• Asian Pacific Journal of Cancer Prevention
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• v.14 no.6
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• pp.3735-3742
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• 2013

Background: Cardamom (Elettaria cardamom), also known as "Queen of Spices", has been traditionally used as a culinary ingredient due to its pleasant aroma and taste. In addition to this role, studies on cardamom have demonstrated cancer chemopreventive potential in in vitro and in vivo systems. Nevertheless, the precise poly-pharmacological nature of naturally occurring chemo-preventive compounds in cardamom has still not been fully demystified. Methods:In this study, an effort has been made to identify the proapoptopic, anti-inflammatory, anti-proliferative, anti-invasive and anti-angiogenic targets of Cardamom's bioactive principles (eucalyptol, alpha-pinene, beta-pinene, d-limonene and geraniol) by employing a dual reverse virtual screening protocol. Experimentally proven target information of the bioactive principles was annotated from bioassay databases and compared with the virtually screened set of targets to evaluate the reliability of the computational identification. To study the molecular interaction pattern of the anti-tumor action, molecular docking simulation was performed with Auto Dock Pyrx. Interaction studies of binding pose of eucalyptol with Caspase 3 were conducted to obtain an insight into the interacting amino acids and their inter-molecular bondings. Results:A prioritized list of target proteins associated with multiple forms of cancer and ranked by their Fit Score (Pharm Mapper) and descending 3D score (Reverse Screen 3D) were obtained from the two independent inverse screening platforms. Molecular docking studies exploring the bioactive principle targeted action revealed that H- bonds and electrostatic interactions forms the chief contributing factor in inter-molecular interactions associated with anti-tumor activity. Eucalyptol binds to the Caspase 3 with a specific framework that is well-suited for nucleophilic attacks by polar residues inside the Caspase 3 catalytic site. Conclusion:This study revealed vital information about the poly-pharmacological anti-tumor mode-of-action of essential oils in cardamom. In addition, a probabilistic set of anti-tumor targets for cardamom was generated, which can be further confirmed by in vivo and in vitro experiments.

• Journal of The Korean Astronomical Society
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• v.49 no.6
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• pp.255-259
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• 2016

We estimate the fractal dimension of the ${\rho}$ Ophiuchus Molecular Cloud Complex, associated with star forming regions. We selected a cube (${\upsilon}$, l, b) database, obtained with J = 1-0 transition lines of $^{12}CO$ and $^{13}CO$ at a resolution of 22" using a multibeam receiver system on the 14-m telescope of the Five College Radio Astronomy Observatory. Using a code developed within IRAF, we identified slice-clouds with two threshold temperatures to estimate the fractal dimension. With threshold temperatures of 2.25 K ($3{\sigma}$) and 3.75 K ($5{\sigma}$), the fractal dimension of the target cloud is estimated to be D = 1.52-1.54, where $P{\propto}A^{D/2}$, which is larger than previous results. We suggest that the sampling rate (spatial resolution) of observed data must be an important parameter when estimating the fractal dimension, and that narrower or wider dispersion around an arbitrary fit line and the intercepts at NP = 100 should be checked whether they relate to firms noise level or characteristic structure of the target cloud. This issue could be investigated by analysing several high resolution databases with different quality (low or moderate sensitivity).

• Journal of KIISE:Databases
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• v.37 no.2
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• pp.113-120
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• 2010

XML is broadly using for data storing and processing. XML is specified its structural characteristic and user can query with XPath when information from data document is needed. XPath query can process when the tern and structure of document and query is matched with each other. However, nowadays there are lots of data documents which are made by using different terminology and structure therefore user can not know the exact idea of target data. In fact, there are many possibilities that target data document has information which user is find or a similar ones. Accordingly user query should be processed when their term usage or structural characteristic is slightly different with data document. In order to do that we suggest a XML document ranking method based on path similarity. The method can measure a semantic similarity between user query and data document using three steps which are position, node and relaxation factors.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.8
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• pp.3711-3719
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• 2016

Drawbacks of conventional cancer treatments, with lack of specificity and cytotoxicity using current approaches, underlies the necessity for development of a novel approach, gene-directed cancer therapy. This has provided novel technological opportunities in vitro and in vivo. This review focuses on a member of an apoptosis inhibitor family, survivin, as a valuable target. Not only the gene but also its promoter are applicable in this context. This article is based on a literature survey, with especial attention to RNA interference as well as tumor-specific promoter action. The search engine and databases utilized were Science direct, PubMed, MEDLINE and Google. In addition to cell-cycle modulation, apoptosis inhibition, interaction in cell-signaling pathways, cancer-selective expression, survivin also may be considered as specific target through its promoter as a novel treatment for cancer. Our purpose in writing this article was to create awareness in researchers, emphasizing relation of survivin gene expression to potential cancer treatment. The principal result and major conclusion of this manuscript are that survivin structure, biological functions and applications of RNA interference systems as well as tumor-specific promoter activity are of major interest for cancer gene therapy.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.9
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• pp.3817-3825
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• 2015

Background: The human protein methyl-transferase DOT1L catalyzes the methylation of histone H3 on lysine 79 (H3K79) at homeobox genes and is also involved in a number of significant processes ranging from gene expression to DNA-damage response and cell cycle progression. Inhibition of DOT1L activity by shRNA or small-molecule inhibitors has been established to prevent proliferation of various MLL-rearranged leukemia cells in vitro, establishing DOT1L an attractive therapeutic target for mixed lineage leukemia (MLL). Most of the drugs currently in use for the MLL treatment are reported to have low efficacy, hence this study focused on various natural compounds which exhibit minimal toxic effects and high efficacy for the target receptor. Materials and Methods: Structures of human protein methyl-transferase DOT1L and natural compound databases were downloaded from various sources. Virtual screening, molecular docking, dynamics simulation and drug likeness studies were performed for those natural compounds to evaluate and analyze their anti-cancer activity. Results: The top five screened compounds possessing good binding affinity were identified as potential high affinity inhibitors against DOT1L's active site. The top ranking molecule amongst the screened ligands had a Glide g-score of -10.940 kcal/mol and Glide e-model score of -86.011 with 5 hydrogen bonds and 12 hydrophobic contacts. This ligand's behaviour also showed consistency during the simulation of protein-ligand complex for 20000 ps, which is indicative of its stability in the receptor pocket. Conclusions: The ligand obtained out of this screening study can be considered as a potential inhibitor for DOT1L and further can be treated as a lead for the drug designing pipeline.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.7
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• pp.4005-4013
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• 2013

Background: Although breast cancer is a major public health worry among Asian women, adherence to screening for the disease remains an obstacle to its prevention. A variety of psycho-social and cultural factors predispose women to delay or avoidance of screening for breast cancer symptoms at the early stages when cure is most likely to be successful. Yet few interventions implemented to date to address this condition in this region have drawn on health behavior theory. Materials and Methods: This paper reviews the existing literature on several cognitive theories and models associated with breast cancer screening, with an emphasis on the work that has been done in relation to Asian women. To conduct this review, a number of electronic databases were searched with context-appropriate inclusion criteria. Results: Little empirical work was found that specifically addressed the applicability of health theories in promoting adherence to the current breast cancer prevention programs Among Asian women. However, a few studies were found that addressed individual cognitive factors that are likely to encourage women's motivation to protect themselves against breast cancer in this region of the world. The findings suggest that multi-level, socio-cultural interventions that focus on cognitive factors have much promise with this issue. Conclusions: Interventions are needed that effectively and efficiently target the personal motivation of at-risk Asian women to seek out and engage in breast cancer prevention. Concerning implications, personal motivation to seek out and engage in individual preventive actions for breast cancer prevention among Asian women is a timely, high priority target with practical implications for community development and health promotion. Further studies using qualitative, anthropologic approaches shaped for implementation in multi-ethnic Asian settings are needed to inform and guide these interventions.

• Journal of the Korea Society of Computer and Information
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• v.13 no.6
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• pp.77-86
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• 2008

The Web information sources can be regarded as the largest distributed database to the users. By virtually integrating the distributed information sources and regarding them as a single huge database, we can query the database to extract information. This capability is important to develop Web application programs. We have to infer a database schema from browsing-oriented Web documents in order to integrate databases. This paper presents a heuristic algorithm to infer the XML Schema fully automatically from semi-structured Web documents. The algorithm first extracts candidate pattern regions based on predefined structure-making tags, and determines a target pattern region using a few heuristic factors, and then derives XML Schema extraction rules from the target pattern region. The schema extraction rule is represented in XQuery, which makes development of various application systems possible using open standard XML tools. We also present the experimental results for several public web sources to show the effectiveness of the algorithm.

• Genomics & Informatics
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• v.14 no.3
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• pp.125-135
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• 2016

Helicobacter pylori is a Gram-negative bacteria that is responsible for gastritis in human. Its spiral flagellated body helps in locomotion and colonization in the host environment. It is capable of living in the highly acidic environment of the stomach with the help of acid adaptive genes. The genome of H. pylori 26695 strain contains 1,555 coding genes that encode 1,445 proteins. Out of these, 340 proteins are characterized as hypothetical proteins (HP). This study involves extensive analysis of the HPs using an established pipeline which comprises various bioinformatics tools and databases to find out probable functions of the HPs and identification of virulence factors. After extensive analysis of all the 340 HPs, we found that 104 HPs are showing characteristic similarities with the proteins with known functions. Thus, on the basis of such similarities, we assigned probable functions to 104 HPs with high confidence and precision. All the predicted HPs contain representative members of diverse functional classes of proteins such as enzymes, transporters, binding proteins, regulatory proteins, proteins involved in cellular processes and other proteins with miscellaneous functions. Therefore, we classified 104 HPs into aforementioned functional groups. During the virulence factors analysis of the HPs, we found 11 HPs are showing significant virulence. The identification of virulence proteins with the help their predicted functions may pave the way for drug target estimation and development of effective drug to counter the activity of that protein.

• Journal of KIISE:Databases
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• v.32 no.2
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• pp.161-176
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• 2005

oping and applying XML techniques. One key aspect of our taxonomy is the support of the credibility of the result by evaluating which XML document types can be processed by a method. Another key aspect is to provide a basis for determining which is the best for target XML document types. Application with preparations for XML document mining shows that our taxonomy may present XML document types to be able to consider during the preparation process and target XML document types to be used for experiments.

• The Korean Journal of Physiology and Pharmacology
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• v.28 no.1
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• pp.59-72
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• 2024

To investigate the mechanism of Wenshen Xuanbi Decoction (WSXB) in treating osteoarthritis (OA) via network pharmacology, bioinformatics analysis, and experimental verification. The active components and prediction targets of WSXB were obtained from the TCMSP database and Swiss Target Prediction website, respectively. OA-related genes were retrieved from GeneCards and OMIM databases. Protein-protein interaction and functional enrichment analyses were performed, resulting in the construction of the Herb-Component-Target network. In addition, differential genes of OA were obtained from the GEO database to verify the potential mechanism of WSXB in OA treatment. Subsequently, potential active components were subjected to molecular verification with the hub targets. Finally, we selected the most crucial hub targets and pathways for experimental verification in vitro. The active components in the study included quercetin, linolenic acid, methyl linoleate, isobergapten, and beta-sitosterol. AKT1, tumor necrosis factor (TNF), interleukin (IL)-6, GAPDH, and CTNNB1 were identified as the most crucial hub targets. Molecular docking revealed that the active components and hub targets exhibited strong binding energy. Experimental verification demonstrated that the mRNA and protein expression levels of IL-6, IL-17, and TNF in the WSXB group were lower than those in the KOA group (p < 0.05). WSXB exhibits a chondroprotective effect on OA and delays disease progression. The mechanism is potentially related to the suppression of IL-17 and TNF signaling pathways and the down-regulation of IL-6.