发布求助
文献互助 智能选刊 最新文献

Ipsj Digital Courier最新文献

筛选
英文 中文
Efficient Lock Algorithm for Shared Objects in SMP Environments SMP环境下共享对象的高效锁算法
Ipsj Digital Courier Pub Date : 2006-12-15 DOI: 10.2197/IPSJDC.2.759
T. Ogasawara, H. Komatsu, T. Nakatani
{"title":"Efficient Lock Algorithm for Shared Objects in SMP Environments","authors":"T. Ogasawara, H. Komatsu, T. Nakatani","doi":"10.2197/IPSJDC.2.759","DOIUrl":"https://doi.org/10.2197/IPSJDC.2.759","url":null,"abstract":"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.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"32 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125914627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Ipsj Digital Courier Pub Date : 2006-11-15 DOI: 10.2197/IPSJDC.2.716
Shigeyuki Oba, N. Tomioka, M. Ohira, S. Ishii
{"title":"Combfit: A Normalization Method for Array CGH Data","authors":"Shigeyuki Oba, N. Tomioka, M. Ohira, S. Ishii","doi":"10.2197/IPSJDC.2.716","DOIUrl":"https://doi.org/10.2197/IPSJDC.2.716","url":null,"abstract":"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.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"116 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128011093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Ipsj Digital Courier Pub Date : 2006-11-15 DOI: 10.2197/IPSJDC.2.710
A. Sasaki, Y. Oshima, Saeko Kishimoto, Akio Fujimura
{"title":"Individual Differences in Gene Expression in Primary Cultured Renal Cortex Cells Derived from Japanese Subjects","authors":"A. Sasaki, Y. Oshima, Saeko Kishimoto, Akio Fujimura","doi":"10.2197/IPSJDC.2.710","DOIUrl":"https://doi.org/10.2197/IPSJDC.2.710","url":null,"abstract":"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.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"63 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114994285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Program Transformation by Templates: A Rewriting Framework 模板程序转换:一个重写框架
Ipsj Digital Courier Pub Date : 2006-11-15 DOI: 10.2197/IPSJDC.2.620
Yuki Chiba, Takahito Aoto, Y. Toyama
{"title":"Program Transformation by Templates: A Rewriting Framework","authors":"Yuki Chiba, Takahito Aoto, Y. Toyama","doi":"10.2197/IPSJDC.2.620","DOIUrl":"https://doi.org/10.2197/IPSJDC.2.620","url":null,"abstract":"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.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"48 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127943289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Ipsj Digital Courier Pub Date : 2006-11-15 DOI: 10.2197/IPSJDC.2.685
Y. Tohsato
{"title":"A Method for Species Comparison of Metabolic Networks Using Reaction Profile","authors":"Y. Tohsato","doi":"10.2197/IPSJDC.2.685","DOIUrl":"https://doi.org/10.2197/IPSJDC.2.685","url":null,"abstract":"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.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"94 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122808086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Ipsj Digital Courier Pub Date : 2006-11-15 DOI: 10.2197/IPSJDC.2.691
Yasuyuki Tomita, H. Asano, H. Izawa, M. Yokota, Takeshi Kobayashi, H. Honda
{"title":"Classification Method for Predicting the Development of Myocardial Infarction by Using the Interaction between Genetic and Environmental Factors","authors":"Yasuyuki Tomita, H. Asano, H. Izawa, M. Yokota, Takeshi Kobayashi, H. Honda","doi":"10.2197/IPSJDC.2.691","DOIUrl":"https://doi.org/10.2197/IPSJDC.2.691","url":null,"abstract":"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.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"117 3","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"113992077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Ipsj Digital Courier 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
{"title":"Comparison of Protein Complexes Predicted from PPI Networks by DPClus and Newman Clustering Algorithms","authors":"Hisashi Tuji, M. Altaf-Ul-Amin, Masanori Arita, Hirokazu Nishio, Y. Shinbo, K. Kurokawa, S. Kanaya","doi":"10.2197/IPSJDC.2.674","DOIUrl":"https://doi.org/10.2197/IPSJDC.2.674","url":null,"abstract":"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.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121860727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Ipsj Digital Courier Pub Date : 2006-11-15 DOI: 10.2197/IPSJDC.2.726
T. Shimayoshi, Kazuhiro Komurasaki, A. Amano, T. Iwashita, T. Matsuda, M. Kanazawa
{"title":"A Method to Support Cell Physiological Modelling Using Description Language and Ontology","authors":"T. Shimayoshi, Kazuhiro Komurasaki, A. Amano, T. Iwashita, T. Matsuda, M. Kanazawa","doi":"10.2197/IPSJDC.2.726","DOIUrl":"https://doi.org/10.2197/IPSJDC.2.726","url":null,"abstract":"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.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134450971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Ipsj Digital Courier Pub Date : 2006-11-15 DOI: 10.2197/IPSJDC.2.736
T. Maeno, S. Date, Y. Kido, S. Shimojo
{"title":"Analytic Space Management for Drug Design Application","authors":"T. Maeno, S. Date, Y. Kido, S. Shimojo","doi":"10.2197/IPSJDC.2.736","DOIUrl":"https://doi.org/10.2197/IPSJDC.2.736","url":null,"abstract":"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.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127072274","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Interactions between Mobile IPv6 and IPsec/IKE 移动IPv6与IPsec/IKE交互
Ipsj Digital Courier Pub Date : 2006-11-15 DOI: 10.2197/IPSJDC.2.635
Shinta Sugimoto, F. Dupont, Ryoji Kato
{"title":"Interactions between Mobile IPv6 and IPsec/IKE","authors":"Shinta Sugimoto, F. Dupont, Ryoji Kato","doi":"10.2197/IPSJDC.2.635","DOIUrl":"https://doi.org/10.2197/IPSJDC.2.635","url":null,"abstract":"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.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130137339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
首页 上一页
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整，为了账户安全，请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们：info@booksci.cn Book学术提供免费学术资源搜索服务，方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号：481959085
Book学术官方微信