• Journal of Life Science
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• v.18 no.8
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• pp.1132-1139
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• 2008

A CpG island is a short stretch of DNA in which the frequency of the CG dinucleotide is higher than other regions. CpG islands are present in the promoters and exonic regions of approximately $30{\sim}60$% of mammalian genes so they are useful markers for genes in organisms containing 5-methylcytosine in their genomes. Recent evidence supports the notion that the hypermethylation of CpG island, by silencing tumor suppressor genes, plays a major causal role in cancer, which has been described in almost every tumor types. In this respect, CpG island search by computational methods is very helpful for cancer research and computational promoter and gene predictions. I therefore developed a window program (called CpGi) on the basis of CpG island criteria defined by D. Takai and P. A. Jones. The program 'CpGi' was implemented in Visual C++ 6.0 and can determine the locations of CpG islands using diverse parameters (%GC, Obs (CpG)/Exp (CpG), window size, step size, gap value, # of CpG, length) specified by user. The analysis result of CpGi provides a graphical map of CpG islands and G+C% plot, where more detailed information on CpG island can be obtained through pop-up window. Two human contigs, i.e. AP00524 (from chromosome 22) and NT_029490.3 (from chromosome 21), were used to compare the performance of CpGi and two other public programs for the accuracy of search results. The two other programs used in the performance comparison are Emboss-CpGPlot and CpG Island Searcher that are web-based public CpG island search programs. The comparison result showed that CpGi is on a level with or outperforms Emboss-CpGPlot and CpG Island Searcher. Having a simple and easy-to-use user interface, CpGi would be a very useful tool for genome analysis and CpG island research. To obtain a copy of CpGi for academic use only, contact corresponding author.

• Journal of the Korean Society of Marine Environment & Safety
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• v.16 no.2
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• pp.141-151
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• 2010

Harmful algal blooms (HABs), commonly known as red tides, are aquatic phenomena caused by the rapid growth and accumulation of certain microalgae, which can lead to marked discoloration of surface waters, and severe impacts on public health, commerce, and the environment. In South Korea, the red tides have been a serious and recurrent problem, especially along the south coast. Plenty of yellow loess was used to control an outbreak of the red tides for 15 years from 1996 until now. Yellow loess was almost sprayed in the vicinity of a large fish farming industry. In this research, the distribution characteristics and density distribution of zooplankton were investigated in autumn (Oct. 2008) and spring (Apr. 2009) using volume backscattering strength (SV) calculated by the zooplankton collected with north pacific standard (NORPAC) net and the echo intensity measured with ADCP at stations on the study area in the spraying ocean of yellow loess (SOYL), and the non-spraying ocean of yellow ocean (NOYL) by the red tide generating every year. The species number and the individuals per unit volume of the zooplankton collected in NOYL was high and it which was collected in SOYL was low. As a result of comparing the volume backscattering strength ($SV_c$) calculated by species and length of the zooplankton collected with NORPAC net with the volume backscattering strength ($SV_m$) calculated by the echo intensity measured with ADCP at stations on the study area, although $SV_c$ and $SV_m$ of NOYL were generally in agreement, $SV_m$ of SOYL was higher than $SV_c$ 4.3dB, i.e. ADCP is greatly influenced by suspended solid in SOYL. The horizontal distribution map of $SV_m$ at the study area in autumn (Oct. 2008) and spring (Apr. 2009) was drawn. $SV_m$ of SOYL is higher than NOYL and autumn is higher than spring. $SV_m$ can suppress the overestimate or underestimate of $SV_c$.

• Journal of the Korean Institute of Traditional Landscape Architecture
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• v.30 no.2
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• pp.64-71
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• 2012

This is a basic study for recovering original form of Nongsanbyeoleop(農山別業) in Gangjin, Jeonnam, created in the latter part of Joseon period and the estimation of originla form at the time of creation was conducted by analyzing related literature and inspecting the actual site. "Joseokruki(朝夕樓記)" of Dasan Jung, Yak Yong could estimate spatial structure and using form of Nongsanbyeoleop and the arrangement of spatial structure in literature could be confirm by on-the-site inspection. The results of this study are as follows. The first, Nongsanbyeoleop managed spatial factors applying natural topography. For the spatial characteristics of Nongsanbyeoleop, the location of ancestral ritual space including deceased father's tomb and tomb house far from the main levee of Yun, Kwang Taek, a father of Yun, Seo Yu by 1.9km and housekeeping could be confirmed. The second, spatial estimation by "Joseokruki" could be possible. "Joseokruki" describes Joseokru.Youngmojae.Hanokkwan.Cheokyunjung.Sangam as construction factors, Wundang.Kookdan.Nokwunoh. as plant factors, Sookyunggan.Keumkoji.Nokeumjung.Uijanghae as hydroponic factors and Pyoeunkok.Aengjakang as natural topography factors. However, most of them were disappeared and at present, only Youngmojae, Keumgoji, Kukdan and Wundang show the past trace. The third is for the changed space of Nongsanbyeoleop and its reason. The surrounding space of Nongsanbyeoleop was planated by land arrangement in 1960s and it played a role of topographical damage because it's recognized as the plane factor including Nongsanbyeoleop's surrounding landscape rather than dotted factor. The forth, the actual measurement of Nongsanbyeoleop and digitalization of manual map of numerical value are judged to be sufficient to apply as the basic material for recovering garden in the future. Because of the diatahce changing method applied at that time, the garden recovery of Nongsanbyeoleop intended to be concreted and 3D model established by digitalized basic materials is considered to apply for multilateral studying. Thus, Nongsanbyeoleop which is byeolseo including the tomb of deceased father based on the conceptual hyo thought shows clear differences from the organized factors of Byolseowonrim of precedent studies and the importance of Byolseowonrim is sufficient. But, the constructional factors which cannot know disappeared spatial factors and accurate location became the limitation of this study. In the future, clear verification of original form must be progressed by excavation which can confirm the location of construction factors.

• The Korean Journal of Nuclear Medicine
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• v.39 no.1
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• pp.57-68
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• 2005

Purpose: The objective of this study was to assess attenuation correction algorithms with the $^{137}Cs$ point source for the brain positron omission tomography (PET) imaging process. Materials & Methods: Four different types of phantoms were used in this study for testing various types of the attenuation correction techniques. Transmission data of a $^{137}Cs$ point source were acquired after infusing the emission source into phantoms and then the emission data were subsequently acquired in 3D acquisition mode. Scatter corrections were performed with a background tail-fitting algorithm. Emission data were then reconstructed using iterative reconstruction method with a measured (MAC), elliptical (ELAC), segmented (SAC) and remapping (RAC) attenuation correction, respectively. Reconstructed images were then both qualitatively and quantitatively assessed. In addition, reconstructed images of a normal subject were assessed by nuclear medicine physicians. Subtracted images were also compared. Results: ELEC, SAC, and RAC provided a uniform phantom image with less noise for a cylindrical phantom. In contrast, a decrease in intensity at the central portion of the attenuation map was noticed at the result of the MAC. Reconstructed images of Jaszack and Hoffan phantoms presented better quality with RAC and SAC. The attenuation of a skull on images of the normal subject was clearly noticed and the attenuation correction without considering the attenuation of the skull resulted in artificial defects on images of the brain. Conclusion: the complicated and improved attenuation correction methods were needed to obtain the better accuracy of the quantitative brain PET images.

• Journal of Korean Society of Forest Science
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• v.40 no.1
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• pp.1-18
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• 1978

Three Pinus densiflora populations as shown in location map (Fig. 1) were studied in 1977. These succeed the population numbers 10, 11 and 12 after the preceeding populations. Following the previous study methods, 20 trees were chosen from each population and the morphological characteristics such as tree forms, branching habit, needle and wood properties were investigated. The results are summerized as follows; 1. The mean stand ages were ranged from 40 to 45. The growth performances of trees of population 10 and 11 was similar, but 12 seemed to be inferior more or less. 2. The ratios of clear bole length was 0.53 in population 12 as the highest but 0.43 for population 10 as the lowest. 3. The population 12 was considered to be a stand of the coarser branching habit having the crown index (The maximum crown diameter/the crown length) 1.65 though the mean branching angle indicates almost horizontal. 4. The differences were observed in the clear bole length ratios and crown-indices between populations as shown in Fig. 3 and 4. 5. No inter-population differences in serration density of needle was shown but significant inter and intra-population and individual differences (within population) in number of stomata rows and resin duct. 6. Population 12 shown 0.119 of resin duct index as the maximum. 7. The pattern of diameter growth, analyses based on the width of 10-year-ring segment unit (for example, the 1st segment denotes the width between pith center and 10th year ring and the 2nd one is from 11th to 20th year ring and so on.), was alike among populations as shown in Fig. 9. 8. No significant differences between population in mean summer wood percentages as well as in wood specific gravity was observed. The values of wood specific gravity were increased with the increase of ages in population 10 and 11 however vice versa in population 12. 9. The fiber length was increased with the increase of age but no differences between populations as shown in Fig. 12.

• Journal of the Korean earth science society
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• v.21 no.4
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• pp.437-448
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• 2000

The Middle Carboniferous Gabsan Formation is distributed in the Cheongrim area of southern Yeongwol and the Mt. Gachang area of Chungbuk Province. This study was carried out to investigate the lithological characters and geochemical composition of the limestones and to find out controlling structures of the limestones of the formation. The limestones of the Gabsan Formation are characterized by the light gray to light brown in color and fine and dense textures. The limestone grains are composed of crinoid fragments, small foraminfers, fusulinids, gastropods, ostracods, etc. Due to the recrystallization, some limestones consist of fine crystalline calcites. The chemical analysis of limestones of the formation was conducted to find out the contents of CaO, MgO, Al$_2$O$_3$, Fe$_2$O$_3$ and SiO$_2$. The content of CaO ranges from 49.78-60.63% and the content of MgO ranges from 0.74 to 4.63% The contents of Al$_2$O$_3$ and Fe$_2$O$_3$ are 0.02-0.55% and 0.02${\sim}$0.84% , respectively. The content of SiO$_2$ varies from 1.55 to 4.80%, but some samples contain more than 6.0%. The limestones of the formation can be grouped into two according to the CaO content: One is a group of which CaO content ranges from 49.78 to 56.26% and the other is a group of which CaO content varies from 59.36 to 60.38%. In the first group, the contents of Al$_2$O$_3$, Fe$_2$O$_3$ and SiO$_2$ range very irregularly according to the CaO content. In the second group, the values of MgO, Al$_2$O$_3$, Fe$_2$O$_3$ and SiO$_2$ are nearly same. Detailed structural analysis of mesoscopic structures and microstructures indicates the five phase of deformation in the study area. The first phase of deformation(D$_1$) is characterized by regional scale isoclinal folds, and bedding parallel S$_1$ axial plane foliation which is locally developed in the mudstone and sandstone. Based on the observations of microstructures, S$_1$ foliations appear to be developed by grain preferred orientation accompanying pressure-solution. During second phase of deformation, outcrop scale E-W trending folds with associated foliations and lineations are developed. Microstructural observations indicate that crenulation foliations were formed by pressure-solution, grain boundary sliding and grain rotation. NNW and SSE trending outcrop scale folds, axial plane foliations, crenulation foliations, crenulation lineations, intersection lineations are developed during the third phase of deformation. On the microscale F$_3$ fold, axial plane foliations which are formed by pressure solution are well developed. Fourth phase of deformation is characterized by map scale NNW trending folds. The pre-existing planar and linear structures are reoriented by F$_4$ folds. Fifth phase of deformation developed joints and faults. The distribution pattern of the limestones is mostly controlled by F$_1$ and F$_4$ folds.

• The Korean Journal of Nuclear Medicine
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• v.32 no.5
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• pp.414-424
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• 1998

Purpose: Cross-modality coregistration of positron emission tomography (PET) and magnetic resonance imaging (MR) could enhance the clinical information. In this study we propose a refined technique to improve the robustness of registration, and to implement more realistic visualization of the coregistered images. Materials and Methods: Using the sinogram of PET emission scan, we extracted the robust head boundary and used boundary-enhanced PET to coregister PET with MR. The pixels having 10% of maximum pixel value were considered as the boundary of sinogram. Boundary pixel values were exchanged with maximum value of sinogram. One hundred eighty boundary points were extracted at intervals of about 2 degree using simple threshold method from each slice of MR images. Best affined transformation between the two point sets was performed using least square fitting which should minimize the sum of Euclidean distance between the point sets. We reduced calculation time using pre-defined distance map. Finally we developed an automatic coregistration program using this boundary detection and surface matching technique. We designed a new weighted normalization technique to display the coregistered PET and MR images simultaneously. Results: Using our newly developed method, robust extraction of head boundary was possible and spatial registration was successfully performed. Mean displacement error was less than 2.0 mm. In visualization of coregistered images using weighted normalization method, structures shown in MR image could be realistically represented. Conclusion: Our refined technique could practically enhance the performance of automated three dimensional coregistration.

• Journal of Korean Society of Forest Science
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• v.44 no.1
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• pp.1-25
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• 1979

Six natural populations of Pinus densiflora S. et Z. as shown in the location map (Flg 1) were studied during 1978. The numerial pouplation codes, 13 to 18. The results of populations 1 to 12 were reported in previous papers. Following the study methods described before, 20 trees were sampled from each population and morpological characteristics such as stem forms, branching habit needle and wood properties investigated. The results are summerized as follows; 1. The mean stand ages were ranged from 36 to 97 of years. The growth performances of trees of population 14. 15 and 18 was similar, but 13, 16, and 17 seemed to be inferior more or less. 2. The ratios of clear bole length were 0.70 in population 18 as the highest but 0.28 for population 16 as the lowest. 3. The population 17 was considered to be a stand of the coarser branching habit having the crown index (The maximum crown diameter/the crown height) 158 though the branching angles were almost horizontal. 4. The differences were observed in the clear bole length ratios and crown-indices between population as shown In Fig. 3 and 4. 5. As to the serration density, number of stomata row and resin duct; the significant differences exist between individual trees within population and also between populations. 6. Population 18 shown resin duct index 0.119 as the maximum. 7. The patterns of diameter growth, based on the width of 10-year-ring segment unit(for example, the 1st segment denotes the with between pith center and 10th year ring and the 2nd one is from 11th to 20th ring and so on.), were alike among populations as shown in Fig 9. 8. Significant differences between population in mean summer wood percentage as well as in wood specific gravity was observed. The values of wood specific gravity were increased with the increase of ages in population 14, 18 however vice versa in population 13, 15, and 17. 9. The fiber length was mereased with the increased of age but no differences between populations as shown in Fig. 12.

• Journal of Wetlands Research
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• v.7 no.3
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• pp.87-95
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• 2005

Vegetation structure of the vascular plants was investigated from March 2003 to October 2003 in Haepyeong wetland, Gumi-si, Gyeongsangbuk-do, Korea. Actual vegetation of Haepyeong wetland largely can be classified by floristic composition and physiognomy into 18 communities; Xanthium strumarium-Digitaria sanguinalis, Humulus japonicus, Persicaria perfoliata-Humulus japonicus, Phragmites japonica-Miscanthus sacchariflorus, Persicaria hydropiper-Phragmites communis, Persicaria hydropiper, Phragmites japonica-Persicaria hydropiper, Miscanthus sacchariflorus- Phragmites japonica, Persicaria hydropiper-Phragmites japonica, Miscanthus sacchariflorus-Salix glandulosa, Salix nipponica-Salix glandulosa, Salix nipponica-Salix koreensis, Salix nipponica, Miscanthus sacchariflorus-Salix nipponica, Phalaris arundinacea-Salix nipponica, Salix glandulosa-Salix nipponica, Trapa japonica, and Ceratophyllum demersum-Trapa japonica. Among them, the area of the Salix nipponica-Salix koreensis community was the largest as 122.2ha(9.23%). The dominant vegetation type was Miscanthus sacchariflorus-Persicaria hydropiper community based on phytosociological method, and it was was classified into three subcommunities; Salix glandulosa-Salix nipponica subcommunity, Digitaria sanguinalis subcommunity, and Cyperus amuricus subcommunity. Differential species of Salix glandulosa-Salix nipponica subcommunity were Salix nipponica, S. glandulosa, S. koreensis, Scirpus radicans, Persicaria maackiana, and Achyranthes japonica; differential species of Digitaria sanguinalis subcommunity were D. sanguinalis, Setaria viridis, Ambrosia artemisiifolia var. elatior, and Cyperus orthostachyus; differential species of Xanthium strumarium subcommunity were X. strumarium, Acalypha australis, Erigeron canadensis, Echinochloa crus-galli, and Vicia tetrasperma. Zonation of vascular hydrophytes and hygrophytes was as followers: Salix glandulosa, S. koreensis, S. nipponica were distributed in the region of land which water table is low, and Persicaria maackiana, Persicaria hydropiper, Scirpus radicans were distributed in the understory. And emergent plants such as Phragmites communis and Scirpus karuizawensis, floating-leaved plant such as Trapa japonica, submersed plant such as Ceratophyllum demersum, and free floating plant such as Spirodela polyrhiza formed the zonation from shoreline to water. The specified wild plants designated by the Korean Association for Conservation of Nature, Ministry of Forest, and Ministry of Environment were not distributed in the study area. It was expected that Haepyeong Wetland worthy of conservation contributed purifying water pollution, giving habitats of many lifes, and providing beautiful scenes of the river.

• Journal of Korean Society of Forest Science
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• v.80 no.1
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• pp.54-71
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• 1991

To classify and analyze the forest communities and their structures, the vegetation in Mt. Joghe was investigated from July, 1980 to August, 1989. The results obtained are as follow ; 1. A total of 750 kinds of vascular plant(49 orders, 122 families, 434 genera, 627 species, 1 subspecies, 111 varieties and 11 forma)were observed in Mt. Ioghe. The newly observed plant species were Dioscorea quingueloba, Spiranthes sinensis, Cephalanthera falcata, Angelica gigas, Clematis patents, Paeonia obovata, Hibiscus mulabilis, Ainsliaea acerifolia, Dictamnus dasycarpus, Cynachum ascyrifolia, Vaccinium koreanum, Erythrortium japonicum, Indigofera kirilowii (17species), Broussonetia kazinoki var, humillis, Euonymus, fortunei var. radicans, Juniperus communis var, nippnnica, Callicarpa japonica var. radicans, Joniperus communis var. rzipponica, Callicarpa japonica var. taquetii (4 varieties) and L indera obtusiloba for. billosum (1 forma). 2. The life spectrum of flora in Mt. Joghe was classified into $CH-D_1-R_5-e$ type. Distribution area was identical to Southern type by Nakai, Lee, and Yim. A few subtropical species were also observed. 3. Simpson's species diversity index(Ds) was 0.9 and Shannon-Weiner's diversity index (H') was 1.004. These indice suggest that the vegetation in Mt. Joghe is of complicated forest communities. 4. Pte-Q was 1.81 which was higher than the nationwide mean of 1.68. Urbanization Index (UI) was 28.75 for naturalized plant species, and 17.49 for exotic woody plant species, which were similar to those of Mt. Baekun and Mt. Naejang. 5. The forest vegetation of Mt. Joghe was grouped in 3 vegetation types : 7 natural plant Communities dominated by Quercus serrat, Quercus acutissima, Quercus variabilis, Carpinus laxiflora, Pinus derasiflora and Platycarya strobilacea, 8 substitutional plant communities Styrax japonica, Stewartia koreana, Lindera erytlrrocarpa, Zelkova serrata, Rhtrs chinensis, Controversa, and Frzrxirtus manrlshurica, and 7 plantation Communities composed of Pinus koraiensis, Pinus rigida, Magnolia nbnvata, Chamecyparis obkrsa, Larie ieptolepis, Castanea crenata and Cryptomeria japonica. 6. Actual vegetation maps and profile diagrams were made by phytosocialogical classification. 7. As the important and unique species in Mt. Joghe, Lindera sericea, Penicaria tilitorme, Hex macropoda, Hex macropoda for. pseudo-macropoda, Steroartia koreana, Adenopkora palustris and Corylop.,is coreana, which were also seported by Lee(1977), Kim and Yark(1989), were identified and Vaccinium coreanum, Cremastra appendiculinium, Juniperus comminis van. nipponica, Cephalanthera falcata, Broussortetia kazinoki var. humilis, paeonia obovata, Deutzia prunifolia, Dictamnus dasyarpus, Angelica gigics and Bupleurum falcatum were odditionally observed.