1.Plasma metabolite based clustering of breast cancer survivors and identification of dietary and health related characteristics: an application of unsupervised machine learning
Ga-Eun YIE ; Woojin KYEONG ; Sihan SONG ; Zisun KIM ; Hyun Jo YOUN ; Jihyoung CHO ; Jun Won MIN ; Yoo Seok KIM ; Jung Eun LEE
Nutrition Research and Practice 2025;19(2):273-291
BACKGROUND/OBJECTIVES:
This study aimed to use plasma metabolites to identify clusters of breast cancer survivors and to compare their dietary characteristics and health-related factors across the clusters using unsupervised machine learning.
SUBJECTS/METHODS:
A total of 419 breast cancer survivors were included in this crosssectional study. We considered 30 plasma metabolites, quantified by high-throughput nuclear magnetic resonance metabolomics. Clusters were obtained based on metabolites using 4 different unsupervised clustering methods: k-means (KM), partitioning around medoids (PAM), self-organizing maps (SOM), and hierarchical agglomerative clustering (HAC). The t-test, χ2 test, and Fisher’s exact test were used to compare sociodemographic, lifestyle, clinical, and dietary characteristics across the clusters. P-values were adjusted through a false discovery rate (FDR).
RESULTS:
Two clusters were identified using the 4 methods. Participants in cluster 2 had lower concentrations of apolipoprotein A1 and large high-density lipoprotein (HDL) particles and smaller HDL particle sizes, but higher concentrations of chylomicrons and extremely large very-low-density-lipoprotein (VLDL) particles and glycoprotein acetyls, a higher ratio of monounsaturated fatty acids to total fatty acids, and larger VLDL particle sizes compared with cluster 1. Body mass index was significantly higher in cluster 2 compared with cluster 1 (FDR adjusted-PKM < 0.001; PPAM = 0.001; PSOM < 0.001; and PHAC = 0.043).
CONCLUSION
The breast cancer survivors clustered on the basis of plasma metabolites had distinct characteristics. Further prospective studies are needed to investigate the associations between metabolites, obesity, dietary factors, and breast cancer prognosis.
2.Plasma metabolite based clustering of breast cancer survivors and identification of dietary and health related characteristics: an application of unsupervised machine learning
Ga-Eun YIE ; Woojin KYEONG ; Sihan SONG ; Zisun KIM ; Hyun Jo YOUN ; Jihyoung CHO ; Jun Won MIN ; Yoo Seok KIM ; Jung Eun LEE
Nutrition Research and Practice 2025;19(2):273-291
BACKGROUND/OBJECTIVES:
This study aimed to use plasma metabolites to identify clusters of breast cancer survivors and to compare their dietary characteristics and health-related factors across the clusters using unsupervised machine learning.
SUBJECTS/METHODS:
A total of 419 breast cancer survivors were included in this crosssectional study. We considered 30 plasma metabolites, quantified by high-throughput nuclear magnetic resonance metabolomics. Clusters were obtained based on metabolites using 4 different unsupervised clustering methods: k-means (KM), partitioning around medoids (PAM), self-organizing maps (SOM), and hierarchical agglomerative clustering (HAC). The t-test, χ2 test, and Fisher’s exact test were used to compare sociodemographic, lifestyle, clinical, and dietary characteristics across the clusters. P-values were adjusted through a false discovery rate (FDR).
RESULTS:
Two clusters were identified using the 4 methods. Participants in cluster 2 had lower concentrations of apolipoprotein A1 and large high-density lipoprotein (HDL) particles and smaller HDL particle sizes, but higher concentrations of chylomicrons and extremely large very-low-density-lipoprotein (VLDL) particles and glycoprotein acetyls, a higher ratio of monounsaturated fatty acids to total fatty acids, and larger VLDL particle sizes compared with cluster 1. Body mass index was significantly higher in cluster 2 compared with cluster 1 (FDR adjusted-PKM < 0.001; PPAM = 0.001; PSOM < 0.001; and PHAC = 0.043).
CONCLUSION
The breast cancer survivors clustered on the basis of plasma metabolites had distinct characteristics. Further prospective studies are needed to investigate the associations between metabolites, obesity, dietary factors, and breast cancer prognosis.
3.Plasma metabolite based clustering of breast cancer survivors and identification of dietary and health related characteristics: an application of unsupervised machine learning
Ga-Eun YIE ; Woojin KYEONG ; Sihan SONG ; Zisun KIM ; Hyun Jo YOUN ; Jihyoung CHO ; Jun Won MIN ; Yoo Seok KIM ; Jung Eun LEE
Nutrition Research and Practice 2025;19(2):273-291
BACKGROUND/OBJECTIVES:
This study aimed to use plasma metabolites to identify clusters of breast cancer survivors and to compare their dietary characteristics and health-related factors across the clusters using unsupervised machine learning.
SUBJECTS/METHODS:
A total of 419 breast cancer survivors were included in this crosssectional study. We considered 30 plasma metabolites, quantified by high-throughput nuclear magnetic resonance metabolomics. Clusters were obtained based on metabolites using 4 different unsupervised clustering methods: k-means (KM), partitioning around medoids (PAM), self-organizing maps (SOM), and hierarchical agglomerative clustering (HAC). The t-test, χ2 test, and Fisher’s exact test were used to compare sociodemographic, lifestyle, clinical, and dietary characteristics across the clusters. P-values were adjusted through a false discovery rate (FDR).
RESULTS:
Two clusters were identified using the 4 methods. Participants in cluster 2 had lower concentrations of apolipoprotein A1 and large high-density lipoprotein (HDL) particles and smaller HDL particle sizes, but higher concentrations of chylomicrons and extremely large very-low-density-lipoprotein (VLDL) particles and glycoprotein acetyls, a higher ratio of monounsaturated fatty acids to total fatty acids, and larger VLDL particle sizes compared with cluster 1. Body mass index was significantly higher in cluster 2 compared with cluster 1 (FDR adjusted-PKM < 0.001; PPAM = 0.001; PSOM < 0.001; and PHAC = 0.043).
CONCLUSION
The breast cancer survivors clustered on the basis of plasma metabolites had distinct characteristics. Further prospective studies are needed to investigate the associations between metabolites, obesity, dietary factors, and breast cancer prognosis.
4.Plasma metabolite based clustering of breast cancer survivors and identification of dietary and health related characteristics: an application of unsupervised machine learning
Ga-Eun YIE ; Woojin KYEONG ; Sihan SONG ; Zisun KIM ; Hyun Jo YOUN ; Jihyoung CHO ; Jun Won MIN ; Yoo Seok KIM ; Jung Eun LEE
Nutrition Research and Practice 2025;19(2):273-291
BACKGROUND/OBJECTIVES:
This study aimed to use plasma metabolites to identify clusters of breast cancer survivors and to compare their dietary characteristics and health-related factors across the clusters using unsupervised machine learning.
SUBJECTS/METHODS:
A total of 419 breast cancer survivors were included in this crosssectional study. We considered 30 plasma metabolites, quantified by high-throughput nuclear magnetic resonance metabolomics. Clusters were obtained based on metabolites using 4 different unsupervised clustering methods: k-means (KM), partitioning around medoids (PAM), self-organizing maps (SOM), and hierarchical agglomerative clustering (HAC). The t-test, χ2 test, and Fisher’s exact test were used to compare sociodemographic, lifestyle, clinical, and dietary characteristics across the clusters. P-values were adjusted through a false discovery rate (FDR).
RESULTS:
Two clusters were identified using the 4 methods. Participants in cluster 2 had lower concentrations of apolipoprotein A1 and large high-density lipoprotein (HDL) particles and smaller HDL particle sizes, but higher concentrations of chylomicrons and extremely large very-low-density-lipoprotein (VLDL) particles and glycoprotein acetyls, a higher ratio of monounsaturated fatty acids to total fatty acids, and larger VLDL particle sizes compared with cluster 1. Body mass index was significantly higher in cluster 2 compared with cluster 1 (FDR adjusted-PKM < 0.001; PPAM = 0.001; PSOM < 0.001; and PHAC = 0.043).
CONCLUSION
The breast cancer survivors clustered on the basis of plasma metabolites had distinct characteristics. Further prospective studies are needed to investigate the associations between metabolites, obesity, dietary factors, and breast cancer prognosis.
5.Plasma metabolite based clustering of breast cancer survivors and identification of dietary and health related characteristics: an application of unsupervised machine learning
Ga-Eun YIE ; Woojin KYEONG ; Sihan SONG ; Zisun KIM ; Hyun Jo YOUN ; Jihyoung CHO ; Jun Won MIN ; Yoo Seok KIM ; Jung Eun LEE
Nutrition Research and Practice 2025;19(2):273-291
BACKGROUND/OBJECTIVES:
This study aimed to use plasma metabolites to identify clusters of breast cancer survivors and to compare their dietary characteristics and health-related factors across the clusters using unsupervised machine learning.
SUBJECTS/METHODS:
A total of 419 breast cancer survivors were included in this crosssectional study. We considered 30 plasma metabolites, quantified by high-throughput nuclear magnetic resonance metabolomics. Clusters were obtained based on metabolites using 4 different unsupervised clustering methods: k-means (KM), partitioning around medoids (PAM), self-organizing maps (SOM), and hierarchical agglomerative clustering (HAC). The t-test, χ2 test, and Fisher’s exact test were used to compare sociodemographic, lifestyle, clinical, and dietary characteristics across the clusters. P-values were adjusted through a false discovery rate (FDR).
RESULTS:
Two clusters were identified using the 4 methods. Participants in cluster 2 had lower concentrations of apolipoprotein A1 and large high-density lipoprotein (HDL) particles and smaller HDL particle sizes, but higher concentrations of chylomicrons and extremely large very-low-density-lipoprotein (VLDL) particles and glycoprotein acetyls, a higher ratio of monounsaturated fatty acids to total fatty acids, and larger VLDL particle sizes compared with cluster 1. Body mass index was significantly higher in cluster 2 compared with cluster 1 (FDR adjusted-PKM < 0.001; PPAM = 0.001; PSOM < 0.001; and PHAC = 0.043).
CONCLUSION
The breast cancer survivors clustered on the basis of plasma metabolites had distinct characteristics. Further prospective studies are needed to investigate the associations between metabolites, obesity, dietary factors, and breast cancer prognosis.
6.Application of cooked meat codes to improve the validity of nutrient content estimation in a recipe-based food ingredient database
Seo-Young YUN ; Hee Joe LEE ; Taenam LEE ; Ga-Eun CHOI ; Minseo CHOI ; Mi-Kyeong CHOI ; Nami JOO ; Mi-Hyun KIM ; Cho-il KIM
Nutrition Research and Practice 2025;19(6):1002-1010
BACKGROUND/OBJECTIVES:
Accurate estimation of nutrient intake from food consumption requires reliable food composition data. However, since nutrient content changes during cooking, the application of raw ingredient composition may lead to overestimation, particularly for energy and fat in meat dishes. In this study, the suitability of applying cooked food codes for meat dishes to improve the validity of recipe-based nutrient content estimation was evaluated.MATERIALS/METHODS: Pork (thin-sliced and thick-cut belly and shoulder butt) and beef (tenderloin, loin, rib meat, and brisket point) were examined for cooking yield after grilling and their nutrient contents were estimated. Each cut was portioned to 100 g of raw meat and cooked in triplicate. Nutrient content was calculated using both raw and cooked meat codes from the Korean Standard Food Composition Table, and differences in energy, fat, and protein content were compared.
RESULTS:
When grilled under standardized conditions, the average cooking yield was approximately 65% for pork and 80% for beef (P < 0.0001). Thin slices of pork belly had a lower yield (62.6%) than thicker cuts (68.0%), while beef brisket point had the lowest yield among beef cuts (63.6%). Applying cooked meat codes and measured cooking yields resulted in overall decreases in energy (−10% to −50%) and fat (−20% to −60%) content, with slight increase in protein (up to +34%, P < 0.0001). For beef tenderloin, additional comparisons using matched raw and grilled data from the United States Department of Agriculture SR Legacy Database showed smaller percent differences in energy, fat, and protein than those obtained from the Korean database.
CONCLUSION
Incorporating measured cooking yields and corresponding cooked meat codes into recipe-based databases can improve the accuracy of nutrient intake estimation. The development of nutrient databases that reflect differences in cooking conditions—including temperature, duration, and doneness—should be prioritized to enhance the validity of national dietary surveys.
7.Kidney biopsy can help to predict renal outcomes of patients with type 2 diabetes mellitus
Wook-Joon KIM ; Taehoon OH ; Nam Hun HEO ; Kyungsup KWON ; Ga-Eun SHIN ; Se-Hwi JEONG ; Ji Hye LEE ; Samel PARK ; Nam-Jun CHO ; Hyo-Wook GIL ; Eun Young LEE
Kidney Research and Clinical Practice 2025;44(1):91-101
In patients with type 2 diabetes mellitus (T2DM), diabetic kidney disease (DKD) is diagnosed based on clinical features. A kidney biopsy is used only in selected cases. This study aimed to reconsider the role of a biopsy in predicting renal outcomes. Methods: Clinical and laboratory parameters and renal biopsy results were obtained from 237 patients with T2DM who underwent renal biopsies at Soonchunhyang University Cheonan Hospital between January 2000 and March 2020 and were analyzed. Results: Of 237 diabetic patients, 29.1% had DKD only, 61.6% had non-DKD (NDKD), and 9.3% had DKD with coexisting NDKD (DKD/NDKD). Of the patients with DKD alone, 43.5% progressed to end-stage kidney disease (ESKD), while 15.8% of NDKD patients and 36.4% of DKD/NDKD patients progressed to ESKD (p < 0.001). In the DKD-alone group, pathologic features like ≥50% global sclerosis (p < 0.001), tubular atrophy (p < 0.001), interstitial fibrosis (p < 0.001), interstitial inflammation (p < 0.001), and the presence of hyalinosis (p = 0.03) were related to worse renal outcomes. The Cox regression model showed a higher risk of progression to ESKD in the DKD/NDKD group compared to the DKD-alone group (hazard ratio [HR], 2.73; p = 0.032), ≥50% global sclerosis (HR, 3.88; p < 0.001), and the degree of mesangial expansion (moderate: HR, 2.45; p = 0.045 and severe: HR, 6.22; p < 0.001). Conclusion: In patients with T2DM, a kidney biopsy can help in identifying patients with NDKD for appropriate treatment, and it has predictive value.
8.Development of an Instrument for Slit-lamp Examination of Donor Corneas in Preservation Medium
Ga Hee NAM ; Da Ran KIM ; Young Chae YOON ; Soon Won YANG ; Woong Joo WHANG ; Yong-Soo BYUN ; Hyung Bin HWANG ; Kyung Sun NA ; Hyun Soo LEE ; So Hyang CHUNG ; Eun Chul KIM ; Yang Kyung CHO ; Hyun Seung KIM ; Ho Sik HWANG
Journal of the Korean Ophthalmological Society 2024;65(2):108-116
Purpose:
To evaluate the effectiveness of an instrument devised for slit-lamp examination of donor corneas suspended in preservation medium.
Methods:
The study examined two donor corneas received at Yeouido St. Mary's Hospital in February 2023 and March 2023. The instrument has three main components: a plastic holder to hold the preservation medium bottle, a cube with a mirror for reflecting the slit beam, and a stand to attach the device to the slit-lamp. Using the instrument, the donor corneas were examined via slit-lamp: microscopy with the endothelium facing upward and downward. Specular microscopy and anterior segment optical coherence tomography (OCT) were also performed on the preserved donor corneas.
Results:
Slit-lamp examination of donor corneas in preservation medium using the instrument showed overall corneal buttoning and optical sections of the donor cornea. Using specular reflection and retroillumination, the endothelial layer was partially visible. However, specular microscopy and anterior segment OCT could not examine the donor cornea in preservation medium using the instrument.
Conclusions
The devised instrument facilitates slit-lamp examination of donor corneas in preservation medium, enabling a qualitative assessment of donor corneas before corneal transplantation surgery.
9.2023 Obesity Fact Sheet: Prevalence of Obesity and Abdominal Obesity in Adults, Adolescents, and Children in Korea from 2012 to 2021
Su-Min JEONG ; Jin-Hyung JUNG ; Ye Seul YANG ; Wonsock KIM ; In Young CHO ; You-Bin LEE ; Kye-Yeung PARK ; Ga Eun NAM ; Kyungdo HAN ;
Journal of Obesity & Metabolic Syndrome 2024;33(1):27-35
Background:
The 2023 Obesity Fact Sheet aims to present an updated overview of obesity prevalence across all age groups, including children and adolescents.
Methods:
This study included individuals aged ≥20 years (n=16,941,423 in 2021) who underwent health checkups provided by the Korean National Health Insurance Service between 2012 and 2021. The prevalence of obesity and abdominal obesity was standardized by age and sex using data from the 2010 population and housing census. For children and adolescents (6 to 18 years) (n= 884 in 2021), we used the Korea National Health and Nutrition Examination Survey (2012 to 2021), and obesity was defined by the corresponding sex- and agespecific body mass index percentile of 95th or greater based on the 2017 Korean National Growth Chart for Children and Adolescents.
Results:
The overall prevalence of obesity in 2021 is 38.4% (49.2% in men and 27.8% in women), which is a 1.27-fold increase from 30.2% in 2012. The prevalence of obesity has increased across all age groups, particularly among those aged 20, 30, and 80 years. The prevalence of class III obesity substantially increased from 0.35% (men) and 0.42% (women) in 2012 to 1.21% and 0.97% in 2021, with 3.46- and 2.31-fold increases, respectively.This increase was particularly pronounced in young adults. The prevalence of obesity in children and adolescents has surged from 9.7% in 2012 to 19.3% in 2021, with a greater increase among boys.
Conclusion
Our study provides information on the current status of obesity prevalence based on the 2023 Obesity Fact Sheet, emphasizing the urgency of implementing timely strategies to reverse this increasing trend.
10.Major clinical research advances in gynecologic cancer in 2023:a tumultuous year for endometrial cancer
Seung-Hyuk SHIM ; Jung-Yun LEE ; Yoo-Young LEE ; Jeong-Yeol PARK ; Yong Jae LEE ; Se Ik KIM ; Gwan Hee HAN ; Eun Jung YANG ; Joseph J NOH ; Ga Won YIM ; Joo-Hyuk SON ; Nam Kyeong KIM ; Tae-Hyun KIM ; Tae-Wook KONG ; Youn Jin CHOI ; Angela CHO ; Hyunji LIM ; Eun Bi JANG ; Hyun Woong CHO ; Dong Hoon SUH
Journal of Gynecologic Oncology 2024;35(2):e66-
In the 2023 series, we summarized the major clinical research advances in gynecologic oncology based on communications at the conference of Asian Society of Gynecologic Oncology Review Course. The review consisted of 1) Endometrial cancer: immune checkpoint inhibitor, antibody drug conjugates (ADCs), selective inhibitor of nuclear export, CDK4/6 inhibitors WEE1 inhibitor, poly (ADP-ribose) polymerase (PARP) inhibitors. 2) Cervical cancer: surgery in low-risk early-stage cervical cancer, therapy for locally advanced stage and advanced, metastatic, or recurrent setting; and 3) Ovarian cancer: immunotherapy, triplet therapies using immune checkpoint inhibitors along with antiangiogenic agents and PARP inhibitors, and ADCs. In 2023, the field of endometrial cancer treatment witnessed a landmark year, marked by several practice-changing outcomes with immune checkpoint inhibitors and the reliable efficacy of PARP inhibitors and ADCs.

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