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Screening for candidate genes related with histological microstructure, meat quality and carcass characteristic in pig based on RNA-seq data

  • Ropka-Molik, Katarzyna;Bereta, Anna;Zukowski, Kacper;Tyra, Miroslaw;Piorkowska, Katarzyna;Zak, Grzegorz;Oczkowicz, Maria
    • Asian-Australasian Journal of Animal Sciences
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    • v.31 no.10
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    • pp.1565-1574
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    • 2018
  • Objective: The aim of the present study was to identify genetic variants based on RNA-seq data, obtained via transcriptome sequencing of muscle tissue of pigs differing in muscle histological structure, and to verify the variants' effect on histological microstructure and production traits in a larger pig population. Methods: RNA-seq data was used to identify the panel of single nucleotide polymorphisms (SNPs) significantly related with percentage and diameter of each fiber type (I, IIA, IIB). Detected polymorphisms were mapped to quantitative trait loci (QTLs) regions. Next, the association study was performed on 944 animals representing five breeds (Landrace, Large White, Pietrain, Duroc, and native Puławska breed) in order to evaluate the relationship of selected SNPs and histological characteristics, meat quality and carcasses traits. Results: Mapping of detected genetic variants to QTL regions showed that chromosome 14 was the most overrepresented with the identification of four QTLs related to percentage of fiber types I and IIA. The association study performed on a 293 longissimus muscle samples confirmed a significant positive effect of transforming acidic coiled-coil-containing protein 2 (TACC2) polymorphisms on fiber diameter, while SNP within forkhead box O1 (FOXO1) locus was associated with decrease of diameter of fiber types IIA and IIB. Moreover, subsequent general linear model analysis showed significant relationship of FOXO1, delta 4-desaturase, sphingolipid 1 (DEGS1), and troponin T2 (TNNT2) genes with loin 'eye' area, FOXO1 with loin weight, as well as FOXO1 and TACC2 with lean meat percentage. Furthermore, the intramuscular fat content was positively associated (p<0.01) with occurrence of polymorphisms within DEGS1, TNNT2 genes and negatively with occurrence of TACC2 polymorphism. Conclusion: This study's results indicate that the SNP calling analysis based on RNA-seq data can be used to search candidate genes and establish the genetic basis of phenotypic traits. The presented results can be used for future studies evaluating the use of selected SNPs as genetic markers related to muscle histological profile and production traits in pig breeding.

Identification of Emerging Research at the national level: Scientometric Approach using Scopus (국가적 차원의 유망연구영역 탐색: Scopus 데이터베이스를 이용한 과학계량학적 접근)

  • Yeo, Woon-Dong;Sohn, Eun-Soo;Jung, Eui-Seob;Lee, Chang-Hoan
    • Journal of Information Management
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    • v.39 no.3
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    • pp.95-113
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    • 2008
  • In todays environment in which scientific technologies are changing very fast than ever, companies have to monitor and search emerging technologies to gain competitiveness. Actually many nations try to do that. Most of them use Dephi approach based on experts review as a searching method. But experts review has been criticised for probability of inclination and its derivative problems in the sense that it is accomplished only by expert's subjectivity. To overcome such problems, we used Scientometric Method for identifying emerging technology that had been done by Delphi as a rule. We made three particular efforts in order to improve the Quality of the result. Firstly, we selected one alternative database between SCI and Scopus hoping to see evenly-distributing results in wide fields on the front burner. Secondly we used Fractional citation counting in counting citation number in the stage of linear regression analysis. Lastly, we verified Scientometric result with experts opinions to minimize probable errors in a Scientometric research. As a result, we derived 290 emerging technologies from Scientometric analysis with Scopus Database, and visualized them on 2-dimension map with data mining system named KnowledgeMatrix which was developed by KISTI.

The Elderly Health and Dietary Management in Gyeonggi Province - Comparison with Gender Difference - (경기지역 노인의 건강과 식생활관리 I - 노인의 성별 비교 -)

  • Won Hyang-Rye;Rhie Seung-Gyo;Choi Mi-Yong
    • The Korean Journal of Community Living Science
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    • v.17 no.1
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    • pp.123-139
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    • 2006
  • The purpose of this study is to search how to promote health and improve nutrition and health care of the elderly people in rural area. Behaviors for health promotion and habits against health risk were surveyed. Dietary management was analyzed for surveyed nutrient intake by 24 hr -recall method. 242 subjects were collected in 12 cities or counties in Gyeonggi Province and 20 elderly people (10 male and 10 female) were selected out of 1 village in each district. Questionnaire for health behavior and dietary management was carried out by trained interviewers. Statistical analyses were made by SAS (version 8.1) and Chi-square tests and General Linear Models were used. Characteristics of the elderly people were 61-74 year-olds (68.2%), elementary school educated (78.4%), with spouse (51.7%), monthly living cost of 500-1,000 thousand won(43.4%), and monthly pocket money of 50-100 or 100-200 thousand won(33.5%, 26.5%). 41.4% of the subjects checked up medical examination regularly. The alcohol drinking status was significantly different according to gender: high no-drink rate of female (52.5%) and low no-drink rate of male (25.6%). Kinds of disease were different according to gender: higher proportion of cardiovascular disease(46.3%) and diabetes mellitus(8.1 %) in male and joint lumbago neuralgia(44.4%) and osteoporosis(8.6%) in female. Gastrointestinal complaints were nausea (69.0%) and chronic indigestion (17.8%). Constipation (12.0%) and vomiting (4.3%) were more frequent in female. Dietary management was good (3 meals per day: 93.4%., dining with family: 72.4%, regular mealtime: 72.4%, and 3-4 times of snacks per week: 44.9%) except side dish taking of 3-4 kinds only. However, almost one-third of the female elderly ate alone (30.6%) which was well compared with one-fifth of the male (19.7%). And food and nutrients intake were not significantly different according to gender except that male elderly's intake of energy and protein was lower than that of female's. The surveyed subjects had no difficulties in Activities of Daily Living (ADL), but some female elderly had some difficulties with Instrumental Activities of Daily Living (IADL) like working at home, using transport, and going shopping. These results suggest that low quality of life linked with low economic status of the rural elderly and that congregate meal at village hall would be required for the female elderly eating alone. For the undernourished male elderly, it would be needed to provide snacks and to establish nutrition and health surveillance system.

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A Study of Career-constitution Process of a Middle-aged Woman (한 중년여성의 진로구성 과정)

  • Kim, Soyeon;Jeong, Heesook
    • The Journal of the Korea Contents Association
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    • v.15 no.5
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    • pp.265-282
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    • 2015
  • This study with qualitative research method explores the process of a middle-aged woman who finds and constructs her career path. As a result, career constitution process of a research participant choosing a career to make a living and carrying out what she is supposed to do, turned out to be more than just a job adaptation process in the workforce. Career constitution process is a journey in search of "genuine self" and a existential process in which the existence of self is understood by sustained choices and "actions." The research participant on the life journey of finding career path sought to return to her intrinsic life and practiced self-realization toward possibility. The result of this study suggests that "work" being different from calling needs to be understood anew in the existential perspective. "work" is not only a passage which makes the meaning of life by existential "actoins" but also a existential method heading toward self-realization. Not only that, career path is a process which doesn't get obvious by one choice but is unfolded by shaking between potential energy and possibilities accumulated by here and now decisions and actions. Thus, the researcher of this study suggests that counselling for career path should go beyond the linear task which figures out a person's aptitude, the features of the workforce and connects both. And there is the need for a paradigm shift in totally understanding the client's life and in making the meaning of a work in the process of finding genuine "self".

Using Numerical Maps to Select Solar Panel Installation Sites no Expressway Slopes (수치지도를 이용한 고속국도 주변 태양광 패널 설치 대상지 선정)

  • Jung, Jaehoon;Kim, Byungil
    • Korean Journal of Construction Engineering and Management
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    • v.17 no.5
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    • pp.71-77
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    • 2016
  • Solar energy is a viable source to replace fossil fuels. However, challenges associated with site selection for solar panel installation inhibit the uptake of solar energy systems. Expressway slopes offer a potentially attractive alternative for solar panel installation for the following reasons: expressway slopes are vacant public sites, they are abundant (about 4,193km in South Korea), and they are linear in nature. Traditoinally when selecting sites for solar systems conventional surveying methods are employed. Unfortunately, these methods can be dangerous, time consuming, and labor intensive. To overcome these limitations of conventional site selection methodologies, we propose an automated approach using numerical maps. First, contour and expressway polylines are extracted separately from numeric maps. The extracted contour lines are then converted into a digital terrain model; this is used to calculate aspect and slope information. Next, the extracted expressway lines are projected onto a binary image and refined to recover the disconnections, and then applied to create a buffer zone to narrow the search space. Finally, all data sets are overlaid to identify candidate sites for solar panel systems and are visually verified through comparisons with aerial photos.

A Genetic Algorithm for Materialized View Selection in Data Warehouses (데이터웨어하우스에서 유전자 알고리즘을 이용한 구체화된 뷰 선택 기법)

  • Lee, Min-Soo
    • The KIPS Transactions:PartD
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    • v.11D no.2
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    • pp.325-338
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    • 2004
  • A data warehouse stores information that is collected from multiple, heterogeneous information sources for the purpose of complex querying and analysis. Information in the warehouse is typically stored In the form of materialized views, which represent pre-computed portions of frequently asked queries. One of the most important tasks of designing a warehouse is the selection of materialized views to be maintained in the warehouse. The goal is to select a set of views so that the total query response time over all queries can be minimized while a limited amount of time for maintaining the views is given(maintenance-cost view selection problem). In this paper, we propose an efficient solution to the maintenance-cost view selection problem using a genetic algorithm for computing a near-optimal set of views. Specifically, we explore the maintenance-cost view selection problem in the context of OR view graphs. We show that our approach represents a dramatic improvement in terms of time complexity over existing search-based approaches that use heuristics. Our analysis shows that the algorithm consistently yields a solution that only has an additional 10% of query cost of over the optimal query cost while at the same time exhibits an impressive performance of only a linear increase in execution time. We have implemented a prototype version of our algorithm that is used to evaluate our approach.

A Method to Develop Security System through the Analysis on Dangerous Case (위해사례분석을 통한 경호제도의 발전방안)

  • Yu, Hyung-Chang;Kim, Tae-Min
    • Korean Security Journal
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    • no.16
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    • pp.161-187
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    • 2008
  • The purpose of this study is to suggest a development method of current Korean security system by analyzing the problems shown in the performance of security work in relation to the terrorism, which is enlarging in the word, from various aspects. In order to perform the study, the researcher considered the basic theory concerned to current Korean law concerned to security, principle and methodology of security, terror and new terrorism. The researcher performed the study by selecting qualitative case study focused on Park Geun-Hye case. Through the study, the methods to develop Korean security system are as follows. First, from the legal aspect, it is necessary to establish the law concerned to terrorism prevention and important person security. Moreover, it is necessary to search for the development of private security by revising Security Industry Act, which is a legal ground of private security. Second, it is necessary to improve and reinforce education & training program, which is not still divided in detail from the aspect of private security cultivation. Moreover, it is necessary to activate personal protection work and enlarge market through Security Industry Act and make an effort to change social recognition over security, which is devaluated in the society. From the viewpoint, national license about private security shall be adopted. The department of president security, which is a representative of official security, shall transfer the advanced technology to private security organization. Third, from the aspect of operation, the operation of security based on SCE principle, human shield principle, the nearest person's protection principle, body extension principle, linear protection principle and evacuation priority principle is required. Therefore, the priority shall be given to preventive security and thorough security plan shall be made for the operation.

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Moderated Mediation effect of Parenting Behaviors on the Relation between Deviant Peer's Influences and Delinquency in Adolescence (청소년 비행행동에 대한 부모양육행동과 비행친구집단간의 조절된 매개효과)

  • Lee, Sang-Gyun
    • Journal of the Korean Society of Child Welfare
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    • no.27
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    • pp.121-151
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    • 2008
  • The purpose of this study is to examine the moderated mediation effects of parenting functioning on the relations between deviant peer's influences and delinquent behaviors in adolescence. To investigate the moderated mediation effects, simple slope test and bootstrapping method based on multiple linear regression(MLR) model were used. This study used data from wave 1-2(2003-2004) of the Korea Youth Panel Survey(KYPS). Results showed that poorer parenting increased the probability that adolescents would affiliated with deviant peers, and more association with deviant peers, in turn, was related to delinquency. There was statistical significant interaction between affiliation with deviant peers and parenting in the model for delinquency. It implied that the relation between deviant peers and delinquency depends on the quality of parenting. Finally, indirect effect of earlier parenting on delinquent behavior through affiliation with deviant peers was moderated by later parenting. These results help clarify the conditions under which exposure to parenting behaviors can buffer the negative effect of deviant best friends on delinquent behaviors in adolescence. Practice and policy implications as well as further research topic were discussed to aid the search for highly effective preventive and treatment interventions.

Path Algorithm for Maximum Tax-Relief in Maximum Profit Tax Problem of Multinational Corporation (다국적기업 최대이익 세금트리 문제의 최대 세금경감 경로 알고리즘)

  • Sang-Un Lee
    • The Journal of the Institute of Internet, Broadcasting and Communication
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    • v.23 no.4
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    • pp.157-164
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    • 2023
  • This paper suggests O(n2) polynomial time heuristic algorithm for corporate tax structure optimization problem that has been classified as NP-complete problem. The proposed algorithm constructs tax tree levels that the target holding company is located at root node of Level 1, and the tax code categories(Te) 1,4,3,2 are located in each level 2,3,4,5 sequentially. To find the maximum tax-relief path from source(S) to target(T), firstly we connect the minimum witholding tax rate minrw(u, v) arc of node u point of view for transfer the profit from u to v node. As a result we construct the spanning tree from all of the source nodes to a target node, and find the initial feasible solution. Nextly, we find the alternate path with minimum foreign tax rate minrfi(u, v) of v point of view. Finally we choose the minimum tax-relief path from of this two paths. The proposed heuristic algorithm performs better optimal results than linear programming and Tabu search method that is a kind of metaheuristic method.

Optimized Image-Based Surrogate Endpoints in Targeted Therapies for Glioblastoma: A Systematic Review and Meta-Analysis of Phase III Randomized Controlled Trials

  • Chong Hyun Suh;Ho Sung Kim;Seung Chai Jung;Choong Gon Choi;Sang Joon Kim;Kyung Won Kim
    • Korean Journal of Radiology
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    • v.21 no.4
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    • pp.471-482
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    • 2020
  • Objective: We aimed to determine the optimized image-based surrogate endpoints (IBSEs) in targeted therapies for glioblastoma through a systematic review and meta-analysis of phase III randomized controlled trials (RCTs). Materials and Methods: A systematic search of OVID-MEDLINE and EMBASE for phase III RCTs on glioblastoma was performed in December 2017. Data on overall survival (OS) and IBSEs, including progression-free survival (PFS), 6-month PFS (6moPFS), 12-month PFS (12moPFS), median PFS, and objective response rate (ORR) were extracted. Weighted linear regression analysis for the hazard ratio for OS and the hazard ratios or odds ratios for IBSEs was performed. The associations between IBSEs and OS were evaluated. Subgroup analyses according to disease stage (newly diagnosed glioblastoma versus recurrent glioblastoma), types of test treatment, and types of response assessment criteria were performed. Results: Twenty-three phase III RCTs published between 2000 and 2017, including 8387 patients, met the inclusion criteria. OS showed strong correlations with PFS (standardized β coefficient [R] = 0.719), 6moPFS (R = 0.647), and 12moPFS (R = 0.638). OS showed no correlations with median PFS and ORR. In subgroup analysis according to types of therapies, PFS showed the highest correlations with OS in targeted therapies for cell cycle pathways (R = 0.913) and growth factor receptors and their downstream pathways (R = 0.962). 12moPFS showed the highest correlation with OS in antiangiogenic therapy (R = 0.821). The response assessment in neuro-oncology criteria provided higher correlation coefficients between OS and IBSEs than the Macdonald criteria. Conclusion: Overall, PFS is an optimized IBSE in targeted therapies for glioblastoma; however, 12moPFS is optimal in antiangiogenic therapy.