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Search Results: 1 - 10 of 768 matches for " Imhoi Koo "
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Smith-Waterman peak alignment for comprehensive two-dimensional gas chromatography-mass spectrometry
Seongho Kim, Imhoi Koo, Aiqin Fang, Xiang Zhang
BMC Bioinformatics , 2011, DOI: 10.1186/1471-2105-12-235
Abstract: We developed novel peak alignment algorithms for both homogeneous (acquired under the identical experimental conditions) and heterogeneous (acquired under the different experimental conditions) GC × GC-MS data using modified Smith-Waterman local alignment algorithms along with mass spectral similarity. Compared with literature reported algorithms, the proposed algorithms eliminated the detection of landmark peaks and the usage of retention time transformation. Furthermore, an automated peak alignment software package was established by implementing a likelihood function for optimal peak alignment.The proposed Smith-Waterman local alignment-based algorithms are capable of aligning both the homogeneous and heterogeneous data of multiple GC × GC-MS experiments without the transformation of retention times and the selection of landmark peaks. An optimal version of the SW-based algorithms was also established based on the associated likelihood function for the automatic peak alignment. The proposed alignment algorithms outperform the literature reported alignment method by analyzing the experiment data of a mixture of compound standards and a metabolite extract of mouse plasma with spiked-in compound standards.Metabolomics examines the structures, functions, interactions, and dynamics of cellular metabolites, identifies their cellular localization (i.e., subcellular membrane compartments and domains), and determines the dynamic changes that occur during physiological and pathophysiological perturbations. Metabolomics, together with other modern omics, has the potential to facilitate the development of preventive, predictive and personalized medicine markets in health and wellness [1]. Multiple high-throughput analytical methods have been developed for metabolomics. One such powerful approach is comprehensive two-dimensional gas chromatography-mass spectrometry (GC × GC-MS) [2-5], which can easily detect a large number of metabolites from a complex sample.The GC × GC-MS s
Multivariate classification of urine metabolome profiles for breast cancer diagnosis
Kim Younghoon,Koo Imhoi,Jung Byung Hwa,Chung Bong Chul
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-s2-s4
Abstract: Background Diagnosis techniques using urine are non-invasive, inexpensive, and easy to perform in clinical settings. The metabolites in urine, as the end products of cellular processes, are closely linked to phenotypes. Therefore, urine metabolome is very useful in marker discoveries and clinical applications. However, only univariate methods have been used in classification studies using urine metabolome. Since multiple genes or proteins would be involved in developments of complex diseases such as breast cancer, multiple compounds including metabolites would be related with the complex diseases, and multivariate methods would be needed to identify those multiple metabolite markers. Moreover, because combinatorial effects among the markers can seriously affect disease developments and there also exist individual differences in genetic makeup or heterogeneity in cancer progressions, single marker is not enough to identify cancers. Results We proposed classification models using multivariate classification techniques and developed an analysis procedure for classification studies using metabolome data. Through this strategy, we identified five potential urinary biomarkers for breast cancer with high accuracy, among which the four biomarker candidates were not identifiable by only univariate methods. We also proposed potential diagnosis rules to help in clinical decision making. Besides, we showed that combinatorial effects among multiple biomarkers can enhance discriminative power for breast cancer. Conclusions In this study, we successfully showed that multivariate classifications are needed to precisely diagnose breast cancer. After further validation with independent cohorts and experimental confirmation, these marker candidates will likely lead to clinically applicable assays for earlier diagnoses of breast cancer.
Feature Selection from a Facial Image for Distinction of Sasang Constitution
Imhoi Koo,Jong Yeol Kim,Myoung Geun Kim,Keun Ho Kim
Evidence-Based Complementary and Alternative Medicine , 2009, DOI: 10.1093/ecam/nep065
Abstract: Recently, oriental medicine has received attention for providing personalized medicine through consideration of the unique nature and constitution of individual patients. With the eventual goal of globalization, the current trend in oriental medicine research is the standardization by adopting western scientific methods, which could represent a scientific revolution. The purpose of this study is to establish methods for finding statistically significant features in a facial image with respect to distinguishing constitution and to show the meaning of those features. From facial photo images, facial elements are analyzed in terms of the distance, angle and the distance ratios, for which there are 1225, 61 250 and 749 700 features, respectively. Due to the very large number of facial features, it is quite difficult to determine truly meaningful features. We suggest a process for the efficient analysis of facial features including the removal of outliers, control for missing data to guarantee data confidence and calculation of statistical significance by applying ANOVA. We show the statistical properties of selected features according to different constitutions using the nine distances, 10 angles and 10 rates of distance features that are finally established. Additionally, the Sasang constitutional meaning of the selected features is shown here.
Association analyses of the INSIG2 polymorphism in the obesity and cholesterol levels of Korean populations
Seongwon Cha, Imhoi Koo, Sun Choi, Byung Park, Kil Kim, Jae-Ryong Kim, Hyoung Shin, Jong Kim
BMC Medical Genetics , 2009, DOI: 10.1186/1471-2350-10-96
Abstract: The rs7566605 polymorphism was genotyped with 2,364 Koreans, and associations with obesity- and cholesterol-related traits were analyzed statistically via an ANOVA or T-test.Replication of an association with BMI, WHR, fat mass, fat percent, and abdominal fat area failed, and the C allele of rs7566605 was not associated significantly with total cholesterol, HDL cholesterol, or triglyceride. However, it was found in a meta-analysis of a dominant model that the C allele of rs7566605 appeared to affect the level of the total cholesterol, especially in female subjects.We failed to show associations of rs7566605 with cholesterol- and obesity-related phenotypes, although we newly suggest the possible involvement of INSIG2 with the plasma level of the total cholesterol in women.INSIG2 is considered to be a candidate gene with respect to involvement in the development of obesity. A common variant located 10 kb upstream of the gene, rs7566605, was found to be associated with BMI in a recent genome-wide association study [1]. This association has been suitably replicated in several white [1-3], African-American [1], and Asian populations [4-6]. However, the SNP did not have a genetic effect on obesity according to other studies including white [2,7-14], Afro-Caribbean [12], and Asian populations [15-17]. Hence, the INSIG2 polymorphism may have an important effect in overweight populations under certain environmental circumstances, given several positive associations found in studies of overweight subjects [3,4].INSIG2 has attracted the attention of researchers due to its role in cholesterol metabolism [18]. The protein is known to reside in the endoplasmic reticulum, where it binds to SCAP to inhibit it from convoying SREBPs to the Golgi apparatus [18]. Eventually, INSIG2 prevents SREBP from activating cholesterol synthesis because SREBP cannot be processed and activated by the Golgi enzymes. These actions of INSIG2 were also reported in subsequent research involving mice [18
Genetic Effects of FTO and MC4R Polymorphisms on Body Mass in Constitutional Types
Seongwon Cha,Imhoi Koo,Byung L. Park,Sangkyun Jeong,Sun M. Choi,Kil S. Kim,Hyoung D. Shin,Jong Y. Kim
Evidence-Based Complementary and Alternative Medicine , 2011, DOI: 10.1093/ecam/nep162
Abstract: Sasang constitutional medicine (SCM), a Korean tailored medicine, categorizes human beings into four types through states of physiological imbalances and responsiveness to herbal medicine. One SCM type susceptible to obesity seems sensitive to energy intake due to an imbalance toward preserving energy. Common variants of fat mass and obesity associated (FTO) and melanocortin 4 receptor (MC4R) genes have been associated with increased body mass index (BMI) by affecting energy intake. Here, we statistically examined the association of FTO and MC4R polymorphisms with BMI in two populations with 1370 Koreans before and after SCM typing, and with the lowering of BMI in 538 individuals who underwent a 1-month lifestyle intervention. The increased BMI replicated the association with FTO haplotypes (effect size ? 1.1 kg/m2) and MC4R variants (effect size ? 0.64 kg/m2). After the lifestyle intervention, the carriers of the haplotype represented by the minor allele of rs1075440 had a tendency to lose more waist-to-hip ratio (0.76%) than non-carriers. The constitutional discrepancy for the accumulation of body mass by the effects of FTO and/or MC4R variants seemed to reflect the physique differences shown in each group of SCM constitutional types. In conclusion, FTO and MC4R polymorphisms appear to play an important role in weight gain, while only FTO variants play a role in weight loss after lifestyle intervention. Different trends were observed among individuals of SCM types, especially for weight gain. Therefore, classification of individuals based on physiological imbalance would offer a good genetic stratification system in assessing the effects of obesity genes.
Internet of Things: Services and Applications Categorization  [PDF]
Matthew Gigli, Simon Koo
Advances in Internet of Things (AIT) , 2011, DOI: 10.4236/ait.2011.12004
Abstract: In this paper we attempt to categorize the services provided by the Internet of Things (IoT) in order to help application developers build upon a base service. First we introduce the four main categories of services, and then follow by providing a number of examples of each of the service categories so as to provide an example of how each type of service might be implemented, and how it can be used to build an IoT application.
Developing Framework for Alternative Funding Options in Water Infrastructure Projects  [PDF]
Matt Nafziger, Dan Koo
Journal of Building Construction and Planning Research (JBCPR) , 2015, DOI: 10.4236/jbcpr.2015.31004
Abstract: The United States is facing a crisis in which less financial resources are available to maintain the quality and to meet increasing demand of our water infrastructure system. Water utility owners across the nation are faced with the incredible challenge of finding ways to invest because of limited government funding, from local to federal levels. The funding gap between available and necessary funds has been increasing and expected to increase in the future. With government unable to provide adequate funding, water utility owners should consider alternative funding sources such as private partnerships and investment. There are many key aspects of an effective funding strategy for water utility owners to achieve successful water infrastructure planning and development. This paper presents various funding alternatives and provides a framework for utilizing alternative funding in water infrastructure planning and development to help alleviate funding gaps while simultaneously encouraging future sustainability in public water infrastructure.
The Influence of Surrounding Ground Floor Facilities on the Use of Privately Owned Public Spaces in Seoul  [PDF]
Bonwoo Koo, Yumi Lee
Journal of Building Construction and Planning Research (JBCPR) , 2015, DOI: 10.4236/jbcpr.2015.32010
Abstract: Seoul’s privately owned public space (POPS) initiative has achieved quantitative success since its introduction in the early 1990s. However, POPSs have been frequently criticized for failing to correspond with the urban context in which they are created and are thus often underused. Association between surrounding urban context and the use of POPS is acknowledged, but specific elements of the urban context associated with the use of POPS and the extent of association are unclear. In this study, the relationship between constituent elements of 48 POPSs including the surrounding ground floor facility use and the use of those spaces in Seoul’s central business district was measured by multiple regression analysis. The results present empirical evidence of a substantial relationship between assembly, mercantile, and business facilities on ground floors of surrounding buildings and the use of POPS. As the surrounding ground floor facility use showed an overriding relationship with the use of POPS that possibly overshadowed the influence of secondary determinants, the 48 POPSs were divided into two groups: those surrounded by commercial facilities and those surrounded by business facilities. The use of POPSs surrounded by commercial facilities was associated with additional variables including the proximity to transit stations and crosswalks. Models using the sample of POPSs surrounded by business facilities were not statistically significant. Based on these results, this paper emphasizes the importance of creating POPSs in connection with desirable surrounding facilities. This study also suggests that anticipation of the usage patterns of POPSs and establishment of guidelines supporting those patterns may be viable by investigating preexisting urban contexts.
Pedagogical Implications Of Some Neglected Differences Between British And American Englishes: Problems For West African Teachers, Examiners And Examinees
KOO Armah
Journal of Science and Technology (Ghana) , 2009,
Abstract: Our premise in this paper is that the fulcrum of pedagogy is two-fold: teaching and examining. Thus, we look at some of the differences between British and American English usage, problems in the teaching situation and how teachers and examiners could handle situations where there is a mixture of British English and American or North American English. The telos of the paper is that since the medium for nearly all examinations conducted in Ghana, and much of West Af-rica is the English Language, and since many Englishes appear to be competing among them-selves for legitimacy and/or supremacy, there is an imperative need to ensure that examinees are not unduly disadvantaged. The paper explores aspects of four broad areas of English grammar where, in pedagogy, there appears a pronounced tendency to ignore the variant usages. The fo-cus is on tense, vocabulary, orthography and preposition. Each of these grammatical categories has been discussed exclusively; that is, no one discussion is contingent on the other albeit they are intertwined by the broad concept of pedagogy in English. The major question that underpins our effort is: what is the teacher and for that matter the examiner to do when caught in such a linguistic labyrinth as we often are, as far as examinations are concerned? It is suggested that as much as possible fairness in evaluating student’s essays should be the paramount objective of the teacher and the examiner. Thus, the paper argues that it is incumbent upon West African teachers and examiners to consciously educate themselves on the variant usages in the English language to ensure consistency and justice in teaching and evaluating student papers.
Stemming the Falling Standard of English: A Semantic Appraisal of Passable but Deviant English Language Usage in Academia
KOO Armah
Journal of Science and Technology (Ghana) , 2008,
Abstract: This paper analyses some of the passable, albeit unacceptable, uses of English in academia and draws attention to the need to be conscious of the deviances. Some recurrent words and phrases have been picked from utterances of teachers, articles by journalists and essays of students for the study. The point is also made that, like Chinua Achebe (1974) who would seize an opportunity to remove ‘structural weaknesses\' from his Arrow of God, intellectuals should not see the acquisition of high qualifications as being necessarily the quintessence of knowledge, nor should deviant use of English be accepted in the name of so-called innovation. The dictionary form has been used to facilitate easy reference.
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