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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
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Interdisciplinary Bio Central
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Journal DOI :
Korean Society for Bioinformatics and Systems Biology
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Volume & Issues
Volume 2, Issue 4 - Dec 2010
Volume 2, Issue 3 - Sep 2010
Volume 2, Issue 2 - Jun 2010
Selecting the target year
Engineered microdevices for single cell immunological assay
Choi, Jong-Hoon ;
Interdisciplinary Bio Central, volume 2, issue 2, 2010, Pages 1.1~1.8
DOI : 10.4051/ibc.2010.2.2.0001
Microdevices have been used as effective experimental tools for the rapid and multiplexed analysis of individual cells in single-cell assays. Technological advances for miniaturizing such systems and the optimization of delicate controls in micron-sized space homing cells have motivated many researchers from diverse fields (e.g., cancer research, stem cell research, therapeutic agent development, etc.) to employ microtools in their scientific research. Microtools allow high-throughput, multiplexed analysis of single cells, and they are not limited by the lack of large samples. These characteristics may significantly benefit the study of immune cells, where the number of cells available for testing is usually limited. In this review, I present an overview of several microtools that are currently available for single-cell analyses in two popular formats: microarrays and microfluidic microdevices. Then, I discuss the potential to study human immunology on the single-cell level, and I highlight several recent examples of immunoassays performed with single-cell microdevice assays. Finally, I discuss the outlook for the development of optimized assay platforms to study human immune cells. The development and application of microdevices for studies on single immune cells presents novel opportunities for the qualitative and quantitative characterization of immune cells and may lead to a comprehensive understanding of fundamental aspects of human immunology.
StrokeMed: an integrated literature database for stroke and the differentiation of stroke syndrome
Kim, Young-Uk ; Kim, Jin-Ho ; Park, Young-Kyu ; Kim, Young-Joo ;
Interdisciplinary Bio Central, volume 2, issue 2, 2010, Pages 2.1~2.4
DOI : 10.4051/ibc.2010.2.2.0002
Complex diseases, such as stroke and cancer, have two or more genetic influences and are affected by environmental factors, which complicate them. Due to the complex characteristics of these diseases, we must search and study comprehensive literature-based article resources. Some disease-related literature databases have been developed through specialized journal issues or major websites. Most of them, however, are scattered throughout a website, and users encounter difficulties in finding accurate and comprehensive information easily and quickly. We developed StrokeMed, an integrated literature database for stroke and the differentiation of stroke syndrome. The system allows users to explore PubMed search results, categorized by MeSH (Medical Subject Headings), and the differentiation of stroke syndrome in Oriental medicine. StrokeMed collects data from important sites, such as PubMed, Scirus, and Scopus, automatically to maintain higher-quality and updated content. Currently, the system indexes more than 20,000 PubMed abstracts that are related to stroke, stroke etiology, and Oriental medicine. The system provides valuable literature information to the scientific and medical fields in stroke.
Utility of Structural Information to Predict Drug Clearance from in Vitro Data
Lee, So-Young ; Kim, Dong-Sup ;
Interdisciplinary Bio Central, volume 2, issue 2, 2010, Pages 3.1~3.4
DOI : 10.4051/ibc.2010.2.2.0003
In the present research, we assessed the utility of the structural information of drugs for predicting human in vivo intrinsic clearance from in vitro intrinsic clearance data obtained by human hepatic microsome experiment. To compare with the observed intrinsic clearance, human intrinsic clearance values for 51 drugs were estimated by the classical methods using in vivo-in vitro scale-up and by the new methods using the in vitro experimental data and selected molecular descriptors of drugs by the forward selection technique together. The results showed that taking consideration of molecular descriptors into prediction from in vitro experimental data could improve the prediction accuracy. The in vitro experiment is very useful when the data can estimate in vivo data accurately since it can reduce the cost of drug development. Improvement of prediction accuracy in the present approach can enhance the utility of in vitro data.
Improved Statistical Testing of Two-class Microarrays with a Robust Statistical Approach
Oh, Hee-Seok ; Jang, Dong-Ik ; Oh, Seung-Yoon ; Kim, Hee-Bal ;
Interdisciplinary Bio Central, volume 2, issue 2, 2010, Pages 4.1~4.6
DOI : 10.4051/ibc.2010.2.2.0004
The most common type of microarray experiment has a simple design using microarray data obtained from two different groups or conditions. A typical method to identify differentially expressed genes (DEGs) between two conditions is the conventional Student's t-test. The t-test is based on the simple estimation of the population variance for a gene using the sample variance of its expression levels. Although empirical Bayes approach improves on the t-statistic by not giving a high rank to genes only because they have a small sample variance, the basic assumption for this is same as the ordinary t-test which is the equality of variances across experimental groups. The t-test and empirical Bayes approach suffer from low statistical power because of the assumption of normal and unimodal distributions for the microarray data analysis. We propose a method to address these problems that is robust to outliers or skewed data, while maintaining the advantages of the classical t-test or modified t-statistics. The resulting data transformation to fit the normality assumption increases the statistical power for identifying DEGs using these statistics.
Flavobacterium columnare / Myxobolus tilapiae Concurrent Infection in the Earthen Pond Reared Nile Tilapia (Oreochromis niloticus) during the Early Summer
Eissa, Alaa E. ; Zaki, Manal M. ; Aziz, A. Abdel ;
Interdisciplinary Bio Central, volume 2, issue 2, 2010, Pages 5.1~5.9
DOI : 10.4051/ibc.2010.2.2.0005
Flavobacterium columnare (F. columnare), the dermotropic Gram negative yellow pigmented bacteria was isolated from different sites of skin ulcerations in the Nile tilapia (Oreochromis niloticus) and Nile catfish (Clarias gariepinus) collected from an earthen pond located at an aquaculture station in Sharkiya Province, Lower Egypt during an acute episode of mass kills during the early summer of 2009. An acute infection with F. columnare was behind the emergent event of mass mortalities among both populations. Many of the Nile tilapias exhibited typical signs of hole - in- the head like lesions from which F. columnare together with the myxosporean spore, Myxobolus tilapiae (M. tilapiae) were retrieved. Most of the cohabitating infected Nile catfishes exhibited severe form of saddle back like ulcer. The identities of the retrieved isolates were confirmed using morphological, biochemical and molecular tools. The research lead us to conclude that the two diverse etiological agents (F. columnare and M. tilapiae) under the triggering effect of the abrupt change in the water quality measures (abrupt rise in the water temperature, ammonia, pH, sharp decrease in dissolved oxygen) have synergized together to induce the above mentioned pathology with the consequent reemergence of fish mass mortalities.
Fragment Molecular Orbital Method: Application to Protein-Ligand Binding
Watanabe, Hirofumi ; Tanaka, Shigenori ;
Interdisciplinary Bio Central, volume 2, issue 2, 2010, Pages 6.1~6.5
DOI : 10.4051/ibc.2010.2.2.0006
Fragment molecular orbital (FMO) method provides a novel tool for ab initio calculations of large biomolecules. This method overcomes the size limitation difficulties in conventional molecular orbital methods and has several advantages compared to classical force field approaches. While there are many features in this method, we here focus on explaining the issues related to protein-ligand binding: FMO method provides useful interaction-analysis tools such as IFIE, CAFI and FILM. FMO calculations can provide not only binding energies, which are well correlated with experimental binding affinity, but also QSAR descriptors. In addition, FMO-derived charges improve the descriptions of electrostatic properties and the correlations between docking scores and experimental binding affinities. These calculations can be performed by the ABINIT-MPX program and the calculation results can be visualized by its proper BioStation Viewer. The acceleration of FMO calculations on various computer facilities is ongoing, and we are also developing methods to deal with cytochrome P450, which belongs to the family of drug metabolic enzymes.