• KSII Transactions on Internet and Information Systems (TIIS)
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• v.14 no.11
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• pp.4310-4330
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• 2020

With the continuous emergence of new applications and cyberattacks and their frequent updates, the need for automatic protocol reverse engineering is gaining recognition. Although several methods for automatic protocol reverse engineering have been proposed, each method still faces major limitations in extracting clear specifications and in its universal application. In order to overcome such limitations, we propose an automatic protocol reverse engineering method using a two-pathway model based on a contiguous sequential pattern (CSP) algorithm. By using this model, the method can infer both command-oriented protocols and non-command-oriented protocols clearly and in detail. The proposed method infers all the key elements of the protocol, which are syntax, semantics, and finite state machine (FSM), and extracts clear syntax by defining fine-grained field types and three types of format: field format, message format, and flow format. We evaluated the efficacy of the proposed method over two non-command-oriented protocols and three command-oriented protocols: the former are HTTP and DNS, and the latter are FTP, SMTP, and POP3. The experimental results show that this method can reverse engineer with high coverage and correctness rates, more than 98.5% and 99.1% respectively, and be general for both command-oriented and non-command-oriented protocols.

• Transactions of the Korean Society of Mechanical Engineers B
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• v.34 no.4
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• pp.365-373
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• 2010

A chemical reactor model (CRM) was developed for a jet stirred reactor (JSR) to predict the emission of exhaust such as NOx. In this study, a two-PSR model was chosen as the chemical reactor model for the JSR. The predictions of NO formation in lean premixed methane-air combustion in the JSR were carried out by using CHEMKIN and GRI 3.0 methane-air combustion mechanism which include the four NO formation mechanisms. The calculated results were compared with Rutar's experimental data for the validation of the model. The effects of important parameters on NO formation and the contributions of the four NO pathways were investigated. In the flame region, the major pathway is the prompt mechanism, and in the post flame region, the major pathway is the Zelodovich mechanism. Under the lean premixed condition, the N2O mechanism is the important pathway in both flame and postflame regions.

• Proceedings of the Microbiological Society of Korea Conference
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• 2002.10a
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• pp.40-50
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• 2002

Fruit fly, Drosophila melanogaster has developed efficient immune mechanisms to prevent microbial infection, which are consisted of cellular and humoral responses. During the systemic or local infection, two distinct pathways (Toll and Imd) play major roles in antimicrobial peptide synthesis. The Toll pathway is required to defend Gram-positive bacterial and fungal infections, whereas the Imd pathway is important in Gram-negative bacterial infection. We have shown that the infection of the opportunistic Gram-negative bacterium, Pseudomonas aeruginosa strain PA14 (PA14) into fly dorsal thorax can kill the flies within 48 h ($100\%$ mortality) in our optimized infection condition, suggesting that the PA14 strain can cause disease progress in fly model system. We found that flies carrying a constitutively activated mutant form of the Toll receptor $(Tl^{10b})$ showed increased resistance to P. aeruginosa infection and that flies carrying mutations in the Toll signaling pathway as well as in the Imd signaling pathway was more susceptible to PA14 infection. All these results imply that the Toll pathway might be important in the resistance to this pathogenic Gram-negative bacterial infection.

• Journal of Microbiology and Biotechnology
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• v.11 no.3
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• pp.384-388
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• 2001

The metabolic pathway synthesis algorithm was applied to estimate the maximum ethanol yield from xylose in a model recombinant Saccharomyces cerevisiae strain containing the genes involved in xylose metabolism. The stoichiometrically independent pathways were identified by constructing a biochemical reaction network for conversion of xylose to ethanol in the recombinant S. cerevisiae. Two independent pathways were obtained in xylose-assimilating recombinant S. cerevisiae as opposed to six independent pathways for conversion of glucose to ethanol. The maximum ethanol yield from xylose was estimated to be 0.46 g/g, which was lower than the known value of 0.51 g/g for glucose-fermenting and wild-type xylose-fermenting yeasts.

• KSII Transactions on Internet and Information Systems (TIIS)
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• v.18 no.1
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• pp.105-125
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• 2024

Gliomas are the most common malignant brain tumor and cause the most deaths. Manual brain tumor segmentation is expensive, time-consuming, error-prone, and dependent on the radiologist's expertise and experience. Manual brain tumor segmentation outcomes by different radiologists for the same patient may differ. Thus, more robust, and dependable methods are needed. Medical imaging researchers produced numerous semi-automatic and fully automatic brain tumor segmentation algorithms using ML pipelines and accurate (handcrafted feature-based, etc.) or data-driven strategies. Current methods use CNN or handmade features such symmetry analysis, alignment-based features analysis, or textural qualities. CNN approaches provide unsupervised features, while manual features model domain knowledge. Cascaded algorithms may outperform feature-based or data-driven like CNN methods. A revolutionary cascaded strategy is presented that intelligently supplies CNN with past information from handmade feature-based ML algorithms. Each patient receives manual ground truth and four MRI modalities (T1, T1c, T2, and FLAIR). Handcrafted characteristics and deep learning are used to segment brain tumors in a Global Convolutional Neural Network (GCNN). The proposed GCNN architecture with two parallel CNNs, CSPathways CNN (CSPCNN) and MRI Pathways CNN (MRIPCNN), segmented BraTS brain tumors with high accuracy. The proposed model achieved a Dice score of 87% higher than the state of the art. This research could improve brain tumor segmentation, helping clinicians diagnose and treat patients.

• Journal of KIISE:Databases
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• v.30 no.6
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• pp.573-584
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• 2003

Recent massive data generation by genomics and proteomics requires bioinformatic tools to extract the biological meaning from the massive results. Here we introduce ROSPath, a database system to deal with information on reactive oxygen species (ROS)-mediated cell signaling pathways. It provides a structured repository for handling pathway related data and tools for querying, displaying, and analyzing pathways. ROSPath data model provides the extensibility for representing incomplete knowledge and the accessibility for linking the existing biochemical databases via the Internet. For flexibility and efficient retrieval, hierarchically structured data model is defined by using the object-oriented model. There are two major data types in ROSPath data model: ‘bio entity’ and ‘interaction’. Bio entity represents a single biochemical entity: a protein or protein state involved in ROS cell-signaling pathways. Interaction, characterized by a list of inputs and outputs, describes various types of relationship among bio entities. Typical interactions are protein state transitions, chemical reactions, and protein-protein interactions. A complex network can be constructed from ROSPath data model and thus provides a foundation for describing and analyzing various biochemical processes.

• Journal of Microbiology and Biotechnology
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• v.16 no.9
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• pp.1331-1337
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• 2006

A mathematical model has been proposed for the batch culture of Agaricus blazei with mixed carbon sources of glucose and dextrin. In the proposed model, the metabolism of A. blazei was divided into three parts: cell growth, exopolysaccharides (EPS) production, and another EPS production pathway activated by dextrin hydrolysis. Each pathway was described mathematically and incorporated into the mechanistic model structure. Batch cultures were carried out with six different carbon source compositions. Although parameters were estimated by using the experimental data from the two extreme cases such as glucose only and dextrin only, the model represented well the profiles of glucose, cell mass, and EPS concentrations for all the six different carbon source mixtures, showing a good interpolation capability. Of note, the lag in EPS production could be quite precisely predicted by assuming that the glucose-to-cell mass ratio was the governing factor for EPS production.

• BMB Reports
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• v.51 no.5
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• pp.209-210
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• 2018

NAFLD induces the development of advanced liver diseases such as NASH and liver cancer. Therefore, understanding the mechanism of NAFLD development is critical for its prevention and treatment. Ablation of PTEN or Hippo pathway components induces liver cancer in a murine model by hyperactive AKT or YAP/TAZ, respectively. Although the regulation of these two pathways occurs in the same hepatocyte, the details of crosstalk between Hippo-YAP/TAZ and PTEN-AKT pathways in liver homeostasis and tumorigenesis still remain unclear. Here, we found that depletion of both PTEN and SAV1 in liver promotes spontaneous NAFLD and liver cancer through hyperactive AKT via YAP/TAZ-mediated up-regulation of IRS2 transcription. Conversely, NAFLD is rescued by both ablation of YAP/TAZ and activation of the Hippo pathway. Furthermore, human HCC patients with NAFLD showed strong correlation between YAP/TAZ and IRS2 or phospho-AKT expression. Finally, the inhibition of AKT by MK-2206 treatment attenuates NAFLD development and tumorigenesis. Our findings indicate that Hippo pathway interacts with AKT signaling during the intervention with IRS2 to prevent NAFLD and liver cancer.

• Journal of Korean Medicine Rehabilitation
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• v.27 no.4
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• pp.111-119
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• 2017

Objectives Clinical pathway (CP), is management plans that display goals for patients and have led to improve outcomes for many diseases. In Korea, Interest in Korean medicine's stabilization (Clinical pathway, Clinical Practice Guideline) is increasing, But the number of studies is scare. Method and Analysis This trials composes nonequivalent control group pretest-posttest design to conduct clincal pathway trial for the acute pain after back surgery. The subjects were 10 control patients with back surgery, and 10 experimental patients with application of integrative CP. Each group patient will observed 6 weeks. We check validation of CP. Also we compared the patient's status using the pain, function, Quality of life index between the two groups. Discussion This trial is the first CP for the acute pain after back surgery using integrative medicine concepts. Aim of this trial is to find the effectiveness and validity of clincal pathway for acute pain after back surgery.

• Molecules and Cells
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• v.37 no.7
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• pp.503-510
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• 2014

Lymphatic vessels provide essential roles in maintaining fluid homeostasis and lipid absorption. Dysfunctions of the lymphatic vessels lead to debilitating pathological conditions, collectively known as lymphedema. In addition, lymphatic vessels are a critical moderator for the onset and progression of diverse human diseases including metastatic cancer and obesity. Despite their clinical importance, there is no currently effective pharmacological therapy to regulate functions of lymphatic vessels. Recent efforts to manipulate the Vascular Endothelial Growth Factor-C (VEGFC) pathway, which is arguably the most important signaling pathway regulating lymphatic endothelial cells, to alleviate lymphedema yielded largely mixed results, necessitating identification of new targetable signaling pathways for therapeutic intervention for lymphedema. Zebrafish, a relatively new model system to investigate lymphatic biology, appears to be an ideal model to identify novel therapeutic targets for lymphatic biology. In this review, we will provide an overview of our current understanding of the lymphatic vessels in vertebrates, and discuss zebrafish as a promising in vivo model to study lymphatic vessels.