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International Joint Conference on Computer science and Software engineering

作者： Miyamura, Hiroko Nakamura Ohzahata, Satoshi Shinano, Yuji Miyashiro, Ryuhei Center for Computational Science and E-systems Japan Atomic Energy Agency Tokyo Japan Graduate School of Information Systems University of Electro-Communications Chofu Tokyo Japan Discrete Mathematics Department Optimization Zuse Institute Berlin Berlin Germany Institute of Engineering Tokyo University of Agriculture and Technology Koganei Tokyo Japan

ISBN: (纸本)9781457706875

This paper proposes an adaptive visualization technique for representing a large-scale hierarchical dataset within a limited display space. A hierarchical dataset has nodes and links that reveal the parent-child relationship between the nodes. These nodes and links are described using graphics primitives. When the number of these primitives is large, it is difficult to recognize the structure of the hierarchical data because several primitives overlap within a display space. In order To overcome this difficulty, we propose an adaptive visualization technique for hierarchical datasets. The proposed technique selects an appropriate graph style according to the nodal density in each area. © 2011 IEEE.

关键词： Forestry

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Synthesis of stable silica-dye hybrid nanomaterial as DNA carrier

Synthesis of stable silica-dye hybrid nanomaterial as DNA ca...

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作者： Lee, Kyoung G. Kim, Jin Chul Wi, Rinbok Min, Jung Sun Ahn, Jeong Keun Kim, Do Hyun Department of Chemical and Biomolecular Engineering Center for Ultramicrochemical Process Systems Korea Advanced Institute of Science and Technology 373-1 Guseong-dong Yuseong-gu Daejeon 305-701 Korea Republic of Department of Microbiology Chungnam National University 220 Gung-dong Yuseong-gu Daejeon 305-764 Korea Republic of

A new method is proposed for the fabrication of fluorescence-labeled and amine-modified silica nanoparticles for application as nonviral vectors in gene delivery. Highly monodisperse, stable fluorescent silica nanoparticles were prepared using 2,5-bis(5-tert-butyl-2-benzoxazolyl)thiophene and the water-in-oil microemulsion method. The green-fluorescent-protein gene can be easily combined onto the positively charged surfaces of nanoparticles to form a nanoparticle-DNA complex. The nanoparticle-DNA complex successfully passed through various barriers into the HeLa and HEK 293 K cells. The cytotoxicity of the PEI-coated and BBOT-encapsulated silica nanoparticles on both the HeLa and HEK 293T cell lines was found to be at an acceptable level for use as gene carriers when the particle concentration was below 125 μg/ml. The fluorescence intracellular images confirm the successful delivery of the nanoparticle-DNA complex and gene expression. The present work suggests the potential use of dye-incorporated silica nanoparticles in nonviral gene delivery. Copyright © 2011 American Scientific Publishers All rights reserved.

关键词： Silica nanoparticles

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Sonochemical preparation of silica nanorods for gene delivery using single-walled carbon nanotubes as templates

Sonochemical preparation of silica nanorods for gene deliver...

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作者： Lee, Kyoung G. Min, Jung Sun Wi, Rinbok Kim, Jin Chul Ahn, Jeong Keun Kim, Do Hyun Department of Chemical and Biomolecular Engineering Center for Ultramicrochemical Process Systems Korea Advanced Institute of Science and Technology 373-1 Guseong-dong Yuseong-gu Daejeon 305-701 Korea Republic of Department of Microbiology Chungnam National University 220 Gung-dong Yuseong-gu Daejeon 305-764 Korea Republic of

Silica nanorods were fabricated with single-walled carbon nanotubes (SWCNTs) via ultrasound. The diameter of the resulting SWCNT-silica particles ranged from 60 to 70 nm. The morphology of this composite material was investigated via scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The individual SWCNTs are uniformly coated with silica and formed a unique nanocomposite material. The important role of ultrasound and the mechanism of silica layer formation on SWCNTs were explained via the hydrolysis of the silica source and the adsorption of the siloxane groups on the SWCNT surfaces under ultrasound irradiation. The amino-functionalized silica nanorods were demonstrated as non-viral vectors for gene delivery. Copyright © 2011 American Scientific Publishers All rights reserved.

关键词： Silica

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Dislocation-Pairing Transitions in Hot Grain Boundaries

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Physical Review Letters 2011年第4期106卷 046101-046101页

作者： David L. Olmsted Dorel Buta Ari Adland Stephen M. Foiles Mark Asta Alain Karma Department of Materials Science and Engineering University of California Berkeley California USA Department of Chemical Engineering and Materials Science University of California Davis California USA Department of Physics and Center for Interdisciplinary Research on Complex Systems Northeastern University Boston Massachusetts USA Computational Materials Science and Engineering Department Sandia National Laboratories Albuquerque New Mexico USA Materials Science Division Lawrence Berkeley National Laboratory Berkeley California USA

We report the finding of a novel grain-boundary structural phase transition in both molecular-dynamics and phase-field-crystal simulations of classical models of bcc Fe. This transition is characterized by pairing of individual dislocations with mixed screw and edge components. We demonstrate that this type of transition is driven by a combination of factors including elastic softening, core interaction, and core disordering. At high homologous temperatures the occurrence of this transition is shown to prevent premelting at misorientation angles where it would otherwise be expected.

关键词： Grain boundaries

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Agile parallel bioinformatics workflow management using Pwrake

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BMC Research Notes 2011年第1期4卷 1-8页

作者： Mishima, Hiroyuki Sasaki, Kensaku Tanaka, Masahiro Tatebe, Osamu Yoshiura, Koh-Ichiro Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences Nagasaki Nagasaki 1-12-4 Sakamoto Japan Nagasaki University Global Center of Excellence Program Nagasaki Nagasaki 1-12-4 Sakamoto Japan Center for Computational Sciences University of Tsukuba Tsukuba Ibaraki 1-1-1 Tennodai Japan Core Research for Evolutional Science and Technology Japan Science and Technology Agency Kawaguchi Saitama 4-1-8 Honcho Japan Departmentent of Computer Science Graduate School of Systems and Information Engineering University of Tsukuba Tsukuba Ibaraki 1-1-1 Tennodai Japan

Background: In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error. Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. Findings. We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Conclusions: Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability

关键词： Ruby Iterative Development Agile Software Development Host Language Bioinformatics Domain

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Self-organization in social tagging systems

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Physical Review E 2011年第6期83卷 066104-066104页

作者： Chuang Liu Chi Ho Yeung Zi-Ke Zhang School of Business East China University of Science and Technology Shanghai 200237 China Engineering Research Center of Process Systems Engineering (Ministry of Education) East China University of Science and Technology Shanghai 200237 China Department of Physics University of Fribourg CH-1700 Fribourg Switzerland The Nonlinearity and Complexity Research Group Aston University Birmingham B4 7ET United Kingdom Web Sciences Center University of Electronic Science and Technology of China Chengdu 610054 China

Individuals often imitate each other to fall into the typical group, leading to a self-organized state of typical behaviors in a community. In this paper, we model self-organization in social tagging systems and illustrate the underlying interaction and dynamics. Specifically, we introduce a model in which individuals adjust their own tagging tendency to imitate the average tagging tendency. We found that when users are of low confidence, they tend to imitate others and lead to a self-organized state with active tagging. On the other hand, when users are of high confidence and are stubborn to change, tagging becomes inactive. We observe a phase transition at a critical level of user confidence when the system changes from one regime to the other. The distributions of post length obtained from the model are compared to real data, which show good agreement.

关键词： TAGS (Metadata) IMITATION SOCIAL interaction CONFIDENCE BEHAVIOR

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Effect of micro voids on stress triaxiality-plastic strain states of notched steels

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Procedia engineering 2011年 10卷 1433-1439页

作者： Zhiguang Zhou Hitoshi Kuwamura Akemi Nishida Center for Computational Science and e-Systems Japan Atomic Energy Agency6-9-3 HigashiuenoTaito-ku Tokyo 110-0015 Japan Department of Architecture School of Engineering the University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan

Brittle fracture of structural steel for building use, in general, is triggered by a ductile crack initiated at notched surface after undergoing a noticeable amount of plastic strain. The initiation of the ductile crack correlates to the stress triaxiality-plastic strain states in the notched section. As stress triaxiality and plastic strain are usually derived from finite element analysis, two material models with voids (Gurson-Tvergaard-Needleman model) and without voids (Mises model) are used to do the analyses to study the stress triaxiality-plastic strain states in notched steels. The results show that the effect of micro voids on stress triaxiality-plastic strain states of notched steels is small until stability limit and become significant gradually after stability limit.

关键词： Stress triaxiality ductile crack equivalent plastic strain notch FEA (Finite Element Analysis)

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Spherical interpolation over graphic processing units

Spherical interpolation over graphic processing units

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ACM SIGSPATIAL 2nd International Workshop on High Performance and Distributed Geographic Information systems, ACM SIGSPATIAL HPDGIS 2011

作者： Ye, Fei Shi, Xuan Wang, Shaowen Liu, Yan Han, Su Yeon School of Computational Science and Engineering College of Computing Georgia Institute of Technology Atlanta GA United States Center for Geographic Information Systems College of Architecture Georgia Institute of Technology Atlanta GA United States University of Illinois at Urbana-Champaign Urbana IL United States Department of Geography University of Illinois at Urbana-Champaign Urbana IL United States University of Illinois at Urbana-Champaign Urbana IL United States

ISBN: (纸本)9781450310406

Spatial interpolation is a widely used GIS function for estimating values at locations where observed values are not available or adequate. One popular method for spatial interpolation is inverse distance weighted, which calculates estimated values based on a weighted sum of the values of a number of nearest neighbors that have observed values. This research focuses on solving a large-scale interpolation problem with a global coverage based on the inverse distance weighted method. Specifically, spherical distance is calculated instead of normal Euclidean distance commonly used in GIS software, which is necessary to find correct neighbors in the regions along the 180° longitude and in the polar areas. The computation of the global-scale interpolation based on spherical distance is intensive especially for achieving high-resolution results. This paper introduces how to accelerate such computation by exploiting massive parallelism provided by Graphic processing Units (GPUs) with significant improvement of computational performance reported. © 2011 ACM.

关键词： Graphics processing unit

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Adaptive view-dependent tree graph visualization

Adaptive view-dependent tree graph visualization

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International Joint Conference on Computer science and Software engineering (JCSSE)

作者： Hiroko Nakamura Miyamura Satoshi Ohzahata Yuji Shinano Ryuhei Miyashiro Center of Computational Science & E-systems Japan Atomic Energy Agency Tokyo Japan Graduate School of Information Systems University of Electro-Communications Chofu Tokyo Japan Discrete Mathematics Department Optimization Zuse Institute Berlin Berlin Germany Institute of Engineering Tokyo University of Agriculture슠and슠Technology Koganei Tokyo Japan

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Tag-based User Topic Discovery Using Twitter Lists

Tag-based User Topic Discovery Using Twitter Lists

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International Conference on Advances in Social Network Analysis and Mining, ASONAM

作者： Yuto Yamaguchi Toshiyuki Amagasa Hiroyuki Kitagawa Graduate School of Systems and Information Engineering University of Tsukuba Tsukuba Ibaraki Japan Institute of Space and Astronautical Science Japan AeroSpace Exploration Agency Sagamihara Kanagawa Japan Center for Computational Sciences University of Tsukuba Tsukuba Ibaraki Japan Tsukuba Daigaku Tsukuba Ibaraki JP

In this paper, we address the problem of tagging users in Twitter, one of the most popular micro-blogging services. There are growing needs to get useful information from Twitter, because an enormous amount of information is transmitted in real time. Twitter users, who play an important role as information sources, typically transmit information about some particular topics which they are interested in. Therefore, to identify useful information, it is very important to know which topics a user tends to transmit. In this paper, we propose a method to discover appropriate topics for a user by using Twitter list. Twitter list is an official functionality to make a"user list, " list members tend to transmit information about the topic represented in the name of the list. From this observation, our idea is to extract tags from list names, and exploit the relationship among lists, tags extracted from the list names, and list members. Experimental results show the effectiveness of the proposed method.

关键词： Twitter Tagging Meteorology Feature extraction Mutual information Correlation Mathematical model

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