1.Genome Characterization of Streptococcus mitis KHUD 011 Isolated from the Oral Microbiome of a Healthy Korean Individual
Eun-Young JANG ; Doyun KU ; Seok Bin YANG ; Cheul KIM ; Jae-Hyung LEE ; Ji-Hoi MOON
Journal of Korean Dental Science 2025;18(1):20-29
Purpose:
This study aimed to perform a genome characterization of Streptococcus mitis KHUD 011, a strain isolated from the oral microbiome of a healthy Korean individual, and to compare its genomic features with other S. mitis strains.
Materials and Methods:
The strain was identified through 16S rRNA gene sequencing, and its genome was sequenced using the PacBio Sequel II platform. De novo assembly and annotation were performed, followed by comparative genomic analysis with three additional strains (S. mitis NCTC 12261, S022-V3-A4, and B6). Pan-genome and phylogenetic analyses were conducted to identify strain-specific genes and assess inter-strain genomic diversity.
Results:
The genome of S. mitis KHUD 011 consisted of 1,782 protein-coding genes, with a G+C content of 40.24%. Pan-genome analysis identified 1,263 core gene clusters (50.0%), 496 dispensable clusters (19.7%), and 763 strain-specific clusters (30.3%). KHUD 011 displayed 88 strain-specific genes, particularly associated with cell wall/membrane biogenesis, transcriptional regulation, and carbohydrate metabolism. Phylogenetic analysis placed KHUD 011 closely with NCTC 12261, forming a distinct cluster apart from other strains.
Conclusion
The genome characterization of S. mitis KHUD 011 underscores substantial inter-strain genomic diversity influenced by host interactions, ecological niches, and health status. The identified strain-specific genes, particularly those associated with cell wall/ membrane biogenesis, transcriptional regulation, and carbohydrate metabolism, suggest adaptations to the oral microbiome and its interaction with the host. These findings highlight the ecological versatility of S. mitis and the importance of exploring strains from diverse environments to better understand their role within the host and the broader microbiome.
2.Cognitive Impairment Screening Test in Korea as a Screening Tool for Dementia: The Correlation Study of Subtest Scores With Korean Version of the Mini Mental State Examination 2nd Edition
Minseong KIM ; Doyun HEO ; Seonkyeong KIM ; Yunjin LEE ; Yong Sung KIM ; Wonjae SUNG ; Hee-Jin KIM
Dementia and Neurocognitive Disorders 2025;24(2):126-134
Background:
and Purpose: The Cognitive Impairment Screening Test in Korea (CIST-K) was designed to detect cognitive decline. Developed independently and widely used in Korea, it is yet to be validated with other screening tests. This study aimed to introduce normative data to the CIST-K and assess its clinical usefulness through correlation analysis with the Korean version of the Mini-Mental State Examination, 2nd edition (K-MMSE-2).
Methods:
We enrolled 85 participants from a tertiary university hospital in Korea, including patients diagnosed with mild cognitive impairment and Alzheimer’s disease by experienced neurologists. Both the CIST-K and K-MMSE-2 were administered to assess the cognitive function of the participants, with scores from each subtest of the neuropsychological tests compared.
Results:
Multivariate correlation analysis, which was adjusted for age, sex, and education level, revealed a significant correlation between the two tests in orientation, memory, and attention. However, no significant correlation was found between the two tests in visuospatial and language functions.
Conclusions
In conclusion, this study demonstrates that some subtests in the CIST-K align with corresponding scores on the K-MMSE-2. However, caution is advised when interpreting visuospatial and language test scores from the CIST-K. Further validity studies are necessary to enhance the sensitivity of each subtest.
3.Genome Characterization of Streptococcus mitis KHUD 011 Isolated from the Oral Microbiome of a Healthy Korean Individual
Eun-Young JANG ; Doyun KU ; Seok Bin YANG ; Cheul KIM ; Jae-Hyung LEE ; Ji-Hoi MOON
Journal of Korean Dental Science 2025;18(1):20-29
Purpose:
This study aimed to perform a genome characterization of Streptococcus mitis KHUD 011, a strain isolated from the oral microbiome of a healthy Korean individual, and to compare its genomic features with other S. mitis strains.
Materials and Methods:
The strain was identified through 16S rRNA gene sequencing, and its genome was sequenced using the PacBio Sequel II platform. De novo assembly and annotation were performed, followed by comparative genomic analysis with three additional strains (S. mitis NCTC 12261, S022-V3-A4, and B6). Pan-genome and phylogenetic analyses were conducted to identify strain-specific genes and assess inter-strain genomic diversity.
Results:
The genome of S. mitis KHUD 011 consisted of 1,782 protein-coding genes, with a G+C content of 40.24%. Pan-genome analysis identified 1,263 core gene clusters (50.0%), 496 dispensable clusters (19.7%), and 763 strain-specific clusters (30.3%). KHUD 011 displayed 88 strain-specific genes, particularly associated with cell wall/membrane biogenesis, transcriptional regulation, and carbohydrate metabolism. Phylogenetic analysis placed KHUD 011 closely with NCTC 12261, forming a distinct cluster apart from other strains.
Conclusion
The genome characterization of S. mitis KHUD 011 underscores substantial inter-strain genomic diversity influenced by host interactions, ecological niches, and health status. The identified strain-specific genes, particularly those associated with cell wall/ membrane biogenesis, transcriptional regulation, and carbohydrate metabolism, suggest adaptations to the oral microbiome and its interaction with the host. These findings highlight the ecological versatility of S. mitis and the importance of exploring strains from diverse environments to better understand their role within the host and the broader microbiome.
4.Genome Characterization of Streptococcus mitis KHUD 011 Isolated from the Oral Microbiome of a Healthy Korean Individual
Eun-Young JANG ; Doyun KU ; Seok Bin YANG ; Cheul KIM ; Jae-Hyung LEE ; Ji-Hoi MOON
Journal of Korean Dental Science 2025;18(1):20-29
Purpose:
This study aimed to perform a genome characterization of Streptococcus mitis KHUD 011, a strain isolated from the oral microbiome of a healthy Korean individual, and to compare its genomic features with other S. mitis strains.
Materials and Methods:
The strain was identified through 16S rRNA gene sequencing, and its genome was sequenced using the PacBio Sequel II platform. De novo assembly and annotation were performed, followed by comparative genomic analysis with three additional strains (S. mitis NCTC 12261, S022-V3-A4, and B6). Pan-genome and phylogenetic analyses were conducted to identify strain-specific genes and assess inter-strain genomic diversity.
Results:
The genome of S. mitis KHUD 011 consisted of 1,782 protein-coding genes, with a G+C content of 40.24%. Pan-genome analysis identified 1,263 core gene clusters (50.0%), 496 dispensable clusters (19.7%), and 763 strain-specific clusters (30.3%). KHUD 011 displayed 88 strain-specific genes, particularly associated with cell wall/membrane biogenesis, transcriptional regulation, and carbohydrate metabolism. Phylogenetic analysis placed KHUD 011 closely with NCTC 12261, forming a distinct cluster apart from other strains.
Conclusion
The genome characterization of S. mitis KHUD 011 underscores substantial inter-strain genomic diversity influenced by host interactions, ecological niches, and health status. The identified strain-specific genes, particularly those associated with cell wall/ membrane biogenesis, transcriptional regulation, and carbohydrate metabolism, suggest adaptations to the oral microbiome and its interaction with the host. These findings highlight the ecological versatility of S. mitis and the importance of exploring strains from diverse environments to better understand their role within the host and the broader microbiome.
5.Genome Characterization of Streptococcus mitis KHUD 011 Isolated from the Oral Microbiome of a Healthy Korean Individual
Eun-Young JANG ; Doyun KU ; Seok Bin YANG ; Cheul KIM ; Jae-Hyung LEE ; Ji-Hoi MOON
Journal of Korean Dental Science 2025;18(1):20-29
Purpose:
This study aimed to perform a genome characterization of Streptococcus mitis KHUD 011, a strain isolated from the oral microbiome of a healthy Korean individual, and to compare its genomic features with other S. mitis strains.
Materials and Methods:
The strain was identified through 16S rRNA gene sequencing, and its genome was sequenced using the PacBio Sequel II platform. De novo assembly and annotation were performed, followed by comparative genomic analysis with three additional strains (S. mitis NCTC 12261, S022-V3-A4, and B6). Pan-genome and phylogenetic analyses were conducted to identify strain-specific genes and assess inter-strain genomic diversity.
Results:
The genome of S. mitis KHUD 011 consisted of 1,782 protein-coding genes, with a G+C content of 40.24%. Pan-genome analysis identified 1,263 core gene clusters (50.0%), 496 dispensable clusters (19.7%), and 763 strain-specific clusters (30.3%). KHUD 011 displayed 88 strain-specific genes, particularly associated with cell wall/membrane biogenesis, transcriptional regulation, and carbohydrate metabolism. Phylogenetic analysis placed KHUD 011 closely with NCTC 12261, forming a distinct cluster apart from other strains.
Conclusion
The genome characterization of S. mitis KHUD 011 underscores substantial inter-strain genomic diversity influenced by host interactions, ecological niches, and health status. The identified strain-specific genes, particularly those associated with cell wall/ membrane biogenesis, transcriptional regulation, and carbohydrate metabolism, suggest adaptations to the oral microbiome and its interaction with the host. These findings highlight the ecological versatility of S. mitis and the importance of exploring strains from diverse environments to better understand their role within the host and the broader microbiome.
6.Cognitive Impairment Screening Test in Korea as a Screening Tool for Dementia: The Correlation Study of Subtest Scores With Korean Version of the Mini Mental State Examination 2nd Edition
Minseong KIM ; Doyun HEO ; Seonkyeong KIM ; Yunjin LEE ; Yong Sung KIM ; Wonjae SUNG ; Hee-Jin KIM
Dementia and Neurocognitive Disorders 2025;24(2):126-134
Background:
and Purpose: The Cognitive Impairment Screening Test in Korea (CIST-K) was designed to detect cognitive decline. Developed independently and widely used in Korea, it is yet to be validated with other screening tests. This study aimed to introduce normative data to the CIST-K and assess its clinical usefulness through correlation analysis with the Korean version of the Mini-Mental State Examination, 2nd edition (K-MMSE-2).
Methods:
We enrolled 85 participants from a tertiary university hospital in Korea, including patients diagnosed with mild cognitive impairment and Alzheimer’s disease by experienced neurologists. Both the CIST-K and K-MMSE-2 were administered to assess the cognitive function of the participants, with scores from each subtest of the neuropsychological tests compared.
Results:
Multivariate correlation analysis, which was adjusted for age, sex, and education level, revealed a significant correlation between the two tests in orientation, memory, and attention. However, no significant correlation was found between the two tests in visuospatial and language functions.
Conclusions
In conclusion, this study demonstrates that some subtests in the CIST-K align with corresponding scores on the K-MMSE-2. However, caution is advised when interpreting visuospatial and language test scores from the CIST-K. Further validity studies are necessary to enhance the sensitivity of each subtest.
7.Cognitive Impairment Screening Test in Korea as a Screening Tool for Dementia: The Correlation Study of Subtest Scores With Korean Version of the Mini Mental State Examination 2nd Edition
Minseong KIM ; Doyun HEO ; Seonkyeong KIM ; Yunjin LEE ; Yong Sung KIM ; Wonjae SUNG ; Hee-Jin KIM
Dementia and Neurocognitive Disorders 2025;24(2):126-134
Background:
and Purpose: The Cognitive Impairment Screening Test in Korea (CIST-K) was designed to detect cognitive decline. Developed independently and widely used in Korea, it is yet to be validated with other screening tests. This study aimed to introduce normative data to the CIST-K and assess its clinical usefulness through correlation analysis with the Korean version of the Mini-Mental State Examination, 2nd edition (K-MMSE-2).
Methods:
We enrolled 85 participants from a tertiary university hospital in Korea, including patients diagnosed with mild cognitive impairment and Alzheimer’s disease by experienced neurologists. Both the CIST-K and K-MMSE-2 were administered to assess the cognitive function of the participants, with scores from each subtest of the neuropsychological tests compared.
Results:
Multivariate correlation analysis, which was adjusted for age, sex, and education level, revealed a significant correlation between the two tests in orientation, memory, and attention. However, no significant correlation was found between the two tests in visuospatial and language functions.
Conclusions
In conclusion, this study demonstrates that some subtests in the CIST-K align with corresponding scores on the K-MMSE-2. However, caution is advised when interpreting visuospatial and language test scores from the CIST-K. Further validity studies are necessary to enhance the sensitivity of each subtest.
8.Cognitive Impairment Screening Test in Korea as a Screening Tool for Dementia: The Correlation Study of Subtest Scores With Korean Version of the Mini Mental State Examination 2nd Edition
Minseong KIM ; Doyun HEO ; Seonkyeong KIM ; Yunjin LEE ; Yong Sung KIM ; Wonjae SUNG ; Hee-Jin KIM
Dementia and Neurocognitive Disorders 2025;24(2):126-134
Background:
and Purpose: The Cognitive Impairment Screening Test in Korea (CIST-K) was designed to detect cognitive decline. Developed independently and widely used in Korea, it is yet to be validated with other screening tests. This study aimed to introduce normative data to the CIST-K and assess its clinical usefulness through correlation analysis with the Korean version of the Mini-Mental State Examination, 2nd edition (K-MMSE-2).
Methods:
We enrolled 85 participants from a tertiary university hospital in Korea, including patients diagnosed with mild cognitive impairment and Alzheimer’s disease by experienced neurologists. Both the CIST-K and K-MMSE-2 were administered to assess the cognitive function of the participants, with scores from each subtest of the neuropsychological tests compared.
Results:
Multivariate correlation analysis, which was adjusted for age, sex, and education level, revealed a significant correlation between the two tests in orientation, memory, and attention. However, no significant correlation was found between the two tests in visuospatial and language functions.
Conclusions
In conclusion, this study demonstrates that some subtests in the CIST-K align with corresponding scores on the K-MMSE-2. However, caution is advised when interpreting visuospatial and language test scores from the CIST-K. Further validity studies are necessary to enhance the sensitivity of each subtest.
9.Changes in Revision Cochlear Implantation and Device Failure Profiles
Bokhyun SONG ; Subi OH ; Doyun KIM ; Young Sang CHO ; Il Joon MOON
Clinical and Experimental Otorhinolaryngology 2024;17(1):37-45
Objectives:
. As cochlear implantation (CI) experiences rapid innovations and its indications expand, the characteristics of revision CI (RCI) are evolving. This study investigated changes in the RCI profile and explored their clinical implications.
Methods:
. A retrospective chart review was conducted of all CIs performed at a tertiary medical institution between October 2001 and January 2023. The rates of and reasons for RCI were evaluated in relation to the manufacturer and device model. Kaplan-Meier analysis was employed to examine cumulative and device survival curves. Cumulative and device survival rates were additionally analyzed based on age group, period of primary CI, and manufacturer. A Cox proportional hazards model was employed to evaluate the association between RCI and the device manufacturer.
Results:
. Among 1,430 CIs, 73 (5.1%) required RCI. The predominant reason for RCI was device failure (40 of 73 RCIs [54.8%]), with an overall device failure rate of 2.8%. This was followed by flap-associated problems and migration (nine of 73 RCIs each [12.3%]). Flap retention issues emerged as a new cause in three cases (two involving the CI 632 and one involving the SYNCHRONY 2 implant), and six instances of electrode tip fold-over arose (four for the CI 600 series and two for the CI 500 series). The overall 10-year cumulative and device survival rates were 93.4% and 95.8%, respectively. After excluding models with recall issues, significant differences in cumulative (P =0.010) and device (P =0.001) survival rates were observed across manufacturers.
Conclusion
. While the overall CI survival rate is stable, device failure persists as the predominant reason for RCI. Moreover, the types of complications leading to revision (including issues with flap retention and electrode tip fold-over) have shifted, particularly for newer implant models. Given the clinical importance of device failure and subsequent reoperation, clinicians should remain informed about and responsive to these trends.
10.An Automated Cell Detection Method for TH-positive Dopaminergic Neurons in a Mouse Model of Parkinson’s Disease Using Convolutional Neural Networks
Doyun KIM ; Myeong Seong BAK ; Haney PARK ; In Seon BAEK ; Geehoon CHUNG ; Jae Hyun PARK ; Sora AHN ; Seon-Young PARK ; Hyunsu BAE ; Hi-Joon PARK ; Sun Kwang KIM
Experimental Neurobiology 2023;32(3):181-194
Quantification of tyrosine hydroxylase (TH)-positive neurons is essential for the preclinical study of Parkinson’s disease (PD). However, manual analysis of immunohistochemical (IHC) images is labor-intensive and has less reproducibility due to the lack of objectivity. Therefore, several automated methods of IHC image analysis have been proposed, although they have limitations of low accuracy and difficulties in practical use. Here, we developed a convolutional neural network-based machine learning algorithm for TH+ cell counting. The developed analytical tool showed higher accuracy than the conventional methods and could be used under diverse experimental conditions of image staining intensity, brightness, and contrast. Our automated cell detection algorithm is available for free and has an intelligible graphical user interface for cell counting to assist practical applications. Overall, we expect that the proposed TH+ cell counting tool will promote preclinical PD research by saving time and enabling objective analysis of IHC images.

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