• Proceeding of EDISON Challenge
• /
• 2014.03a
• /
• pp.63-74
• /
• 2014

Predicting protein loop structures is an important modeling problem since protein loops are often involved in diverse biological functions by participating in enzyme active sites, ligand binding sites, etc. However, loop structure prediction is difficult even when structures of homologous proteins are known due to large sequence and structure variability among loops of homologous proteins. Therefore, an ab initio approach is necessary to solve loop modeling problems. One of the difficulties in the development of ab initio loop modeling method is to derive an accurate scoring function that closely approximates the true free energy function. In particular, entropy as well as energy contribution have to be considered adequately for loops because loops tend to be flexible compared to other parts of protein. In this study, the contribution of conformational entropy is considered in scoring loop conformations by employing "colony energy" which was previously proposed to estimate the free energy for an ensemble of conformations. Loop conformations were generated by using two EDISON_Chem programs GalaxyFill and GalaxySC, and colony energy was designed for this sampling by tuning relevant parameters. On a test set of 40 loops, the accuracy of predicted loop structure improved on average by scoring with the colony energy compared to scoring by energy alone. In addition, high correlation between colony energy and deviation from the native structure suggested that more extensive sampling can further improve the prediction accuracy. In another test on 6 ligand-binding loops that show conformational changes by ligand binding, both ligand-free and ligand-bound states could be identified by using colony energy when no information on the ligand-bound conformation is used.

• Bulletin of the Korean Chemical Society
• /
• v.29 no.5
• /
• pp.921-927
• /
• 2008

Discovery of $\alpha$-glucosidase inhibitors has been actively pursued with the aim to develop therapeutics for the treatment of diabetes and the other carbohydrate mediated diseases. As a method for the discovery of new novel inhibitors of $\alpha$-glucosidase, we have addressed the performance of the computer-aided drug design protocol involving the homology modeling of $\alpha$-glucosidase and the structure-based virtual screening with the two docking tools: FlexX and the automated and improved AutoDock implementing the effects of ligand solvation in the scoring function. The homology modeling of $\alpha$-glucosidase from baker’s yeast provides a high-quality 3-D structure enabling the structure-based inhibitor design. Of the two docking programs under consideration, AutoDock is found to be more accurate than FlexX in terms of scoring putative ligands to the extent of 5-fold enhancement of hit rate in database screening when 1% of database coverage is used as a cutoff. A detailed binding mode analysis of the known inhibitors shows that they can be stabilized in the active site of $\alpha$- glucosidase through the simultaneous establishment of the multiple hydrogen bond and hydrophobic interactions. The present study demonstrates the usefulness of the automated AutoDock program with the improved scoring function as a docking tool for virtual screening of new $\alpha$-glucosidase inhibitors as well as for binding mode analysis to elucidate the activities of known inhibitors.

• Radiation Oncology Journal
• /
• v.7 no.2
• /
• pp.189-196
• /
• 1989

Twenty five patients with tumors of the brain stem were treated with radiotherapy between 1979 and 1987. Histological diagnosis could be obtained in 6 cases, and other 19 patients were diagnosed by neurologic findings and CT or MRI. Eighteen patients were treated by radical radiotherapy and 6 patients received both operation and radiotherapy, while 1 patient received chemotherapy after radiotherapy. Total dose ranged from 50 Gy to 55 Gy. By an clinical scoring scale at 2 months after radiotherapy, no complete response was obtained, but 16 cases achieved partial response, 2 cases were stable, and 4 cases were deteriorated. The overall survival rate at 3 years was $36\%$ Age, performance status at diagnosis, degree of cranial nerve involvement, CT pattern of post-contrast enhancement, and clinical responese by scoring scale were correlated with survival.

• Journal of the Korea Institute of Information and Communication Engineering
• /
• v.11 no.10
• /
• pp.1880-1885
• /
• 2007

In this paper, we propose the method that improve the performance of the Mowse. Mowse is the tool of the peptide mass fingerprinting that is used the identification of protein. In Mowse, frequency factor matrix is generated to regular interval for protein and peptide mass and the value of each elements is calculated to frequency of peptide. We propose new method for calculation of exact scoring value maintaining same size of matrix. The proposed method is that decide interval of matrix considering distribution of protein database. That is, interval of matrix is decided to small in many value of protein mass and is decided to large in few value of protein mass. We present the performance result both Mowse scoring method and the proposed scoring method.

• Journal of the Korea Institute of Information Security & Cryptology
• /
• v.22 no.3
• /
• pp.601-613
• /
• 2012

It is required to design and implement secure web applications to provide safe web services. For this reason, there are several scoring frameworks to measure vulnerabilities in web applications. However, these frameworks do not classify according to seriousness of vulnerability because these frameworks simply accumulate score of individual factors in a vulnerability. We rate and score vulnerabilities according to probability of privilege acquisition so that we can prioritize vulnerabilities found in web applications. Also, our proposed framework provides a method to score all web applications provided by an organization so that which web applications is the worst secure and should be treated first. Our scoring framework is applied to the data which lists vulnerabilities in web applications found by a web scanner based on crawling, and we show the importance of categorizing vulnerabilities according to privilege acquisition.

• Applied Microscopy
• /
• v.51
• /
• pp.4.1-4.12
• /
• 2021

Fluorescence in situ hybridization (FISH) is a technique to visualize specific DNA/RNA sequences within the cell nuclei and provide the presence, location and structural integrity of genes on chromosomes. A confocal Whole Slide Imaging (WSI) scanner technology has superior depth resolution compared to wide-field fluorescence imaging. Confocal WSI has the ability to perform serial optical sections with specimen imaging, which is critical for 3D tissue reconstruction for volumetric spatial analysis. The standard clinical manual scoring for FISH is labor-intensive, time-consuming and subjective. Application of multi-gene FISH analysis alongside 3D imaging, significantly increase the level of complexity required for an accurate 3D analysis. Therefore, the purpose of this study is to establish automated 3D FISH scoring for z-stack images from confocal WSI scanner. The algorithm and the application we developed, SHIMARIS PAFQ, successfully employs 3D calculations for clear individual cell nuclei segmentation, gene signals detection and distribution of break-apart probes signal patterns, including standard break-apart, and variant patterns due to truncation, and deletion, etc. The analysis was accurate and precise when compared with ground truth clinical manual counting and scoring reported in ten lymphoma and solid tumors cases. The algorithm and the application we developed, SHIMARIS PAFQ, is objective and more efficient than the conventional procedure. It enables the automated counting of more nuclei, precisely detecting additional abnormal signal variations in nuclei patterns and analyzes gigabyte multi-layer stacking imaging data of tissue samples from patients. Currently, we are developing a deep learning algorithm for automated tumor area detection to be integrated with SHIMARIS PAFQ.

• Journal of Practical Engineering Education
• /
• v.15 no.1
• /
• pp.193-198
• /
• 2023

This paper analyzed the validity of exercise problems for each unit in Python programming education. Practice questions presented for each unit are presented through an online learning system, and each student uploads an answer code and is automatically graded. Data such as students' mid-term exam scores, final exam scores, and practice questions scores for each unit are collected through Python lecture that lasts for one semester. Through the collected data, it is possible to improve the exercise problems for each unit by analyzing the validity of the automatic scoring exercise problems. In this paper, Orange machine learning tool was used to analyze the validity of automatic scoring exercises. The data collected in the Python subject are analyzed and compared comprehensively by total, top, and bottom groups. From the prediction accuracy of the machine learning model that predicts the student's final grade from the Python unit-by-unit practice problem scores, the validity of the automatic scoring exercises for each unit was analyzed.

• Korean Journal of Radiology
• /
• v.22 no.9
• /
• pp.1481-1489
• /
• 2021

Objective: To construct a CT-based Fagotti scoring system by analyzing the correlations between laparoscopic findings and CT features in patients with advanced ovarian cancer. Materials and Methods: This retrospective cohort study included patients diagnosed with stage III/IV ovarian cancer who underwent diagnostic laparoscopy and debulking surgery between January 2010 and June 2018. Two radiologists independently reviewed preoperative CT scans and assessed ten CT features known as predictors of suboptimal cytoreduction. Correlation analysis between ten CT features and seven laparoscopic parameters based on the Fagotti scoring system was performed using Spearman's correlation. Variable selection and model construction were performed by logistic regression with the least absolute shrinkage and selection operator method using a predictive index value (PIV) ≥ 8 as an indicator of suboptimal cytoreduction. The final CT-based scoring system was internally validated using 5-fold cross-validation. Results: A total of 157 patients (median age, 56 years; range, 27-79 years) were evaluated. Among 120 (76.4%) patients with a PIV ≥ 8, 105 patients received neoadjuvant chemotherapy followed by interval debulking surgery, and the optimal cytoreduction rate was 90.5% (95 of 105). Among 37 (23.6%) patients with PIV < 8, 29 patients underwent primary debulking surgery, and the optimal cytoreduction rate was 93.1% (27 of 29). CT features showing significant correlations with PIV ≥ 8 were mesenteric involvement, gastro-transverse mesocolon-splenic space involvement, diaphragmatic involvement, and para-aortic lymphadenopathy. The area under the receiver operating curve of the final model for prediction of PIV ≥ 8 was 0.72 (95% confidence interval: 0.62-0.82). Conclusion: Central tumor burden and upper abdominal spread features on preoperative CT were identified as distinct predictive factors for high PIV on diagnostic laparoscopy. The CT-based PIV prediction model might be useful for patient stratification before cytoreduction surgery for advanced ovarian cancer.

• Communications of Mathematical Education
• /
• v.26 no.3
• /
• pp.251-271
• /
• 2012

The purpose of this study is: 1) to determine error sources and the effects of each error source, 2) to investigate optimal measuring conditions from holistic and analytic scoring methods, and 3) to compare the value of reliability between Cronbach's alpha and the generalizability coefficient in self-introduction letter and teacher's recommendation letter based on the generalizability theory in identification of mathematical gifted students by observations and nominations. Data of this study were collected from the science education institute for the gifted attached to the university located within in a capital city for the 2011 academic year. Scores form two raters using holistic and analytic scoring methods in both assessment types were used. The results of this study were as follows. First, as to both assessment types, error sources for people were relatively large regardless of scoring methods. However, error sources for raters in holistic scoring methods had a more significant impact than those of analytic scoring methods. Second, to set optimal measuring conditions in the self-introduction letter and teacher's recommendation letter, if we fixed the number of raters into 2 based on holistic scoring methods, at least 5 and 10 content domains were needed, respectively. In addition, the number of items in teacher's recommendation letter should be more than 3 when we fixed the number of content domains into 4, and the number of items in self-introduction letter should be more than 8 when we fixed the number of content domains into 6 using analytic scoring methods. Third, Cronbach's alpha having only a single source of errors was higher than the generalizability coefficient regardless of assessment types and scoring methods. Hence we recommend that generalizability coefficient based on various error sources such as raters, content domains, and items should be considered to keep a satisfactory level of reliability in both assessment types.

• Asian-Australasian Journal of Animal Sciences
• /
• v.24 no.11
• /
• pp.1587-1594
• /
• 2011

Live weight, body length, hip and shoulder heights, heart girth, and metatarsal length were measured on 100 one to two years old Bali (Bos javanicus) bulls. Multiple regression of these measurements on live weight gave a prediction equation involving heart girth and body length (prediction $R^2$ = 0.845). These measurements were also used to derive several frame scores (FS). Live weight (Lwt) divided by FS was used as an index of body condition. Lwt/(length+hip height) was normally distributed and highly correlated with other normally-distributed condition indexes. This index was used to define five body condition scores. These were used to develop a five-point body condition scoring system in which the amount of fleshing over the vertebral processes, ribs, hindquarters, tail head, hooks, at the top of the neck, and the shoulders, the development of wrinkles in the skin above the hock and the neck, and the size of the dewlap, were used to describe the different body condition scores. Animals of score 1 had prominent hooks, shoulders, vertebrae and ribs, and hollow hindquarters and flat tailhead. Score 5 animals had rounded hindquarters, well-filled upper hind legs, small mounds of soft tissue were apparent on the tailhead, their hooks, necks, shoulders, vertebrae and ribs were well covered, and the dewlap was prominent.