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Development of a Window Program for Searching CpG Island (CpG Island 검색용 윈도우 프로그램 개발)

  • Kim, Ki-Bong
    • 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.

The PRISM-based Rainfall Mapping at an Enhanced Grid Cell Resolution in Complex Terrain (복잡지형 고해상도 격자망에서의 PRISM 기반 강수추정법)

  • Chung, U-Ran;Yun, Kyung-Dahm;Cho, Kyung-Sook;Yi, Jae-Hyun;Yun, Jin-I.
    • Korean Journal of Agricultural and Forest Meteorology
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    • v.11 no.2
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    • pp.72-78
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    • 2009
  • The demand for rainfall data in gridded digital formats has increased in recent years due to the close linkage between hydrological models and decision support systems using the geographic information system. One of the most widely used tools for digital rainfall mapping is the PRISM (parameter-elevation regressions on independent slopes model) which uses point data (rain gauge stations), a digital elevation model (DEM), and other spatial datasets to generate repeatable estimates of monthly and annual precipitation. In the PRISM, rain gauge stations are assigned with weights that account for other climatically important factors besides elevation, and aspects and the topographic exposure are simulated by dividing the terrain into topographic facets. The size of facet or grid cell resolution is determined by the density of rain gauge stations and a $5{\times}5km$ grid cell is considered as the lowest limit under the situation in Korea. The PRISM algorithms using a 270m DEM for South Korea were implemented in a script language environment (Python) and relevant weights for each 270m grid cell were derived from the monthly data from 432 official rain gauge stations. Weighted monthly precipitation data from at least 5 nearby stations for each grid cell were regressed to the elevation and the selected linear regression equations with the 270m DEM were used to generate a digital precipitation map of South Korea at 270m resolution. Among 1.25 million grid cells, precipitation estimates at 166 cells, where the measurements were made by the Korea Water Corporation rain gauge network, were extracted and the monthly estimation errors were evaluated. An average of 10% reduction in the root mean square error (RMSE) was found for any months with more than 100mm monthly precipitation compared to the RMSE associated with the original 5km PRISM estimates. This modified PRISM may be used for rainfall mapping in rainy season (May to September) at much higher spatial resolution than the original PRISM without losing the data accuracy.

An Experiment and Analysis for Standardize Measurement on CCFL (냉음극 형광램프의 표준화 계측을 위한 실험과 분석)

  • Jin, Dong-Jun;Jeong, Jong-Mun;Jeong, Hee-Suk;Kim, Jin-Shon;Lee, Min-Kyu;Kim, Jung-Hyun;Koo, Je-Huan;Gwon, Gi-Cheong;Kang, June-Gill;Choi, Eun-Ha;Cho, Guang-Sup
    • Journal of the Korean Vacuum Society
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    • v.17 no.4
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    • pp.331-340
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    • 2008
  • A method of measuring the current and voltage is suggested in the circuit of cold cathode fluorescent lamps (CCFLs) which are driven at a high frequency of $50{\sim}100\;kHz$ and a high voltage of several kV. It is difficult to measure the current and voltage in the lamp circuit, because the impedance of the probe at high voltage side causes the leakage current and the variation of luminance. According to the analysis of equivalence circuit with the probe impedance and leakage current, the proper measuring method is to adjust the input DC voltage and to keep the specific luminance when the probe is installed at a high voltage circuit. The lamp current is detected with a current probe or a high frequency current meter at the ground side and the voltage is measured with a high voltage probe at the high voltage side of lamp. The lamp voltage($V_C$) is measured between the ballast capacitor and the lamp electrode, and the output voltage($V_I$) of inverter is measured between inverter output and ballast capacitor. As the phases of lamp voltage($V_C$) and current ($I_G$) are nearly the same values, the real power of lamp is the product of the lamp voltage($V_C$) by the lamp current($I_G$). The measured value of the phase difference between inverter output voltage($V_I$) and lamp current($I_G$) is appreciably deviated from the calculated value at $cos{\theta}=V_C/V_I$.

Environmental Damage to Nearby Crops by Hydrogen Fluoride Accident (불화수소 누출사고 사례를 통한 주변 농작물의 환경피해)

  • Kim, Jae-Young;Lee, Eunbyul;Lee, Myeong Ji
    • Korean Journal of Environmental Agriculture
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    • v.38 no.1
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    • pp.54-60
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    • 2019
  • BACKGROUND: Hydrogen fluoride is one of the 97 accident preparedness substances regulated by the Ministry of Environment (Republic of Korea) and chemical accidents should be managed centrally due to continual occurrence. Especially, hydrogen fluoride has a characteristic of rapid diffusion and very toxic when leaking into the environment. Therefore, it is important to predict the impact range quickly and to evaluate the residual contamination immediately to minimize the human and environmental damages. METHODS AND RESULTS: In order to estimate the accident impact range, the off-site consequence analysis (OCA) was performed to the worst and alternative scenarios. Also, in order to evaluate the residual contamination of hydrogen fluoride in crop, the samples in accident site were collected from 15-divided regions (East direction from accident sites based on the main wind direction), and the concentration was measured by fluoride ($F^-$) ion-selective electrode potentiometer (ISE). As a result of the OCA, the affected distance by the worst scenario was estimated to be >10 km from the accident site and the range by the alternative scenario was estimated to be about 1.9 km. The residual contamination of hydrogen fluoride was highest in the samples near the site of the accident (E-1, 276.82 mg/kg) and tended to decrease as it moved eastward. Meanwhile, the concentrations from SE and NE (4.96~28.98 mg/kg) tended to be lower than the samples near the accident site. As a result, the concentration of hydrogen fluoride was reduced to a low concentration within 2 km from the accident site (<5 mg/kg), and the actual damage range was estimated to be around 2.2 km. Therefore, it is suggested that the results are similar to those of alternative accident scenarios calculated by OCA (about 1.9 km). CONCLUSION: It is difficult to estimate the chemical accident-affecting range/region by the OCA evaluation, because it is not possible to input all physicochemical parameters. However simultaneous measurement of the residual contamination in the environment will be very helpful in determining the diffusion range of actual chemical accident.

BVOCs Estimates Using MEGAN in South Korea: A Case Study of June in 2012 (MEGAN을 이용한 국내 BVOCs 배출량 산정: 2012년 6월 사례 연구)

  • Kim, Kyeongsu;Lee, Seung-Jae
    • Korean Journal of Agricultural and Forest Meteorology
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    • v.24 no.1
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    • pp.48-61
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    • 2022
  • South Korea is quite vegetation rich country which has 63% forests and 16% cropland area. Massive NOx emissions from megacities, therefore, are easily combined with BVOCs emitted from the forest and cropland area, then produce high ozone concentration. BVOCs emissions have been estimated using well-known emission models, such as BEIS (Biogenic Emission Inventory System) or MEGAN (Model of Emission of Gases and Aerosol from Nature) which were developed using non-Korean emission factors. In this study, we ran MEGAN v2.1 model to estimate BVO Cs emissions in Korea. The MO DIS Land Cover and LAI (Leaf Area Index) products over Korea were used to run the MEGAN model for June 2012. Isoprene and Monoterpenes emissions from the model were inter-compared against the enclosure chamber measurements from Taehwa research forest in Korea, during June 11 and 12, 2012. For estimating emission from the enclosed chamber measurement data. The initial results show that isoprene emissions from the MEGAN model were up to 6.4 times higher than those from the enclosure chamber measurement. Monoterpenes from enclosure chamber measurement were up to 5.6 times higher than MEGAN emission. The differences between two datasets, however, were much smaller during the time of high emissions. More inter-comparison results and the possibilities of improving the MEGAN modeling performance using local measurement data over Korea will be presented and discussed.

An accuracy analysis of Cyberknife tumor tracking radiotherapy according to unpredictable change of respiration (예측 불가능한 호흡 변화에 따른 사이버나이프 종양 추적 방사선 치료의 정확도 분석)

  • Seo, jung min;Lee, chang yeol;Huh, hyun do;Kim, wan sun
    • The Journal of Korean Society for Radiation Therapy
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    • v.27 no.2
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    • pp.157-166
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    • 2015
  • Purpose : Cyber-Knife tumor tracking system, based on the correlation relationship between the position of a tumor which moves in response to the real time respiratory cycle signal and respiration was obtained by the LED marker attached to the outside of the patient, the location of the tumor to predict in advance, the movement of the tumor in synchronization with the therapeutic device to track real-time tumor, is a system for treating. The purpose of this study, in the cyber knife tumor tracking radiation therapy, trying to evaluate the accuracy of tumor tracking radiation therapy system due to the change in the form of unpredictable sudden breathing due to cough and sleep. Materials and Methods : Breathing Log files that were used in the study, based on the Respiratory gating radiotherapy and Cyber-knife tracking radiosurgery breathing Log files of patients who received herein, measured using the Log files in the form of a Sinusoidal pattern and Sudden change pattern. it has been reconstituted as possible. Enter the reconstructed respiratory Log file cyber knife dynamic chest Phantom, so that it is possible to implement a motion due to respiration, add manufacturing the driving apparatus of the existing dynamic chest Phantom, Phantom the form of respiration we have developed a program that can be applied to. Movement of the phantom inside the target (Ball cube target) was driven by the displacement of three sizes of according to the size of the respiratory vertical (Superior-Inferior) direction to the 5 mm, 10 mm, 20 mm. Insert crosses two EBT3 films in phantom inside the target in response to changes in the target movement, the End-to-End (E2E) test provided in Cyber-Knife manufacturer depending on the form of the breathing five times each. It was determined by carrying. Accuracy of tumor tracking system is indicated by the target error by analyzing the inserted film, additional E2E test is analyzed by measuring the correlation error while being advanced. Results : If the target error is a sine curve breathing form, the size of the target of the movement is in response to the 5 mm, 10 mm, 20 mm, respectively, of the average $1.14{\pm}0.13mm$, $1.05{\pm}0.20mm$, with $2.37{\pm}0.17mm$, suddenly for it is variations in breathing, respective average $1.87{\pm}0.19mm$, $2.15{\pm}0.21mm$, and analyzed with $2.44{\pm}0.26mm$. If the correlation error can be defined by the length of the displacement vector in the target track is a sinusoidal breathing mode, the size of the target of the movement in response to 5 mm, 10 mm, 20 mm, respective average $0.84{\pm}0.01mm$, $0.70{\pm}0.13mm$, with $1.63{\pm}0.10mm$, if it is a variant of sudden breathing respective average $0.97{\pm}0.06mm$, $1.44{\pm}0.11mm$, and analyzed with $1.98{\pm}0.10mm$. The larger the correlation error values in both the both the respiratory form, the target error value is large. If the motion size of the target of the sine curve breathing form is greater than or equal to 20 mm, was measured at 1.5 mm or more is a recommendation value of both cyber knife manufacturer of both error value. Conclusion : There is a tendency that the correlation error value between about target error value magnitude of the target motion is large is increased, the error value becomes large in variation of rapid respiration than breathing the form of a sine curve. The more the shape of the breathing large movements regular shape of sine curves target accuracy of the tumor tracking system can be judged to be reduced. Using the algorithm of Cyber-Knife tumor tracking system, when there is a change in the sudden unpredictable respiratory due patient coughing during treatment enforcement is to stop the treatment, it is assumed to carry out the internal target validation process again, it is necessary to readjust the form of respiration. Patients under treatment is determined to be able to improve the treatment of accuracy to induce the observed form of regular breathing and put like to see the goggles monitor capable of the respiratory form of the person.

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