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  1. Article ; Online: PCTC-Net: A Crack Segmentation Network with Parallel Dual Encoder Network Fusing Pre-Conv-Based Transformers and Convolutional Neural Networks.

    Moon, Ji-Hwan / Choi, Gyuho / Kim, Yu-Hwan / Kim, Won-Yeol

    Sensors (Basel, Switzerland)

    2024  Volume 24, Issue 5

    Abstract: Cracks are common defects that occur on the surfaces of objects and structures. Crack detection is a critical maintenance task that traditionally requires manual labor. Large-scale manual inspections are expensive. Research has been conducted to replace ... ...

    Abstract Cracks are common defects that occur on the surfaces of objects and structures. Crack detection is a critical maintenance task that traditionally requires manual labor. Large-scale manual inspections are expensive. Research has been conducted to replace expensive human labor with cheaper computing resources. Recently, crack segmentation based on convolutional neural networks (CNNs) and transformers has been actively investigated for local and global information. However, the transformer is data-intensive owing to its weak inductive bias. Existing labeled datasets for crack segmentation are relatively small. Additionally, a limited amount of fine-grained crack data is available. To address this data-intensive problem, we propose a parallel dual encoder network fusing Pre-Conv-based Transformers and convolutional neural networks (PCTC-Net). The Pre-Conv module automatically optimizes each color channel with a small spatial kernel before the input of the transformer. The proposed model, PCTC-Net, was tested with the DeepCrack, Crack500, and Crackseg9k datasets. The experimental results showed that our model achieved higher generalization performance, stability, and F1 scores than the SOTA model DTrC-Net.
    Language English
    Publishing date 2024-02-24
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2052857-7
    ISSN 1424-8220 ; 1424-8220
    ISSN (online) 1424-8220
    ISSN 1424-8220
    DOI 10.3390/s24051467
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Environment-Adaptable Rotational Energy Harvesters Based on Nylon-core Coiled Carbon Nanotube Yarns.

    Mun, Tae Jin / Moon, Ji Hwan / Park, Jong Woo / Baughman, Ray H / Kim, Seon Jeong

    Small methods

    2023  Volume 7, Issue 10, Page(s) e2300526

    Abstract: Owing to increasing amount of research on energy harvesting, studies on harvesters for practical application and their performance are attracting attention. Therefore, studies on the use of continuous energy as an energy source for energy-harvesting ... ...

    Abstract Owing to increasing amount of research on energy harvesting, studies on harvesters for practical application and their performance are attracting attention. Therefore, studies on the use of continuous energy as an energy source for energy-harvesting devices are being conducted, and fluid flows, e.g., wind, river flow, and sea wave, are widely used as input energy sources for continuous energy harvesting. A new energy-harvesting technology has emerged based on the mechanical stretch and release of coiled carbon nanotube (CNT) yarns, which generate energy based on the change in the electrochemical double-layer capacitance. First, this CNT yarn-based mechanical energy harvester is demonstrated, which is applicable to various environments where fluid flow exists. This environment-adaptable harvester uses rotational energy as the mechanical energy source and is tested in river and ocean environments. Moreover, an attachable-type harvester for the application of the existing rotational system is devised. In the case of a slow rotational environment, a square-wave strain-applying harvester has been implemented, which can convert sinusoidal strain motion into square-wave strain motion for high output voltages. To achieve high performance of practical harvesting applications, a scale-up method for powering signal-transmitting devices has been implemented.
    Language English
    Publishing date 2023-06-14
    Publishing country Germany
    Document type Journal Article
    ISSN 2366-9608
    ISSN (online) 2366-9608
    DOI 10.1002/smtd.202300526
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: MLDEG: A Machine Learning Approach to Identify Differentially Expressed Genes Using Network Property and Network Propagation.

    Moon, Ji Hwan / Lee, Sangseon / Pak, Minwoo / Hur, Benjamin / Kim, Sun

    IEEE/ACM transactions on computational biology and bioinformatics

    2022  Volume 19, Issue 4, Page(s) 2356–2364

    Abstract: Motivation: Identifying differentially expressed genes (DEGs) in transcriptome data is a very important task. However, performances of existing DEG methods vary significantly for data sets measured in different conditions and no single statistical or ... ...

    Abstract Motivation: Identifying differentially expressed genes (DEGs) in transcriptome data is a very important task. However, performances of existing DEG methods vary significantly for data sets measured in different conditions and no single statistical or machine learning model for DEG detection perform consistently well for data sets of different traits. In addition, setting a cutoff value for the significance of differential expressions is one of confounding factors to determine DEGs.
    Results: We address these problems by developing an ensemble model that refines the heterogeneous and inconsistent results of the existing methods by taking accounts into network information such as network propagation and network property. DEG candidates that are predicted with weak evidence by the existing tools are re-classified by our proposed ensemble model for the transcriptome data. Tested on 10 RNA-seq datasets downloaded from gene expression omnibus (GEO), our method showed excellent performance of winning the first place in detecting ground truth (GT) genes in eight datasets and find almost all GT genes in six datasets. On the other hand, performances of all existing methods varied significantly for the 10 data sets. Because of the design principle, our method can accommodate any new DEG methods naturally.
    Availability: The source code of our method is available at https://github.com/jihmoon/MLDEG.
    MeSH term(s) Gene Expression Profiling/methods ; Machine Learning ; Software ; Transcriptome
    Language English
    Publishing date 2022-08-08
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1557-9964
    ISSN (online) 1557-9964
    DOI 10.1109/TCBB.2021.3067613
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: High-Performance One-Body Electrochemical Torsional Artificial Muscles Built Using Carbon Nanotubes and Ion-Exchange Polymers.

    Hyeon, Jae Sang / Kim, Seongjun / Song, Gyu Hyeon / Moon, Ji Hwan / Park, Jong Woo / Baughman, Ray H / Kim, Seon Jeong

    ACS applied materials & interfaces

    2023  Volume 15, Issue 51, Page(s) 59939–59945

    Abstract: Electrochemical torsional artificial muscles have the potential to replace electric motors in the field of miniaturization. In particular, carbon nanotubes (CNTs) are some of the best materials for electrochemical torsional artificial muscles due to ... ...

    Abstract Electrochemical torsional artificial muscles have the potential to replace electric motors in the field of miniaturization. In particular, carbon nanotubes (CNTs) are some of the best materials for electrochemical torsional artificial muscles due to their remarkable mechanical strength and high electrical conductivity. However, previous studies on CNT torsional muscle utilize only half of the whole potential range for torsional actuation because the actuations in the positive and negative voltage ranges offset each other. Here, we used an ion-exchange polymer, poly(sodium 4-styrenesulfonate) (PSS), which leads to the participation of only positive ions in the actuation of CNT muscles so that the whole potential range can be used for torsional actuation. As a result, PSS-coated CNT muscle can provide 1.9 times higher torsional actuation compared to neat CNT torsional muscle. This PSS-coated CNT muscle not only provides high performance but also facilitates a one-body system for electrochemical torsional actuation. From these advantages, we implement a one-body torsional muscle for the realization of the forward motion of a model boat. This high performance and one-body structure for electrochemical torsional muscles can be used for further applications, such as soft robotics and implantable devices.
    Language English
    Publishing date 2023-12-12
    Publishing country United States
    Document type Journal Article
    ISSN 1944-8252
    ISSN (online) 1944-8252
    DOI 10.1021/acsami.3c14772
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Mesenchymal stem cell-derived extracellular vesicles subvert Th17 cells by destabilizing RORγt through posttranslational modification.

    Jung, Sunyoung / Lee, Sunho / Kim, Hyun Je / Kim, Sueon / Moon, Ji Hwan / Chung, Hyunwoo / Kang, Seong-Jun / Park, Chung-Gyu

    Experimental & molecular medicine

    2023  Volume 55, Issue 3, Page(s) 665–679

    Abstract: Mesenchymal stem cell (MSC)-derived small extracellular vesicles (MSC-sEVs) are known to exert immunosuppressive functions. This study showed that MSC-sEVs specifically convert T helper 17 (Th17) cells into IL-17 low-producer (ex-Th17) cells by degrading ...

    Abstract Mesenchymal stem cell (MSC)-derived small extracellular vesicles (MSC-sEVs) are known to exert immunosuppressive functions. This study showed that MSC-sEVs specifically convert T helper 17 (Th17) cells into IL-17 low-producer (ex-Th17) cells by degrading RAR-related orphan receptor γt (RORγt) at the protein level. In experimental autoimmune encephalomyelitis (EAE)-induced mice, treatment with MSC-sEVs was found to not only ameliorate clinical symptoms but also to reduce the number of Th17 cells in draining lymph nodes and the central nervous system. MSC-sEVs were found to destabilize RORγt by K63 deubiquitination and deacetylation, which was attributed to the EP300-interacting inhibitor of differentiation 3 (Eid3) contained in the MSC-sEVs. Small extracellular vesicles isolated from the Eid3 knockdown MSCs by Eid3-shRNA failed to downregulate RORγt. Moreover, forced expression of Eid3 by gene transfection was found to significantly decrease the protein level of RORγt in Th17 cells. Altogether, this study reveals the novel immunosuppressive mechanisms of MSC-sEVs, which suggests the feasibility of MSC-sEVs as an attractive therapeutic tool for curing Th17-mediated inflammatory diseases.
    MeSH term(s) Animals ; Mice ; Nuclear Receptor Subfamily 1, Group F, Member 3/genetics ; Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism ; Th17 Cells ; Encephalomyelitis, Autoimmune, Experimental ; Cell Differentiation/genetics ; Protein Processing, Post-Translational ; Mesenchymal Stem Cells/metabolism ; Extracellular Vesicles/metabolism
    Chemical Substances Nuclear Receptor Subfamily 1, Group F, Member 3
    Language English
    Publishing date 2023-03-24
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1328915-9
    ISSN 2092-6413 ; 1226-3613 ; 0378-8512
    ISSN (online) 2092-6413
    ISSN 1226-3613 ; 0378-8512
    DOI 10.1038/s12276-023-00949-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Author Correction: Mesenchymal stem cell-derived extracellular vesicles subvert Th17 cells by destabilizing RORγt through posttranslational modification.

    Jung, Sunyoung / Lee, Sunho / Kim, Hyun Je / Kim, Sueon / Moon, Ji Hwan / Chung, Hyunwoo / Kang, Seong-Jun / Park, Chung-Gyu

    Experimental & molecular medicine

    2023  Volume 55, Issue 4, Page(s) 870

    Language English
    Publishing date 2023-04-26
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 1328915-9
    ISSN 2092-6413 ; 1226-3613 ; 0378-8512
    ISSN (online) 2092-6413
    ISSN 1226-3613 ; 0378-8512
    DOI 10.1038/s12276-023-01001-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Spatial transcriptomic analysis of tumour-immune cell interactions in melanoma arising from congenital melanocytic nevus.

    Lim, Youngkyoung / Cho, Beom Keun / Kang, Seong-Jun / Jeong, Soyoung / Kim, Hyun Je / Baek, Jiyoon / Moon, Ji Hwan / Lee, Cheol / Park, Chan-Sik / Mun, Je-Ho / Won, Chong Hyun / Park, Chung-Gyu

    Journal of the European Academy of Dermatology and Venereology : JEADV

    2024  

    Abstract: Background: Studies on the interaction between tumour-infiltrating immune cells (TIICs) and tumour cells in melanoma arising from congenital melanocytic nevus (CMN) are lacking.: Objective: The aim of this study was to determine the intratumoral ... ...

    Abstract Background: Studies on the interaction between tumour-infiltrating immune cells (TIICs) and tumour cells in melanoma arising from congenital melanocytic nevus (CMN) are lacking.
    Objective: The aim of this study was to determine the intratumoral immune landscape of TIICs and tumour cells during invasion and metastasis.
    Methods: Tissue specimens were obtained from patients with melanoma originating from CMN. Differential gene expression in melanoma cells and TIICs during invasion and metastasis was determined using spatial transcriptomics.
    Results: As invasion depth increased, the expression of LGALS3, known to induce tumour-driven immunosuppression, increased in melanoma cells. In T cells, the expression of genes that inhibit T-cell activation increased with increasing invasion depth. In macrophages, the expression of genes related to the anti-inflammatory M2 phenotype was upregulated with increasing invasion depth. Compared to primary tumour cells, melanoma cells in metastatic lesions showed upregulated expression of genes associated with cancer immune evasion, including AXL and EPHA2, which impede T-cell recruitment, and BST2, associated with M2 polarization. Furthermore, T cells showed increased expression of genes related to immunosuppression, and macrophages exhibited increased expression of genes associated with the M2 phenotype.
    Conclusions: The interaction between melanomas arising from CMN and TIICs may be important for tumour progression and metastasis.
    Language English
    Publishing date 2024-02-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 1128828-0
    ISSN 1468-3083 ; 0926-9959
    ISSN (online) 1468-3083
    ISSN 0926-9959
    DOI 10.1111/jdv.19881
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Impact of mutations in DNA methylation modification genes on genome-wide methylation landscapes and downstream gene activations in pan-cancer.

    Lee, Chai-Jin / Ahn, Hongryul / Jeong, Dabin / Pak, Minwoo / Moon, Ji Hwan / Kim, Sun

    BMC medical genomics

    2020  Volume 13, Issue Suppl 3, Page(s) 27

    Abstract: Background: In cancer, mutations of DNA methylation modification genes have crucial roles for epigenetic modifications genome-wide, which lead to the activation or suppression of important genes including tumor suppressor genes. Mutations on the ... ...

    Abstract Background: In cancer, mutations of DNA methylation modification genes have crucial roles for epigenetic modifications genome-wide, which lead to the activation or suppression of important genes including tumor suppressor genes. Mutations on the epigenetic modifiers could affect the enzyme activity, which would result in the difference in genome-wide methylation profiles and, activation of downstream genes. Therefore, we investigated the effect of mutations on DNA methylation modification genes such as DNMT1, DNMT3A, MBD1, MBD4, TET1, TET2 and TET3 through a pan-cancer analysis.
    Methods: First, we investigated the effect of mutations in DNA methylation modification genes on genome-wide methylation profiles. We collected 3,644 samples that have both of mRNA and methylation data from 12 major cancer types in The Cancer Genome Atlas (TCGA). The samples were divided into two groups according to the mutational signature. Differentially methylated regions (DMR) that overlapped with the promoter region were selected using minfi and differentially expressed genes (DEG) were identified using EBSeq. By integrating the DMR and DEG results, we constructed a comprehensive DNA methylome profiles on a pan-cancer scale. Second, we investigated the effect of DNA methylations in the promoter regions on downstream genes by comparing the two groups of samples in 11 cancer types. To investigate the effects of promoter methylation on downstream gene activations, we performed clustering analysis of DEGs. Among the DEGs, we selected highly correlated gene set that had differentially methylated promoter regions using graph based sub-network clustering methods.
    Results: We chose an up-regulated DEGs cluster where had hypomethylated promoter in acute myeloid leukemia (LAML) and another down-regulated DEGs cluster where had hypermethylated promoter in colon adenocarcinoma (COAD). To rule out effects of gene regulation by transcription factor (TF), if differentially expressed TFs bound to the promoter of DEGs, that DEGs did not included to the gene set that effected by DNA methylation modifiers. Consequently, we identified 54 hypomethylated promoter DMR up-regulated DEGs in LAML and 45 hypermethylated promoter DMR down-regulated DEGs in COAD.
    Conclusions: Our study on DNA methylation modification genes in mutated vs. non-mutated groups could provide useful insight into the epigenetic regulation of DEGs in cancer.
    MeSH term(s) DNA Methylation/genetics ; DNA, Neoplasm/metabolism ; Epigenesis, Genetic ; Epigenome ; Gene Expression Regulation, Neoplastic ; Genome, Human ; Humans ; Mutation ; Neoplasms/genetics ; Promoter Regions, Genetic
    Chemical Substances DNA, Neoplasm
    Language English
    Publishing date 2020-02-24
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1755-8794
    ISSN (online) 1755-8794
    DOI 10.1186/s12920-020-0659-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Mesenchymal stem cell-derived exosomes suppress proliferation of T cells by inducing cell cycle arrest through p27kip1/Cdk2 signaling.

    Lee, Sunho / Kim, Sueon / Chung, Hyunwoo / Moon, Ji Hwan / Kang, Seong Jun / Park, Chung-Gyu

    Immunology letters

    2020  Volume 225, Page(s) 16–22

    Abstract: Mouse mesenchymal stem cells (MSCs) have been shown to suppress T cells. Especially, MSC-cultured media have shown suppressive functions against various immune cells including the T cells. However, the underlying immunosuppressive mechanisms of the MSC- ... ...

    Abstract Mouse mesenchymal stem cells (MSCs) have been shown to suppress T cells. Especially, MSC-cultured media have shown suppressive functions against various immune cells including the T cells. However, the underlying immunosuppressive mechanisms of the MSC-cultured medium are not yet fully understood. In this study, we confirmed the T cell-suppression capacity of MSC culture supernatant (MSC-CS) through both apoptosis and cell cycle arrest, and hypothesized that the exosomes were the major immunosuppressive agents in the MSC-CS. MSC-derived exosomes (MSC-exo) exhibited potent suppressive effects on T cell proliferation while the rest of the supernatant fraction did not. Interestingly, the exosomes derived from MSC only induced the cell cycle arrest, and it was through the upregulation of p27kip1 protein and downregulation of Cdk2 protein. In conclusion, the exosomes secreted from MSCs could suppress the activated T cell proliferation through the induction of cell cycle arrest.
    MeSH term(s) Animals ; Cell Cycle Checkpoints ; Cell Proliferation ; Cells, Cultured ; Cyclin-Dependent Kinase 2/metabolism ; Cyclin-Dependent Kinase Inhibitor p27/metabolism ; Exosomes/metabolism ; Female ; Immune Tolerance ; Lymphocyte Activation ; Mesenchymal Stem Cells/physiology ; Mice ; Mice, Inbred C57BL ; Signal Transduction ; T-Lymphocytes/immunology
    Chemical Substances Cyclin-Dependent Kinase Inhibitor p27 (147604-94-2) ; Cyclin-Dependent Kinase 2 (EC 2.7.11.22)
    Language English
    Publishing date 2020-06-15
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 445150-8
    ISSN 1879-0542 ; 0165-2478
    ISSN (online) 1879-0542
    ISSN 0165-2478
    DOI 10.1016/j.imlet.2020.06.006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: The patient-specific mouse model with Foxg1 frameshift mutation uncovers the pathophysiology of FOXG1 syndrome.

    Park, Jaein / Moon, Ji Hwan / O'Shea, Holly / Shin, Dongjun / Hwang, Seon Ung / Li, Liwen / Lee, Hyojong / Brimble, Elise / Lee, Jae / Clark, Stewart / Lee, Soo-Kyung / Jeon, Shin

    Research square

    2023  

    Abstract: Single allelic mutations in the gene encoding the forebrain-specific transcription factor FOXG1 lead to FOXG1 syndrome (FS). Patient-specific animal models are needed to understand the etiology of FS, as FS patients show a wide spectrum of symptoms ... ...

    Abstract Single allelic mutations in the gene encoding the forebrain-specific transcription factor FOXG1 lead to FOXG1 syndrome (FS). Patient-specific animal models are needed to understand the etiology of FS, as FS patients show a wide spectrum of symptoms correlated with location and mutation type in the FOXG1 gene. Here we report the first patient-specific FS mouse model, Q84Pfs heterozygous (Q84Pfs-Het) mice, mimicking one of the most predominant single nucleotide variants in FS. Intriguingly, we found that Q84Pfs-Het mice faithfully recapitulate human FS phenotypes at the cellular, brain structural, and behavioral levels. Importantly, Q84Pfs-Het mice exhibited myelination deficits like FS patients. Further, our transcriptome analysis of Q84Pfs-Het cortex revealed a new role for FOXG1 in synapse and oligodendrocyte development. The dysregulated genes in Q84Pfs-Het brains also predicted motor dysfunction and autism-like phenotypes. Correspondingly, Q84Pfs-Het mice showed movement deficits, repetitive behaviors, increased anxiety, and prolonged behavior arrest. Together, our study revealed the crucial postnatal role of FOXG1 in neuronal maturation and myelination and elucidated the essential pathophysiology mechanisms of FS.
    Language English
    Publishing date 2023-06-02
    Publishing country United States
    Document type Preprint
    DOI 10.21203/rs.3.rs-2953760/v1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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