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IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming

BIOINFORMATICS 2011年第13期27卷 I85-I93页

作者： Sato, Kengo Kato, Yuki Hamada, Michiaki Akutsu, Tatsuya Asai, Kiyoshi Univ Tokyo Grad Sch Frontier Sci Chiba 2778561 Japan Nara Inst Sci & Technol Grad Sch Informat Sci Nara 6300192 Japan Kyoto Univ Bioinformat Ctr Inst Chem Res Kyoto 6110011 Japan Natl Inst Adv Ind Sci & Technol CBRC Koto Ku Tokyo 1350064 Japan

Motivation: Pseudoknots found in secondary structures of a number of functional RNAs play various roles in biological processes. Recent methods for predicting RNA secondary structures cover certain classes of pseudoknotted structures, but only a few of them achieve satisfying predictions in terms of both speed and accuracy. Results: We propose IPknot, a novel computational method for predicting RNA secondary structures with pseudoknots based on maximizing expected accuracy of a predicted structure. IPknot decomposes a pseudoknotted structure into a set of pseudoknot-free substructures and approximates a base-pairing probability distribution that considers pseudoknots, leading to the capability of modeling a wide class of pseudoknots and running quite fast. In addition, we propose a heuristic algorithm for refining base-paring probabilities to improve the prediction accuracy of IPknot. the problem of maximizing expected accuracy is solved by using integer programming with threshold cut. We also extend IPknot so that it can predict the consensus secondary structure with pseudoknots when a multiple sequence alignment is given. IPknot is validated through extensive experiments on various datasets, showing that IPknot achieves better prediction accuracy and faster running time as compared with several competitive prediction methods.

关键词： Algorithms Nucleic Acid Conformation* RNA/chemistry* Sequence Analysis, RNA Software*

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Uncertain: a first-order type for uncertain data 14

Uncertain<T>: a first-order type for uncertain data

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Proceedings of the 19th international conference on Architectural support for programming languages and operating systems

作者： James Bornholt Todd Mytkowicz Kathryn S. McKinley Australian National University Canberra Australia Microsoft Research Redmond WA USA

ISBN: (纸本)9781450323055

Emerging applications increasingly use estimates such as sensor data (GPS), probabilistic models, machine learning, big data, and human data. Unfortunately, representing this uncertain data with discrete types (floats, integers, and booleans) encourages developers to pretend it is not probabilistic, which causes three types of uncertainty bugs. (1) Using estimates as facts ignores random error in estimates. (2) Computation compounds that error. (3) Boolean questions on probabilistic data induce false positives and negatives. this paper introduces Uncertain, a new programming language abstraction for uncertain data. We implement a Bayesian network semantics for computation and conditionals that improves program correctness. the runtime uses sampling and hypothesis tests to evaluate computation and conditionals lazily and efficiently. We illustrate with sensor and machine learning applications that Uncertain improves expressiveness and *** previous probabilistic programming languages focus on experts, Uncertain serves a wide range of developers. Experts still identify error distributions. However, both experts and application writers compute with distributions, improve estimates with domain knowledge, and ask questions with conditionals. the Uncertain type system and operators encourage developers to expose and reason about uncertainty explicitly, controlling false positives and false negatives. these benefits make Uncertain a compelling programming model for modern applications facing the challenge of uncertainty.

关键词： uncertain data estimates probabilistic programming

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thz and microwave properties of 3D-printed nanocarbon based multilayers 19

THz and microwave properties of 3D-printed nanocarbon based ...

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19th international conference on Electromagnetics in Advanced Applications (ICEAA)

作者： Kuzhir, P. Paddubskaya, A. Volynets, N. Kotsilkova, R. Ivanov, E. Biro, I. Mark, G. I. Biro, L. P. Maksimenko, S. Belarusian State Univ Inst Nucl Problems Minsk BELARUS Bulgarian Acad Sci Inst Mech Open Lab Expt Micro & Nano Mech Sofia Bulgaria NanoTech Lab Ltd Sofia Bulgaria 3D Wishes Birou Hungary Ctr Energy Res Inst Tech Phys & Mat Sci Ctr Energy Res Budapest Hungary

ISBN: (纸本)9781509044511

We propose a new type of light-weight conductive thin film material having good mechanical properties and electromagnetic shielding efficiency. For that 3D printing through layer-to-layer deposition of nanocarbon containing plastic layers and neat polymer layers was combined with hot pressing to obtain 10 mu m thick films. We show that such composite has Re epsilon = Im epsilon in very broad frequency range, 200GHz - 0.6 thz.

关键词： three-dimensional displays Pressing Programmable logic arrays Mechanical factors Polymers Dielectrics Graphene

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20 kV, 2 cm2, 4H-SiC gate turn-off thyristors for advanced pulsed power applications

20 kV, 2 cm2, 4H-SiC gate turn-off thyristors for advanced p...

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international conference on Pulsed Power

作者： L. Cheng A. K. Agarwal C. Capell M. O'Loughlin K. Lam J. Richmond Edward Van Brunt A. Burk J. W. Palmour H. O'Brien A. Ogunniyi C. Scozzie Cree Inc. Durham North Carolina USA U S. Army Research Laboratory Adelphi MD USA

the need for high voltage solid-state power electronic devices for advanced power distribution and energy conversion has grown rapidly in recent years, especially for pulsed power applications that require high turn-on di/dt. However, current power converters built with silicon (Si) switches are quite bulky and inefficient, making their utilization difficult in practical energy conversion and power distribution systems. the development of high-voltage power devices based on wide bandgap semiconductor such as silicon carbide (SiC) has attracted great attention due to its superior material properties over silicon. Among the high-voltage SiC power devices, SiC gate turn-off thyristor (GTO) offers excellent current handling, very high voltage blocking, and fast turn-off capabilities. SiC GTO also exhibits lower forward voltage drop than the IGBT-based switch at high injection-level currents, resulting in lower power losses during normal operation. In this paper, we report our recently developed 2 cm 2 , 20 kV SiC p-type gate turnoff GTO thyristor with very low differential on-resistance for advanced pulsed power applications.

关键词： Silicon carbide logic gates Silicon Charge carrier lifetime Insulated gate bipolar transistors thyristors Anodes

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Design and development of a 6.25 kV/1 kA PFN to supply the new PS Booster distributor magnets

Design and development of a 6.25 kV/1 kA PFN to supply the n...

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international conference on Pulsed Power

作者： R. Rosol P. Adraktas R. A. Barlow E. Carlier L. Ducimetière P. Faure A. Fowler J. Schipper L. Sermeus M. Stjepic CERN Geneva Switzerland

Linac4 is an H - ion linear accelerator at CERN, intended to replace Linac2 as injector to the PS Booster (PSB). In order to distribute the 160 MeV beam from Linac4 to the four rings of the PSB, new distributor magnets (***) and magnetic septa (***) need to be built. the proposed distribution scheme requires the construction of five new pulse generators of Pulse Forming Network (PFN) type, to double the magnitude of the *** field pulse and to increase the maximum duration of the pulse from 140 μs to 620 μs. A prototype PFN featuring 60 cells assembled in a Guillemin type E network was built. A PFN impedance of 6.25 Ω was chosen in order to achieve a magnetic field rise time of 1 μs (1 %-99 %) and a current amplitude of 1 kA in the lumped inductance magnet with a flat top ripple of ± 1%. the nominal operating voltage of 6.25 kV (maximum of 10 kV) and the repetition rate of 1.1 Hz allow operation in air. A switch comprising two commercial IGBTs connected in series will be used to initiate the transfer of the energy from the PFN to the magnet. this document presents the design of the new PFN and the measurements performed with switches from four different suppliers. IGBT rise time improvements, synchronization problems and ideas for timing drift stabilization are discussed. the general layout of the foreseen control system is shown.

关键词： Insulated gate bipolar transistors Optical switches logic gates Inductors Voltage measurement Inductance

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Restricted optical proximity effect correction pattern generation based on optical proximity effect correction-design for manufacturability rule in model-based optical proximity effect correction: Application for metal layer in complementary metal-oxide-semiconductor logic process

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JAPANESE JOURNAL OF APPLIED PHYSICS PART 1-REGULAR PAPERS BRIEF COMMUNICATIONS & REVIEW PAPERS 2007年第9B期46卷 6140-6144页

作者： Harazaki, Katsuhiko Yoshioka, Tasuku Ohmori, Kiyoshige Satoh, Masayuki Kawamura, Akio Sharp Co Ltd Elect Components & Devices Dev Grp Adv Technol Dev Labs Nara 6328567 Japan

In the recent submicron technologies, the pattern formation on photomasks is increasing in its difficulty owing to the complexity of optical proximity effect correction (OPC) and resolution enhancement techniques (RET). the detection and repair of critical patterns after OPC or RET have become essential procedures for photomask preparation, and design rule check (DRC) or lithography simulation tools have often been used to verify these patterns. However, the detection and repair of critical patterns have been becoming an excessive burden in the development of lithography processes and mask data processing. In this paper, we describe how to detect and repair these OPC critical patterns in lithography using the OPC-DFM rule, which can be derived from the OPC extraction test element group (TEG) effectively and easily. this technology enables the removal of OPC critical patterns before photomask preparation.

关键词： optical proximity effect correction simulation lithography design for manufacturability

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Characterization of commercial IGBT modules for pulsed power applications

Characterization of commercial IGBT modules for pulsed power...

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international conference on Pulsed Power

作者： W. Hartmann R. Fleck R. Graba M. Hergt Siemens AG Erlangen Germany

An analysis of commercial semiconductor switches favors the IGBT for pulsed power applications, in particular for high average power, high pulse repetition rate applications, due to its availability based on its widespread use in drive applications. High power IGBT modules rated at 6.5 kV/700 A of two different technologies have been investigated in this work: the planar technology and the trench technology. Both types of semiconductor switches were tested in a special low inductance setup to characterize the IGBT for pulsed power applications. A dedicated gate drive unit enables the IGBT to generate fast rise times for the collector current and fast fall times for the collector - emitter voltage. the IGBT with planar technology [1] was characterized at a DC link voltage of 4 kV and a peak current of 2 kA. the switching time of the IGBT stays in the region of 200 ns (t fall time(20-80%) ) of the collector-emitter voltage, while the rise time of the collector current is 160ns (t rise time(10-90%) ) with peak power losses of 1.41MW. this allows to use the IGBT at higher pulse repetition rates (PRF) up to 2 kHz, at a pulse duration of 1 μs. the IGBT with trench technology [2] shows gate voltage oscillations at peak currents above 1 kA, which infers that the gate source capacitance will be slowly destroyed by overvoltage spikes. In addition, minimizing the on-state losses by using higher gate voltages is not possible due to this effect. It is thus concluded that the planar technology is preferable for pulsed power applications, in particular for hard-wired configurations to achieve higher peak currents [3] and in IVA concepts [4], eventually using solid-state switching technology.

关键词： Insulated gate bipolar transistors logic gates Resistance Resistors Delays Inductance Switches

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Semi-planar power combiner structure for IGBT-based pulsed power modulators

Semi-planar power combiner structure for IGBT-based pulsed p...

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international conference on Pulsed Power

作者： W. Hartmann R. Fleck R. Graba M. Hergt Corporate Technology Siemens AG Erlangen Germany Healthcare Siemens AG Erlangen Germany Healthcare Corporate Technology Erlangen Germany

A semi-planar, rotationally symmetric power combiner has been realized using a hard-wired parallel circuit of four power transfer stages which feed into a common radial transmission line. For testing purposes, the radial transmission line is terminated with a matched ohmic resistor. the power combiner is designed to produce a double exponential pulse by optimizing the transmission line geometry with the help of electrodynamic modeling using CST Microwave Suite. Each of the four stages contains three parallel capacitors of 200nF each, the geometrical circuit inductance, a switch, and are discharged into the common resistive load. the switch is realized with an industrial type IGBT module, at a DC link voltage of up to 4.5 kV. Lifetime estimations show a permissible peak current of up to 2kA for a single IGBT module, at pulse durations of around 1 μs. Hence, a peak current of over 6 kA can be achieved by paralleling four of these power transfer stages in the semi-planar power combiner structure. First experimental results show that the semi-planar power combiner is a suitable functional unit for pulsed power applications. the circuit was characterized at a DC link voltage of up to 4 kV, a peak current of 1.68kA, and a pulse duration of 1μs per IGBT module. the low switching losses of the IGBT when using a hard gate drive allow using the IGBT at high pulse repetition rates (PRF) up to kHz, at pulse durations around 1μs. the circuit presented is suitable to be used as a modular component of an inductive voltage adder to increase the available voltage and peak power levels, respectively.

关键词： Insulated gate bipolar transistors Power combiners Switches Resistors logic gates Jitter Current measurement

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DSML4JaCaMo: A Modelling tool for Multi-agent programming with JaCaMo

DSML4JaCaMo: A Modelling tool for Multi-agent Programming wi...

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Federated conference on Computer Science and Information Systems (FedCSIS)

作者： Burak Karaduman Baris Tekin Tezel Geylani Kardas Moharram Challenger Department of Computer Science University of Antwerp and Flanders Make Antwerp Belgium Department of Computer Science Dokuz Eylul University Izmir Türkiye International Computer Institute Ege University Izmir Türkiye

ISBN: (数字)9788396960160

ISBN: (纸本)9798350359718

this paper introduces a domain-specific modelling language (DSML) called DSML4JaCaMo to develop belief-desire-intention (BDI) agents. the DSML’s design covers aspects of Jason, Cartago, and Moise from viewpoints that follow the meta-modelling approach. In this way, the DSML4JaCaMo enables graphical modelling of JaCaMo’s multi-agent systems (MASs), providing comprehensive support for defining agents’ beliefs, desires, and intentions (BDI) using Jason, specifying artifacts and their operations with Cartago, and outlining organizational structures and norms via Moise. the DSML’s operational semantics ensure seamless integration of these components, facilitating automatic code generation and artifact construction for creating a JaCaMo-based system. the graphical syntax contributes to ease of use, making it accessible for novice and experienced developers. this work aims to enhance the JaCaMo ecosystem by offering a model-driven approach to provide abstraction on MAS development as well as facilitating design and implementation.

关键词： Codes Systematics Biological system modeling Semantics Ecosystems Syntactics programming Complexity theory Usability Multi-agent systems

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Learnability in information design 01

Learnability in information design

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Proceedings of the 19th annual international conference on Computer documentation

作者： Kathy Haramundanis Compaq Computer Corporation Nashua NH

ISBN: (纸本)9781581132953

Design of information used for technical communication of complex products should consider how learnable that information is, and strive to deliver materials that are inherently *** speed of information interchange and the demands of the workplace and school curricula require increasingly minimalist approaches to the material that is made available. People are frustrated by long learning times, and new users of software tools demand rapid absorption of tool capabilities. In addition, many readers of technical information are people for whom English is not their native *** and practices that worked in the period when people were willing to commit to hours of study to understand a topic, or days of practice to master a tool, no longer work in a world based on ?internet time.? To assist our understanding of these trends in learning, this paper addresses three key areas related to learnability: proposing a definition of learnability, showing where learnability and usability intersect, and providing a basis for learnability based on some attributes of human beings.

关键词： information development guidelines information design mathematics learnability logic heuristic model learning times cognitive science

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