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Design of MAHA Supercomputing System for Human Genome Analysis (대용량 유전체 분석을 위한 고성능 컴퓨팅 시스템 MAHA)

  • Kim, Young Woo;Kim, Hong-Yeon;Bae, Seungjo;Kim, Hag-Young;Woo, Young-Choon;Park, Soo-Jun;Choi, Wan
    • KIPS Transactions on Software and Data Engineering
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    • v.2 no.2
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    • pp.81-90
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    • 2013
  • During the past decade, many changes and attempts have been tried and are continued developing new technologies in the computing area. The brick wall in computing area, especially power wall, changes computing paradigm from computing hardwares including processor and system architecture to programming environment and application usage. The high performance computing (HPC) area, especially, has been experienced catastrophic changes, and it is now considered as a key to the national competitiveness. In the late 2000's, many leading countries rushed to develop Exascale supercomputing systems, and as a results tens of PetaFLOPS system are prevalent now. In Korea, ICT is well developed and Korea is considered as a one of leading countries in the world, but not for supercomputing area. In this paper, we describe architecture design of MAHA supercomputing system which is aimed to develop 300 TeraFLOPS system for bio-informatics applications like human genome analysis and protein-protein docking. MAHA supercomputing system is consists of four major parts - computing hardware, file system, system software and bio-applications. MAHA supercomputing system is designed to utilize heterogeneous computing accelerators (co-processors like GPGPUs and MICs) to get more performance/$, performance/area, and performance/power. To provide high speed data movement and large capacity, MAHA file system is designed to have asymmetric cluster architecture, and consists of metadata server, data server, and client file system on top of SSD and MAID storage servers. MAHA system softwares are designed to provide user-friendliness and easy-to-use based on integrated system management component - like Bio Workflow management, Integrated Cluster management and Heterogeneous Resource management. MAHA supercomputing system was first installed in Dec., 2011. The theoretical performance of MAHA system was 50 TeraFLOPS and measured performance of 30.3 TeraFLOPS with 32 computing nodes. MAHA system will be upgraded to have 100 TeraFLOPS performance at Jan., 2013.

Effect of Reaction Factors on the Properties of Complex Oxide Powder Produced by Spray Roasting Process (분무배소법에 의해 생성되는 복합산화물 분말들의 특성에 미치는 반응인자들의 영향)

  • 유재근;이성수;박희범;안주삼;남용현;손진군
    • Resources Recycling
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    • v.9 no.4
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    • pp.16-27
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    • 2000
  • In order to produce raw material powder of advanced magnetic material by spray roasting process, newly modified spray roasting system was developed in this work. In this spray roasting system, raw material solution was effectively atomized and sprayed into the reaction furnace. Also, uniform temperature distribution inside reaction furnace made thermal decomposition process fully completed, and produced powder was effectively collected in cyclone and bag filter. This system equipped with apparatus which can purify hazard produced gas. In this study complex acid solution was prepared by dissolution of mill scale and ferro-Mn into the acid solution, and the pH of this complex acid solution was controlled about to 4. It was conformed that mill scale and ferro-Mn containing a lot of impurities such as $SiO_2$, P and Al could be used as raw material by reducing the impurities content of complex acid solution below 20 ppm. Complex oxide powder of Fe-Mn system was produced by spraying purified complex acid solution into the spray roaster through nozzle, and the variations of produced powder characters were studied by changing he reaction conditions such as reaction temperature, the injection velocity of solution and air, nozzle tip size and concentration of solution. The morphology of produced powder had spherical shape under the most experimental conditions, and concentration of solution. The morphology of produced powder has spherical shape under the most experimental conditions, and the composition and the particle size distribution were almost uniform, which tells the excellence of this spray roasting system. The grain size of most produced powder was below 100 nm. From the above results, it will be possible to produce ultra fine oxide powder from the chloride of Fe, Mn, Ni, Cu and rare earth by using this spray roasting system, and also to produce ultra fine pure metal powder by changing reaction atmosphere.

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The Study on the Factors for Detection of Renal Stone on Ultrasound (초음파 검사에서 신장 결석의 검출 요인에 관한 연구)

  • Sim, Hyun-Sun;Jung, Hong-Ryang;Lim, Cheong-Hwan
    • Journal of radiological science and technology
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    • v.29 no.1
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    • pp.1-6
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    • 2006
  • Purpose: Renal stones are common and typically arise within the collecting system. The renal sinus are contains the collection system, the renal vessels, lymphatcs, fat, and fibrous tissue. Because of the compression of all the large echoes in signal processing, the echo from the renal stone generally cannot be distinguished from large echoes emanating from normal structures of the renal sinus. Use of ultrasonography has been difficult for detecting small renal stone without posterior shadowing and chemical composition of stone. The aim of study was measuring for posterior acoustic shadowing to a stone for various scan parameter and it examines a help in renal stone diagnosis. Material & Methods: The stone was place on sponge examined in a water bath with a 3.5MHz or 7.5MHz transducer(LOGIQ 400, USA). First, tested a variety of gain. Second, tested a variety of dynamic range. Third, tested a variety of focal zone. Fourth, measuring of the echo level for low and high frequency for depth. Results: 1) Average echo level was 98 for low total gain(10 dB) and was 142 for high total gain(40 dB). Posterior acoustic shadowing of renal stone was clear for low gain. 2) Average echo level was 129 for low dynamic range(42 dB) and was 101 for high dynamic range(72 dB). Posterior acoustic shadowing of renal stone was clear for high dynamic range. 3) When stone is in focal zone of transducer, definite posterior acoustic shadow is identified. 4) Stone was clear appeared for high frequency(7.5 MHz) than low frequency(3.5 MHz) and it is not distorted. Conclusion: The demonstration of an posterior acoustic shadow of renal stone dependents on several technical factors such as gain, dynamic range, focus, and frequency. This various factors are a help in renal stone diagnosis.

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Effects of the mascara and eye shadow on theMR image distortion (자기공명영상 왜곡에서 마스카라와 아이섀도의 영향)

  • Lee, Hyun-Yong;Shin, Oun-Jae;Park, Byung-Rae
    • Journal of radiological science and technology
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    • v.28 no.1
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    • pp.25-32
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    • 2005
  • Purpose : To evaluate the degree of the artifact which is caused by the mascara and the eye shadow when acquiring MR images and compare the difference of the image distortion according to the change of various pulse sequence. Material and Method : The popular domestic mascara and eye shadow products were selected from three different companies respectively and divided into two groups mascara (M1, M2, M3 ), eye shadow (E1, E2, E3). Self-designed quadrature type saddle coil which has 4 cm inside diameter, 8 cm length and which is for both Tx and Rx was used. MR image was acquired respectively after applying the mascara to the tape from study 1, the eye shadow to the tape from study 2 and adding the eye shadow to the mascara from study 3. The FSE(fast spin echo), the SE(spin echo), the GE(gradient echo) were used as pulse sequences. The degree of the image distortion which was measured from each sequence was analyzed in quality and quantity. Result : The mascara and the eye shadow caused the artifacts to the MR images partially and induced the image distortion. There was a little difference in terms of the degree of artifact according to the change of pulse sequence. From the study 3 in which the eye shadow was applied to the mascara, on the axial plane image, the width of artifact was 16.73 mm in the GE pulse sequence, 6.64 mm in the SE pulse sequence, and 6.19 mm in the FSE pulse sequence. The degree of the artifact appeared highly in order of the GE, the SE and the FSE. On the sagittal plane image, the length of artifact was 22.84 mm in the GE, 17.81 mm in the SE and it appeared highly with the SE and the FSE technique order. Conclusion : When examining the eyeball and the brain of a woman with the mascara and the eye shadow, we have to consider that the artifact caused by them can have an effect on the image diagnosis. We concluded that it is more suitable for a brain and a eyeball T2 emphasizing image to use the FSE technique than the GE technique.

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Effects of Milk with Boiled-Dried Large Anchovy, Calcium-Fortifying Materials and Fortified-Calcium Milk on Calcium Absorption Rate and Bone Metabolism in Rats (자건대멸, 칼슘강화소재를 첨가한 우유 및 칼슘강화우유가 흰쥐의 칼슘흡수율과 골대사에 미치는 영향)

  • Jo, Jin-Ho;Kim, Byung-Gi;Han, Chan-Kyu;Jung, Eun-Bong;Cho, Seung-Mock
    • Journal of the Korean Society of Food Science and Nutrition
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    • v.37 no.4
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    • pp.459-464
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    • 2008
  • This study was performed to investigate the effect of calcium-rich large anchovy on calcium metabolism in rats for 5 weeks. Experimental animals were randomly assigned to 5 treatments with 14 heads of Spraque Dawley male rats in each group. The experimental diets were as follows; market milk group (M) as control, market milk+calcium-rich large anchovy group (MA), market milk+calcium carbonate group (MC), market milk+calcium lactate group (ML), and enriched-calcium market milk group (M2), which were formulated with commercially semi-purified rat chow (AIN-diet) to maintain the same level of calcium (1%) in all groups. Femur lengths of M and M2 groups were significantly higher than other groups. Bone mineral density (BMD) and bone mineral content (BMC) and calcium content of femur were the highest in MA group than other groups. In vitro and in vivo calcium absorption rates were high in MA group (7.30% vs 27.50%) compared with those of the other groups. Serum total-cholesterol and HDL-cholesterol levels were significantly different between M group and MA group (p<0.05). Creatinine levels were significantly higher in M, MA and MC groups than in M2 group (p<0.05). Serum calcium, osteocalcin and ALPase activities were higher in calcium-rich large anchovy (MA) group among the treatments, but there was no significant difference. SGOT activity was significantly lower in M2 group than those of M, MA and MC groups (p<0.05). These results may indicate that the calcium-rich large anchovy has enforced the BMD, BMC and calcium absorption rates of in vitro and in vivo compared with the other groups and might be a calcium-enriched food with large anchovy.

Effects of Edge Area and Burn Severity on Early Vegetation Regeneration in Damaged Area (가장자리와 산불피해강도가 산불피해지역 초기식생재생에 미치는 효과)

  • Lee, Joo-Mee;Won, Myoung-Soo;Lim, Joo-Hoon;Lee, Sang-Woo
    • Journal of Korean Society of Forest Science
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    • v.101 no.1
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    • pp.121-129
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    • 2012
  • The edge area with burn severity is known as significant factor that has great effects on the ecosystem recovery. However, there is little study on the edge area and its effects in the South Korea. Thus, this study aimed to analyze immediate responses of vegetation following forest fires due to combined effect of burn severity and edge-interior effect. Burn Severity (BS), or ${\Delta}NBR$ values were computed using satellite images of pre and post-forest fire in Samcheock areas. The burn forest was classified 231 $1-km^2$ girds and these grids were further reclassified into 4 groups by BS type (low BS and high BS areas) and forest areas (edge areas and interior areas). These four groups of grids including low BS-interior (group A), low BS-edge (group B), high BS-interior (group C) and high BS-edge (group D). Post-fire vegetation responses measured with (${\Delta}NDVI$) among four groups were then compared and tested by T-test. The results indicated that group C (${\Delta}NDVI$=0.047) and D (${\Delta}NDVI$ = 0.059) showed considerably greater vegetation regeneration than those of low BS areas including group A (${\Delta}NDVI$ = -0.039) and group B (${\Delta}NDVI$ = -0.036). It was also observed that edges areas showed greater vegetation regeneration than interior areas when BS is the same. Group B (${\Delta}NDVI$ = -0.036) showed greater (${\Delta}NDVI$) values than group A (${\Delta}NDVI$ = -0.039) in low BS condition. Similar relationship is observed between group C and group D in high BS condition. Thus adequate restoration practices for burned areas might need to pay close attention to interior areas with low BS to minimize the secondary damages and to rehabilitate the burned forests.

Critiques of 'The Endangered and Protected Wild Species List in Korea' Proposed by Korea Ministry of Environment and Listing Process - Is This the Best Process for the Current National Management of Endangered Wildlife and Plants in Korea? - (2011년 환경부 멸종위기종 등록절차 및 대상 멸종위기종 식물 목록 재고-과연 현재 국가 멸종위기종 관리가 최선의 방안인가? -)

  • Kim, Hui;Lee, Byong Cheon;Kim, Yong Shik;Chang, Chin-Sung
    • Journal of Korean Society of Forest Science
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    • v.101 no.1
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    • pp.7-19
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    • 2012
  • After having announced legislation for threatened or endangered species on the List of Endangered and Threatened Wildlife and Plants in 2005, the Korea Ministry of Environment proposed (in June 2011) amending the list, thereby delisting or reclassifying endangered species using new quantitative criteria for two levels (I and II), as well as status reviews. The new legislation included 40 species remained in their original endangered status, but 19 species were delisted, 5 species were proposed as candidates for delisting, 29 species were given a new endangered listing, and 3 species were proposed for an endangered listing in Korea. We assessed the threatened status of 98 plants using the IUCN Red List Criteria (version 3.1) at the global level, and compared the Ministry's revised criteria with the IUCN Red List Criteria and ESA criteria used in the USA. Most species proposed by the Ministry do not qualify as threatened and one of the major difficulties found in applying IUCN Red List Criteria at the global scale was a lack of knowledge on the status of species at broader geographic scales and the perceived difficulty this causes. Under the current classification process, many endangered species, such as Abeliophyllum distichum, Leontice microrhyncha, Echinosophora koreensis, Leontopodium coreanum, Iris odaesanensis, and Corylopsis coreana at global level were excluded here. Knowledge gaps and uncertainties mean that the number of taxa at high risk of extinction may be substantially greater than is currently understood. Due to a lack of information on its taxonomic status, currently there is controversy over the Red List status of Physocarpus insularis. Also, Caragana koreana, which was an invalidly published name, should be excluded here. Although the Korea Ministry of Environment insisted this procedure was conducted by applying the modified IUCN threat categories and definitions, this evaluation has been carried out based only on subjective views and misapplication of the IUCN Red List Criteria. The current listings by the Korea Ministry of Environment should be challenged. We suggest that broad species concepts on endemic species are applied and also criteria that adequately address the proper quantitative knowledge should be used. It is suggested that the highest priorities for the Red List should be given to endemic species at least in the Korean peninsula first at global scale.

An Analysis on Consumers' Awareness of a Rural Specialties Exhibition Shop and the Design Development : Focusing on Rural Tourism Village (농촌 농특산품 전시판매시설 디자인 소비자 의식 분석 및 디자인 개발 - 농촌관광마을을 중심으로 -)

  • Jin, Hye-Ryeon;Seo, Ji-Ye;Jo, Lok-Hwan
    • Journal of Korean Society of Rural Planning
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    • v.20 no.4
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    • pp.253-262
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    • 2014
  • This, an association research for design-improvement and model-development of exhibition shops at rural tourism communities, is to secure objective data by analyzing customers' awareness-tendency of and demand for agricultural-specialty exhibition shops. Survey-questions for finding out consumers' awareness-tendency and demand were determined through brainstorming of a professional council, 30 rural communities of which visit-rate by consumers is considerably high were selected for the recruit of 200 consumers. For investigation and analysis, survey and in-depth interview were carried out at the scene with the application of frequency analysis and summarization of their opinions, which revealed that they have a strong will to visit the rural tourism communities for the purchase of agricultural specialties along with the experience of learning-program and on-the-scene direct dealing and that their viewpoint on the direct dealing at the scene was very positive. Also it was confirmed hat their satisfaction with the purchase of agricultural specialties by on-the-scene direct dealing, their pleasure at the purchase, their satisfaction with services and their intention for re-purchase of them were very high while their satisfaction with the exhibition shops was very low. With on-the-scene survey, the consumers' opinions could be listened to in depth. Almost all of them said their satisfaction with the trip to those rural tourism communities was considerably high since they could go to those communities themselves to relieve the stress from their modern life, to experience healing and to see the goods on the scene. Their satisfaction also was attributed to the fact that they have enough trust in purchase along with feeling the warm-heartedness of rural residents. As to their awareness of exhibition shops, they showed a positive response to the on-the-scene direct dealing at rural communities while they, thinking that the space in those exhibition shops was not sufficiently wide, demanded for more systematic counters in more accessible and affordable exhibition shops so that they might be more satisfied with the exhibition shops. Their demand for the necessity of exhibition shops selling agricultural specialties was found to be over 80%, which indicates that the necessity is very high. As to the suitability of function, they have the opinion that the business at those shops had better be focused on sales since they have the understanding of information when they take a trip to the rural communities, while there was another opinion: since agricultural products are seasonal items they should be exhibited and sold at the same time. More than 90% of the respondents had a positive viewpoint on direct dealing of agricultural specialties on the scene, which showed that their response to it was very high. They preferred the permanent shops equipped with roll-around table-booths. In addition, it was revealed that they want systematic exhibition shops in rural communities because they frequent those communities for on-the-scene direct purchase. The preferred type and opinion resulting from estimation of consumers' demands have been reflected for development of practical designs. The structure of variable principles has been designed so that the types of display-case and table-booth might be created. The result of this study is a positive data as a design model which can be utilized at rural communities and will be commercialized for the verification of its validity.

Clinical Findings on Vertebral Compression Fracture Diagnosed with MRI (자기공명영상으로 진단된 척추 압박골절의 임상적 소견)

  • Kim, Ham-Gyum
    • Journal of radiological science and technology
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    • v.28 no.3
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    • pp.219-226
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    • 2005
  • By analyzing the severally clinical characteristics such as the prevalence by gender and age, and the developmental region, and the developmental factor in terms of vertebral compression fracture, which was diagnosed by MRI(Magnetic Resonance Imaging), the following conclusions were obtained. 1. The general characteristics in 183 research subjects, were 70 men (38.0%) and 113 women (62.0%), and aged from the minimum 16 years old to the maximum 84 years old. 2. Among 183 persons with abnormal findings in vertebral compression fracture, the single compression fracture was included 111 persons (60.7%) with 38 men (34.0%) and 73 women (66.0%), and women in their 60s were largest with 32 persons. 3. As the multiple compression fracture was included 72 persons (39.3%) among 183 research subjects, and as the incidence had 182 cases, this is what classified the case in which one person with abnormal findings has the compression fracture at the levels with more than one, and there were 70 cases (38.0%) in men and 112 cases (62.0%) in women, and it is being indicated the large frequency in women in their 60s and in their 70s. 4. The developmental regions in the single compression fracture and the multiple compression fracture, were generated about 70% of the whole at $T11{\sim}L2$. 5. In terms of the prevalence by cause for compression fracture in 183 whole subjects, it was largest with 41.4% in the fracture caused by trauma in case of men, and with 70.0% in what was caused by the osteoporosis in case of women, and as for a case that combined men and women, it was largest with 56.8% in the vertebral compression fracture caused by osteoporosis.

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Development of $14"{\times}8.5"$ active matrix flat-panel digital x-ray detector system and Imaging performance (평판 디지털 X-ray 검출기의 개발과 성능 평가에 관한 연구)

  • Park, Ji-Koon;Choi, Jang-Yong;Kang, Sang-Sik;Lee, Dong-Gil;Seok, Dae-Woo;Nam, Sang Hee
    • Journal of radiological science and technology
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    • v.26 no.4
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    • pp.39-46
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    • 2003
  • Digital radiographic systems based on solid-state detectors, commonly referred to as flat-panel detectors, are gaining popularity in clinical practice. Large area, flat panel solid state detectors are being investigated for digital radiography. The purpose of this work was to evaluate the active matrix flat panel digital x-ray detectors in terms of their modulation transfer function (MTF), noise power spectrum (NPS), and detective quantum efficiency (DQE). In this paper, development and evaluation of a selenium-based flat-panel digital x-ray detector are described. The prototype detector has a pixel pitch of $139\;{\mu}m$ and a total active imaging area of $14{\times}8.5\;inch^2$, giving a total 3.9 million pixels. This detector include a x-ray imaging layer of amorphous selenium as a photoconductor which is evaporated in vacuum state on a TFT flat panel, to make signals in proportion to incident x-ray. The film thickness was about $500\;{\mu}m$. To evaluate the imaging performance of the digital radiography(DR) system developed in our group, sensitivity, linearity, the modulation transfer function(MTF), noise power spectrum (NPS) and detective quantum efficiency(DQE) of detector was measured. The measured sensitivity was $4.16{\times}10^6\;ehp/pixel{\cdot}mR$ at the bias field of $10\;V/{\mu}m$ : The beam condition was 41.9\;KeV. Measured MTF at 2.5\;lp/mm was 52%, and the DQE at 1.5\;lp/mm was 75%. And the excellent linearity was showed where the coefficient of determination ($r^2$) is 0.9693.

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