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Computational Approaches for Structural and Functional Genomics

  • Brenner, Steven-E.
    • Proceedings of the Korean Society for Bioinformatics Conference
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    • 2000.11a
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    • pp.17-20
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    • 2000
  • Structural genomics aims to provide a good experimental structure or computational model of every tractable protein in a complete genome. Underlying this goal is the immense value of protein structure, especially in permitting recognition of distant evolutionary relationships for proteins whose sequence analysis has failed to find any significant homolog. A considerable fraction of the genes in all sequenced genomes have no known function, and structure determination provides a direct means of revealing homology that may be used to infer their putative molecular function. The solved structures will be similarly useful for elucidating the biochemical or biophysical role of proteins that have been previously ascribed only phenotypic functions. More generally, knowledge of an increasingly complete repertoire of protein structures will aid structure prediction methods, improve understanding of protein structure, and ultimately lend insight into molecular interactions and pathways. We use computational methods to select families whose structures cannot be predicted and which are likely to be amenable to experimental characterization. Methods to be employed included modern sequence analysis and clustering algorithms. A critical component is consultation of the presage database for structural genomics, which records the community's experimental work underway and computational predictions. The protein families are ranked according to several criteria including taxonomic diversity and known functional information. Individual proteins, often homologs from hyperthermophiles, are selected from these families as targets for structure determination. The solved structures are examined for structural similarity to other proteins of known structure. Homologous proteins in sequence databases are computationally modeled, to provide a resource of protein structure models complementing the experimentally solved protein structures.

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Optimal monitoring instruments selection using innovative decision support system framework

  • Masoumi, Isa;Ahangari, Kaveh;Noorzad, Ali
    • Smart Structures and Systems
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    • v.21 no.1
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    • pp.123-137
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    • 2018
  • Structural monitoring is the most important part of the construction and operation of the embankment dams. Appropriate instruments selection for dams is vital, as inappropriate selection causes irreparable loss in critical condition. Due to the lack of a systematic approach to determine adequate instruments, a framework based on three comparable Multi-Attribute Decision Making (MADM) methods, which are VIKOR, technique of order preference by similarity to ideal solution (TOPSIS) and Preference ranking organization method for enrichment evaluation (PROMETHEE), has been developed. MADM techniques have been widely used for optimizing priorities and determination of the most suitable alternatives. However, the results of the different methods of MADM have indicated inconsistency in ranking alternatives due to closeness of judgements from decision makers. In this study, 9 criteria and 42 geotechnical instruments have been applied. A new method has been developed to determine the decision makers' importance weights and an aggregation method has been introduced to optimally select the most suitable instruments. Consequently, the outcomes of the aggregation ranking correlate about 94% with TOPSIS and VIKOR, and 83% with PROMETHEE methods' results providing remarkably appropriate prioritisation of instruments for embankment dams.

Paenibacillus gyeongsangnamensis sp. nov., Isolated from Soil

  • Hyosun Lee;Dhiraj Kumar Chaudhary;Dong-Uk Kim
    • Journal of Microbiology and Biotechnology
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    • v.34 no.8
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    • pp.1636-1641
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    • 2024
  • A Gram-stain-positive, aerobic, white-coloured, rod-shaped bacteria, designated as a strain dW9T, was isolated from soil. Strain dW9T was catalase-positive and oxidase-negative. Strain dW9T grew at temperature of 20-37℃ and at pH of 5.0-7.0. Phylogenetic and 16S rRNA gene analysis indicated that strain dW9T belonged to the genus Paenibacillus with its closest relative being Paenibacillus filicis S4T (97.4% sequence similarity). The genome size of dW9T was 7,787,916 bp with DNA G+C G+C content of 51.3%. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of dW9T with its closest relatives were found to be <22.0% and <74.0%, respectively. The only respiratory quinone was MK-7, and the major fatty acids were antiso-C15:0 and iso-C16:0. Overall, the comprehensive taxonomic analysis revealed that strain dW9T met all the fundamental criteria to be classified as a novel species within the genus Paenibacillus. Accordingly, we propose the name Paenibacillus gyeongsangnamensis sp. nov., with the type strain dW9T (=KCTC 43431T =NBRC 116022T).

Types of Students' Responses to Anomalous Data (변칙 사례에 대한 학생들의 반응 유형)

  • Noh, Tae-Hee;Lim, Hee-Yeon;Kang, Suk-Jin
    • Journal of The Korean Association For Science Education
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    • v.20 no.2
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    • pp.288-296
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    • 2000
  • In this study, the types and the characteristics of students' responses to anomalous data were investigated. The criteria for classifying students' responses were 'acceptance of validity of anomalous data', 'acceptance of inconsistency between anomalous data and initial theory', and 'change of belief in initial theory'. Seven types of responses were identified as follows: Rejection, reinterpretation, exclusion, uncertainty, peripheral theory change, partial belief change, and theory change. Absolute belief in the intial theory and doubts about methodological accuracy were found to be the major reasons for rejecting anomalous data. The students did not accept the inconsistency between anomalous data and initial theory because they ignored the experimental procedures and focused on the similarity of the experimental results.

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Molecular Typing of Listeria monocytogenes Isolated from Different Sources by Pulsed-Field Gel Electrophoresis

  • Kim Hwan Deuk;Lee Jae Youl;Suh Dong Kyun
    • Biomedical Science Letters
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    • v.11 no.2
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    • pp.121-128
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    • 2005
  • A total of 30L monocytogenes strains from different sources including 13 strains isolated from the foreign imported meat were genotyped in order to establish their genetic relatedness and to compare them with the foreign isolates. PFGE analysis of genomic DNA showed the 11\~16 fragments ranging in size from 38 to 504 kb. Eleven different PFGE types (1\~11) were identified in the dendrogram at 75% similarity, and the two major PFGE types, type 1 and 2, contained 94% of domestic isolates (16/17). All isolates from domestic beef and pork carcass were grouped in each different type, however, isolates from chicken were clustered together with those from pork and beef. We also found all foreign strains were unrelated with each other, regardless of geographic criteria and that they could be differentiated from those from the domestic isolates by PFGE pattern. The PFGE pattern of one isolate from chicken wing, which the chicken meat was found to be imported from foreign country, was closely related to that of isolate from the Thailand.

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A study on Forced Ventilation Rate for Bedroom Indoor Air Quality Improvement (침실 공기질 개선을 위한 강제 환기횟수에 관한 연구)

  • Kim, Dong-Gyu;Lee, Sung;Kim, Se-Hwan
    • KIEAE Journal
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    • v.9 no.1
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    • pp.85-90
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    • 2009
  • The indoor air quality is one of the most important issues of designing ventilation in high rise apartment buildings. This study suggested proper ventilation rate in the apartment bedroom where mechanical ventilation system has installed. Six university students(four male and two female) were participating in the experiment. Experiments were performed in environmental chamber. Experimental conditions were combinations from three ventilation rate 0, 0.4 and 0.7. Measurement items during 8 hours of experimental time were temperature, humidity, carbon dioxide concentrations and questionnaire surveyed aftrer sleeping. The concentration of Carbon Dioxide depending on ventilation rate in the chamber was analyzed for proper ventilation rate. The results of this paper can be summarized as follows. (1) When two persons experiment, 0.7 ventilation rate was in excess of 1000ppm. (2) When one person experiment, 0.7 and 0.4 ventilation rates were satisfied the criteria of IAQ. (3) It compared 0.4 with 0.7 in the ventilation rate, 0.4 ventilation rate could reduced about 80% of the power by fan similarity law.

Evaluation of research performances for 28 national universities (국내 28개 국공립대학교의 연구성과에 대한 평가)

  • Jeong, Dong Bin
    • Journal of the Korean Data and Information Science Society
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    • v.25 no.6
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    • pp.1241-1251
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    • 2014
  • Based on the 4 principal research-performance criteria in 28 national universities in Korea, both cluster analysis and multidimensional scaling are performed in this paper. We can classify and/or specialize the initially unknown groups into a group of relatively homogeneous universities and then create new groupings without any preconceived notion of what clusters may arise. Furthermore, the level of similarity of individual universities can be visualized on the multidimensional space so that each university is then assigned coordinates in each of the 2 dimensions. Both types and characteristics of each university can be relatively evaluated and be practically exploited for the policy of the university authority through these results.

Literature Evaluation: The Focus on the Difference between Job-based Pay and Skill-based Pay Scheme

  • Eungoo KANG
    • The Journal of Industrial Distribution & Business
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    • v.14 no.7
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    • pp.1-7
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    • 2023
  • Purpose: The present research is to explore and investigate the meaningful difference between job-based pay and skill-based pay in the current literature to shed light on the advantages and caveats of two compensation approach, providing direction for human resource practitioners looking to develop efficient and fair compensation plans. Research design, data and methodology: The methodology based on Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) was used for this research. The PRISMA technique is generally considered the gold standard since it guarantees openness, repeatability, and rigor. Studies comparing salaries based on work duties versus those based on individual skills published in English and accepted for publication in peer-reviewed journals are eligible for inclusion. Results: According to the comprehensive literature analysis, the present research provides clear comparison between Job-based pay and skilled-based pay, pointing out a similarity and four differences (1. Criteria for pay determination, 2. Flexibility, 2. Job Scope, and 4. Career progression. Conclusions: The result of the current research implies that human resource professionals would be well to learn the effects of various compensation structures on career advancement, and suggests for them that employees can take advantage of chances to advance in their careers based on right compensation schemes.

DNA Based Cloud Storage Security Framework Using Fuzzy Decision Making Technique

  • Majumdar, Abhishek;Biswas, Arpita;Baishnab, Krishna Lal;Sood, Sandeep K.
    • KSII Transactions on Internet and Information Systems (TIIS)
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    • v.13 no.7
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    • pp.3794-3820
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    • 2019
  • In recent years, a cloud environment with the ability to detect illegal behaviours along with a secured data storage capability is much needed. This study presents a cloud storage framework, wherein a 128-bit encryption key has been generated by combining deoxyribonucleic acid (DNA) cryptography and the Hill Cipher algorithm to make the framework unbreakable and ensure a better and secured distributed cloud storage environment. Moreover, the study proposes a DNA-based encryption technique, followed by a 256-bit secure socket layer (SSL) to secure data storage. The 256-bit SSL provides secured connections during data transmission. The data herein are classified based on different qualitative security parameters obtained using a specialized fuzzy-based classification technique. The model also has an additional advantage of being able to decide on selecting suitable storage servers from an existing pool of storage servers. A fuzzy-based technique for order of preference by similarity to ideal solution (TOPSIS) multi-criteria decision-making (MCDM) model has been employed for this, which can decide on the set of suitable storage servers on which the data must be stored and results in a reduction in execution time by keeping up the level of security to an improved grade.

Development of a Clustering Model for Automatic Knowledge Classification (지식 분류의 자동화를 위한 클러스터링 모형 연구)

  • 정영미;이재윤
    • Journal of the Korean Society for information Management
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    • v.18 no.2
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    • pp.203-230
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    • 2001
  • The purpose of this study is to develop a document clustering model for automatic classification of knowledge. Two test collections of newspaper article texts and journal article abstracts are built for the clustering experiment. Various feature reduction criteria as well as term weighting methods are applied to the term sets of the test collections, and cosine and Jaccard coefficients are used as similarity measures. The performances of complete linkage and K-means clustering algorithms are compared using different feature selection methods and various term weights. It was found that complete linkage clustering outperforms K-means algorithm and feature reduction up to almost 10% of the total feature sets does not lower the performance of document clustering to any significant extent.

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