• Proceedings of the KIEE Conference
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• 2002.07d
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• pp.2815-2817
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• 2002

Classification method of cancers using cDNA microarrays data was developed using genetic algorithms and neural networks. For gene selection, 2308 genes were ranked using genetic algorithms, and selected by frequency number of selection from 1000 of genetic iterative runs. To calculate fitness values, artificial neural networks are used as classifier. The small, round blue cell tumors (SRBCTs) which is difficult to distinguish via pathological single test was used as test diseases for classification, and the test results showed the 96% of exact classification capability for 25 test samples.

• Molecules and Cells
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• v.40 no.1
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• pp.10-16
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• 2017

When peripheral axons are damaged, neuronal injury signaling pathways induce transcriptional changes that support axon regeneration and consequent functional recovery. The recent development of bioinformatics techniques has allowed for the identification of many of the regeneration-associated genes that are regulated by neural injury, yet it remains unclear how global changes in transcriptome are coordinated. In this article, we review recent studies on the epigenetic mechanisms orchestrating changes in gene expression in response to nerve injury. We highlight the importance of epigenetic mechanisms in discriminating efficient axon regeneration in the peripheral nervous system and very limited axon regrowth in the central nervous system and discuss the therapeutic potential of targeting epigenetic regulators to improve neural recovery.

• Journal of Photoscience
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• v.9 no.2
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• pp.287-289
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• 2002

Planarians show negative phototaxis and have extensive regenerative ability, including the ability to regenerate the brain. Recently the process of regeneration of the planarian brain has been divided into three steps based on the expression of neural markers. In this study, we have analyzed the process of recovery of the light response during head regeneration. Although morphological observations indicated that regeneration of the eyes and optic nerves appeared to be completed by the fourth day, the recovery of the evasion behavior against light was not recovered within 4 days after amputation. Functional recovery of the evasion behavior could be detected starting 5 days after amputation and then gradually recovered. We previously identified genes which are specifically expressed in the brain after the recovery of morphological structures. This characteristic suggested that these genes may be involved in functional recovery of the brain. To investigate the function of these genes, we performed gene knockout analysis using the RNA interference method. The results clearly indicated that these genes are involved in the functional recovery of the visual system.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.15 no.9
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• pp.2032-2037
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• 2011

Marker genes are defined as genes in which the expression level characterizes a specific experimental condition. Such genes in which the expression levels differ significantly between different groups are highly informative relevant to the studied phenomenon. In this paper, first the system can detect marker genes that are selected by ranking genes according to statistics after normalizing data with methods that are the most widely used among several normalization methods proposed the while, And it compare and analyze a performance of each of normalization methods with mult-perceptron neural network layer. The Result that apply Multi-Layer perceptron algorithm at Microarray data set including eight of marker gene that are selected using ANOVA method after Lowess normalization represent the highest classification accuracy of 99.32% and the lowest prediction error estimate.

• The Journal of Korean Medicine
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• v.25 no.2
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• pp.127-137
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• 2004

Objectives : The purpose of this investigation was to evaluate the effects of Sohaphyang-won (SH) on the alteration in gene expression in a hypoxia model using cultured rat cortical cells. Methods : E18 rat cortical cells were grown in neurobasal medium containing B27 supplement. On 12 DIV, SH was added ($20\mu\textrm{g}/ml$) to the culture media for 24 hrs. On 14 DIV, cells were given a hypoxic insult (2% O2/5% CO2, $37^{\circ}C$, 3 hrs), returned to normoxia and cultured for another 24 hrs. Total RNA was prepared from SH-untreated (control) and -treated cultures and alteration in gene expression was analyzed by microarray using rat 5K-TwinChips. Results : Effects on some of the genes whose functions are implicated in neural viability are as follows: 1) For most of the genes altered in expression, the global M values were between -05 to +0.5, Among these, 1517 genes were increased in their expression by more than global M +0.1, while 1480 genes were decreased by more than global M -0.1. 2) The expression of apoptosis-related genes such as Bad (global M =0.35), tumor protein p53 (T53) (global M =0.28) were increased, while v-akt murine thymoma viral oncogene homolog 1 (Akt1) was decreased. 3) The expression of hemoglobin alpha 1 (probably neuroglobin) was increased by about 3.2-fold (global M =1.7). 4) The expression of antioxidation-related catalase gene was increased (global M =0.26). 5) The expression of PKCzeta (prkcz), an upstream kinase of MAPK, was increased (global M =0.29). 6) The expression of retinoic acid receptor alpha (RAR), which may regulate transcription in hypoxic stress, was increased (global M =10.27). Conclusions : In summary, the microarray data suggest that SH doesn't increase the expression of oxygen capture-, anti-oxidation- and 'response to stress' -related genes but decreases some anti-apoptosis genes which would help protect the hypoxic cells from apoptosis.

• Animal cells and systems
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• v.12 no.1
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• pp.23-33
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• 2008

The Zic family is a group of genes encoding zinc finger proteins that are highly expressed in the mammalian cerebellum. Zic genes are the vertebrate homologue of Drosophila pair-rule gene, odd-paired(opa), which plays important roles in the parasegmental subdivision as well as in the visceral mesoderm development of Drosophila embryos. Recent studies on human, mouse, frog, fish and ascidian Zic homologues support that Zic genes are involved in a variety of developmental processes, including neurogenesis, myogenesis, skeletal patterning, and left-right axis establishment. In an effort to explore possible functions of Zic proteins during vertebrate embryogenesis, we initially examined more detailed expression pattern of zebrafish homologue of zic3(zic3z). zic3z transcripts are detected in the neuroectoderm, neural plate, dorsal neural tube, and brain regions including eye field during early embryonic development. Marker DNA studies found that zic3z transcription is modulated by BMP, Wnt, and Nodal signals particularly in the dorsal and vegetal neuroectoderm at gastrula. Interfering with zic3z translation with zic3z-specific morpholino causes abnormal brain formation and expansion of the optic stalk cells. Retinal ganglion cells(RGCs) undergo abnormal neuronal differentiation. These findings suggest that zic3z defines the dorsal and vegetal neuroectoderm to specify brain formation and retinal neurogenesis during early embryonic development.

• Proceedings of the Korean Society of Toxicology Conference
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• 2006.11a
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• pp.55-64
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• 2006

The fetal central nervous system (CNS) is sensitive to diverse environmental factors, such as alcohol, heavy metals, irradiation, mycotoxins, neurotransmitters, and DNA damage, because a large number of processes occur during an extended period of development. Fetal neural damage is an important issue affecting the completion of normal CNS development. As many concepts about the brain development have been recently revealed, it is necessary to compare the mechanism of developmental abnormalities induced by extrinsic factors with the normal brain development. To clarify the mechanism of fetal CNS damage, we used one experimental model in which 5-azacytidine (5AZC), a DNA damaging and demethylating agent, was injected to the dams of rodents to damage the fetal brain. 5AzC induced cell death (apoptosis)and cell cycle arrest in the fetal brain, and it lead to microencephaly in the neonatal brain. We investigated the mechanism of apoptosis and cell cycle arrest in the neural progenitor cells in detail, and demonstrated that various cell cycle regulators were changed in response to DNA damage. p53, the guardian of genome, played a main role in these processes. Further, using DNA microarray analysis, tile signal cascades of cell cycle regulation were clearly shown. Our results indicate that neural progenitor cells have the potential to repair the DNA damages via cell cyclearrest and to exclude highly affected cells through the apoptotic process. If the stimulus and subsequent DNA damage are high, brain development proceeds abnormally and results in malformation in the neonatal brain. Although the mechanisms of fetal brain injury and features of brain malformation afterbirth have been well studied, the process between those stages is largely unknown. We hypothesized that the fetal CNS has the ability to repair itself post-injuring, and investigated the repair process after 5AZC-induced damage. Wefound that the damages were repaired by 60 h after the treatment and developmental processes continued. During the repair process, amoeboid microglial cells infiltrated in the brain tissue, some of which ingested apoptotic cells. The expressions of genes categorized to glial cells, inflammation, extracellular matrix, glycolysis, and neurogenesis were upregulated in the DNA microarray analysis. We show here that the developing brain has a capacity to repair the damage induced by the extrinsic stresses, including changing the expression of numerous genes and the induction of microglia to aid the repair process.

• Journal of KIISE:Software and Applications
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• v.33 no.4
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• pp.440-448
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• 2006

Self-Organizing Map (SOM) is an unsupervised learning neural network and it is used for preserving the structural relationships in the data without prior knowledge. SOM has been applied in the study of complex problems such as vector quantization, combinatorial optimization, and pattern recognition. This paper proposes a new usage of SOM as a tool for schema transformation hoping to achieve more efficient genetic process. Every offspring is transformed into an isomorphic neural network with more desirable shape for genetic search. This helps genes with strong epistasis to stay close together in the chromosome. Experimental results showed considerable improvement over previous results.

• BMB Reports
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• v.42 no.5
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• pp.245-259
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• 2009

The process by which adult neural stem cells generate new and functionally integrated neurons in the adult mammalian brain has been intensely studied, but much more remains to be discovered. It is known that neural progenitors progress through distinct stages to become mature neurons, and this progression is tightly controlled by cell-cell interactions and signals in the neurogenic niche. However, less is known about the cell-intrinsic signaling required for proper progression through stages of adult neurogenesis. Techniques have recently been developed to manipulate genes specifically in adult neural stem cells and progenitors in vivo, such as the use of inducible transgenic mice and viral-mediated gene transduction. A critical mass of publications utilizing these techniques has been reached, making it timely to review which molecules are now known to play a cell-intrinsic role in regulating adult neurogenesis in vivo. By drawing attention to these isolated molecules (e.g. Notch), we hope to stimulate a broad effort to understand the complex and compelling cascades of intrinsic signaling molecules important to adult neurogenesis. Understanding this process opens the possibility of understanding brain functions subserved by neurogenesis, such as memory, and also of harnessing neural stem cells for repair of the diseased and injured brain.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.6 no.1
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• pp.108-115
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• 2006

The inherent biology of neural stem cells (NSCs) endows them with capabilities that not only circumvent many of the limitations of other gene transfer vehicles, but that enable a variety of novel therapeutic strategies heretofore regarded as beyond the purview of neural transplantation, Most neurodegenerative diseases are characterized not by discrete, focal abnormalities but rather by extensive, multifocal, or even global neuropathology. Such widely disseminated lesions have not conventionally been regarded as amenable to neural transplantation. However, the ability of NSCs to engraft diffusely and become integral members of structures throughout the host CNS while also expressing therapeutic molecules may permit these cells to address that challenge. Intriguingly, while NSCs can be readily engineered to express specified foreign genes, other intrinsic factors appear to emanate spontaneously from NSCs and, in the context of reciprocal donor-host signaling, seem to be capable of neuroprotective and/or neuroregenerative functions. Stem cells additionally have the appealing ability to "home in" on pathology, even over great distances. Such observations help to advance the idea that NSCs - as a prototype for stem cells from other solid organs - might aid in reconstructing the molecular and cellular milieu of maid eve loped or damaged organs.