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Integrated genome sizing (IGS) approach for the parallelization of whole genome analysis
Sona, Peter,Hong, Jong Hui,Lee, Sunho,Kim, Byong Joon,Hong, Woon-Young,Jung, Jongcheol,Kim, Han-Na,Kim, Hyung-Lae,Christopher, David,Herviou, Laurent,Im, Young Hwan,Lee, Kwee-Yum,Kim, Tae Soon,Jung, J BioMed Central 2018 BMC bioinformatics Vol.19 No.1
<P><B>Background</B></P><P>The use of whole genome sequence has increased recently with rapid progression of next-generation sequencing (NGS) technologies. However, storing raw sequence reads to perform large-scale genome analysis pose hardware challenges. Despite advancement in genome analytic platforms, efficient approaches remain relevant especially as applied to the human genome. In this study, an Integrated Genome Sizing (IGS) approach is adopted to speed up multiple whole genome analysis in high-performance computing (HPC) environment. The approach splits a genome (GRCh37) into 630 chunks (fragments) wherein multiple chunks can simultaneously be parallelized for sequence analyses across cohorts.</P><P><B>Results</B></P><P>IGS was integrated on Maha-Fs (HPC) system, to provide the parallelization required to analyze 2504 whole genomes. Using a single reference pilot genome, NA12878, we compared the NGS process time between Maha-Fs (NFS SATA hard disk drive) and SGI-UV300 (solid state drive memory). It was observed that SGI-UV300 was faster, having 32.5 mins of process time, while that of the Maha-Fs was 55.2 mins.</P><P><B>Conclusions</B></P><P>The implementation of IGS can leverage the ability of HPC systems to analyze multiple genomes simultaneously. We believe this approach will accelerate research advancement in personalized genomic medicine. Our method is comparable to the fastest methods for sequence alignment.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (10.1186/s12859-018-2499-1) contains supplementary material, which is available to authorized users.</P>
Artificial Intelligence in Diagnostic Dermatology
( Jung-im Na ) 한국피부장벽학회 2020 한국피부장벽학회지 Vol.22 No.1
Recent advancement of deep learning technologies enabled expert-level image classification. Artificial intelligence (AI) algorithms showing dermatologist-level performances or surpassing dermatologists have been reported. Most AI studies have been focused to binary classification of malignant versus benign skin tumors, especially melanoma versus nevi, either from standard digital photographs or dermoscopic images. Recent AI studies are expanding to multiclass-classification of various skin diseases including infectious and inflammatory conditions. Studies for dermatopathology are also increasing. However, the use of AI in real practices still requires further substantiation by data and prospective studies. Cinicians need to understand benefits and limitations of current AI algorithms.
Artificial Intelligence in Diagnostic Dermatology
( Jung-im Na ) 한국피부장벽학회 2020 한국피부장벽학회지 Vol.22 No.1
Artificial intelligence (AI) is gaining high visibility in diagnostic dermatology. Algorithms showing dermatologist-level performances or surpassing dermatologists have been reported. Most AI applications focus on differentiating malignant and benign skin lesions, however, other applications such as differentiating inflammatory and infectious skin diseases are increasingly available. Although many applications are technologically feasible, there is a strong need for clinical validation of these applications. This review summarizes research on the automated classification of skin lesions for diagnostic dermatology and discusses barriers to clinical application.
( Jung Im Na ),( Sang Young Byun ),( Mi Young Jeong ),( Kyoung Chan Park ),( Chang Hun Huh ) 대한피부과학회 2014 Annals of Dermatology Vol.26 No.6
Background: Formaldehyde (FA) and other volatile organic compounds (VOCs) are considered among the main causes of atopic aggravation. Their main sources include wallpapers, paints, adhesives, and flooring materials. Objective: To assess the effects of environmentally friendly wallpaper and flooring material on indoor air quality and atopic dermatitis severity. Methods: Thirty patients with atopic dermatitis were enrolled in this study. To improve air quality, the wallpaper and flooring in the homes of the subjects were replaced with plant- or silica-based materials. The indoor air concentration of FA and the total VOCs (TVOCs) were measured before remodeling and 2, 6, and 10 weeks thereafter. Pruritus and the severity of atopic eczema were evaluated by using a questionnaire and the eczema area and severity index (EASI) score before and at 4, 8, and 12 weeks after remodeling. The subjects were instructed to continue their therapy for atopic dermatitis. Results: The houses of 24 subjects were remodeled; all subjects completed the study. The concentration of FA in ambient air significantly decreased within 2 weeks after remodeling. The TVOC level showed a decrease at week 2 but increased again at weeks 6 and 10. The reduction of pruritus and EASI score was statistically significant in patients whose baseline EASI score was >3. Conclusion: Replacing the wallpaper and flooring of houses with environmentally friendly material reduced FA in ambient air and improved pruritus and the severity of atopic eczema. The improvement of pruritus and eczema was statistically significant in patients whose baseline EASI score was >3. (Ann Dermatol 26(6) 688∼692, 2014)
( Jung Im Na ),( Jung Won Shin ),( Sang Young Byun ),( Hye Ryung Choi ),( Kyoung Chan Park ) 대한피부과학회 2014 대한피부과학회 학술발표대회집 Vol.66 No.2
Background: There are many whitening agents for melasma treatment, but in aspects of potency and safety, few treatment agents exist. To evaluate whitening agents we previoulsy suggested a new parameter: a ratio of lesion/non-lesional melanin index (MI ratio) to compensate the seasonal effects. Objectives: In this study, we evaluated the efficacy of 4n-butyl resorcinol and resveratrol containing cream using MI ratio and compared the efficacy with other whitening agents. Methods: 21 females with melasma were enrolled. Subjects used 4n-butyl resorcinol and resveratrol containing cream for 4 weeks. Skin color of the lesional and preauricular non-lesional skin was measured with a Mexameter at baseline, week 2 and week 4, and MI ratio was obtained. To compare the efficacy with other whitening agents for melasma, MI ratio was obtained from the data of seven other clinical trials performed in Seoul National University Bundang Hospital. Results: Mean MI of lesional skin decreased from 201.1 to 189.4 at week 2 and 182.8 at week 4, and the difference was statistically significant from week 2. MI ratio decreased from 155.9% at baseline to 142.5% at week 4 (-13.4%). This result was compared with that of seven other clinical trials on whitening agents. Among eight different whitening agents, 4n-butyl resorcinol and resveratrol containing cream showed the biggest decrease of MI ratio at week 4. Conclusion: 4n-butyl resorcinol and resveratrol containing cream has fast and potent whitening effect on melasma.