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Efficient Lock Algorithm for Shared Objects in SMP Environments SMP环境下共享对象的高效锁算法
Pub Date : 2006-12-15 DOI: 10.2197/IPSJDC.2.759
T. Ogasawara, H. Komatsu, T. Nakatani
We propose a new algorithm that is effective for objects that are shared among threads but are not contended for in SMP environments. We can remove the overhead of the serialization between lock and other non-lock operations and avoid the latency of complex atomic operations in most cases. We established the safety of the algorithm by using a software tool called Spin. The experimental results from our benchmarking on an SMP machine using Intel Xeon processors revealed that our algorithm could significantly improve efficiency by 80% on average compared to using complex atomic instruction.
我们提出了一种新的算法,该算法对线程之间共享但在SMP环境中不争用的对象有效。我们可以消除锁和其他非锁操作之间序列化的开销,并在大多数情况下避免复杂原子操作的延迟。我们通过使用一个名为Spin的软件工具来建立算法的安全性。我们在使用Intel至强处理器的SMP机器上进行基准测试的实验结果表明,与使用复杂的原子指令相比,我们的算法可以显着提高效率,平均提高80%。
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引用次数: 0
Combfit: A Normalization Method for Array CGH Data Combfit:一种阵列CGH数据的归一化方法
Pub Date : 2006-11-15 DOI: 10.2197/IPSJDC.2.716
Shigeyuki Oba, N. Tomioka, M. Ohira, S. Ishii
The recently developed array-based comparative genomic hybridization(array CGH) technique measures DNA copy number aberrations that occur as causes or consequences of cell diseases such as cancers. Conventional array CGH analysis classifies DNA copy number aberrations into three categories: no significant change, significant gain, and significant loss. However, recent improvements in microarray measurement precision enable more quantitative analysis of copy number aberrations. We propose a method, called comb fitting, that extracts a quantitative interpretation from array CGH data. We also propose modifications that allow us to apply comb fitting to cases featuring heterogeneity of local aberrations in DNA copy numbers. By using comb fitting, we can correct the baseline of the fluorescence ratio data measured by array CGH and simultaneously translate them into the amount of changed copy numbers for each small part of the chromosome, such as 0, ±1, ±2, ···. Comb fitting is applicable even when a considerable amount of contamination by normal cells exists and when heterogeneity in the ploidy number cannot be neglected.
最近开发的基于阵列的比较基因组杂交(array CGH)技术可以测量DNA拷贝数畸变,这些畸变是癌症等细胞疾病的原因或后果。传统的阵列CGH分析将DNA拷贝数畸变分为三种类型:无显著变化、显著增加和显著损失。然而,最近微阵列测量精度的提高使拷贝数畸变的定量分析成为可能。我们提出了一种称为梳状拟合的方法,从阵列CGH数据中提取定量解释。我们还提出了一些修改,使我们能够将梳状拟合应用于DNA拷贝数局部畸变异质性的情况。通过梳状拟合,我们可以对阵列CGH测得的荧光比数据进行基线校正,同时将其转化为染色体各小部分拷贝数的变化量,如0、±1、±2、···。即使存在相当数量的正常细胞污染,当倍性数目的异质性不能被忽视时,梳状拟合也适用。
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引用次数: 2
Individual Differences in Gene Expression in Primary Cultured Renal Cortex Cells Derived from Japanese Subjects 日本人原代培养肾皮质细胞基因表达的个体差异
Pub Date : 2006-11-15 DOI: 10.2197/IPSJDC.2.710
A. Sasaki, Y. Oshima, Saeko Kishimoto, Akio Fujimura
We used microarrays to examine individual-based differences in gene expression in primary cultures of renal tubular cells derived from Japanese subjects. The subjects had solitary tumors in the kidney or urinary tract, which were diagnosed pathologically as renal cell carcinoma or transitional cell carcinoma. Renal tissue samples collected from a non-tumorous portion of the tissue were regarded as normal tissues, as there were no abnormal microscopic findings and no evidence of renal dysfunction from the clinical laboratory data. The genome-wide gene expression profiles of nine human renal cell cultures were analyzed using the Affymetrix GeneChip HG-U133A and HG-U133B arrays. Approximately 8, 500 transcripts exhibited significant differential expression (p < 0.05) among the subjects, and the coefficients of variation for 1, 338 transcripts were greater than 50%. Some of these transcripts encode drug-metabolizing enzymes (e.g., UGT1A8 and UGT1A9) or sodium/phosphate cotransporters (e.g., PDZK1). These data provide the basis for toxicogenomic studies using primary cultured renal cortical cells from Japanese subjects.
我们使用微阵列来检测源自日本受试者的肾小管细胞原代培养中基因表达的个体差异。患者均为肾或尿路单发肿瘤,病理诊断为肾细胞癌或移行细胞癌。从组织的非肿瘤部分采集的肾组织样本被认为是正常组织,因为从临床实验室数据来看,没有异常的显微镜发现和肾功能障碍的证据。采用Affymetrix基因芯片HG-U133A和HG-U133B阵列分析了9个人肾细胞培养物的全基因组基因表达谱。约有8500个转录本在被试中表现出显著差异表达(p < 0.05),其中1338个转录本变异系数大于50%。其中一些转录物编码药物代谢酶(如UGT1A8和UGT1A9)或钠/磷酸盐共转运蛋白(如PDZK1)。这些数据为利用原代培养的日本受试者肾皮质细胞进行毒性基因组学研究提供了基础。
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引用次数: 0
Program Transformation by Templates: A Rewriting Framework 模板程序转换:一个重写框架
Pub Date : 2006-11-15 DOI: 10.2197/IPSJDC.2.620
Yuki Chiba, Takahito Aoto, Y. Toyama
y We propose a framework in this paper for transforming programs with templates based on term rewriting. The programs are given by term rewriting systems. We discuss how to validate the correctness of program transformation within our framework. We introduce a notion of developed templates and a simple method of constructing such templates without explicit use of induction. We then show that in any transformation of programs using the developed templates, their correctness can be verifled automatically. The correctness of pro- gram transformation within our framework is discussed based on operational semantics. We also present some examples of program transformations in our framework.
我们提出了一个基于术语重写的模板程序转换框架。程序是由术语重写系统给出的。我们讨论了如何在我们的框架内验证程序转换的正确性。我们引入了一个已开发模板的概念和一种无需显式使用归纳法来构造这样的模板的简单方法。然后我们表明,在使用开发的模板的任何程序转换中,它们的正确性都可以自动验证。从操作语义的角度讨论了框架内程序转换的正确性。我们还在我们的框架中提供了一些程序转换的示例。
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引用次数: 5
A Method for Species Comparison of Metabolic Networks Using Reaction Profile 一种利用反应谱进行代谢网络物种比较的方法
Pub Date : 2006-11-15 DOI: 10.2197/IPSJDC.2.685
Y. Tohsato
Comparative analyses of the metabolic networks among different species provide important information regarding the evolution of organisms as well as pharmacological targets. In this paper, a method is proposed for comparing metabolic networks based on enzymatic reactions within different species. Specifically, metabolic networks are handled as sets of enzymatic reactions. Based on the presence or absence of metabolic reactions, the metabolic network of an organism is represented by a bit string comprised of the digits “1” and “0, ” called the “reaction profile.” Then, the degree of similarity between bit strings is defined, followed by clustering of metabolic networks by different species. By applying our method to the metabolic networks of 33 representative organisms selected from bacteria, archaea, and eukaryotes in the MetaCyc database, a phylogenetic tree was reconstructed that represents the similarity of metabolic network based on metabolic phenotypes.
不同物种间代谢网络的比较分析为生物进化和药理靶点提供了重要信息。本文提出了一种比较不同物种体内酶促反应代谢网络的方法。具体来说,代谢网络是作为一系列酶促反应来处理的。根据代谢反应的存在与否,生物体的代谢网络由数字“1”和“0”组成的位串表示,称为“反应概况”。然后,定义位串之间的相似度,然后对不同物种的代谢网络进行聚类。通过将我们的方法应用于MetaCyc数据库中从细菌、古细菌和真核生物中选择的33种具有代表性的生物的代谢网络,构建了一个基于代谢表型的代表代谢网络相似性的系统发育树。
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引用次数: 8
Classification Method for Predicting the Development of Myocardial Infarction by Using the Interaction between Genetic and Environmental Factors 利用遗传与环境因素相互作用预测心肌梗死发展的分类方法
Pub Date : 2006-11-15 DOI: 10.2197/IPSJDC.2.691
Yasuyuki Tomita, H. Asano, H. Izawa, M. Yokota, Takeshi Kobayashi, H. Honda
Multifactorial diseases, such as lifestyle-related diseases, for example, cancer, diabetes mellitus, and myocardial infarction, are believed to be caused by the complex interactions between various environmental factors on a polygenic basis. In addition, it is believed that genetic risk factors for the same disease differ on an individual basis according to their susceptible environmental factors. In the present study, to predict the development of myocardial infarction (MI) and classify the subjects into personally optimum development patterns, we have extracted risk factor candidates (RFCs) that comprised a state that is a derivative form of polymorphisms and environmental factors using a statistical test. We then selected the risk factors using a criterion for detecting personal group (CDPG), which is defined in the present study. By using CDPG, we could predict the development of MI in blinded subjects with an accuracy greater than 75%. In addition, the risk percentage for MI was higher with an increase in the number of selected risk factors in the blinded data. Since sensitivity using the CDPG was high, it can be an effective and useful tool in preventive medicine and its use may provide a high quality of life and reduce medical costs.
多因素疾病,如与生活方式有关的疾病,如癌症、糖尿病和心肌梗死,被认为是由各种环境因素在多基因基础上的复杂相互作用引起的。此外,据信同一疾病的遗传风险因素因其易受影响的环境因素而因人而异。在本研究中,为了预测心肌梗死(MI)的发展并将受试者分类为个人最佳发展模式,我们提取了风险因素候选(rfc),这些风险因素候选包括一种状态,这种状态是多态性和环境因素的衍生形式,使用统计检验。然后,我们使用检测个人群体(CDPG)的标准选择危险因素,这是在本研究中定义的。通过使用CDPG,我们可以预测盲法受试者心肌梗死的发展,准确率大于75%。此外,随着盲法数据中所选危险因素数量的增加,心肌梗死的风险百分比也更高。由于使用CDPG的敏感性高,它可以成为预防医学中有效和有用的工具,它的使用可以提供高质量的生活和降低医疗费用。
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引用次数: 3
Comparison of Protein Complexes Predicted from PPI Networks by DPClus and Newman Clustering Algorithms 用DPClus和Newman聚类算法预测PPI网络中蛋白质复合物的比较
Pub Date : 2006-11-15 DOI: 10.2197/IPSJDC.2.674
Hisashi Tuji, M. Altaf-Ul-Amin, Masanori Arita, Hirokazu Nishio, Y. Shinbo, K. Kurokawa, S. Kanaya
A Protein-Protein Interaction network, what we call a PPI network is considered as an important source of information for prediction of protein functions. However, it is quite difficult to analyze such networks for their complexity. We expected that if we could develop a good visualizing method for PPI networks, we could predict protein functions visually because of the close relation between protein functions and protein interactions. Previously, we proposed one, which is based on clustering concepts, by extracting clusters defined as relatively densely connected group of nodes. But the results of visualization of a network differ very much depending on the clustering algorithm. Therefore, in this paper, we compare the outcome of two different clustering algorithms, namely DPClus and Newman algorithms, by applying them to a PPI network, and point out some advantages and limitations of both.
蛋白质-蛋白质相互作用网络,我们称之为PPI网络,被认为是预测蛋白质功能的重要信息来源。然而,由于网络的复杂性,对其进行分析是相当困难的。由于蛋白质功能与蛋白质相互作用之间的密切关系,我们期望如果我们能够开发出一种良好的PPI网络可视化方法,我们可以直观地预测蛋白质的功能。在此之前,我们提出了一种基于聚类概念的聚类方法,通过提取定义为相对紧密连接的节点组的聚类。但是不同的聚类算法对网络的可视化效果有很大的不同。因此,在本文中,我们通过将DPClus和Newman算法两种不同的聚类算法应用于PPI网络,比较它们的聚类结果,并指出两者的一些优点和局限性。
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引用次数: 4
A Method to Support Cell Physiological Modelling Using Description Language and Ontology 一种基于描述语言和本体的细胞生理建模支持方法
Pub Date : 2006-11-15 DOI: 10.2197/IPSJDC.2.726
T. Shimayoshi, Kazuhiro Komurasaki, A. Amano, T. Iwashita, T. Matsuda, M. Kanazawa
The development of physiological cell models to support the understanding of biological mechanisms gains increasingly importance. Due to the complexity of biological systems, whole cell models, which are composed of many imported component models of functional elements, get quite complex, making modifications difficult. Here, we propose a method to enhance structural changes of cell models, employing the markup languages of CellML and our original PMSML (Physiological Model Structure Markup Language), in addition to a new ontology for cell physiological modelling, the Cell Model Ontology. In particular, a method to make references from CellML files to the ontology and a method to assist with manipulation of model structures using PMSML together with the Cell Model Ontology are reported. Using these methods two software utilities, an interactive ontology ID assigner, the CellML Ontologizer, and a graphical cell model editor, the Cell Structure Editor, are implemented. Experimental results proved that the proposed method and the implemented software are useful for the modification of physiological models.
发展生理细胞模型以支持对生物机制的理解变得越来越重要。由于生物系统的复杂性,整个细胞模型是由许多导入的功能元件组件模型组成的,变得非常复杂,给修改带来了困难。在这里,我们提出了一种增强细胞模型结构变化的方法,采用CellML标记语言和我们原始的PMSML(生理模型结构标记语言),以及一个新的细胞生理建模本体——细胞模型本体。特别地,报告了一种从Cell ml文件引用到本体的方法,以及一种使用PMSML和Cell model ontology辅助操作模型结构的方法。使用这些方法,实现了两个软件实用程序,一个交互式本体ID分配器(CellML ontology - gizer)和一个图形单元模型编辑器(cell Structure editor)。实验结果表明,所提出的方法和实现的软件可用于生理模型的修正。
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引用次数: 3
Analytic Space Management for Drug Design Application 药物设计应用的分析空间管理
Pub Date : 2006-11-15 DOI: 10.2197/IPSJDC.2.736
T. Maeno, S. Date, Y. Kido, S. Shimojo
Demands on efficient drug design have been increasing with the advancement of computing technology and bioinformatics. A variety of information technologies pertaining to drug design have been proposed recently and such technology mostly contributes to drug design research. Molecular docking simulation is a promising application for drug design, and can be realized with current information technology. However although docking simulation and the related information technology have advanced in recent years, scientists still have difficulty finding a suitable parameter set of docking simulations for accuracy of simulation. The parameter-tuning step takes a long time, and existing computing technology can hardly assist in this step. This is because the parameter-tuning step involves factors that are difficult to automate with computers. In this paper, we propose a new architecture for assisting procedures that require the decisions of scientists, especially when they need to tune parameters in a docking simulation.
随着计算机技术和生物信息学的发展,对高效药物设计的要求越来越高。最近提出了各种与药物设计有关的信息技术,这些技术主要有助于药物设计研究。分子对接模拟在药物设计中具有广阔的应用前景,并且可以在现有的信息技术条件下实现。然而,尽管近年来对接仿真和相关的信息技术取得了很大的进步,但科学家们仍然很难找到一个合适的对接仿真参数集来保证仿真的准确性。参数整定步骤耗时较长,现有的计算技术难以辅助这一步骤。这是因为参数调整步骤涉及难以用计算机自动化的因素。在本文中,我们提出了一种新的架构,用于辅助需要科学家决策的程序,特别是当他们需要在对接模拟中调整参数时。
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引用次数: 2
Interactions between Mobile IPv6 and IPsec/IKE 移动IPv6与IPsec/IKE交互
Pub Date : 2006-11-15 DOI: 10.2197/IPSJDC.2.635
Shinta Sugimoto, F. Dupont, Ryoji Kato
We specified a mechanism with which Mobile IPv6 and IPsec/IKE can work together efficiently. The interaction is necessary for updating the endpoint address of an IPsec tunnel in accordance with movement performed by a mobile node. Based on an analysis of needs for interaction between Mobile IPv6 and IPsec/IKE, we designed and implemented a mechanism that is an extension to the PF_KEY framework. The proposed mechanism allows Mobile IPv6 to inform IPsec/IKE of the movement so that necessary updates to the security policy database and security association database can be taken by IPsec/IKE.This notification helps IKE to update its internal state. The mechanism is also applicable to the other scenarios, such as NEMO, Mobile VPN and its variants.
我们指定了一种机制,使移动IPv6和IPsec/IKE可以有效地协同工作。这种交互是根据移动节点的移动来更新IPsec隧道端点地址所必需的。在分析移动IPv6与IPsec/IKE交互需求的基础上,设计并实现了PF_KEY框架的扩展机制。提议的机制允许移动IPv6通知IPsec/IKE移动,以便IPsec/IKE可以对安全策略数据库和安全关联数据库进行必要的更新。此通知有助于IKE更新其内部状态。该机制也适用于其他场景,如NEMO、移动VPN及其变体。
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引用次数: 2
期刊
Ipsj Digital Courier
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