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Naito Y.,University of Tokyo | Naito Y.,Database Systems | Ui-Tei K.,University of Tokyo
Frontiers in Genetics | Year: 2012

RNA interference (RNAi) is a mechanism through which small interfering RNA (siRNA) induces sequence-specific posttranscriptional gene silencing. RNAi is commonly recognized as a powerful tool not only for functional genomics but also for therapeutic applications. Twenty-one-nucleotide-long siRNA suppresses the expression of the intended gene whose transcript possesses perfect complementarity to the siRNA guide strand. Hence, its silencing effect has been assumed to be extremely specific. However, accumulated evidences revealed that siRNA could downregulate unintended genes with partial complementarities mainly to the seven-nucleotide seed region of siRNA. This phenomenon is referred to as off-target effect. We have revealed that the capability to induce off-target effect is strongly correlated to the thermodynamic stability in siRNA seed-target duplex. For understanding accurate target gene function and successful therapeutic application, it may be critical to select a target gene-specific siRNA with minimized off-target effect. Here we present our siRNA design software for a target-specific RNAi. In addition, we also introduce the software programs open to the public for designing functional siRNAs. © 2012 Naito and Ui-Tei. Source


Lehner W.,TU Dresden | Sattler K.-U.,Database Systems
Proceedings - International Conference on Data Engineering | Year: 2010

Modern Web or "Eternal-Beta" applications necessitate a flexible and easy-to-use data management platform that allows the evolutionary development of databases and applications. The classical approach of relational database systems following strictly the ACID properties has to be extended by an extensible and easy-to-use persistency layer with specialized DB features. Using the underlying concept of Software as a Service (SaaS) also enables an economic advantage based on the "economy of the scale", where application and system environments only need to be provided once but can be used by thousands of users. Within this tutorial, we are looking at the current state-of-the-art from different perspectives. We outline foundations and techniques to build database services based on the SaaS-paradigm. We discuss requirements from a programming perspective, show different dimensions in the context of consistency and reliability, and also describe different non-functional properties under the umbrella of Service-Level agreements (SLA). © 2010 IEEE. Source


Goto N.,Osaka University | Prins P.,Wageningen University | Nakao M.,Database Systems | Bonnal R.,CNR Institute of Molecular Genetics | And 2 more authors.
Bioinformatics | Year: 2010

Summary: The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser. © The Author(s) 2010. Published by Oxford University Press. Source


Barker K.,Database Systems
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2012

Protecting data privacy is an area of increasing concern as the general public has become increasingly impacted by its inability to guarantee that those things we wish to hold private remain private. The concept of privacy is found in the earliest writing ofmankind and continues today to be a very high value inmodern society.Unfortunately, challenges to privacy have always existed and at times, these challenges have become so strong that any real sense of personal privacy was assumed to unattainable. This occurred in the middle-ages when communal living was normative, at least among the poor, so it was necessary to accept this as a simple matter of fact. This does not mean that privacy was not valued at the time, simply that it was assumed to be unachievable so the absence of it was accepted. A poll in a recent undergraduate/graduate class at the University of Calgary revealed that over half of the students felt that there was no way to protect their privacy in online systems. It was not that they did not value their privacy but simply felt, much like those in the middle-ages, there was nothing they could do about it. In addition, about half of the students felt that there was value in their private information and felt that they would consider trading it for an economic return under certain conditions that varied widely from individual to individual. © 2012 Springer-Verlag. Source


Rao V.S.H.,Jawaharlal Nehru Technological University | Kumar M.N.,Database Systems
IEEE Transactions on Information Technology in Biomedicine | Year: 2012

Identification of the influential clinical symptoms and laboratory features that help in the diagnosis of dengue fever (DF) in early phase of the illness would aid in designing effective public health management and virological surveillance strategies. Keeping this as our main objective, we develop in this paper a new computational intelligence-based methodology that predicts the diagnosis in real time, minimizing the number of false positives and false negatives. Our methodology consists of three major components: 1) a novel missing value imputation procedure that can be applied on any dataset consisting of categorical (nominal) and/or numeric (real or integer); 2) a wrapper-based feature selection method with genetic search for extracting a subset of most influential symptoms that can diagnose the illness; and 3) an alternating decision tree method that employs boosting for generating highly accurate decision rules. The predictivemodels developed using our methodology are found to be more accurate than the state-of-theart methodologies used in the diagnosis of the DF. © 2012 IEEE. Source

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