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Construction of PANM Database (Protostome DB) for rapid annotation of NGS data in Mollusks

  • Kang, Se Won;Park, So Young;Patnaik, Bharat Bhusan;Hwang, Hee Ju;Kim, Changmu;Kim, Soonok;Lee, Jun Sang;Han, Yeon Soo;Lee, Yong Seok
    • The Korean Journal of Malacology
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    • v.31 no.3
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    • pp.243-247
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    • 2015
  • A stand-alone BLAST server is available that provides a convenient and amenable platform for the analysis of molluscan sequence information especially the EST sequences generated by traditional sequencing methods. However, it is found that the server has limitations in the annotation of molluscan sequences generated using next-generation sequencing (NGS) platforms due to inconsistencies in molluscan sequence available at NCBI. We constructed a web-based interface for a new stand-alone BLAST, called PANM-DB (Protostome DB) for the analysis of molluscan NGS data. The PANM-DB includes the amino acid sequences from the protostome groups-Arthropoda, Nematoda, and Mollusca downloaded from GenBank with the NCBI taxonomy Browser. The sequences were translated into multi-FASTA format and stored in the database by using the formatdb program at NCBI. PANM-DB contains 6% of NCBInr database sequences (as of 24-06-2015), and for an input of 10,000 RNA-seq sequences the processing speed was 15 times faster by using PANM-DB when compared with NCBInr DB. It was also noted that PANM-DB show two times more significant hits with diverse annotation profiles as compared with Mollusks DB. Hence, the construction of PANM-DB is a significant step in the annotation of molluscan sequence information obtained from NGS platforms. The PANM-DB is freely downloadable from the web-based interface (Malacological Society of Korea, http://malacol.or/kr/blast) as compressed file system and can run on any compatible operating system.

Meaning of Housing through Oral Life History of Korean Chineses in Harbin, China : Focused on experiences of housing structure type and pathway approach (생애구술을 통해 본 중국 할빈 지역 조선족의 주거의 의미 : 주거유형 경험과 경로접근을 중심으로)

  • Hong, Hyung-Ock
    • Journal of Families and Better Life
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    • v.28 no.5
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    • pp.167-181
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    • 2010
  • This research was designed to explore the meaning of housing among Korean Chinese in Harbin, China. In particular, the meaning of housing was examined by using the pathway approach. Utilizing qualitative research methods, this study administered the in-depth interview on the oral history of an individual life, and the 5 elderly persons in their 60s and 70s participated in the individualized interviews that were conducted from May 28 to 31 in 2010. The main findings of meaning of housing were as follows; 1. Similarly to the meaning of housing in 1970s and 1980s in Korea, house was viewed as both a shelter for family members and relatives and a place for their comfort. 2. Prior to multi-story residences, Harbin had only 3 different forms of single-story houses available; Chinese style with Kang and soil room(地室), Korean style with 'Ondol', and Russian style with open floor and Pechka, The promotion at work enabled participants to move to multi-story residences, their moving time varied from 1970 to 1991, and the residential moving determined their current housing status. 3. Multi-story residences were available around 1970s, floor-heating system was introduced from 1990s, and high-rise apartments were built from 1998. Korean Chinese(朝鮮族) weren't satisfied with the spatial composition of individual units embedded into the Chinese culture, especially, entrance, kitchen, bathroom and veranda. 4. Based on assimilation through socialism, adaptation to socialist society and capitalist acculturation, the lifestyles of the interviewees were categorized into five types - capitalist-proactive(Ms. KS), socialist-pragmatic(Ms. J), socialist-inducive(Ms. KY), family centered-conservative(Ms. L), and socialist-adaptive(Ms. P). This study implies that housing-related services for Korean Chinese are necessarily provided so as to embrace their life style and cultural identity in housing design, and further studies need to be explored.

A Study on the Categorization of Interface for the Flexibility in the Wall System of Long Life Housing (장수명 공동주택의 가변성 확보를 위한 벽체 인터페이스 유형화 연구)

  • Bahc, Yo Han;Choi, Young Ho;Kim, Sung Wan
    • KIEAE Journal
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    • v.8 no.3
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    • pp.37-42
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    • 2008
  • The purpose of this study was to comprehend specific characteristic of interface and present the standardized interface of Long Life Housing, which could be obtained by the total and various approaches. With this in mind we analyzed related studies of interface through previous studies, and based on the analysis we created standardized factors of categorization in view of characteristic of interface. Using these factors, we can determine whether the interface could be used systematically in Long Life Housing. And as these were presented in the form of Key Map for expedite the synthetic understanding of interface, we could easily reconize types of interface. Especially, we only dealt the wall of flexible interface of Long Life Housing. Throughout systemizing and standardizing works, we can expedite the understanding of interface of Long Life Housing and finally, we want to make basic data used for date base of interface which can be available for Long Life Housing.

Effects of the smartphone addiction on adjustment to college life - Moderating effect of impulsivity -

  • Jeong, ByeongIl;Baek, SangUk
    • Journal of the Korea Society of Computer and Information
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    • v.20 no.12
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    • pp.129-136
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    • 2015
  • In this paper, we propose a smartphone addiction affected adjustment to college life and the moderating effects of impulsivity in the relations between smartphone addiction and adjustment to college life. For this, it conducted the questionnaire with 348 college students who showed higher use of smartphone and analyzed the data from the questionnaire. The results of the analysis are as follows. It was found that smartphone addiction had significant influences on the adjustment to college life. As a result of examining the moderating effects of impulsivity in the relations between smartphone addiction and adjustment to college life, there were the moderating effects of impulsivity. This study was available in giving useful suggestions to prevent smartphone addiction and help college students adjust to their college life through impulsivity control.

Changes in Available Lysine and Extractable Nitrogen, and Extent of Browning during the Storage of Dried Fish Meat (건어육저장중의 유효 Lysine 및 Ex분질소의 변화와 갈변)

  • LEE Kang-Ho;SONG Dong-Suck;You Byeong-Jin;KIM Mu-Nam
    • Korean Journal of Fisheries and Aquatic Sciences
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    • v.15 no.4
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    • pp.271-282
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    • 1982
  • The browning development, mainly through the Maillard reaction, occurring in the dried fish meat products during storage causes reduction of the nutritional value due to the loss of the essential amino acid such as available lysine as well as off -flavor resulting in the deterioration of the food quality thus shortening the shelflife. In the work, the changes in the amount of available lysine, extractable nitrogenous compounds (nonprotein-N, amino-N, trimethylamine oxide, trimethylamine, and free lysine) and development of browning were measured to assess the relationship between the shelflife and the quality loss in dried filefish under the steady state conditions (35,45, and $55^{\circ}C;a_{w}'s$ of 0.44 0.52, 0.65 and 0.75 at each temperature) and fluctuating temperature condition of $35/55^{\circ}C$ will. alternating 7 day periods at each water activity. The results indicated that the amount of available lysine and extractable nitrogenous compounds except TMA decreased rapidly with increasing temperatures and water activities while the rate of available lysine and extractable nitrogenous compounds must be involved in the initial stage of brown pigment formation. The available lysine loss of the dried filefish products stored under the fluctuating temperature conditions was greater than that stored under its fixed mean temperature, $45^{\circ}C$. The activation energies for lysine loss obtained from the Arrhenius plot ranged 6.9 to 4.4 Kcal/mol and $Q_{10}$ values at $40^{\circ}C$ were 1.4 to 1.2. The values for browning were 15.7 to 14.4 Kcal/mol and 2.2 to 2.0 respectively. Shelf-life, defined as the time to reach 0.15 O. D./g solid or the limit of off-color deterioration by browning reaction, was extented longer than the halflife of Iysine loss, actually corresponding $75\%$ loss of available lysine. This suggested that the halflife of lysine loss might not be adequate to assess the shelf-life of the food system with high potential of protein, nonproteinous nitrogen compounds, and lipids.

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Effects of Source and Application Rate of Phosphorus on Growth and Arbuscular Mycorrhizae Formation of Trifoliate Orange in Volcanic Ash Soil (화산회토양에서 인 공급원과 시용 수준이 탱자유묘의 생육과 공생균근 형성에 미치는 영향)

  • Kang, Seok-Beom;Jwa, Sung-Min;Moon, Doo-Khil;Han, Hae-Ryong;Chung, Jong-Bae
    • Korean Journal of Environmental Agriculture
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    • v.19 no.3
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    • pp.206-212
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    • 2000
  • The effects of two phosphorus sources (fused phosphate and rock phosphate), applied at different rates, on growth, arbuscular-mycorrhizae(AM) formation in roots and nutrient contents of trifoliate orange grown in an uncultivated volcanic ash soil were investigated in a greenhouse. The seedlings were either inoculated with AM fungi or left uninnoculated. Growth of seedlings were best in the treatments of 156-272 mg P/kg with fused phosphate. Although the applied P in the rack phosphate treatments were nearly same or much higher comparing to the fused phosphate treatments, seedling growth were significantly less. Soil available P in the treatment of 272 mg P/kg of fused phosphate was maintained in the range of 3-5 mg/kg during the experiment, and the AM formation was about 60% in average. In the treatments of lower rates of fused phosphate application or of rock phosphate application, soil available P were lower than 3 mg P/kg and AM formations were less than 30%. Significant increases were found in seedling growth and nutrient absorption due to AM fungi inoculation, and the effects were much more significant in the treatments of higher AM formation. In most of citrus groves in Cheju island, soil available P is much higher than 200 mg P/kg, and average AM formation in citrus roots is less than 30%. Results obtained in this study show that the formation of AM can be increased at much lower level of available P than the present levels found in citrus groves.

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Economic Effect of Local Feed Utilization in Korea

  • Lee, Byung Oh;Yang, Jeong Hee;Park, Sang Youn;Lee, Byeong Soon
    • International Journal of Advanced Culture Technology
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    • v.6 no.4
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    • pp.214-225
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    • 2018
  • Rice straw is the principal forage for Korean cattle. Limited supply of domestic forage forces Korea to depend on imported forage. Utilizing locally available domestic feed as an alternative would lead to self-sufficiency and stability in cattle farm management. Locally available feed can be utilized as forage. The challenge of collecting local feed has been overcome by machines that have been developed to harvest feed. Local feed can be completely consumed in the production regions, thus reducing transportation costs and increasing price competitiveness. Hitherto, studies have focused on feed technologies and price competitiveness, among other factors, while the substitution of forage has not been examined. This study conducts a quantitative analysis to estimate the extent to which local feed can replace existing forage. We find that local feed is cheaper, and abundantly available, and can thus replace high-quality forage.

Biological Pretreatment of Softwood Pinus densiflora by Three White Rot Fungi

  • Lee, Jae-Won;Gwak, Ki-Seob;Park, Jun-Yeong;Park, Mi-Jin;Choi, Don-Ha;Kwon, Mi;Choi, In-Gyu
    • Journal of Microbiology
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    • v.45 no.6
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    • pp.485-491
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    • 2007
  • The effects of biological pretreatment on the Japanese red pine Pinus densiflora, was evaluated after exposure to three white rot fungi Ceriporia lacerata, Stereum hirsutum, and Polyporus brumalis. Change in chemical composition, structural modification, and their susceptibility to enzymatic saccharification in the degraded wood were analyzed. Of the three white rot fungi tested, S. hirsutum selectively degraded the lignin of this sortwood rather than the holocellulose component. After eight weeks of pretreatment with S. hirsutum, total weight loss was 10.7%, while lignin loss was the highest at 14.52% among the tested samples. However, holocellulose loss was lower at 7.81 % compared to those of C. lacerata and P. brumalis. Extracelluar enzymes from S. hirsutum showed higher activity of ligninase and lower activity of cellulase than those from other white rot fungi. Thus, total weight loss and changes in chemical composition of the Japanese red pine was well correlated with the enzyme activities related with lignin- and cellulose degradation in these fungi. Based on the data obtained from analysis of physical characterization of degraded wood by X-ray Diffractometry (XRD) and pore size distribution, S. hirsutum was considered as an effective potential fungus for biological pretreatment. In particular, the increase of available pore size of over 120 nm in pretreated wood powder with S. hirsutum made enzymes accessible for further enzymatic saccharification. When Japanese red pine chips treated with S. hirsutum were enzymatically saccharified using commercial enzymes (Cellulclast 1.5 L and Novozyme 188), sugar yield was greatly increased (21.01 %) compared to non-pre treated control samples, indicating that white rot fungus S. hirsutum provides an effective process in increasing sugar yield from woody biomass.

A Study for the Enhancement of Korean Married Women's Quality of Life: The level of the Quality of Life and It's Influential Factors (한국 기혼여성의 일상적 삶의 질 향상에 관한 연구 (II) 한국 기혼여성의 삶의 질 실태 및 영향 요인)

  • 김정자
    • Journal of the Korean Home Economics Association
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    • v.36 no.12
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    • pp.87-104
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    • 1998
  • This study explores the life quality(LQ) of Korean married women compared to Korean married men's LQ, examines personal factors' and home environmental factors' influences to Korean married women's LQ via psychological factors such as social belongingness, positive emotion, self-esteem, and sense of intemal control in causal model, and explores Korean married women's perceived important factors and perceived enhancement required factors in life. The questionnaire was administered to 941 Korean married women and their husbands who have one or more children in Pusan. The results indicated that: 1. The overal and most sub dimensional LQ of Korean married women mark medium level and were lower than that of Korean married men's. Korean married women who is highly educated, keeps efficient communication with their husband, self-esteem, sense of internal control, social belongingness, and positive emotion, and possess high SES and much available resources shows higher LQ than those who doesn't. 2. The efficient communication with husband and available resources have direct and indirect influences on Korean married women's LQ. The psychological mediatory factors of these two variables' influences on women's LQ are such as social belongingness, positive emotion, self-esteem and sense of intemal control. SES has direct influence only and the educational level has indirect influence via social belongingness only on Korean married women's LQ. All these factors explain 58% of Korean married women's LQ variance. 3. Korean married women rank family health, family reconciliation, husband's success, and children's achievement as the very important factors in life. They also rank husbands success, economic abundant, family reconciliation, family health, and their self-actualization as the very required factors for enhancing the given LQ.

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Diversity and its Characteristics of Life Phenomenon (생명현상의 다양성과 특징에 관한 고찰 - 보건의료에 미치는 영향을 중심으로 -)

  • Lee, Sun-Dong
    • Journal of Society of Preventive Korean Medicine
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    • v.14 no.1
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    • pp.1-12
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    • 2010
  • This research was intended to delve into the diversity of life phenomenon and its characteristics. First of all, this research gave real examples to compare the differences in men's health, disease, and longevity in order to confirm the existence of diversity of life phenomenon. In addition, it also studied the process and mechanism of manifestation of life phenomenon, as well as the influence and problems of existing studies' results and implications. The results are as follow. 1. Differences in health, diseases, and longevity were very big and diverse in researches on different races, nations, ages, socioeconomic status, positions, and even (monozygotic) twins. 2. The basic foundation of all organisms is DNA, and environmental factors change DNA methylation and the structure of chromatin by constantly influencing DNA. Due to this, the manifestation, control, and phenotype of DNA change, resulting in diversified life phenomenon. Therefore, it is the environmental factors, not DNA, that has more influence on the diversity of life. 3. Looking at available studies, the most reasonable perspective on human requires focusing on the diversity of life phenomenon, holistic thinking, and reversible change instead of irreversible determinism. Considerable differences in life phenomenon between entities require a change in malformed perspective on life. Public health and medicine deals with live human beings, a more precise and accurate perspective on life is very important. Because management methods of health and disease, such as structure and approaches of medical research, prevention and cure, must be different by life perspectives.