverable Coupling technology into the shipyard. Presently he is assigned to the Naval Sea Systems Command (NAVSEA) in the Sonar Dome Office. Prior assignments within NAVSEA have been as Assistant Ship Systems Design Manager for the SSNX and FA-SSN preliminary designs in the Submarine Propulsion Analysis Branch in the Submarine Hydrodynamics Branch and in the Gear Coupling and Clutch Branch. He received his Bachelor of Engineering degree from Vanderbilt University in 1971 and in 1977 graduated from Massachusetts Institute of Technology with his M.S. degree in Naval Architecture and Marine Engineering and his Professional degree of Ocean Engineer. A member of ASNE since 1975 LCdr. Liberatore also is a member of IEEE SNAME the Naval Institute and Sigma Xi. Cdr. James E. Baskerville USN: is presently assigned to NAVSEA as the Ship Manager for the DDG 51 the Navy's next generation surface combatant. In a previous tour at Naval Shipyard Pearl Harbor he was the Navy's Program Manager for Heat Recoverable Coupling introduction in ship repair and maintenance. A graduate of the U.S. Naval Academy Class of 1969 he is a qualified Surface Warfare Officer and a designated Engineering Duty Officer (ED). He received his M.S. degree in Mechanical Engineering and his Professional degree of Ocean Engineer from Massachusetts Institute of Technology and also holds a patent right on an Electronic Control and Response System. His naval assignments have included tours in the USS Ramey (FFG-2) as Aide and Flag Lieutenant to the Commander Naval Electronic Systems Command and as Ship Superintendent Surface Type Desk Officer and Assistant Design Superintendent at Naval Shipyard Pearl Harbor. Cdr. Baskervi

Although Heat Recoverable Couplings (HRCs), used to join pipe, may be labeled innovative “state-of-the-art” technology for U.S. Naval Shipyards, they have been in use in foreign ships and high technology industries for over a decade. HRCs provide a permanent leak-proof pipe joint in specified applications without the use of high temperature and the inherent hazards of an open flame. Manufactured from NITINOL, a nickel-titanium alloy developed by the U.S. Navy, the couplings exhibit a “shape memory” characteristic. That is, they return (shrink) to a specified shape (pipe diameter) thus forming a mechanical seal when the expanded coupling is removed from a cryogenic environment and warmed above approximately —130°C. This paper provides background information into the development of NITINOL, technical explanation of shape memory metallurgy, and a summary of results, with specific examples, describing the trial use of HRCs at Pearl Harbor and Norfolk Naval Shipyards. Limited return cost data and recommendations for future use are presented. Then, using the HRC program as a basis, the Authors discuss the conservative nature of the ship repair and maintenance environment. This environment, in the Authors' opinion, couples with complex contractual constraints and requirements which serve to restrict the introduction of new ideas. An analogy is made to Russian tenacity of recent years which promotes “exploring and doing” while we in the U.S. Navy are frequently content to study.

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The role of CSP in Brazil: A multi-model analysis

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AIP Conference Proceedings 2016年第1期1734卷

作者： Rafael Soria André F. P. Lucena Jan Tomaschek Tobias Fichter Thomas Haasz Alexandre Szklo Roberto Schaeffer Pedro Rochedo Ulrich Fahl Jürgen Kern Susanne Hoffmann 1Energy Planning Program Graduate School of Engineering Universidade Federal do Rio de Janeiro (UFRJ) Centro de Tecnologia Bloco C Sala 211 Cidade Universitária Ilha do Fundão 21941-972 Rio de Janeiro RJ Brazil 2Institute of Energy Economics and the Rational Use of Energy University of Stuttgart Hessbruehlstr. 49a D-70565 Stuttgart Germany 3German Aerospace Center (DLR) Institute of Engineering Thermodynamics Department of Systems Analysis and Technology Assessment Pfaffenwaldring 38-40 70569 Stuttgart Germany

MESSAGE, TIMES and REMIX-CEM are potential tools for modelling a larger penetration of variable renewable energy (VRE) into the Brazilian power system. They also allow devising the opportunities that concentrated solar power (CSP) plants offer to the power system and to the wider energy system. There are different opportunities for CSP in Brazil in the short and medium term, consolidating this technology as a feasible alternative for greenhouse gas (GHG) mitigation in Brazil. This work verified that CSP is a cost-effective option only under very stringent mitigation scenarios (4DS and 2DS) and when carbon capture and storage (CCS) is not available. Still, according to the findings of REMIX-CEM-B, CSP can provide firm energy and dispatchable capacity in the Northeast region of Brazil, optimally complementing wind and PV generation. Moreover, CSP can offer additional flexibility to the Northeast power system, especially during winter and after 2030.

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SWATH—THE VSTOL AIRCRAFT CARRIER FOR THE POST‐1990's

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Naval Engineers Journal 1977年第1期89卷 47-54页

作者： CHILDERS, RADM.K.C. GLOECKLER, FREDERICK M. STEVENS, ROBERT M. USN (RET.) RAdm. K.C. Childers USN (Ret.):graduated from the U.S. Naval Academy in 1939. and later completed his graduate studies at California Institute of Technology from which he received his MS and AE degrees. He was a fighter pilot in the aircraft carriers USS Ranger and USS Essex during World War II and an instructor at the Guided Missile School. Ft. Bliss Texas from 1947 until 1949 at which time he came to Washington. D.C. as an Assistant Division Director Ships Installation Division Bureau of Aeronautics. In addition his active duty career included assignments as Naval Air Systems Command Representative Atlantic Assistant Commander for Material Acquisition Naval Air Systems Command and Deputy Project Manager for the FlllB/Phoenix Program. Bureau of Naval Weapons. During the first five years of the Polaris Program he was responsible for all testing at the Atlantic Missile Range. He also served as Commander of the Naval Missile Center where he directed the test and evaluation of Airborne Weapon Systems and had been on an earlier assignment the Missile Test Officer. His military decorations include the Silver Star the Legion of Merit two Air Medals the Navy Commendation Medal and a Presidential Unit Citation. Currently he is employed as the Manager of the Analysis and Evaluation Department at CERBERONICS. Inc. Falls Church. Va. Mr. Frederick M. Gloeckler: currently a Consultant to CERBERONICS Inc. graduated from New York University from which he received his BS degree. He began his career with the Department of the Navy in 1938. and culminated it with his retirement in 1972 at which time he was engaged in VSTOL aircraft analysis and was the Director Advanced Systems Division Naval Air Systems Command (and its predecessor organizations). During this period he made major contributions to the Fleet Ballistic Missile Program the F-14 A-7 and S-3 Aircraft Programs and the Phoenix Condor and Harpoon Missile Programs. In 1951 Mr. Gloeckler organized‘ and directed the Systems Engineering Divis

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THE “TRADE—OFF” BETWEEN LEARNING AND INFLATION IN SHIPBUILDING

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Naval Engineers Journal 1978年第4期90卷 23-40页

作者： FRISCH, FRANZ A.P. TODD, CHARLES Dr. Franz A.P. Frischgraduated from the Technical University of Vienna in Austria. He has thirty years' experience in shipbuilding and related subjects. He has worked as a Naval Architect Guarantee Engineer Chief Estimator Production Manager and Director for Shipyard Planning and Maintenance in Austria Denmark Sweden and Germany. In 1956 he was first invited to the United States to testify on foreign cost and production in subsidy cases before the Maritime Administration. From 1957 through 1962 he was associated with several U.S. Naval Architect firms: was Owner's Representative in Europe and Japan conducted studies on transport economy for Venezuela ICC and shipowners and was a consultant for shipyard planning in Brazil and Europe. In 1963 he joined the Staff of the Center for Naval Analysis (CNA) and became Head of the Logistic Section and Study Director. There he originated the FDL ship and ship concept and was assigned as advisor to the Project Manager. From 1968 through 1974 Dr. Frisch was a Faculty member and visiting lecturer at Massachusetts Institute of Technology he lectured on Shipyard Management Ocean Transportation Systems Theory in Transportation and in Interdisciplinary Seminars. In 1972 and 1973 he was consultant to Dubai Drydock. Ltd. for layout of a new shipyard in the Arabian Gulf but since 1973 he has been with the Naval Sea Systems Command mostly involved in special projects. Dr. Frisch is also Adj. Professor for Virginia Polytechnic Institute & State University (VPI) where he teaches graduate courses in Advanced Engineering Economy and Management Concepts. Mr. Charles Toddis a graduate of Howard University School of Engineering Washington D.C where he has also pursued his graduate work. He has fifteen years' experience in New Construction Shipbuilding Acquisition Programs concentrating in the areas of Major Ship Class Project Engineering and Program Management. He worked in this capacity on the LSD 36 and 37 Class ships and in the Special Craft Section of the Combatant Craft

Learning leads to a decrease in program cost and inflation leads to an increase in program cost. At a certain time, the benefits of leaming and the penalty due to inflation will balance each other. This time is defined as the “critical time.” The “critical tune” depends upon the number of ships to be built because this determines the possible gain in learning. The “Critical time” also depends upon the assumed inflation, upon the achievable learning rate, and upon the material/labor ratio of the first ship. Learning expectation can be influenced by planning and the material/labor ration by a make– or buydecision. Assumptions on future learning are as vague as assumptions on inflation. The paper shows that it is almost impossible to beat inflation. It shows that accelerated programs are preferable and that make—decisions supersede the value of buy—decisions. The result is derived from an abstract treatment of the subject. © 1978 American Society of Naval Engineers

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THE UNIMAST CONCEPT - A MAJOR DEPARTURE IN SHIPBOARD RADAR ANTENNA INSTALLATION PHILOSOPHY

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NAVAL ENGINEERS JOURNAL 1981年第2期93卷 82-89页

作者： BIONDI, RJ KRUGER, BE THE AUTHORS: Mr. Roy J. Biondi:received his B.S.E.E. degree from the University of Illinois and has since taken additional graduate studies at The George Washington University. Currently he is Head of the Ship Type Combat System Integration Branch (Code-6141) Naval Sea Systems Command. Prior to his present appointment he served as Radar Branch Head in the former Naval Ship Engineering Center (NA VSEC) and was responsible for development and production of shipboard radars such as the AN/SPS-48 AN/SPS-49 AN/SPS-52 and AN/SPS-55. His primary Navy Radar and Combat System experience was attained during his earlier career in the Navy's Bureau of Ships where he was the AN/SPS-48 Radar Project Manager as well as the Navy Tactical Data System Data Processing and Display Project Engineer - a total of twenty years of Navy Radar and NTDS experience. In addition to ASNE which he joined in 1977 he is a member of IEEE and ASE and has had several technical papers published on Radar Radar Processing and Transmission Lines. Mr. Bradford E. Kruger:is a Senior Member of the Technical Staff at ITT Gilfillan Los Angeles Calif. He received his B.S.E.E. and M.S.E.E. degrees from the University of California at Berkeley in 1955 and 1956 respectively and has been with Gilfillan since then. For the past fifteen years he has been involved in the concept formulation and design of numerous radar systems for the Army Navy and Marine Corps. Most recently he has been the Principal Radar Systems Engineer for the SSURADS then the DDGX Program. In addition to ASNE which he joined in June 1980 he is a member of IEEE and holds several patents in Radar and Antenna Technology.

The best topside location for an antenna is on top of the highest mast on the ship, thus affording all-around coverage and minimum interference. However, usually only one antenna can occupy that site. Modern naval combatants have numerous antennas, and the necessary compromises in mounting all of them means that even the best site is often electro-magnetically compromised by adjacent structures and other antennas. A contrary approach is to mount larger antennas lower, and to design the ship to minimize blockage. This is “The UNIMAST Concept,” which argues for a single mast on which are mounted all the ship's major rotating surveillance antennas. The larger antennas rotate around the lower part of the mast, while lighter antennas, e.g., surface search, are sited above. This paper discusses the degradation of sidelobes due to present topside design and numerically relates degradation to Electronic Counter-Countermeasures (ECCM) performance. Removal of that degradation via the UNIMAST Concept requires that a device known as an Annular Rotary Coupler (ARC) be used. The development of just such a high power, wide-band ARC on a Navy-sponsored R&D contract is herein described. Also described is the potential backfitting of the UNIMAST Concept to existing ships; e.g., the DDG-993. Battle damage vulnerability of the UNIMAST Concept with respect to a conventional two mast design is addressed. It is argued that the UNIMAST Concept affords no degradation in vulnerability due to improved potential for protecting vital antenna parts.

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Uncovering the HOXA9 Translational Regulatory Complex That Promotes AML Leukemic Stem Cells

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Blood 2024年 144卷 4106-4106页

作者： Xueqin Xie Florisela Herrejon Chavez Ilyes Baali Eren L. Chu Chiara Evans Xuejing Yang Wei Wei Hanzhi Luo Sun Mi Park Kathryn Chang Aspen Pierson Grace Han Emily Batchelor Quaid D. Morris Ly Vu Diu T.T. Nguyen Michael G. Kharas Molecular Pharmacology Program Memorial Sloan Kettering Cancer Center New York NY Memorial Sloan Kettering Cancer Center NY Weill Cornell Graduate School of Medical Sciences NY Memorial Sloan Kettering Cancer Center New York Molecular Pharmacology Program Center for Cell Engineering Center for Stem Cell Biology Center for Experimental Therapeutics Center for Hematologic Malignancies Memorial Sloan Kettering Cancer Center New York City NY Memorial Sloan Kettering Cancer Center ny Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York Memorial Sloan-Kettering Cancer Center Vancouver Canada The University of British Columbia Vancouver Canada Simon Fraser University Vancouver Canada Center for Hemato-Oncology Barts Cancer Institute Queen Mary University of London London United Kingdom

HOXA9 is a master transcription factor of hematopoiesis and essential for maintaining self-renewal of leukemia stem cells (LSCs). Although mechanisms associated with its transcriptional regulation are extensively studied, how Hoxa9 mRNA translation is controlled remain poorly understood. We have previously identified the RNA binding protein (RBP) MUSASHI-2 (MSI2) as a central regulator of myeloid LSCs by controlling translation of crucial transcription factors including Hoxa9 (Park et al. JCI, 2015; Nguyen et al. Nature Comm, 2020) . However, the mechanisms by which HOXA9 translation is modulated and the role of MSI2 remain unknown. To characterize the HOXA9 3'UTR mRNA regulon, we used it as a bait to perform an RNA-pull down followed by mass spectrometry (MS) with control or MSI2 depleted cells. To determine the direct MSI2's protein interactors on HOXA9 , we also performed MSI2 co-immunoprecipitation (co-IP) MS in control or MSI2 deficient AML cells. We identified 10 RBPs that directly bind to MSI2 and are dependent on MSI2 for their binding to the HOXA9 -3'UTR mRNA. Among these, we focused on SYNCRIP, a known MSI2 interactor ( Vu et al. Nat Gen , 2017 ), HNRNPC and MOV10, of which binding ability on HOXA 9 3'UTR was most reduced and enhanced, respectively, upon MSI2 loss. Reciprocal co-IP confirmed the interactions between these RBPs with MSI2. We then reasoned that if these RBPs are in the same regulatory complex with MSI2, they might phenocopy MSI2 loss of function in LSCs. To understand how each selected factor impacts LSC function and gene control, we first assessed MSI2's global regulation by performing integrative omic studies including MSI2-HyperTRIBE, RNA-seq and proteomics in MLL-AF9 murine LSCs that have acutely deleted (68hrs) of Msi2. We found that MSI2 binding promotes translation of 264 genes while suppresses 8 genes; and only 10 genes affected at mRNA level. These data found that MSI2 mediates translation of the self-renewal program in LSCs. We the

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