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An Installation and Model Assessment of the UM, U.K. Earth System Model, in a Linux Cluster (U.K. 지구시스템모델 UM의 리눅스 클러스터 설치와 성능 평가)

  • Daeok Youn;Hyunggyu Song;Sungsu Park
    • Journal of the Korean earth science society
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    • v.43 no.6
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    • pp.691-711
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    • 2022
  • The state-of-the-art Earth system model as a virtual Earth is required for studies of current and future climate change or climate crises. This complex numerical model can account for almost all human activities and natural phenomena affecting the atmosphere of Earth. The Unified Model (UM) from the United Kingdom Meteorological Office (UK Met Office) is among the best Earth system models as a scientific tool for studying the atmosphere. However, owing to the expansive numerical integration cost and substantial output size required to maintain the UM, individual research groups have had to rely only on supercomputers. The limitations of computer resources, especially the computer environment being blocked from outside network connections, reduce the efficiency and effectiveness of conducting research using the model, as well as improving the component codes. Therefore, this study has presented detailed guidance for installing a new version of the UM on high-performance parallel computers (Linux clusters) owned by individual researchers, which would help researchers to easily work with the UM. The numerical integration performance of the UM on Linux clusters was also evaluated for two different model resolutions, namely N96L85 (1.875° ×1.25° with 85 vertical levels up to 85 km) and N48L70 (3.75° ×2.5° with 70 vertical levels up to 80 km). The one-month integration times using 256 cores for the AMIP and CMIP simulations of N96L85 resolution were 169 and 205 min, respectively. The one-month integration time for an N48L70 AMIP run using 252 cores was 33 min. Simulated results on 2-m surface temperature and precipitation intensity were compared with ERA5 re-analysis data. The spatial distributions of the simulated results were qualitatively compared to those of ERA5 in terms of spatial distribution, despite the quantitative differences caused by different resolutions and atmosphere-ocean coupling. In conclusion, this study has confirmed that UM can be successfully installed and used in high-performance Linux clusters.

A Study on Tile from the Early Period of the Three Kingdoms Period Excavated in Bonghwang-dong (김해 봉황동 유적 일대 출토 삼국시대 초기 기와 검토)

  • YUN Sunkyung;KIM Jiyeon
    • Korean Journal of Heritage: History & Science
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    • v.56 no.4
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    • pp.40-52
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    • 2023
  • The basic purpose of building material called tiles is waterproofing and damp proofing, and they were restricted to use on important buildings to symbolize authority. This is especially true during the Three Kingdoms period, although unearthed examples are rare. Most of these tiles are found in ruins in the Silla and Baekje regions. Tiles were excavated from the Buwon-dong ruins that show the oldest manufacturing technique in the Gaya region to date, and tiles from the early Three Kingdoms period were recently excavated from the Gimhae Bonghwang-dong ruins, which is presumed to be the site of the royal palace of Geumgwan Gaya. These are important materials that show the appearance of tiles from the early days of Gimhae, the ancient capital of Geumgwan Gaya. The tiles excavated from the Bonghwang-dong ruins are reddish-yellow because a small amount of sand was mixed in the tile material and baked at a low temperature. The tiles are thin, no traces of fabric were identified, but traces of clay bands were identified. Tapping tool marks and traces of an anvil used in pottery production are clearly observed on the inside and outside, indicating that the tiles were made in the same way as earthenware manufacturing methods. If this is connected to the genealogy of the potters who made Gaya earthenware, it is estimated that tiles and earthenware were produced together as in the Songrim-ri ruins in Bulo-dong, Incheon, Songgok-dong ruins in Gyeongju, and Mulcheon-ri ruins. To date, tiles excavated from the Gimhae area have been identified only in places believed to be the Geumgwan Gaya City Wall (Royal Palace) in the Gimhae Basin. Considering what has been recorded so far and the geographical scenery, the Bonghwang-dong remains are the only city wall candidate site, and this is clearly revealed through the existence of the excavated tiles, which proves this. Considering that a small number of tiles were excavated during this time, it is estimated that the role of tiles as a luxury product with a symbolic meaning was greater than that of roofing materials, and there were strict restrictions and controls on its use.

Gap-Filling of Sentinel-2 NDVI Using Sentinel-1 Radar Vegetation Indices and AutoML (Sentinel-1 레이더 식생지수와 AutoML을 이용한 Sentinel-2 NDVI 결측화소 복원)

  • Youjeong Youn;Jonggu Kang;Seoyeon Kim;Yemin Jeong;Soyeon Choi;Yungyo Im;Youngmin Seo;Myoungsoo Won;Junghwa Chun;Kyungmin Kim;Keunchang Jang;Joongbin Lim;Yangwon Lee
    • Korean Journal of Remote Sensing
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    • v.39 no.6_1
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    • pp.1341-1352
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    • 2023
  • The normalized difference vegetation index (NDVI) derived from satellite images is a crucial tool to monitor forests and agriculture for broad areas because the periodic acquisition of the data is ensured. However, optical sensor-based vegetation indices(VI) are not accessible in some areas covered by clouds. This paper presented a synthetic aperture radar (SAR) based approach to retrieval of the optical sensor-based NDVI using machine learning. SAR system can observe the land surface day and night in all weather conditions. Radar vegetation indices (RVI) from the Sentinel-1 vertical-vertical (VV) and vertical-horizontal (VH) polarizations, surface elevation, and air temperature are used as the input features for an automated machine learning (AutoML) model to conduct the gap-filling of the Sentinel-2 NDVI. The mean bias error (MAE) was 7.214E-05, and the correlation coefficient (CC) was 0.878, demonstrating the feasibility of the proposed method. This approach can be applied to gap-free nationwide NDVI construction using Sentinel-1 and Sentinel-2 images for environmental monitoring and resource management.

Removal of ${\alpha}$-Gal Epitopes in Aortic Valve and Pericardium of Pig Using Green Coffee Bean ${\alpha}$-Galactosidase (돼지의 대동맥 판막 및 심낭에서 녹색콩 알파-갈락토시다아제를 이용한 알파-갈 항원결정인자 제거)

  • Park, Seong-Sik;Kim, Woong-Han;Kim, Kyung-Hwan;Lee, Chang-Ha;Choi, Sun-Young;Lee, Cheul;Oh, Sam-Sae;Kim, Kwan-Chang;Kim, Yong-Jin
    • Journal of Chest Surgery
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    • v.41 no.1
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    • pp.12-24
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    • 2008
  • Background: It is currently thought that tissue valve degeneration is related to an animal's immune response, which is mainly due to cell surface ${\alpha}$-Gal epitopes. Cell surface ${\alpha}$-Gal epitopes are known to be degraded by the enzyme called green coffee bean ${\alpha}$-Galactosidase. It is also well known that ${\alpha}$-Gal epitopes are immunologically stained by Griffonia Simplicifolia isolectin type B4. We know that many commercially available tissue valves are made of aortic valves and pericardial tissue of pig. So, we investigated whether ${\alpha}$-Gal epitopes of the aortic valve and pericardial tissue of a pig can be removed by green coffee bean ${\alpha}$-Galactosidase, and we did so by comparing immunologic staining of the tissues before and after the enzyme treatment. Material and method: After treating fresh porcine aortic valve and pericardial tissue with green coffee bean ${\alpha}$-Galactosidase at concentrations of 0.5 unit/mL, 1.0 unit/mL, 2.0 unit/mL, respectively, under the condition of pH 6.5, temperature. $4^{\circ}C$ and 24 hours of incubation, each sample was stained with Griffonia Simplicifolia isolectin type B4 immunpfluorescent labeling. We then examined whether the ${\alpha}$-Gal epitopes were reduced or abolished in each consecutive. concentration of green coffee bean ${\alpha}$-Galactosidase by comparing the degree of the Griffonia Simplicifolia isolectin B4 staining in each sample. Result: In the pig aortic valve tissue, a 1.0 unit/mL concentration of green coffee bean ${\alpha}$-Galactosidase at pH 6.5, $4^{\circ}C$ and reaction for 24 hours was enough for complete removal of ${\alpha}$-Gal epitopes from the cell sur face on the immunostaining with Griffonia Simplicifolia isolectin B4. On the other hand, more ${\alpha}$-Gal epitopes were present in the pig pericardial tissue on Griffonia Simplicifolia isolectin B4 staining before the enzyme treatment, and 1.0 unit/mL of galactosidase was not sufficient for complete removal of ${\alpha}$-Gal from the tissue. 2.0 units/mL of green coffee bean ${\alpha}$-Galactosidase was needed to completely remove the ${\alpha}$-Gal epitopes from the pericardial tissue on immunostaining. Conclusion: The ${\alpha}$-Gal epitopes of the pig's aortic valve and pericardial tissue were successfully stained with Griffonia Simplicifolia isolectin B4. We could remove nearly all the ${\alpha}$-Gal epitopes using green coffee bean ${\alpha}$-Galactosidase at the concentration of 1.0 unit/mL in the aortic valve. Of pig, and 2.0 unit/mL was need to nearly completely remove all the ${\alpha}$-Gal epitopes in the pericardial tissue of pig under the condition of pH 6.5, $4^{\circ}C$ and 24 hours of reaction time. In the near future, removal of ${\alpha}$-Gal epitapes in the pig's aortic valve and pericardial tissue will become a powerful tool for the improvement of the tissue valve durability. It needs to be determined if ${\alpha}$-galactosidase treated pig tissue is immune to human anti-Gal antibody or anit-Gal mooclonal antibodies.

Sesquiterpenoids Bioconversion Analysis by Wood Rot Fungi

  • Lee, Su-Yeon;Ryu, Sun-Hwa;Choi, In-Gyu;Kim, Myungkil
    • 한국균학회소식:학술대회논문집
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    • 2016.05a
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    • pp.19-20
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    • 2016
  • Sesquiterpenoids are defined as $C_{15}$ compounds derived from farnesyl pyrophosphate (FPP), and their complex structures are found in the tissue of many diverse plants (Degenhardt et al. 2009). FPP's long chain length and additional double bond enables its conversion to a huge range of mono-, di-, and tri-cyclic structures. A number of cyclic sesquiterpenes with alcohol, aldehyde, and ketone derivatives have key biological and medicinal properties (Fraga 1999). Fungi, such as the wood-rotting Polyporus brumalis, are excellent sources of pharmaceutically interesting natural products such as sesquiterpenoids. In this study, we investigated the biosynthesis of P. brumalis sesquiterpenoids on modified medium. Fungal suspensions of 11 white rot species were inoculated in modified medium containing $C_6H_{12}O_6$, $C_4H_{12}N_2O_6$, $KH_2PO_4$, $MgSO_4$, and $CaCl_2$ for 20 days. Cultivation was stopped by solvent extraction via separation of the mycelium. The metabolites were identified as follows: propionic acid (1), mevalonic acid lactone (2), ${\beta}$-eudesmane (3), and ${\beta}$-eudesmol (4), respectively (Figure 1). The main peaks of ${\beta}$-eudesmane and ${\beta}$-eudesmol, which were indicative of sesquiterpene structures, were consistently detected for 5, 7, 12, and 15 days These results demonstrated the existence of terpene metabolism in the mycelium of P. brumalis. Polyporus spp. are known to generate flavor components such as methyl 2,4-dihydroxy-3,6-dimethyl benzoate; 2-hydroxy-4-methoxy-6-methyl benzoic acid; 3-hydroxy-5-methyl phenol; and 3-methoxy-2,5-dimethyl phenol in submerged cultures (Hoffmann and Esser 1978). Drimanes of sesquiterpenes were reported as metabolites from P. arcularius and shown to exhibit antimicrobial activity against Gram-positive bacteria such as Staphylococcus aureus (Fleck et al. 1996). The main metabolites of P. brumalis, ${\beta}$-Eudesmol and ${\beta}$-eudesmane, were categorized as eudesmane-type sesquiterpene structures. The eudesmane skeleton could be biosynthesized from FPP-derived IPP, and approximately 1,000 structures have been identified in plants as essential oils. The biosynthesis of eudesmol from P. brumalis may thus be an important tool for the production of useful natural compounds as presumed from its identified potent bioactivity in plants. Essential oils comprising eudesmane-type sesquiterpenoids have been previously and extensively researched (Wu et al. 2006). ${\beta}$-Eudesmol is a well-known and important eudesmane alcohol with an anticholinergic effect in the vascular endothelium (Tsuneki et al. 2005). Additionally, recent studies demonstrated that ${\beta}$-eudesmol acts as a channel blocker for nicotinic acetylcholine receptors at the neuromuscular junction, and it can inhibit angiogenesis in vitro and in vivo by blocking the mitogen-activated protein kinase (MAPK) signaling pathway (Seo et al. 2011). Variation of nutrients was conducted to determine an optimum condition for the biosynthesis of sesquiterpenes by P. brumalis. Genes encoding terpene synthases, which are crucial to the terpene synthesis pathway, generally respond to environmental factors such as pH, temperature, and available nutrients (Hoffmeister and Keller 2007, Yu and Keller 2005). Calvo et al. described the effect of major nutrients, carbon and nitrogen, on the synthesis of secondary metabolites (Calvo et al. 2002). P. brumalis did not prefer to synthesize sesquiterpenes under all growth conditions. Results of differences in metabolites observed in P. brumalis grown in PDB and modified medium highlighted the potential effect inorganic sources such as $C_4H_{12}N_2O_6$, $KH_2PO_4$, $MgSO_4$, and $CaCl_2$ on sesquiterpene synthesis. ${\beta}$-eudesmol was apparent during cultivation except for when P. brumalis was grown on $MgSO_4$-free medium. These results demonstrated that $MgSO_4$ can specifically control the biosynthesis of ${\beta}$-eudesmol. Magnesium has been reported as a cofactor that binds to sesquiterpene synthase (Agger et al. 2008). Specifically, the $Mg^{2+}$ ions bind to two conserved metal-binding motifs. These metal ions complex to the substrate pyrophosphate, thereby promoting the ionization of the leaving groups of FPP and resulting in the generation of a highly reactive allylic cation. Effect of magnesium source on the sesquiterpene biosynthesis was also identified via analysis of the concentration of total carbohydrates. Our current study offered further insight that fungal sesquiterpene biosynthesis can be controlled by nutrients. To profile the metabolites of P. brumalis, the cultures were extracted based on the growth curve. Despite metabolites produced during mycelia growth, there was difficulty in detecting significant changes in metabolite production, especially those at low concentrations. These compounds may be of interest in understanding their synthetic mechanisms in P. brumalis. The synthesis of terpene compounds began during the growth phase at day 9. Sesquiterpene synthesis occurred after growth was complete. At day 9, drimenol, farnesol, and mevalonic lactone (or mevalonic acid lactone) were identified. Mevalonic acid lactone is the precursor of the mevalonic pathway, and particularly, it is a precursor for a number of biologically important lipids, including cholesterol hormones (Buckley et al. 2002). Farnesol is the precursor of sesquiterpenoids. Drimenol compounds, bi-cyclic-sesquiterpene alcohols, can be synthesized from trans-trans farnesol via cyclization and rearrangement (Polovinka et al. 1994). They have also been identified in the basidiomycota Lentinus lepideus as secondary metabolites. After 12 days in the growth phase, ${\beta}$-elemene caryophyllene, ${\delta}$-cadiene, and eudesmane were detected with ${\beta}$-eudesmol. The data showed the synthesis of sesquiterpene hydrocarbons with bi-cyclic structures. These compounds can be synthesized from FPP by cyclization. Cyclic terpenoids are synthesized through the formation of a carbon skeleton from linear precursors by terpene cyclase, which is followed by chemical modification by oxidation, reduction, methylation, etc. Sesquiterpene cyclase is a key branch-point enzyme that catalyzes the complex intermolecular cyclization of the linear prenyl diphosphate into cyclic hydrocarbons (Toyomasu et al. 2007). After 20 days in stationary phase, the oxygenated structures eudesmol, elemol, and caryophyllene oxide were detected. Thus, after growth, sesquiterpenes were identified. Per these results, we showed that terpene metabolism in wood-rotting fungi occurs in the stationary phase. We also showed that such metabolism can be controlled by magnesium supplementation in the growth medium. In conclusion, we identified P. brumalis as a wood-rotting fungus that can produce sesquiterpenes. To mechanistically understand eudesmane-type sesquiterpene biosynthesis in P. brumalis, further research into the genes regulating the dynamics of such biosynthesis is warranted.

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