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Integration and Reanalysis of Four RNA-Seq Datasets Including BALF, Nasopharyngeal Swabs, Lung Biopsy, and Mouse Models Reveals Common Immune Features of COVID-19

  • Rudi Alberts;Sze Chun Chan;Qian-Fang Meng;Shan He;Lang Rao;Xindong Liu;Yongliang Zhang
    • IMMUNE NETWORK
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    • v.22 no.3
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    • pp.22.1-22.25
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    • 2022
  • Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndromecoronavirus-2 (SARS-CoV-2), has spread over the world causing a pandemic which is still ongoing since its emergence in late 2019. A great amount of effort has been devoted to understanding the pathogenesis of COVID-19 with the hope of developing better therapeutic strategies. Transcriptome analysis using technologies such as RNA sequencing became a commonly used approach in study of host immune responses to SARS-CoV-2. Although substantial amount of information can be gathered from transcriptome analysis, different analysis tools used in these studies may lead to conclusions that differ dramatically from each other. Here, we re-analyzed four RNA-sequencing datasets of COVID-19 samples including human bronchoalveolar lavage fluid, nasopharyngeal swabs, lung biopsy and hACE2 transgenic mice using the same standardized method. The results showed that common features of COVID-19 include upregulation of chemokines including CCL2, CXCL1, and CXCL10, inflammatory cytokine IL-1β and alarmin S100A8/S100A9, which are associated with dysregulated innate immunity marked by abundant neutrophil and mast cell accumulation. Downregulation of chemokine receptor genes that are associated with impaired adaptive immunity such as lymphopenia is another common feather of COVID-19 observed. In addition, a few interferon-stimulated genes but no type I IFN genes were identified to be enriched in COVID-19 samples compared to their respective control in these datasets. These features are in line with results from single-cell RNA sequencing studies in the field. Therefore, our re-analysis of the RNA-seq datasets revealed common features of dysregulated immune responses to SARS-CoV-2 and shed light to the pathogenesis of COVID-19.

Genetic diversity and population structure in five Inner Mongolia cashmere goat populations using whole-genome genotyping

  • Tao Zhang;Zhiying Wang;Yaming Li;Bohan Zhou;Yifan Liu;Jinquan Li;Ruijun Wang;Qi Lv;Chun Li;Yanjun Zhang;Rui Su
    • Animal Bioscience
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    • v.37 no.7
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    • pp.1168-1176
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    • 2024
  • Objective: As a charismatic species, cashmere goats have rich genetic resources. In the Inner Mongolia Autonomous Region, there are three cashmere goat varieties named and approved by the state. These goats are renowned for their high cashmere production and superior cashmere quality. Therefore, it is vitally important to protect their genetic resources as they will serve as breeding material for developing new varieties in the future. Methods: Three breeds including Inner Mongolia cashmere goats (IMCG), Hanshan White cashmere goats (HS), and Ujimqin white cashmere goats (WZMQ) were studied. IMCG were of three types: Aerbas (AEBS), Erlangshan (ELS), and Alashan (ALS). Nine DNA samples were collected for each population, and they were genomically re-sequenced to obtain high-depth data. The genetic diversity parameters of each population were estimated to determine selection intensity. Principal component analysis, phylogenetic tree construction and genetic differentiation parameter estimation were performed to determine genetic relationships among populations. Results: Samples from the 45 individuals from the five goat populations were sequenced, and 30,601,671 raw single nucleotide polymorphisms (SNPs) obtained. Then, variant calling was conducted using the reference genome, and 17,214,526 SNPs were retained after quality control. Individual sequencing depth of individuals ranged from 21.13× to 46.18×, with an average of 28.5×. In the AEBS, locus polymorphism (79.28) and expected heterozygosity (0.2554) proportions were the lowest, and the homologous consistency ratio (0.1021) and average inbreeding coefficient (0.1348) were the highest, indicating that this population had strong selection intensity. Conversely, ALS and WZMQ selection intensity was relatively low. Genetic distance between HS and the other four populations was relatively high, and genetic exchange existed among the other four populations. Conclusion: The Inner Mongolia cashmere goat (AEBS type) population has a relatively high selection intensity and a low genetic diversity. The IMCG (ALS type) and WZMQ populations had relatively low selection intensity and high genetic diversity. The genetic distance between HS and the other four populations was relatively high, with a moderate degree of differentiation. Overall, these genetic variations provide a solid foundation for resource identification of Inner Mongolia Autonomous Region cashmere goats in the future.

A Study on the Development of Guidelines for Place Name Authority Standardization (지명 전거 표준화를 위한 지명 전거데이터 기술 지침 개발에 관한 연구)

  • Ji-won Baek;Sungsook Lee
    • Journal of the Korean BIBLIA Society for library and Information Science
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    • v.35 no.1
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    • pp.169-192
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    • 2024
  • This study was conducted with the aim of providing a foundation for high-quality national place name authority data by developing Korean-specific guidelines for place name authority data in response to the need for systematic construction and standardization of authority databases. To this end, a survey of domestic and international trends and cases related to place name authority data was conducted, and the rules and guidelines of each country for establishing place name authority data were analyzed. Based on these surveys and rule analyses, the scope of concepts and terminology required to build a place name authority database were defined and the direction for the development of place name authority data guidelines was set. The analysis also determined the scope and framework of the guidelines, and how they should be referenced to existing rules. The structure of the guidelines proposed in this study is based on the original RDA and NCR. Based on the implications derived from the analysis process, the guidelines were organized and presented in terms of scope of construction, selection and recording of preferred place names, recording of variant place names, and attributes of place names to propose a technical guideline for place name authority data that fits the Korean situation. Future discussions were revealed accordingly.

Research on Optimized Operating Systems for Implementing High-Efficiency Small Wind Power Plants (고효율 소형 풍력 발전소 구현을 위한 최적화 운영 체계 연구)

  • Young-Bu Kim;Jun-Mo Park
    • Journal of the Institute of Convergence Signal Processing
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    • v.25 no.2
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    • pp.94-99
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    • 2024
  • Recently, wind power has been gaining attention as a highly efficient renewable energy source, leading to various technological developments worldwide. Typically, wind power is operated in the form of large wind farms with many wind turbines installed in areas rich in wind resources. However, in developing countries or regions isolated from the power grid, off-grid small wind power systems are emerging as an efficient solution. To efficiently operate and expand off-grid small-scale power systems, the development of real-time monitoring systems is required. For the efficient operation of small wind power systems, it is essential to develop real-time monitoring systems that can actively respond to excessive wind speeds and various environmental factors, as well as ensure the stable supply of produced power to small areas or facilities through an Energy Storage System (ESS). The implemented system monitors turbine RPM, power generation, brake operation, and more to create an optimal operating environment. The developed small wind power system can be utilized in remote road lighting, marine leisure facilities, mobile communication base stations, and other applications, contributing to the development of the RE100 industry ecosystem.

Status and Prospect of Herbicide Resistant Weeds in Rice Field of Korea (한국 논에서 제초제 저항성잡초 발생 현황과 전망)

  • Park, Tae-Seon;Lee, In-Yong;Seong, Ki-Yeong;Cho, Hyeon-Suk;Park, Hong-Kyu;Ko, Jae-Kwon;Kang, Ui-Gum
    • Korean Journal of Weed Science
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    • v.31 no.2
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    • pp.119-133
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    • 2011
  • Sulfonylurea (SU)-resistant weeds include seven annual weeds such as Monochoria vaginalis, Scirpus juncoides and Cyperus difformis, etc., and three perennial weeds of Scirpus planiculmis, Sagittaria pigmaea and Eleocharis acicularis as of 2010 since identification Monochoria korsakowii in the reclaimed rice field in 1998. The Echinochloa oryzoides resistant to acetyl CoA carboxylase (ACCase) and acetolactate synthase (ALS) inhibitors has been confirmed in wet-direct seeding rice field of the southern province, Korea in 2009. In the beginning of occurrence of SU-resistant weeds the M. vaginalis, S. juncoides and C. difformis were rapidly and individually spreaded in different fields, however, theses resistant weeds have been occurring simultaneously in the same filed as time goes by. The resistant biotype by weed species demonstrated about 10- to 1,000-fold resistance, base on $GR_{50}$ (50% growth reduction) values of the SU herbicides tested. And the resistant biotype of E. oryzoides to cyhalofop-butyl, pyriminobac-methyl, and penoxsulam was about 14, 8, and 11 times more resistant than the susceptible biotype base on $GR_{50}$ values. In history of paddy herbicides in Korea, the introduction of SU herbicides including besulfuron-metyl and pyrazosulfuron-ethyl that control many troublesome weeds at low use rates and provide excellent crop safety gave farmers and many workers for herbicide business refreshing jolt. The products and applied area of SU-included herbicides have been rapidly increased, and have accounted for about 69% and 96%, respectively, in Korea. The top ten herbicides by applied area were composed of all SU-included herbicides by 2003. The concentrated and successive treatment of ACCase and ALS inhibitors for control of barnyardgrass in direct-seeded rice led up to the resistance of E. oryzoides. Also, SU-herbicides like pyrazosulfuron-ethyl and imazosulfuron which are effective to barnyardgrass can be bound up with the resistance of E. oryzoides. The ALS activity isolated from the resistant biotype of M. korsakowii to SU-herbicides tested was less sensitive than that of susceptible biotype. The concentration of herbicide required for 50% inhibition of ALS activity ($I_{50}$) of the SU-resistant M. korsakowii was 14- to 76-fold higher as compared to the susceptible biotype. No differences were observed in the rates of [$^{14}C$]bensulfuron uptake and translocation. ALS genes from M. vaginalis resistant and susceptible biotypes against SU-herbicides revealed a single amino acid substitution of proline (CCT), at 197th position based on the M. korsakowii ALS sequence numbering, to serin (TCT) in conserved domain A of the gene. Carfentrazone-ethyl and pyrazolate were used mainly to control SU-resistant M. vaginalis by 2006, the early period, in Korea. However, the alternative herbicides such as benzobicyclone, to be possible to control simultaneously the several resistant weeds, have been developing and using broadly because the several resistant weeds have been occurring simultaneously in the same filed. The top ten herbicides by applied area in Korea have been occupied by products of 3-way mixture type including herbicides with alternative mode of action for the herbicide resistant weeds. Mefenacet, fentrazamide and cafenstrole had excellent controlling effects on the ACCase and ALS inhibitors resistant when they were applied within 2 leaf stage.

Development and Research into Functional Foods from Hydrolyzed Whey Protein Powder with Sialic Acid as Its Index Component - I. Repeated 90-day Oral Administration Toxicity Test using Rats Administered Hydrolyzed Whey Protein Powder containing Normal Concentration of Sialic Acid (7%) with Enzyme Separation Method - (Sialic Acid를 지표성분으로 하는 유청가수분해단백분말의 기능성식품 개발연구 - I. 효소분리로 7% Siailc Acid가 표준적으로 함유된 유청가수분해단백분말(7%)의 랫드를 이용한 90일 반복경구투여 독성시험 평가 연구 -)

  • Noh, Hye-Ji;Cho, Hyang-Hyun;Kim, Hee-Kyong
    • Journal of Dairy Science and Biotechnology
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    • v.34 no.2
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    • pp.99-116
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    • 2016
  • We herein performed animal safety assessment in accordance with Good Laboratory Practice (GLP) regulations with the aim of developing sialic acid from glycomacropeptide (hereafter referred to as "GMP") as an index ingredient and functional component in functional foods. GMP is a type of whey protein derived from milk and a safe food, with multiple functions, such as antiviral activity. A test substance was produced containing 7% (w/w) sialic acid and mostly-hydrolyzed whey protein (hereafter referred to as "7%-GNANA") by enzymatic treatment of substrate GMP. The maximum intake test dose level was selected based on 5,000 mg/kg/day dose set for male NOEL (no-observed-effect-level) and female NOAEL (no-observed-adverse-effect-level) determined by a dose-range finding (DRF) test (GLP Center of Catholic University of Daegu, Report No. 15-NREO-001) that was previously conducted with the same test substance. To evaluate the toxicity of a repeated oral dose of the test substance in connection with the previous DRF study, 1,250, 2,500, and 5,000 mg/kg of the substance were administered by a probe into the stomachs of 6-week-old SPF Sprague-Dawley male and female rats for 90 d. Each test group consisted of 10 male and 10 female rats. To determine the toxicity index, all parameters, such as observation of common signs; measurements of body weight and food consumption; ophthalmic examination; urinalysis, electrolyte, hematological, and serum biochemical examination; measurement of organ weights during autopsy; and visual and histopathological examinations were conducted according to GLP standards. After evaluating the results based on the test toxicity assessment criteria, it was determined that NOAEL of the test substance, 7%-GNANA, was 5,000 mg/kg/day, for both male and female rats. No animal death was noted in any of the test groups, including the control group, during the study period, and there was no significant difference associated with test substance, as compared with the control group, with respect to general symptoms, body weight changes, food consumption, ophthalmic examination, urinalysis, hematological and serum biochemical examination, and electrolyte and blood coagulation tests during the administration period (P<0.05). As assessed by the effects of the test substance on organ weights, food consumption, autopsy, and histopathological safety, change in kidney weight as an indicator of male NOAEL revealed up to 20% kidney weight increase in the high-dose group (5,000 mg/kg/day) compared with the change in the control group. However, it was concluded that this effect of the test substance was minor. In the case of female rats, reduction of food consumption, increase of kidney weight, and decrease of thymus weight were observed in the high-dose group. The kidney weight increased by 10.2% (left) and 8.9% (right) in the high-dose group, with a slight dose-dependency compared with that of the control group. It was observed that the thymus weight decreased by 25.3% in the high-dose group, but it was a minor test substance-associated effect. During the autopsy, botryoid tumor was detected on the ribs of one subject in the high-dose group, but we concluded that the tumor has been caused by a naturally occurring (non-test) substance. Histopathological examination revealed lesions on the kidney, liver, spleen, and other organs in the low-dose test group. Since these lesions were considered a separate phenomenon, or naturally occurring and associated with aging, it was checked whether any target organ showed clear symptoms caused by the test substance. In conclusion, different concentrations of the test substance were fed to rats and, consequently, it was verified that only a minor effect was associated with the test substance in the high-dose (5,000 mg/kg/day) group of both male and female rats, without any other significant effects associated with the test substance. Therefore, it was concluded that NOAEL of 7%-GNANA (product name: Helicobactrol) with male and female rats as test animals was 5,000 mg/kg/day, and it thus was determined that the substance is safe for the ultimate use as an ingredient of health functional foods.

N- and P-doping of Transition Metal Dichalcogenide (TMD) using Artificially Designed DNA with Lanthanide and Metal Ions

  • Kang, Dong-Ho;Park, Jin-Hong
    • Proceedings of the Korean Vacuum Society Conference
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    • 2016.02a
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    • pp.292-292
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    • 2016
  • Transition metal dichalcogenides (TMDs) with a two-dimensional layered structure have been considered highly promising materials for next-generation flexible, wearable, stretchable and transparent devices due to their unique physical, electrical and optical properties. Recent studies on TMD devices have focused on developing a suitable doping technique because precise control of the threshold voltage ($V_{TH}$) and the number of tightly-bound trions are required to achieve high performance electronic and optoelectronic devices, respectively. In particular, it is critical to develop an ultra-low level doping technique for the proper design and optimization of TMD-based devices because high level doping (about $10^{12}cm^{-2}$) causes TMD to act as a near-metallic layer. However, it is difficult to apply an ion implantation technique to TMD materials due to crystal damage that occurs during the implantation process. Although safe doping techniques have recently been developed, most of the previous TMD doping techniques presented very high doping levels of ${\sim}10^{12}cm^{-2}$. Recently, low-level n- and p-doping of TMD materials was achieved using cesium carbonate ($Cs_2CO_3$), octadecyltrichlorosilane (OTS), and M-DNA, but further studies are needed to reduce the doping level down to an intrinsic level. Here, we propose a novel DNA-based doping method on $MoS_2$ and $WSe_2$ films, which enables ultra-low n- and p-doping control and allows for proper adjustments in device performance. This is achieved by selecting and/or combining different types of divalent metal and trivalent lanthanide (Ln) ions on DNA nanostructures. The available n-doping range (${\Delta}n$) on the $MoS_2$ by Ln-DNA (DNA functionalized by trivalent Ln ions) is between $6{\times}10^9cm^{-2}$ and $2.6{\times}10^{10}cm^{-2}$, which is even lower than that provided by pristine DNA (${\sim}6.4{\times}10^{10}cm^{-2}$). The p-doping change (${\Delta}p$) on $WSe_2$ by Ln-DNA is adjusted between $-1.0{\times}10^{10}cm^{-2}$ and $-2.4{\times}10^{10}cm^{-2}$. In the case of Co-DNA (DNA functionalized by both divalent metal and trivalent Ln ions) doping where $Eu^{3+}$ or $Gd^{3+}$ ions were incorporated, a light p-doping phenomenon is observed on $MoS_2$ and $WSe_2$ (respectively, negative ${\Delta}n$ below $-9{\times}10^9cm^{-2}$ and positive ${\Delta}p$ above $1.4{\times}10^{10}cm^{-2}$) because the added $Cu^{2+}$ ions probably reduce the strength of negative charges in Ln-DNA. However, a light n-doping phenomenon (positive ${\Delta}n$ above $10^{10}cm^{-2}$ and negative ${\Delta}p$ below $-1.1{\times}10^{10}cm^{-2}$) occurs in the TMD devices doped by Co-DNA with $Tb^{3+}$ or $Er^{3+}$ ions. A significant (factor of ~5) increase in field-effect mobility is also observed on the $MoS_2$ and $WSe_2$ devices, which are, respectively, doped by $Tb^{3+}$-based Co-DNA (n-doping) and $Gd^{3+}$-based Co-DNA (p-doping), due to the reduction of effective electron and hole barrier heights after the doping. In terms of optoelectronic device performance (photoresponsivity and detectivity), the $Tb^{3+}$ or $Er^{3+}$-Co-DNA (n-doping) and the $Eu^{3+}$ or $Gd^{3+}$-Co-DNA (p-doping) improve the $MoS_2$ and $WSe_2$ photodetectors, respectively.

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Recent Progress in Air Conditioning and Refrigeration Research -A Review of Papers Published in the Korean Journal of Air-Conditioning and Refrigeration Engineering in 2000 and 2001- (공기조화, 냉동 분야의 최근 연구 동향 -2000년 및 2001년 학회지 논문에 대한 종합적 고찰 -)

  • 강신형;한화택;조금남;이승복;조형희;김민수
    • Korean Journal of Air-Conditioning and Refrigeration Engineering
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    • v.14 no.12
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    • pp.1102-1139
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    • 2002
  • A review on the papers published in the Korean Journal of Air-Conditioning and Refrigerating Engineering in 2000 and 2001 has been done. Focus has been put on current status of research in the aspect of heating, cooling, ventilation, sanitation and building environment. The conclusions are as follows. (1) Most of fundamental studies on fluid flow were related with heat transportation of facilities. Drop formation and rivulet flow on solid surfaces were interesting topics related with condensation augmentation. Research on micro environment considering flow, heat, humidity was also interesting for comfortable living environment. It can be extended considering biological aspects. Development of fans and blowers of high performance and low noise were continuing topics. Well developed CFD technologies were widely applied for developing facilities and their systems. (2) Most of papers related with heat transfer analysis and heat exchanger shows dealt with convection, evaporation, and channel flow for the design application of heat exchanger. The numerical heat transfer simulation studies have been peformed and reported to show heat transfer characteristics. Experimental as well as numerical studies on heat exchanger were reported, while not many papers are available for the system analysis including heat exchanger. (3) A review of the recent studies on heat pump system shows that performance analysis and control of heat pump have been peformed by various simulations and experiments. The research papers on multi-type heat pump system increased significantly. The studies on heat pipe have been examined experimently for change of working characteristics and strut lure. Research on the phase change has been carried out steadily and operation strategies of encapsulated ice storage tank are reported experimentally in several papers. (4) A review of recent studies on refrigeration/air conditioning system have focused on the system performance and efficiency for new alternative refrigerants. Evaporation and condensation heat transfer characteristics are investigated for tube shapes and new alternative refrigerants. Studies on components of refrigeration/air conditioning system are carried to examine efficiency for various compressors and performance of new expansion devices. In addition to thermophysical properties of refrigerant mixtures, studies on new refrigerants are also carried out, however research works on two-phase flow seemed to be insufficient. (5) A review of the recent studies on absorption cooling system indicates that heat and mass transfer phenomena have been investigated to improve absorber performance. Various experimental data have been presented and several simulation models have been proposed. A review of the recent studies on duct and ventilation shows that ventilation indices have been proposed to quantify the ventilation performance in buildings and tunnels. Main efforts have been focused on the applications of ventilation effectiveness in practice, either numerically using computational fluid dynamics or experimentally using tracer gas techniques. (6) Based on a review of recent studies on indoor thermal environment and building service systems, research issues have mainly focused on many innovative ideas such as underfloor air-conditioning system, personal environmental modules, radiant floor cooling and etc. Also, the new approaches for minimizing energy consumption as well as improving indoor environmental conditions through predictive control of HVAC systems, various activities of building energy management and cost-benefit analysis for economic evaluation were highlighted.

Effect of Drying Methods and Gamma Irradiation on the Color Changes and Antioxidant Activity of Grape By-Products (건조방법과 감마선 조사에 따른 포도가공부산물의 색상 변화 및 항산화활성)

  • Jo, Ji-Eun;Yook, Hong-Sun;Kim, Kyoung-Hee;Baek, Jong-Yeon;Moon, Young-Ja;Park, Sung-Jin;Jang, Soon-Ae
    • Journal of the Korean Society of Food Science and Nutrition
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    • v.39 no.12
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    • pp.1826-1831
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    • 2010
  • This study was carried out to examine the changes of the quality feature and antioxidant activity of grape by-products. This experiment was to arrange the basic data for developing a functional material using grape by-products which were useless resources. Hot-air and freeze drying were followed by the gamma irradiation of 1~20 kGy. Hunter's color value, in case of hot-air drying, showed the highest L and a value in the 3 kGy, and it decreased according to the increase of the exposure dose. In the case of fre ze drying it showed the highest L and b value at the highest exposure, 20 kGy. It was considered that the breakdown of the pigment through high temperature processing was launched and the influence according to the gamma irradiation was not shown. The gamma irradiation of 3 kGy appeared to have a good influence on the color of the grape by-products which went through hot-air drying. The contents of the total phenolic compounds, in case of hot-air drying, showed the highest total polyphenol contents in the 3 kGy irradiation and it decreased according to the increase of the exposure dose; in contrast, the higher phenolic contents showed in the irradiated group than in the control. In case of freeze drying, the highest phenolic contents appeared in the control but 3 kGy showed the highest one in the irradiated group. Results of radical scavenging activity using DPPH and ABTS indicated that 3 kGy showed the highest radical scavenging activity in hot-air and freeze drying. Therefore, it was found that gamma irradiation of 3 kGy could improve the color and antioxidant activity of grape by-products, but an antioxidant activity of grape by-product due to the gamma irradiation was a little affected in the aspects of by-product utilization.

Studies on Growth Responses of Tomato and Environmental Characteristics of Various Rain Shelter Types (간이시설 형태별 환경특성과 토마토 생장반응 연구)

  • 김현환;조삼증;이시영;권영삼;신만균;남윤일;최규홍
    • Journal of Bio-Environment Control
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    • v.2 no.2
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    • pp.89-98
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    • 1993
  • The purpose of this study was to investigate crop growth responses under various rain shelters which were devised to improve the indoor environment in summer season. For developing the proper type of rain shelter, the improved rain shelters with the roof of saw - tooth type(saw-tooth type) and 3 span-arch type(improved arch type) were compared with the conventional one with the roof of single arch type(conventional arch type) and no rain shelter (open field ). The results were summarized as follows ; 1. The air temperature in the improved arch type was 4$^{\circ}C$ and 1$^{\circ}C$ lower than those in the conventional arch type and the saw - tooth type, respectively. 2. The air temperature drop by the evaporative cooling + improved drainage was 1.3$^{\circ}C$ which was 0.9$^{\circ}C$lower than that by the improved drainage only. 3. The effect of labour saving in the saw-tooth type was superior to any other type because its frames were used as props and the labour for ventilation was not needed. 4. The highest marketable yield of tomato was 4,897kg/10a in the improved arch type and the total leaf areas which related to photosynthesis was the largest in the saw - tooth type. 5. The improved arch type was proved to be proper to raise yield potential. The effect of the underground environment treatment on the quality and quantity of vegetable showed to be outstanding in the saw- tooth type with the evaporative cooling + improved drainage, and in the improved and conventional arch type with the trickle improved drainage. 6. In conclusion, the saw - tooth type and the improved arch type were proved to be labour saving rain shelters and the indoor environments in both types were better than that in the conventional arch type.

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