• Title/Summary/Keyword: least common ancestor

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Altering LCA of dependency parse trees for improving relation extraction from adjective clauses (형용사구에서의 관계추출 개선을 위한 의존구문트리의 최소공동조상 (LCA) 변경)

  • Lee, Dae-Seok;Myaeng, Sung-Hyon
    • Annual Conference on Human and Language Technology
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    • 2018.10a
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    • pp.552-556
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    • 2018
  • 본 논문에서는 텍스트에서 개체(entity) 간 관계(relation) 추출 문제에서 의존구문트리를 이용하여 자질을 추출할 때 형용사구 내에 관계가 나타나는 경우의 성능을 향상시키는 방법을 제안한다. 일률적으로 의존구문트리의 최소공동조상(LCA: Least Common Ancestor)을 이용하는 일반적인 방법보다 형용사구가 나타날 때는 형용사구의 술어를 대신 이용하는 것이 더 좋은 자질이 된다는 것을 제안하고 로지스틱 회귀분석, SVM(linear), SVM(exponential kernel)을 이용한 실험들을 통해 그 효과를 확인하였다. 이는 트리커널을 이용한 것과 같이 의존구문트리의 최소공동조상이 주요한 역할을 하는 관계추출 모델들의 성능을 높일 수 있음을 보여 준다. 수행한 실험 과정을 통해 관계추출 데이터 셋에서 형용사구 내 관계를 포함하는 문장이 전체에서 차지하는 비율이 낮을 경우 생길 수 있는 문제를 추가적으로 얻을 수 있었다.

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Protein Interaction Network Visualization System Combined with Gene Ontology (유전자 온톨로지와 연계한 단백질 상호작용 네트워크 시각화 시스템)

  • Choi, Yun-Kyu;Kim, Seok;Yi, Gwan-Su;Park, Jin-Ah
    • Journal of KIISE:Computer Systems and Theory
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    • v.36 no.2
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    • pp.60-67
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    • 2009
  • Analyzing protein-protein interactions(PPI) is an important task in bioinformatics as it can help in new drugs' discovery process. However, due to vast amount of PPI data and their complexity, efficient visualization of the data is still remained as a challenging problem. We have developed efficient and effective visualization system that integrates Gene Ontology(GO) and PPI network to provide better insights to scientists. To provide efficient data visualization, we have employed dynamic interactive graph drawing methods and context-based browsing strategy. In addition, quick and flexible cross-reference system between GO and PPI; LCA(Least Common Ancestor) finding for GO; and etc are supported as special features. In terms of interface, our visualization system provides two separate graphical windows side-by-side for GO graphs and PPI network, and also provides cross-reference functions between them.

Evolutionary History of Two Paralogous Glyceraldehyde 3-Phosphate Dehydrogenase Genes in Teleosts

  • Kim, Keun-Yong;Nam, Yoon-Kwon
    • Fisheries and Aquatic Sciences
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    • v.11 no.3
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    • pp.177-181
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    • 2008
  • Glyceraldehyde 3-phosphate dehydrogenase(GAPDH) is a key enzyme for carbohydrate metabolism in most living organisms. Recent reports and our own searches of teleost species in publicly available genomic databases have identified at least two distinct GAPDH genes in a given species. The two GAPDH genes are located on the same chromosome in teleosts, whereas they are located on the different chromosomes in mammals. Thus, we reconstructed a phylogenetic tree to better understand the evolutionary history of the GAPDH genes in the vertebrate lineage. Our phylogenetic analysis revealed unambiguously that the two GAPDH genes of teleosts are phylogenetically closely affiliated to one of the cytosolic GAPDH and spermatogenic GAPDH-S of mammals. This indicates that the two paralogous GAPDH genes shared a common ancestor and subsequently underwent a gene duplication event during early vertebrate evolution. However, GAPDH-S of teleosts showed significant differences in the polypeptide residues and tissue distribution of its mRNA transcripts from that of mammals, implying they have undergone a different history of functionalization.

The Chloroplast rpl23 Gene Cluster of Spirogyra maxima (Charophyceae) Shares Many Similarities with the Angiosperm rpl23 Operon

  • Lee, Jung-Ho;James R. Manhart
    • ALGAE
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    • v.17 no.1
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    • pp.59-68
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    • 2002
  • A phylogenetic affinity between charophytes and embryophytes (land plants) has been explained by a few chloroplast genomic characters including gene and intron (Manhart and Palmer 1990; Baldauf et al. 1990; Lew and Manhart 1993). Here we show that a charophyte, Spirogyra maxima, has the largest operon of angiosperm chloroplast genomes, rpl23 operon (trnⅠ-rpl23-rpl2-rps19-rpl22-rps3-rpl16-rpl14-rps8-infA-rpl36-rps11-rpoA) containing both embryophyte introns, rpl16.i and rpl2.i. The rpl23 gene cluster of Spirogyra contains a distinct eubacterial promoter sequence upstream of rpl23, which is the first gene of the green algal rpl23 gene cluster. This sequence is completely absent in angiosperms but is present in non-flowering plants. The results imply that, in the rpl23 gene cluster, early charophytes had at least two promoters, one upstream of trnⅠ and and another upstream of rpl23, which partially or completely lost its function in land plants. A comparison of gene clusters of prokaryotes, algal chloroplast DNAs and land plant cpDNAs indicated a loss of numerous genes in chlorophyll a+b eukaryotes. A phylogenetic analysis using presence/absence of genes and introns as characters produced trees with a strongly supported clade containing chlorophyll a+b eukaryotes. Spirogyra and embryophytes formed a clade characterized by the loss of rpl5 and rps9 and the gain of trnⅠ (CAU) and introns in rpl2 and rpl16. The analyses support the hypothesis that the rpl23 gene cluster and the rpl2 and rpl16 introns of land plants originated from a common ancestor of Spirogyra and land plants.

Cloning and Sequencing Analysis of the Repressor Gene of Temperate Mycobacteriophage L1

  • Sau, Subrata;Chattoraj, Partho;Ganguly, Tridib;Lee, Chia Yen;Mandal, Nitai Chandra
    • BMB Reports
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    • v.37 no.2
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    • pp.254-259
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    • 2004
  • The wild-type and temperature-sensitive (ts) repressor genes were cloned from the temperate mycobacteriophage L1 and its mutant L1cIts391, respectively. A sequencing analysis revealed that the $131^{st}$ proline residue of the wild-type repressor was changed to leucine in the ts mutant repressor. The 100% identity that was discovered between the two DNA regions of phages L1 and L5, carrying the same sets of genes including their repressor genes, strengthened the speculation that L1 is a minor variant of phage L5 or vice versa. A comparative analysis of the repressor proteins of different mycobacteriophages suggests that the mycobacteriophage-specific repressor proteins constitute a new family of repressors, which were possibly evolved from a common ancestor. Alignment of the mycobacteriophage-specific repressor proteins showed at least 7 blocks (designated I-VII) that carried 3-8 identical amino acid residues. The amino acid residues of blocks V, VI, and some residues downstream to block VI are crucial for the function of the L1 (or L5) repressor. Blocks I and II possibly form the turn and helix 2 regions of the HTH motif of the repressor. Block IV in the L1 repressor is part of the most charged region encompassing amino acid residues 72-92, which flanks the putative N-terminal basic (residues 1-71) and C-terminal acidic (residues 93-183) domains of L1 repressor.

Some Instances of Manchurian Naturalization and Settlement in Choson Dynasty (향화인의 조선 정착 사례 연구 - 여진 향화인을 중심으로 -)

  • Won, Chang-Ae
    • (The)Study of the Eastern Classic
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    • no.37
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    • pp.33-61
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    • 2009
  • In the late Koryo period, until 14th century, there had been at least two groups of Manchurians who were conferred citizenships; one group was living as an original inhabitant in the coastal area of north­eastern part of Korean peninsular, long time ago, and they were over one thousand households. The other was coming down from inland, eastern part of Yoha River, to the area of Tuman River to settle down and they were at least around one hundred and sixty households, including such tribes as Al-tha-ry, Ol-lyang-hap, Ol-jok-hap and others. They were treated courteously, from the early days of Choson dynasty, with governmental policies in an economic, political, and social ways. They were given, for instance, a house, a land, household furniture, and clothes. They were allowed to get marry with a native Korean to settle down. They were educated how to cultivate their lands. It was also possible for them to be given an official position politically or allowed to take a National Civil Official Examination. The fact they could take such an Examination, in particular, means they were treated fairly and equally, because they also had a privilege to improve their social positions through the formal system as much as common people. Two typical families were scrutinized, in this paper, family Chong-hae Lee and family Chon-ju Ju. All of them were successful to settle down with different backgrounds each other. The former were from a headman, Lee Jee-ran, who controlled his tribe, over five hundred households. He was given three titles of a meritorious retainer at the founding of Chosun dynasty, at the retrieval of armies, and an enshrined retainer. His son, Lee Wha-yong, was also given a vassal of merit who kept a close tie successfully with the king's family through a marriage. Upon the foundation of their ancestors, their grandsons, family Lee Hyo-yang and family Lee Hyo-gang, each, had taken solid root as an aristocratic Yang-ban class. The former became a high officer family, generation by generation, while the latter changed into a civil official family through Civil Official Examinations. They lived mainly around Seoul, Kyong-gi Province and some lived in their original places, Ham-kyong Province. Chu-man, the first ancestor, was given a meritorious retainer at the founding of the dynasty and Chu-in was also given a high officer position from the government. They kept living at the original place, Ham-heung, Ham-kyong Province, and then became an outstanding local family there. They began to pass the Civil Official Examinations. After 17th century on the passers were 17 in Civil Official Examinations and 40 were passed in lower civil examinations. The positions in government they attained usually were remonstrance which position was prohibited particularly to North­Western people at that time. The Chosun dynasty was open to Machurians widely through the system of envoy, convoy, and naturalization. It was intended to build up an enclosure policy through a friendly diplomatic relation with them against any possible invasion from outside. This is one reason why they were supported fully that much in a various way.