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.TNF in Human Tuberculosis: A Double-Edged Sword
Jae-Min YUK ; Jin Kyung KIM ; In Soo KIM ; Eun-Kyeong JO
Immune Network 2024;24(1):e4-
TNF, a pleiotropic proinflammatory cytokine, is important for protective immunity and immunopathology during Mycobacterium tuberculosis (Mtb) infection, which causes tuberculosis (TB) in humans. TNF is produced primarily by phagocytes in the lungs during the early stages of Mtb infection and performs diverse physiological and pathological functions by binding to its receptors in a context-dependent manner. TNF is essential for granuloma formation, chronic infection prevention, and macrophage recruitment to and activation at the site of infection. In animal models, TNF, in cooperation with chemokines, contributes to the initiation, maintenance, and clearance of mycobacteria in granulomas. Although anti-TNF therapy is effective against immune diseases such as rheumatoid arthritis, it carries the risk of reactivating TB. Furthermore, TNF-associated inflammation contributes to cachexia in patients with TB. This review focuses on the multifaceted role of TNF in the pathogenesis and prevention of TB and underscores the importance of investigating the functions of TNF and its receptors in the establishment of protective immunity against and in the pathology of TB.Such investigations will facilitate the development of therapeutic strategies that target TNF signaling, which makes beneficial and detrimental contributions to the pathogenesis of TB.
7.Improved immune responses and safety of foot-and-mouth disease vaccine containing immunostimulating components in pigs
Joo-Hyung CHOI ; Su-Hwa YOU ; Mi-Kyeong KO ; Hye Eun JO ; Sung Ho SHIN ; Hyundong JO ; Min Ja LEE ; Su-Mi KIM ; Byounghan KIM ; Jong-Soo LEE ; Jong-Hyeon PARK
Journal of Veterinary Science 2020;21(5):e74-
Background:
The quality of a vaccine depends strongly on the effects of the adjuvants applied simultaneously with the antigen in the vaccine. The adjuvants enhance the protective effect of the vaccine against a viral challenge. Conversely, oil-type adjuvants leave oil residue inside the bodies of the injected animals that can produce a local reaction in the muscle. The longterm immunogenicity of mice after vaccination was examined. ISA206 or ISA15 oil adjuvants maintained the best immunity, protective capability, and safety among the oil adjuvants in the experimental group.
Objectives:
This study screened the adjuvant composites aimed at enhancing foot-andmouth disease (FMD) immunity. The C-type lectin or toll-like receptor (TLR) agonist showed the most improved protection rate.
Methods:
Experimental vaccines were fabricated by mixing various known oil adjuvants and composites that can act as immunogenic adjuvants (gel, saponin, and other components) and examined the enhancement effect on the vaccine.
Results:
The water in oil (W/O) and water in oil in water (W/O/W) adjuvants showed better immune effects than the oil in water (O/W) adjuvants, which have a small volume of oil component. The W/O type left the largest amount of oil residue, followed by W/O/W and O/W types. In the mouse model, intramuscular inoculation showed a better protection rate than subcutaneous inoculation. Moreover, the protective effect was particularly weak in the case of inoculation in fatty tissue. The initial immune reaction and persistence of long-term immunity were also confirmed in an immune reaction on pigs.
Conclusions
The new experimental vaccine with immunostimulants produces improved immune responses and safety in pigs than general oil-adjuvanted vaccines.
8.Coxsackievirus A6-induced HandFoot-and-Mouth Disease Mimicking Stevens-Johnson Syndrome in an Immunocompetent Adult
Tae-Hoon NO ; Kyeong Min JO ; So Young JUNG ; Mi Ra KIM ; Joo Yeon KIM ; Chan Sun PARK ; Sungmin KYMC
Infection and Chemotherapy 2020;52(4):634-640
Hand-foot-and-mouth disease, a highly contagious viral infection, occurs more common in children than in adults. However, there was a recent outbreak of Coxsackievirus A6-induced infection with an atypical presentation among the adult population. Stevens– Johnson syndrome is a severe mucocutaneous disease characterized by extensive necrosis and detachment of the epidermis, and this condition is commonly caused by medications.Herein, we describe a 30-year-old male patient taking allopurinol for the management of gout. The patient presented with numerous erythematous papules, vesicles, and patches with mucosal eruptions on the whole body, oral mucositis, and fever, and he was finally diagnosed with hand-foot-and-mouth disease.
9.Coxsackievirus A6-induced HandFoot-and-Mouth Disease Mimicking Stevens-Johnson Syndrome in an Immunocompetent Adult
Tae-Hoon NO ; Kyeong Min JO ; So Young JUNG ; Mi Ra KIM ; Joo Yeon KIM ; Chan Sun PARK ; Sungmin KYMC
Infection and Chemotherapy 2020;52(4):634-640
Hand-foot-and-mouth disease, a highly contagious viral infection, occurs more common in children than in adults. However, there was a recent outbreak of Coxsackievirus A6-induced infection with an atypical presentation among the adult population. Stevens– Johnson syndrome is a severe mucocutaneous disease characterized by extensive necrosis and detachment of the epidermis, and this condition is commonly caused by medications.Herein, we describe a 30-year-old male patient taking allopurinol for the management of gout. The patient presented with numerous erythematous papules, vesicles, and patches with mucosal eruptions on the whole body, oral mucositis, and fever, and he was finally diagnosed with hand-foot-and-mouth disease.
10.New foot-and-mouth disease vaccine, O JC-R, induce complete protection to pigs against SEA topotype viruses occurred in South Korea, 2014–2015
Hye Eun JO ; Mi Kyeong KO ; Joo Hyung CHOI ; Sung Ho SHIN ; Hyundong JO ; Su Hwa YOU ; Min Ja LEE ; Su Mi KIM ; Byounghan KIM ; Jong Hyeon PARK
Journal of Veterinary Science 2019;20(4):e42-
Foot-and-mouth disease (FMD) is an acute epidemic that spreads rapidly among cattle and pigs. In 2014, in Korea, despite enforced vaccination, the type O Southeast Asia (SEA) topotype viruses (Mya-98 lineage) infected mainly cattle and pigs simultaneously, thereby causing enormous damage. If a vaccine that is completely protective against this FMD virus is developed and used, it can become a very important preventive measure in Asia, which is where this type of virus mainly circulates. The SEA topotype has been steadily evolving and transforming into new variations since it became epidemic in Asia. Therefore, it became necessary to develop a new vaccine that could provide protection against the FMD virus strain that was responsible for the 2014–2015 outbreak in Korea. This study aimed to develop a vaccine that would provide complete protection against the SEA topotype FMD virus to control sporadic FMD outbreaks, which occur despite the enforcement of vaccination, and to completely prevent virus shedding, thereby preventing the virus from spreading. The vaccine candidate virus developed in this study showed low pathogenicity and can be distinguished from the wild-type FMD virus strain. The developed vaccine was able to protect mice from SEA and Middle East–South Asia topotype virus strains and induced high titers of antibodies against both virus strains in pigs, thereby confirming the sufficiency of its protective function. In particular, the results of the SEA topotype virus challenge test in pigs revealed that perfect immunity was created in the vaccinated pigs, without virus shedding and viremia.
Animals
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Antibodies
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Asia
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Asia, Southeastern
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Cattle
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Disease Outbreaks
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Foot-and-Mouth Disease
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Korea
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Mice
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Swine
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Vaccination
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Viremia
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Virulence
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Virus Shedding

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