• Molecules and Cells
• /
• v.44 no.11
• /
• pp.843-850
• /
• 2021

The rapid increase in collateral omics and phenotypic data has enabled data-driven studies for the fast discovery of cancer targets and biomarkers. Thus, it is necessary to develop convenient tools for general oncologists and cancer scientists to carry out customized data mining without computational expertise. For this purpose, we developed innovative software that enables user-driven analyses assisted by knowledge-based smart systems. Publicly available data on mutations, gene expression, patient survival, immune score, drug screening and RNAi screening were integrated from the TCGA, GDSC, CCLE, NCI, and DepMap databases. The optimal selection of samples and other filtering options were guided by the smart function of the software for data mining and visualization on Kaplan-Meier plots, box plots and scatter plots of publication quality. We implemented unique algorithms for both data mining and visualization, thus simplifying and accelerating user-driven discovery activities on large multiomics datasets. The present Q-omics software program (v0.95) is available at http://qomics.sookmyung.ac.kr.

• Journal of KIISE:Databases
• /
• v.31 no.6
• /
• pp.641-649
• /
• 2004

The relationship between chemical structures and biological activities is researched briskly in the area of 'Medicinal Chemistry' At the base of these structure-based drug design tries, medicinal chemists search the existing drugs of similar chemical structure to target drug for the development of a new drug. Therefore, it is such necessary that an automatic system selects drug files that have a set of chemical moieties matching a user-defined query moiety. Substructure searching is the process of identifying a set of chemical moieties that match a specific query moiety. Testing for substructure searching was developed in the late 1950s. In graph theoretical terms, this problem corresponds to determining which graphs in a set are subgraph isomorphic to a specified query moiety. Testing for subgraph isomorphism has been proved, in the general case, to be an NP- complete problem. For the purpose of overcoming this difficulty, there were computational approaches. On the 1990s, a US patent has been granted on an atom-centered indexing scheme, used by the RS3 system; this has the virtue that the indexes generated can be searched by direct text comparison. This system is commercially used(http://www.acelrys.com/rs3). We define the RS3 system's drawback and present a new indexing scheme. The RS3 system treats substructure searching with substring matching by means of expressing chemical structure aspredefined strings. However, it has insufficient 'rerall' and 'precision‘ because it is impossible to index structures uniquely for same atom and same bond. To resolve this problem, we make the minimum-cost- spanning tree for one centered atom and describe a structure with paths per levels. Expressing 2D chemical structure into 1D a string has limit. Therefore, we break 2D chemical structure into 1D structure fragments. We present in this paper a new index technique to improve recall and precision surprisingly.

• Korean Journal of Clinical Pharmacy
• /
• v.29 no.2
• /
• pp.125-132
• /
• 2019

Objective: To examine the perceptions and attitudes toward spontaneous adverse drug reaction (ADR) reporting system among community pharmacists and identify factors that influence reporting, by implementing a survey. Methods: A structured questionnaire was developed and distributed online. Request for the survey was posted on the website of pharmacy's billing program, and the survey was conducted for 8 days. We collected the participants' response on their work environment, experience of ADR reporting, and their perception and attitude on the reporting system. Multivariate logistic regression was used to evaluate factors influencing ADR reporting. Results: A total of 382 pharmacists participated in the survey. Significant contributing factors for reporting level were age (odds ratio [OR], 0.90; 95% confidence interval [CI], 0.84-0.96), knowledge of reporting method (OR, 53.56; 95% CI, 9.10-315.41), installation of reporting program (OR, 31.92; 95% CI, 4.16-244.75), and encouragement from the Korean pharmaceutical association (OR, 4.13; 95% CI, 1.11-15.35). Regarding the attitude toward spontaneous ADR reporting system, 'lack of time for reporting' (OR, 0.29; 95% CI, 0.15-0.53) and 'complexity of reporting procedure' (OR, 0.51; 95% CI, 0.31-0.84), were associated with a low likelihood of reporting. Conclusion: Our results indicated that the knowledge of ADR reporting method, installation of the reporting program, and encouragement from the Korean Pharmaceutical Association contribute to active reporting. It is necessary to simplify the reporting method, make the ADR reporting program user-friendly, and provide educational interventions to increase participation in spontaneous reporting by the community pharmacists.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2003.10a
• /
• pp.236-244
• /
• 2003

Summary: The analysis of human genetic variation is one of the key issues far the understanding of the different drug response among individuals and many programs are developed for this purpose. However, current publicly available programs have so many limitations such as time complexity problem for the analysis of large amount of alleles or SNPs, difficult manipulation for installation, data import, and usage, and low-quality visual output. Here we present workbench for SNP anlaysis, SNPAnalyzer. SNPAnalyzer consists of 3 main modules: 1)Hardy-Weinberg Equilibrium ,2) Haplotype Estimation, and 3) Linkage Disequilibrium. Each module has several different widely-used algorithms for the extensive analysis and can handle large amount of alleles and SNPs with simple format. Analysis results are displayed in user-friendly formats such as table, graph and map. SNPAnalyzer is developed using C and C$^{++}$ and users can easily access through web-interftce. Availability: SNPAnalyzer can be freely implemented at http://www.istech.info/istech/board/login_form.jsp

• Journal of Biomedical Engineering Research
• /
• v.24 no.1
• /
• pp.45-53
• /
• 2003

Based on the 4-compartmental pharmacokinetic model developed in PART1, target-controlled infusion(TCI) pump system was designed and evaluated. The TCI system consists of digital board including microcontroller and digital signal process(DSP), analog board, motor-driven actuator, user friendly interface, power management and controller. It provides two modes according to the drugs: plasma target concentration and effect target concentration. Anaesthetist controls the depth of anaesthesia for patients by adjusting the required concentration to maintain both plasma and effect site in drug concentration. The data estimated in DSP include infusion rate, initial load dose, and rotation number of motor encoder. During TCI operation, plasma concentration. effect site concentration, awaken concentration, context-sensitive decrement time and system error information are displayed in real time. Li-ion battery guarantees above 2 hours without power line failure. For high reliability of the system, two microprocessors were used to perform independent functions for both pharmacokinetic algorithm and motor control strategy.

• Genomics & Informatics
• /
• v.11 no.1
• /
• pp.55-57
• /
• 2013

Growing numbers of studies employ cell line-based systematic short interfering RNA (siRNA) screens to study gene functions and to identify drug targets. As multiple sources of variations that are unique to siRNA screens exist, there is a growing demand for a computational tool that generates normalized values and standardized scores. However, only a few tools have been available so far with limited usability. Here, we present siMacro, a fast and easy-to-use Microsoft Office Excel-based tool with a graphic user interface, designed to process single-condition or two-condition synthetic screen datasets. siMacro normalizes position and batch effects, censors outlier samples, and calculates Z-scores and robust Z-scores, with a spreadsheet output of >120,000 samples in under 1 minute.

• Molecules and Cells
• /
• v.25 no.2
• /
• pp.279-288
• /
• 2008

The analysis of microarray data is essential for large amounts of gene expression data. In this review we focus on clustering techniques. The biological rationale for this approach is the fact that many co-expressed genes are co-regulated, and identifying co-expressed genes could aid in functional annotation of novel genes, de novo identification of transcription factor binding sites and elucidation of complex biological pathways. Co-expressed genes are usually identified in microarray experiments by clustering techniques. There are many such methods, and the results obtained even for the same datasets may vary considerably depending on the algorithms and metrics for dissimilarity measures used, as well as on user-selectable parameters such as desired number of clusters and initial values. Therefore, biologists who want to interpret microarray data should be aware of the weakness and strengths of the clustering methods used. In this review, we survey the basic principles of clustering of DNA microarray data from crisp clustering algorithms such as hierarchical clustering, K-means and self-organizing maps, to complex clustering algorithms like fuzzy clustering.

• International Journal of Internet, Broadcasting and Communication
• /
• v.14 no.2
• /
• pp.147-161
• /
• 2022

Video on demand (VOD) platforms provide immersive, inspiring, and commercial-free binge watching experiences. Recently, the number of these platform users increased dramatically as users can enjoy various contents without physical and time constraints during COVID-19. However, such platforms do not provide sufficient video censorship services while there is a strong need. In this study, we investigated the users' desire for video censorship when choosing and watching movies on VOD platforms, and how video censorship can be applied to different types of scenes to increase the censoring effect without diminishing the enjoyment. We first conducted an online survey with 98 respondents to identify the types of discomfort while watching sexual, violent, or drug-related scenes. We then conducted an in-depth online interview with 18 participants to identify the effective video filtering types and regions for each of the three scenes. Based on the findings, we suggest implications for designing a censor application for videos that contain uncomfortable scenes.

• Journal of Society of Preventive Korean Medicine
• /
• v.8 no.2
• /
• pp.157-169
• /
• 2004

We have conducted questionnaire and measured serum kidney function tests on 156 patients whom have received a treatment at a local Oriental medicine clinic in Seoul from Sept. 1, 2002 to Dec. 31, 2002. Patients were categorized into five groups. The groups are control(10 samples), herbal extract group(41 samples), herbal pills group(5samples), western medicines(45samples), and combination group(55 samples). This study was conducted to investigate how these treatment methods can affect the kidney functions. Following results were obtained : 1) Most of the research subjects were male(103 individuals) living in large urban area, with a drinking habit, highly educated, and with normal marriage. For the treatment history, 45 individuals received western medicine treatment(28.85%), 46 with Oriental medicine(29.49%), and 55patients (35.26%) experienced both forms of the treatment. 2) For measuring Mean(SD) of serum kidney functions for all the research subjects, Bun was 12.16(3.90)g/dl, 0.51(0.19) g/dl for Creatinine, and 4.64(1.49)g/dl for Uric acid. All the measurements were within the normal range. 3) Confounding variables which may affect the kidney functions such as age, smoking, drinking, occupation, and residency were eliminated in calculation and no significant differences were witnessed between the control and experiment groups. 4) In measuring affects of treatment duration on the kidney functions, no statistical significances were shown in multiple regression's ${\beta}(SE)$ values. 5) Correlations affecting the kidney functions are duration of drinking, drinking volume per round, drinking volume per week, smoking, gender, and age difference caused significant correlations. From the above results, we can deduce that taking herbal and western medicine didn't cause significant effects between the control and experiment groups in the kidney functions. Further research is needed in this field to verify this evidence by adding odds ratios and etc.

• Communications for Statistical Applications and Methods
• /
• v.29 no.4
• /
• pp.421-439
• /
• 2022

Phase I dose-finding trials are essential in drug development. By finding the maximum tolerated dose (MTD) of a new drug or treatment, a Phase I trial establishes the recommended doses for later-phase testing. The primary toxicity endpoint of interest is often a binary variable, which describes an event of a patient who experiences dose-limiting toxicity. However, there is a growing interest in dose-finding studies regarding non-binary outcomes, defined by either the weighted sum of rates of various toxicity grades or a continuous outcome. Although several novel methods have been proposed in the literature, accessible software is still lacking to implement these methods. This study introduces a newly developed R package, UnifiedDoseFinding, which implements three phase I dose-finding methods with non-binary outcomes (Quasi- and Robust Quasi-CRM designs by Yuan et al. (2007) and Pan et al. (2014), gBOIN design by Mu et al. (2019), and by a method by Ivanova and Kim (2009)). For each of the methods, UnifiedDoseFinding provides corresponding functions that begin with next that determines the dose for the next cohort of patients, select, which selects the MTD defined by the non-binary toxicity endpoint when the trial is completed, and get oc, which obtains the operating characteristics. Three real examples are provided to help practitioners use these methods. The R package UnifiedDoseFinding, which is accessible in R CRAN, provides a user-friendly tool to facilitate the implementation of innovative dose-finding studies with nonbinary outcomes.