• Journal of Integrative Natural Science
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• v.3 no.1
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• pp.49-53
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• 2010

Molecular docking is a critical event which mostly forms Van der waals complex in molecular recognition. Since the majority of developed drugs are small molecules, docking them into proteins has been a prime concern in drug discovery community. Since the binding pose space is too vast to cover completely, many search algorithms such as genetic algorithm, Monte Carlo, simulated annealing, distance geometry have been developed. Proper evaluation of the quality of binding is an essential problem. Scoring functions derived from force fields handle the ligand binding prediction with the use of potential energies and sometimes in combination with solvation and entropy contributions. Knowledge-based scoring functions are based on atom pair potentials derived from structural databases. Forces and potentials are collected from known protein-ligand complexes to get a score for their binding affinities (e.g. PME). Empirical scoring functions are derived from training sets of protein-ligand complexes with determined affinity data. Because non of any single scoring function performs generally better than others, some other approaches have been tried. Although numerous scoring functions have been developed to locate the correct binding poses, it still remains a major hurdle to derive an accurate scoring function for general targets. Recently, consensus scoring functions and target specific scoring functions have been studied to overcome the current limitations.

• Bulletin of the Korean Chemical Society
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• v.33 no.2
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• pp.717-720
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• 2012

• Bulletin of the Korean Chemical Society
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• v.28 no.7
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• pp.1141-1150
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• 2007

Molecular modeling study has been performed to assist in the design of PTP1B inhibitors using FlexX. FlexX dockings with 19 test ligands, whose structures have been determined by X-ray crystallography, were successful in reproducing the experimental conformations within the protein. An increase in biological activity is observed as hydrophobic character of formylchromone derivatives increases. Most ligands bind to the activesite regions of the protein successfully in two different score runs. The Drug score run gave better results than the FlexX score run based on the score, rank, binding modes and bond distance of docked structures. Consensus values from the CScore scoring function are between 3 and 5, suggesting that the scoring scheme is reliable. All formylchromone inhibitors considered in this work show unidirectional binding modes in the active site pocket, which is contrary to the bidirectional X-ray results by Malamas et al. and amino acid residues responsible for such orientation are identified to help further development of the inhibitors.

• Journal of the Korean Academy of Child and Adolescent Psychiatry
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• v.34 no.2
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• pp.141-149
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• 2023

Objectives: Most developmental screening tests have been built as parent-performed questionnaires. However, they often do not guide parents on how to answer the questionnaire. This study aimed to develop easily applicable parent guidelines. Methods: We implemented the Delphi procedure with 20 panelists. The development of the initial questionnaire was based on the results of two surveys of parents and experts provided by a policy research report that investigated the item adequacy of the Korean Developmental Screening Test. Round one included 33 items comprising all possible measurements in six categories that were identified as difficult to understand or confusing. Round two merged and modified some items and included 32 items. We defined consensus as a median agreement value of one or less and convergence and stability values of 0.5 or less. The subjective usefulness of the parent guidelines was examined based on their previous test experiences. Results: Consensus was reached after the second round, reflecting the items with the highest level of accuracy in each category. Of the 167 parents who participated in the survey, 113 (67.7%) affirmed the usefulness of the guidelines, while 10 (6.0%) answered that they were not useful. Items that recommended a different scoring strategy in answering the questionnaire from their previous measurements were found to be more useful by the parents. Conclusion: The parent guidelines, composed of five bullet points, drew on the consensus of the experts. Further studies are required to assess whether these guidelines improve the accuracy of screening tests in clinical settings.

• 한국균학회소식:학술대회논문집
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• 2018.05a
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• pp.22-22
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• 2018

Fungal genome sequencing and assembly have been trivial in these days. Genome analysis relies on high quality of gene prediction and annotation. Automatic fungal genome annotation pipeline is essential for handling genomic sequence data accumulated exponentially. However, building an automatic annotation procedure for fungal genomes is not an easy task. FunGAP (Fungal Genome Annotation Pipeline) is developed for precise and accurate prediction of gene models from any fungal genome assembly. To make high-quality gene models, this pipeline employs multiple gene prediction programs encompassing ab initio, evidence-, and homology-based evaluation. FunGAP aims to evaluate all predicted genes by filtering gene models. To make a successful filtering guide for removal of false-positive genes, we used a scoring function that seeks for a consensus by estimating each gene model based on homology to the known proteins or domains. FunGAP is freely available for non-commercial users at the GitHub site (https://github.com/CompSynBioLab-KoreaUniv/FunGAP).

• Education of Primary School Mathematics
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• v.16 no.3
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• pp.229-250
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• 2013

The purpose of this study is analyzing 'observation and recommendation letter by teacher', which is being submitted to screen and enhance the utilization of gifted students in accordance with recently introduced gifted students observation, recommendation and screening system. For the purpose, this study will provide with objective securing plan of 'observation and recommendation letter by teacher' by developing an optimum evaluation model. The research findings were as follows: First, the result of analysis on the mathematically gifted students behavior characteristic as appeared in 'observation and recommendation letter by teacher' suggested that the recommending teachers have the tendency of giving superficial statement instead of giving concrete case description. When it was analyzed for frequency by the 'observation and recommendation letter by teacher' analysis framework devised by the author, the teachers showed the tendency of concentrating on specific questions. Meanwhile, there was a tendency that teachers concentrate on specific gifted behavior characteristic or area for which concrete case had been suggested. The reason is believed that such part is easy to observe and state while others are not, or, teachers did not judge the other part as the characteristic of gifted students. Second, the gifted students behavior characteristics as appeared in 'observation and recommendation letter by teacher' were made into scores by Rubric model. When the interrater reliability was analyzed based on these scores, the correlation coefficient of 1st scoring was .641. After a discussion session was taken and 2nd scoring was done 3 weeks later, the correlation coefficient of 2nd scoring increased to .732. The reason is believed that; i) the severity among scorers was adjusted by the discussion session after the 1st scoring, ii) the scorers established detail judgment standard on various situations which can appear because of the descriptive nature, and, (iii) they found a consensus on scoring for a new situation appeared. It implies that thorough understanding and application of scorers on evaluation model is as important as the development of optimum model for the differentiation of mathematically gifted elementary students.

• Archives of Plastic Surgery
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• v.41 no.2
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• pp.111-115
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• 2014

Analysis of scars in various conditions is essential, but no consensus had been reached on the scar assessment scale to select for a given condition. We reviewed papers to determine the scar assessment scale selected depending on the scar condition and treatment method. We searched PubMed for articles published since 2000 with the contents of the scar evaluation using a scar assessment scale with a Journal Citation Report impact factor >0.5. Among them, 96 articles that conducted a scar evaluation using a scar assessment scale were reviewed and analyzed. The scar assessment scales were identified and organized by various criteria. Among the types of scar assessment scales, the Patient and Observer Scar Assessment Scale (POSAS) was found to be the most frequently used scale. As for the assessment of newly developed operative scars, the POSAS was most used. Meanwhile, for categories depending on the treatment methods for preexisting scars, the Vancouver Scar Scale (VSS) was used in 6 studies following a laser treatment, the POSAS was used in 7 studies following surgical treatment, and the POSAS was used in 7 studies following a conservative treatment. Within the 12 categories of scar status, the VSS showed the highest frequency in 6 categories and the POSAS showed the highest frequency in the other 6 categories. According to our reviews, the POSAS and VSS are the most frequently used scar assessment scales. In the future, an optimal, universal scar scoring system is needed in order to better evaluate and treat pathologic scarring.

• Physical Therapy Korea
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• v.23 no.4
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• pp.71-80
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• 2016

Background: Functional capacity evaluations (FCEs) are designed to systematically assess the capacity to perform work-related tasks and to determine worker's ability to return to the previous job following work-related injuries. These evaluations may be rated either by clinician or worker. There has been a lack of consensus between the two scoring methods. Objects: This study aimed: 1) to confirm if the data are fit to the Rasch rating scale model and 2) to investigate the item-level concordance rate between the ratings of clinician and injured worker of the FCE. Methods: A cross-sectional study was conducted with a sample (n=124) of a rehabilitation program with the Occupational Rehabilitation Data Base for workers with low back pain. The functional capacity evaluation at admission and discharge was administered to clinicians and workers. The data were analyzed using both classical test theory-based Pearson's r and intra-class coefficient followed by item-level analysis with Rasch rating scale model. Results: All items of the FCE, except sitting items rated by clinician at admission and handling items rated by both clinician and worker throughout admission and discharge, were acceptable fit statistics with minor out of ranges for a misfit criterion. This may indicate that the items of the FCE overall fit to the Rasch rating scale model. Few problematic items responding differently to clinician and worker both at admission and discharge were detected with the differential item functioning analysis despite the excellent concordance rate using the two conventional statistics-sitting and handling items at admission and handling item at discharge. Conclusion: The item-level speculations using Rasch analysis of the FCE demonstrate that the ratings of clinician and self ratings of worker were psychometrically acceptable though there was an apparent discrepancy between the raters both at admission and discharge.

• Clinical and Experimental Pediatrics
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• v.60 no.4
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• pp.118-123
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• 2017

Purpose: Tuberculosis (TB) remains a problem in the community. TB patients usually experience malnutrition, which is characterized by both decreased body weight (BW) and body fat percentage (BFP). Leptin, an important regulator of BW, also plays an important role in cellular immunity, which is integral to defense against Mycobacterium tuberculosis infection. We analyzed the effect of an anti-TB treatment regimen on the leptin level, BW, and BFP of children with TB. Methods: The design of this study was a group interrupted time series. The subjects were children with probable TB according to clinical criteria based on an Indonesian scoring system adopted from the Consensus of Expert Panel. BW; BFP; energy intake; fat and protein intake; and leptin levels before, 2 months after (intensive phase), and 6 months after (continuation phase) anti-TB treatment, were measured. About 40 children, aged 5-14 years, participated in this study. Results: The BW, BFP and leptin level increased from before treatment to after completion of the intensive phase and still showed an increased during the continuation phase: BW 18.65 kg, 19.75 kg, and 20.85 kg; BFP 18.3%, 19.5%, and 20.2%; and leptin level 1.9 mg/dL, 3.07 mg/dL, and 3.4 mg/dL, respectively (P<0.01). Conclusion: Leptin level, BW, and BFP increased throughout the course of anti-TB treatment, compared with pretreatment values. Further research is needed to compare the results with data for healthy children.

• Journal of Preventive Medicine and Public Health
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• v.55 no.4
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• pp.334-341
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• 2022

Objectives: This study was conducted to develop the Mobility to Participation Assessment Scale for Stroke (MPASS) and assess its content validity, internal consistency, inter-rater and intra-rater reliability, and convergent validity in people with stroke living in the community. Methods: The MPASS was developed using published data on mobility-related activity and participation timing in elderly individuals, and then reviewed by community physical therapists. Content validity was established by reaching a consensus of experienced physical therapists in a focus group. The MPASS was scored for 32 participants with stroke (mean age 61.75±4.92 years) by 3 individual testers. Reliability was examined using the intraclass correlation coefficient (ICC), internal consistency using the Cronbach alpha coefficient (α), and convergent validity using the Pearson correlation coefficient (r) to compare the MPASS to the Modified Rivermead Mobility Index as a referent test of mobility. Results: The MPASS consists of 8 items, and its scoring system provides information on the ability of people with stroke to reach a movement level enabling them to live in society, including interactions with other people and safe living in the community. The interrater and intra-rater reliability were excellent (ICC, 0.948; 95% confidence interval [CI], 0.893 to 0.982 and ICC, 0.967; 95% CI, 0.933 to 0.989, respectively). Internal consistency was good (α=0.877). The convergent validity was moderate (r=0.646; p<0.001). Conclusions: The newly developed MPASS showed acceptable construct validity and high reliability. The MPASS is suitable for use in people with stroke, especially those who have been discharged and live in the community with the ability to initiate sitting.