• The Plant Pathology Journal
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• 제33권2호
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• pp.148-162
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• 2017

As a step towards discovering novel pathogenesis-related proteins, we performed a genome scale computational identification and characterization of secreted and transmembrane (TM) proteins, which are mainly responsible for bacteria-host interactions and interactions with other bacteria, in the genomes of six representative Burkholderia species. The species comprised plant pathogens (B. glumae BGR1, B. gladioli BSR3), human pathogens (B. pseudomallei K96243, B. cepacia LO6), and plant-growth promoting endophytes (Burkholderia sp. KJ006, B. phytofirmans PsJN). The proportions of putative classically secreted proteins (CSPs) and TM proteins among the species were relatively high, up to approximately 20%. Lower proportions of putative type 3 non-classically secreted proteins (T3NCSPs) (~10%) and unclassified non-classically secreted proteins (NCSPs) (~5%) were observed. The numbers of TM proteins among the three clusters (plant pathogens, human pathogens, and endophytes) were different, while the distribution of these proteins according to the number of TM domains was conserved in which TM proteins possessing 1, 2, 4, or 12 TM domains were the dominant groups in all species. In addition, we observed conservation in the protein size distribution of the secreted protein groups among the species. There were species-specific differences in the functional characteristics of these proteins in the various groups of CSPs, T3NCSPs, and unclassified NCSPs. Furthermore, we assigned the complete sets of the conserved and unique NCSP candidates of the collected Burkholderia species using sequence similarity searching. This study could provide new insights into the relationship among plant-pathogenic, humanpathogenic, and endophytic bacteria.

• Clinical Endoscopy
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• 제56권1호
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• pp.55-64
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• 2023

Background/Aims: Endoscopic submucosal dissection (ESD) has been established as a treatment modality for superficial esophageal squamous cell carcinoma (ESCC). Long-term follow-up data are lacking in Western countries. The aim of this study was to analyze long-term survival in a Western center. Methods: Patients undergoing ESD for ESCC were included. The analysis was performed retrospectively using a prospectively collected database. Results: R0 resection rate was 96.7% (59/61 lesions in 58 patients). Twenty-seven patients (46.6%) fulfilled the curative resection criteria (M1/M2) (group A), 11 patients (19.0%) had M3 lesions without lymphovascular invasion (LVI) (group B), and 20 patients (34.5%) had lesions with submucosal invasion or LVI (group C). Additional treatment was recommended after non-curative resection. It was not performed in 20/31 patients (64.5%), mainly because of comorbidities (75%). Twenty-nine out of 58 (50.0%) patients died during a mean follow-up of 3.7 years. Death was related to ESCC in 17.2% (5/29) of patients. The disease-specific survival rate after curative resection was 100%. Overall survival rates after 5 years were 61.5%, 63.6% and 28.1% for groups A, B, and C, respectively. The overall survival was significantly worse after non-curative resection (p=0.038). Conclusions: Non-curative resection is frequent after ESD for ESCC in Western patients. The long-term prognosis is limited and mainly determined by comorbidity. Early diagnosis and pre-interventional assessments need to be improved.

• Molecular & Cellular Toxicology
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• 제5권4호
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• pp.335-345
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• 2009

A major source of paeoniflorin (PF) which was from the Paeonia lactiflora root, has been used as a herbal medicine in East Asia for its antiallergic, antiinflammatory, and immunoregulatory effects. However, only few details are known about the mechanism of apoptosis induced by this compound. The present study was undertaken to further elucidate the molecular mechanism of apoptosis and the changes of gene expression elicited by PF using DNA microarrays and computational gene-expression analysis tools in human leukemia U937 cells. A comparative global transcription analysis between treatment with PF and anisomycin (AM) that induces apoptosis in U937 cells revealed that c-Jun-$NH_2$-kinase (JNK) pathway related genes were less expressed in PF-treated cells. Elucidation of the mechanisms by which PF conducts its anti-cancer activities through comparative analysis of the gene expression is necessary to provide a solid foundation for its use as a promising agent in prevention and treatment strategies.

• 동의생리병리학회지
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• 제30권6호
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• pp.376-384
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• 2016

Systems biology is an emerging field aiming at a systems level understanding of living organisms and focusing on the characteristics of the whole network of them. The emergence of systems biology is partly because of the availability of huge amounts of data on organisms and the extensive support of computational technologies as the tools for understanding complex biological systems. The scientific understanding of Korean medicine has been obstructed because of the lack of proper methods examining the complex nature and the unique property of it. However, systems biology could give a chance understanding Korean medicine objectively and scientifically. Pattern classification is a unique tool of Korean medicine to diagnose and treat patients and systems biology would give a useful tool to interpret pattern classification. Various omics technologies has been used to explain the relations between pattern classification and biological factors and then many characteristics of pattern classification in various diseases have been discovered. Therefore, pattern classification could be a bridge to understand the features and differences of western medicine and Korean medicine and it could be a basis to develop pattern-based personalized medicine.

• The Korean Journal of Physiology and Pharmacology
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• 제24권1호
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• pp.89-99
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• 2020

Although microscopic analysis of tissue slides has been the basis for disease diagnosis for decades, intra- and inter-observer variabilities remain issues to be resolved. The recent introduction of digital scanners has allowed for using deep learning in the analysis of tissue images because many whole slide images (WSIs) are accessible to researchers. In the present study, we investigated the possibility of a deep learning-based, fully automated, computer-aided diagnosis system with WSIs from a stomach adenocarcinoma dataset. Three different convolutional neural network architectures were tested to determine the better architecture for tissue classifier. Each network was trained to classify small tissue patches into normal or tumor. Based on the patch-level classification, tumor probability heatmaps can be overlaid on tissue images. We observed three different tissue patterns, including clear normal, clear tumor and ambiguous cases. We suggest that longer inspection time can be assigned to ambiguous cases compared to clear normal cases, increasing the accuracy and efficiency of histopathologic diagnosis by pre-evaluating the status of the WSIs. When the classifier was tested with completely different WSI dataset, the performance was not optimal because of the different tissue preparation quality. By including a small amount of data from the new dataset for training, the performance for the new dataset was much enhanced. These results indicated that WSI dataset should include tissues prepared from many different preparation conditions to construct a generalized tissue classifier. Thus, multi-national/multi-center dataset should be built for the application of deep learning in the real world medical practice.

• BMB Reports
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• 제42권6호
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• pp.356-360
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• 2009

In the present study we have examined human-mouse homologous intronless disease and non-disease genes alongside their extent of sequence conservation, tissue expression, domain and gene ontology composition to get an idea regarding evolutionary and functional attributes. We show that selection has significantly discriminated between the two groups and the disease associated genes in particular exhibit lower $K_{a}$ and $K_{a}/K_{s}$ while $K_{s}$ although smaller is not significantly different. Our analyses suggest that majority of disease related intronless human genes have homology limited to eukaryotic genomes and their expression is localized. Also we observed that different classes of intronless disease related genes have experienced diverse selective pressures and are enriched for higher level functionality that is essentially needed for developmental processes in complex organisms. It is expected that these insights will enhance our understanding of the nature of these genes and also improve our ability to identify disease related intronless genes.

• 전자통신동향분석
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• 제35권2호
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• pp.1-16
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• 2020

"Artificial Intelligence+" is a key strategic direction that has garnered the attention of several global medical device manufacturers and internet companies. Large hospitals are actively involved in different types of medical AI research and cooperation projects. Medical AI is expected to create numerous opportunities and advancements in areas such as medical imaging, computer aided diagnostics and clinical decision support, new drug development, personal healthcare, pathology analysis, and genetic disease prediction. On the contrary, some studies on the limitations and problems in current conditions such as lack of clinical validation, difficulty in performance comparison, lack of interoperability, adversarial attacks, and computational manipulations are being published. Overall, the medical AI field is in a paradigm shift. Regarding international standardization, the work on the top 10 standardization issues is witnessing rapid progress and the competition for standard development has become fierce.

• Genomics & Informatics
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• 제17권1호
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• pp.2.1-2.12
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• 2019

Chronic obstructive pulmonary disease (COPD) is a type of progressive lung disease, featured by airflow obstruction. Recently, a comprehensive analysis of the transcriptome in lung tissue of COPD patients was performed, but the heterogeneity of the sample was not seriously considered in characterizing the mechanistic dysregulation of COPD. Here, we established a new transcriptome analysis pipeline using a deconvolution process to reduce the heterogeneity and clearly identified that these transcriptome data originated from the mild or moderate stage of COPD patients. Differentially expressed or co-expressed genes in the protein interaction subnetworks were linked with mitochondrial dysfunction and the immune response, as expected. Computational protein localization prediction revealed that 19 proteins showing changes in subcellular localization were mostly related to mitochondria, suggesting that mislocalization of mitochondria-targeting proteins plays an important role in COPD pathology. Our extensive evaluation of COPD transcriptome data could provide guidelines for analyzing heterogeneous gene expression profiles and classifying potential candidate genes that are responsible for the pathogenesis of COPD.

• Advances in Computational Design
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• 제8권2호
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• pp.179-190
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• 2023

In this paper, building information modelling (BIM) associated to the principle of significant items emerged at quantities and costs in the optimization of productivity related to the rehabilitation of the building where proposed and discussed. A quantitative and qualitative study related to the field of application based on some parameters such as pathology diagnosis, projects documents and bills of quantities were used for model development at the preliminary stage of this work. The study identified 14 quantities significant items specified to cost value based on the use of the 80/20 Pareto rule, through the integration of building information modelling (BIM) in the optimisation of labour productivity for rehabilitation of buildings. The results of this study reveal the reliability and the improvement of labour productivity using building information modelling process integrating quantities and cost significant items.

• The Plant Pathology Journal
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• 제34권1호
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• pp.11-22
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• 2018

Type VI secretion system (T6SS) has been discovered in a variety of gram-negative bacteria as a versatile weapon to stimulate the killing of eukaryotic cells or prokaryotic competitors. Type VI secretion effectors (T6SEs) are well known as key virulence factors for important pathogenic bacteria. In many Burkholderia species, T6SS has evolved as the most complicated secretion pathway with distinguished types to translocate diverse T6SEs, suggesting their essential roles in this genus. Here we attempted to detect and characterize T6SSs and potential T6SEs in target genomes of plant-associated and environmental Burkholderia species based on computational analyses. In total, 66 potential functional T6SS clusters were found in 30 target Burkholderia bacterial genomes, of which 33% possess three or four clusters. The core proteins in each cluster were specified and phylogenetic trees of three components (i.e., TssC, TssD, TssL) were constructed to elucidate the relationship among the identified T6SS clusters. Next, we identified 322 potential T6SEs in the target genomes based on homology searches and explored the important domains conserved in effector candidates. In addition, using the screening approach based on the profile hidden Markov model (pHMM) of T6SEs that possess markers for type VI effectors (MIX motif) (MIX T6SEs), 57 revealed proteins that were not included in training datasets were recognized as novel MIX T6SE candidates from the Burkholderia species. This approach could be useful to identify potential T6SEs from other bacterial genomes.