• Title/Summary/Keyword: library discovery

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Development of an efficient genotyping-by-sequencing (GBS) library construction method for genomic analysis of grapevine

  • Jang, Hyun A;Oh, Sang-Keun
    • Korean Journal of Agricultural Science
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    • v.44 no.4
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    • pp.495-503
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    • 2017
  • Genotyping-by-sequencing (GBS) is an outstanding technology for genotyping and single nucleotide polymorphism (SNP) discovery compared to next generation sequencing (NGS) because it can save time when analyzing large-scale samples and carries a low cost per sample. Recently, studies using GBS have been conducted on major crops and, to a greater extent, on fruit crops. However, many researchers have some problems due to low GBS efficiency resulting from low quality GBS libraries. To overcome this limitation, we developed an efficient GBS library construction method that regulates important conditions such as restriction enzymes (RE) digestion and a PCR procedure for grapevine. For RE digestion, DNA samples are digested with ApeKI (3.6U) at $75^{\circ}C$ for 5 hours and adapters are ligated to the ends of gDNA products. To produce suitable PCR fragments for sequencing, we modified the PCR amplification conditions; temperature cycling consisted of $72^{\circ}C$ (5 min), $98^{\circ}C$ (30 s), followed by 16 cycles of $98^{\circ}C$ (30 s), $65^{\circ}C$ (30 s), $72^{\circ}C$ (20 s) with a final extension step. As a result, we had obtained optimal library construct sizes (200 to 400 bp) for GBS analysis. Furthermore, it not only increased the mapping efficiency by approximately 10.17% compared to the previous method, but also produced mapped reads which were distributed equally on the19 chromosomes in the grape genome. Therefore, we suggest that this system can be used for various fruit crops and is expected to increase the efficiency of various genomic analysis performed.

Deployment of BIBFRAME as a New Bibliographic Framework in Linked Data (링크드 데이터 환경에서의 서지기술형식 BIBFRAME과 그 활용에 대한 고찰)

  • Park, Ok Nam;Oh, Jung Sun
    • Journal of the Korean BIBLIA Society for library and Information Science
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    • v.25 no.4
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    • pp.235-263
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    • 2014
  • Library of Congress introduced BIBFRAME as a new bibliographic framework to enhance web accessibility of bibliographic records and their integration to Web of data. This study introduces BIBFRAME model and its current status, reviews BIBFRAME classes and properties, and presents a mapping between MARC21 and BIBFRAME. The study aims to help the understanding the deployment of BIBFRAME in bibliographic description. BIBFRAME categorizes bibliographic entities into Work-Instance, and employs RDF/XML and URIs to identify resources and specify semantics of the resources on the Web. It also suggests an Annotation entity to provide additional information produced by users and external organizations. BIBFRAME is significant in that it presents a new paradigm of bibliographic description and expands users' information discovery in the context of Linked Data. Continuous researches are required to support its content model agnostic application to diverse resource type, which may entail a modification of BIBFRAME model and vocabulary. It also calls for guidelines for using the complicated vocabulary in a coherent way.

DDC in DSpace: Integration of Multi-lingual Subject Access System in Institutional Digital Repositories

  • Roy, Bijan Kumar;Biswas, Subal Chandra;Mukhopadhyay, Parthasarathi
    • International Journal of Knowledge Content Development & Technology
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    • v.7 no.4
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    • pp.71-84
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    • 2017
  • The paper discusses the nature of Knowledge Organization Systems (KOSs) and shows how these can support digital library users. It demonstrates processes related to integration of KOS like the Dewey Decimal Classification, $22^{nd}$ edition (DDC22) in DSpace software (http://www.dspace.org/) for organizing and retrieving (browsing and searching) scholarly objects. An attempt has been made to use the DDC22 available in Bengali language and highlights the required mechanisms for system-level integration. It may help a repository administrator to build an IDR (Institutional Digital Repository) integrated with SKOS-enabled multilingual subject access systems for supporting subject descriptors based indexing (DC.Subject metadata element), structured navigation (browsing) and efficient searching.

Drug Target Identification of a natural anticancer agent plumbagin using $GPScreen^{TM}$: An innovative Technology for Drug Target Discovery using Drug-induced haploinsufficiency in S. pombe Genome-wide Heterozygous Deletion Mutant Library ($GPScreen^{TM}$ 이용한 천연 항암물질인 plumbagin의 약물 작용점 연구: 분열 효모인 S. pombe 유전체 이종 결손 변이 라이브러리에서의 약물에 의한 haploinsufficiency를 이용한 약물 작용점 규명을 위한 혁신 기술)

  • Lee, Ju-Hee;Yeon, Ji-Hyun;Yoon, Pyoung-Oh;Roh, Whi-Jae;Park, Han-Oh;Kim, Dong-Myung
    • 한국약용작물학회:학술대회논문집
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    • 2011.04a
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    • pp.106-107
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    • 2011
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A literature study about the satisfaction with oriental medical services (한방의료 만족도에 대한 문헌적 고찰)

  • Lim, Jung-Hun;Lim, Sung-Min
    • The Journal of the Society of Korean Medicine Diagnostics
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    • v.17 no.1
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    • pp.51-62
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    • 2013
  • Objectives This study aimed to analyze and summarize the satisfaction with oriental medical services in korea. Methods From 3 Korean databases (National Assembly Library, Korea Education Research Information Sharing Service, and National Discovery for Science Leaders), published between 2001 and 2011, we were obtained 13 studies that involved the satisfaction of oriental medical services. Results We found that the kindness of doctors and other staffs was significant determinant of satisfaction with oriental medical services. The positive recognition about treatment effect and the preference to combined medical system were also influenced to satisfaction with oriental medical services. Generally it was necessary for evaluation of satisfaction to improve facilities and environments of hospitals. Conclusions The satisfaction with oriental medical services would be related with the kindness of doctors and other staffs, the recognition about treatment effect, the preference to combined medical system and environments of hospitals. Also to confirm the reasons for the satisfaction with oriental medical services, further studies should be conducted using the highest methodological standards.

Plant Extracts Inhibiting Biofilm Formation by Streptococcus mutans without Antibiotic Activity

  • Ham, Youngseok;Kim, Tae-Jong
    • Journal of the Korean Wood Science and Technology
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    • v.46 no.6
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    • pp.692-702
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    • 2018
  • Streptococcus mutans causes oral diseases, including tooth decay, by producing a biofilm called plaque. Therefore, inhibition of biofilm formation is essential for maintaining oral health. Plants produce a variety of secondary metabolites, which act as starting sources for the discovery of new bioactive chemicals that inhibit biofilm formation of S. mutans. Previous studies have reported on chemicals with antibiotic activity for the inhibition of biofilm formation by S. mutans. In this study, nine plant extracts from Melonis Pedicellus, Agastachis Herba, Mori Cortex Radicis, Diospyros kaki leaves, Agrimoniae Herba, Polygoni Multiflori Radix, Lycopi Herba, Elsholtziae Herba, and Schizonepetae Spica were screened for the inhibition of biofilm formation from a plant extract library. The water-soluble compounds of the extracts did not affect cell growth but selectively inhibited biofilm formation. These results suggest that the selected plant extracts constitute novel biofilm formation inhibitors, with a novel biological mechanism, for improving oral hygiene.

A literature study about utilization of oriental medical services (한방의료 이용에 대한 문헌적 고찰)

  • Lim, Jung-Hun;Lim, Sung-Min
    • The Journal of the Society of Korean Medicine Diagnostics
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    • v.16 no.2
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    • pp.11-22
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    • 2012
  • Objectives : This study aimed to analyze and summarize the utilization of oriental medical services in korea. Methods : From 3 Korean databases (National Assembly Library, Korea Education Research Information Sharing Service, and National Discovery for Science Leaders), published between 2001 and 2011, we were obtained 17 studies that involved the utilization of oriental medical services. Results : We found that women, elderly patients, and patients with low education levels and those with musculoskeletal and cerebrovascular diseases preferred to use oriental medical services. Other variables such as trust and kindness of staff and positive perceptions of the treatment effect were found to be significant determinants for utilizing oriental medical services. Conclusions : The utilization of oriental medical services would be related with gender, age, education levels and diseases. Also to confirm the reasons for patients to choose oriental medical services, further studies should be conducted using the highest methodological standards.

Screening for bioactive compounds from natural products by ELISA assay

  • Iwanami, Naoko
    • Proceedings of the Korean Society of Applied Pharmacology
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    • 1998.11a
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    • pp.34-37
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    • 1998
  • Combinatorial chemistry is one of the most interested topics in the area of drug discovery. One of the most important points is how to find a lead compound that gives the seed structure for designing of a combinatorial library. Natural products is suitable for searching a new bioactive compound with new structure. We have carried out systematic screening works to find natural products possessing the effects on inter-and intra-cellular signaling. Two hundreds extracts of medical plants and two thousands microbial culture broth samples have been tested for the induction and inhibition of IL-2 or IL-6 production (Fig. 1). ELISA is an efficient method for screenings from such a large number of samples. Now, we apply this method to search prion- binding agents.

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Reviewing Research on Korean medical treatment of Psoriasis (건선의 한의학적 치료에 관한 논문 경향 분석 - 국내 논문을 중심으로)

  • Hong, Seok-Hoon
    • The Journal of Korean Medicine Ophthalmology and Otolaryngology and Dermatology
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    • v.26 no.4
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    • pp.26-42
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    • 2013
  • Background : The purpose of this study is to analyze research trends on the korean medical treatment and develop the way of psoriasis cure. Object & Method : This study is based on analysis of recent paper about korean medical treatment of psoriasis using WKUCL(Wonkwang University Central Library) and NDSL(National Discovery for Science Leader). I searched papers using the keyword "Psoriasis". Inclusion criteria was last 13 years. Result : A total 19 studies were found. They turned out to be effective treatment methods of acupuncture, moxibustion, internal medicines, external applications, and evaluation tool of PASI(psoriasis area and severity index). Conclusion : According to the results, korean medical treatments have good effects on psoriasis. If we accumulate the more clinical reports, it will be helpful to map out a systematic treatment of korean medicine on psoriasis.

Exploratory Study of Developing a Synchronization-Based Approach for Multi-step Discovery of Knowledge Structures

  • Yu, So Young
    • Journal of Information Science Theory and Practice
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    • v.2 no.2
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    • pp.16-32
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    • 2014
  • As Topic Modeling has been applied in increasingly various domains, the difficulty in naming and characterizing topics also has been recognized more. This study, therefore, explores an approach of combining text mining with network analysis in a multi-step approach. The concept of synchronization was applied to re-assign the top author keywords in more than one topic category, in order to improve the visibility of the topic-author keyword network, and to increase the topical cohesion in each topic. The suggested approach was applied using 16,548 articles with 2,881 unique author keywords in construction and building engineering indexed by KSCI. As a result, it was revealed that the combined approach could improve both the visibility of the topic-author keyword map and topical cohesion in most of the detected topic categories. There should be more cases of applying the approach in various domains for generalization and advancement of the approach. Also, more sophisticated evaluation methods should also be necessary to develop the suggested approach.