• Title/Summary/Keyword: Mixed-effect model

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Genomic partitioning of growth traits using a high-density single nucleotide polymorphism array in Hanwoo (Korean cattle)

  • Park, Mi Na;Seo, Dongwon;Chung, Ki-Yong;Lee, Soo-Hyun;Chung, Yoon-Ji;Lee, Hyo-Jun;Lee, Jun-Heon;Park, Byoungho;Choi, Tae-Jeong;Lee, Seung-Hwan
    • Asian-Australasian Journal of Animal Sciences
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    • v.33 no.10
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    • pp.1558-1565
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    • 2020
  • Objective: The objective of this study was to characterize the number of loci affecting growth traits and the distribution of single nucleotide polymorphism (SNP) effects on growth traits, and to understand the genetic architecture for growth traits in Hanwoo (Korean cattle) using genome-wide association study (GWAS), genomic partitioning, and hierarchical Bayesian mixture models. Methods: GWAS: A single-marker regression-based mixed model was used to test the association between SNPs and causal variants. A genotype relationship matrix was fitted as a random effect in this linear mixed model to correct the genetic structure of a sire family. Genomic restricted maximum likelihood and BayesR: A priori information included setting the fixed additive genetic variance to a pre-specified value; the first mixture component was set to zero, the second to 0.0001×σ2g, the third 0.001×σ2g, and the fourth to 0.01×σ2g. BayesR fixed a priori information was not more than 1% of the genetic variance for each of the SNPs affecting the mixed distribution. Results: The GWAS revealed common genomic regions of 2 Mb on bovine chromosome 14 (BTA14) and 3 had a moderate effect that may contain causal variants for body weight at 6, 12, 18, and 24 months. This genomic region explained approximately 10% of the variance against total additive genetic variance and body weight heritability at 12, 18, and 24 months. BayesR identified the exact genomic region containing causal SNPs on BTA14, 3, and 22. However, the genetic variance explained by each chromosome or SNP was estimated to be very small compared to the total additive genetic variance. Causal SNPs for growth trait on BTA14 explained only 0.04% to 0.5% of the genetic variance Conclusion: Segregating mutations have a moderate effect on BTA14, 3, and 19; many other loci with small effects on growth traits at different ages were also identified.

Numerical Modeling of Soil-Cement based on Discrete Element Method (개별요소법을 이용한 시멘트 혼합토의 수치모델링)

  • Jeong, Sang-Guk
    • Journal of the Korean Geosynthetics Society
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    • v.15 no.4
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    • pp.33-42
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    • 2016
  • Discrete Element Method was conducted for rock and coarse-grained materials in development of granular mechanics and related numerical model due to analyze and apply micromechanical property. And it was verified that the analysis to consider bonding effect was insufficient. In this study, to overcome limits of existing method, it was conducted to analyze difference between indoor test result and bonding effect using $PFC^{3D)}$. For indoor test of mixed soil, uniaxial compression tests by curing time and by cement content were performed. And, DEM to suitable for each condition of indoor test was conducted. In the result of this study, in terms of geotechnics, it was verified that DEM can be used for application as numerical laboratory as well as prediction of micro and macro behavior about bonding effect of mixed soil.

SNP-based and pedigree-based estimation of heritability and maternal effect for body weight traits in an F2 intercross between Landrace and Jeju native black pigs (제주재래흑돼지와 랜드레이스 F2 교배축군의 생체중에 대한 유전체와 가계도 기반의 유전력 및 모체효과 추정)

  • Park, Hee-Bok;Han, Sang-Hyun;Lee, Jae-Bong;Kim, Sang-Geum;Kang, Yong-Jun;Shin, Hyun-Sook;Shin, Sang-Min;Kim, Ji-Hyang;Son, Jun-Kyu;Baek, Kwang-Soo;Cho, Sang-Rae;Cho, In-Cheol
    • Journal of Embryo Transfer
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    • v.31 no.3
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    • pp.243-247
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    • 2016
  • Growth traits, such as body weight, directly influence productivity and economic efficiency in the swine industry. In this study, we estimate heritability for body weight traits usinginformation from pedigree and genome-wide single nucleotide polymorphism (SNP) chip data. Four body weight phenotypes were measured in 1,105 $F_2$ progeny from an intercross between Landrace and Jeju native black pigs. All experimental animals were subjected to genotypic analysis using PorcineSNP60K BeadChip platform, and 39,992 autosomal SNP markers filtered by quality control criteria were used to construct genomic relationship matrix for heritability estimation. Restricted maximum likelihood estimates of heritability were obtained using both genomic- and pedigree- relationship matrix in a linear mixed model. The heritability estimates using SNP information were smaller (0.36-0.55) than those which were estimated using pedigree information (0.62-0.97). To investigate effect of common environment, such as maternal effect, on heritability estimation, we included maternal effect as an additional random effect term in the linear mixed model analysis. We detected substantial proportions of phenotypic variance components were explained by maternal effect. And the heritability estimates using both pedigree and SNP information were decreased. Therefore, heritability estimates must be interpreted cautiously when there are obvious common environmental variance components.

Development of the Public Practice Center's teaching-learning model by applying Blended Learning Strategies (Blended Learning 전략을 적용한 공동실습소 교수-학습 모형 개발)

  • Bae, Dong-Yoon;Lee, Byung-Wook;Ahn, Kwang-Sik;Choi, Won-Sik
    • 대한공업교육학회지
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    • v.30 no.1
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    • pp.19-36
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    • 2005
  • The purpose of this study is to develop the Public Practice Center's teaching-learning model by applying blended learning strategies which is complementary to the expected problems such as expansion of the educational object and diversity of the curriculum to maximize the educational effect and to analyze activation types of the Practical Practice Center to expand the Public Practice Center's function and role by studying the document. Blended Learning Strategies are established in consideration of the following eight (8) factors ; learning environment, learning purpose, learning contents, learning time, learning place, learning type, learning media, type of interaction. It is redesigned and amended to the KEDI's individual confirmation instruction model for skill learning (1975) which is considered to be effective in the filed of education by applying features, educational contents of the Public Practice Center's teaching and merit of Blended Learning Strategies simultaneous. This model is composed of six (6) steps as shown below; 1. Understanding on the purpose and orientation 2. Observation for demonstration of fundamental skill 3. Ex on-line learning 4. Acquirement of element skill 5. Confirmation for acquirement of fundamental skill 6. After on-line learning. Further to this, this model is designed so that the above eight factors will be applied to the students effectively and the merit of e-learning and off-line practice will be mixed to the learner's expectation and satisfaction.

Variations of 'Rightward Bias' with Typhoon Using an Ideal 3D Primitive Equation Numerical Model (3차원 수치모델상에서 태풍통과시 '우측쏠림현상')

  • Hong, Chul-Hoon;Masuda, Akira;Hirose, Naoki
    • Korean Journal of Fisheries and Aquatic Sciences
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    • v.53 no.4
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    • pp.637-649
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    • 2020
  • An ideal 3D primitive equation model is implemented to investigate upper ocean response to typhoons, focusing on rightward bias (RWB) which means an appearance of an intensified sea surface cooling to the right side of the typhoon track. The model has 26-stratified levels and a flat bottom (1000 m), covering a rectangular domain of about 3,060 km×3,300 km with four open boundaries. The sea water is forced by an atmospheric pressure and a gradient wind of the typhoon. The model well reproduces the RWB in previous observations and theoretical analyses. For the fast moving typhoon (FMT) (-8m/sec), the model shows that in the mixed layer (ML), the RWB in the SST noticeably appears clearly illustrating the coupling between inertial motion and wind stress, but in the subsurface layer (-100m), the RWB does not emerge since a cyclonic current field (CCF) caused by wind stress curl is primarily dominant. For the slowly moving typhoon (SMT) (-3m/sec), however, the RWB does not emerge because the coupling is weakened and the CCF is rather predominant even in the ML. In the model, we conclude that the RWB noticeably emerges in the FMT but does not emerge in the SMT related to predominance of CCF.

Antioxidant and Neuroprotective Effects of Doenjang Prepared with Rhizopus, Pichia, and Bacillus

  • Kang, Su Jin;Seo, Ji Yeon;Cho, Kye Man;Lee, Chang Kwon;Kim, Jeong Hwan;Kim, Jong-Sang
    • Preventive Nutrition and Food Science
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    • v.21 no.3
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    • pp.221-226
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    • 2016
  • A new type of doenjang was manufactured by mixing soaked soybean, koji (Rhizopus oryzae), cheonggukjang (Bacillus amyloliquefaciens MJ1-4 and B. amyloliquefaciens EMD17), and Pichia farinosa SY80 as a yeast, salt, and water, followed by fermentation with koji that was made by fermenting whole wheat with R. oryzae. The mixed culture doenjang was designed to have a more palatable flavor and stronger biological activities than the conventional product. The extract of mixed culture doenjang showed higher antioxidant activity than the commercial doenjang as evaluated by the ferric reducing antioxidant power assay although it was not significantly different from the commercial product in 2,2-diphenyl-1-picrylhydrazyl and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) radical scavenging activities. Further, the mixed culture doenjang reduced intracellular reactive oxygen species levels and protected cells from glutamate-induced cytotoxicity more efficiently in human hippocampal HT22 neuroblastoma cells than the commercial doenjang. In conclusion, a newly-developed mixed culture doenjang had a strong antioxidant activity in vitro and cultured cell model systems, exhibited a potential to prevent oxidative stress-associated disorders although animal and clinical studies are needed to confirm its in vivo efficacy.

The Effectiveness of Jeju Island Mixed Reality Tourism Application: Focusing on the Moderating Role of Users' K-Culture Involvement

  • Yoo, Seungchul;Jung, Kwanghee;Nguyen, Vinh T.;Piscarac, Diana
    • International Journal of Advanced Culture Technology
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    • v.8 no.2
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    • pp.116-128
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    • 2020
  • In this study, we introduce a multi-modal mixed reality (MR) application for advertising the main touristic landmarks on Jeju Island, and evaluate its effectiveness based on the Technology Acceptance Model (TAM) with a focus on the user's involvement in Korean culture (K-Culture). Specifically, we deployed several stimuli to enable users to retrieve information, visualize a variety of heritage content such as text, images, videos, virtual artifacts, and immerse in a VR environment to experience the heritage locations. The results of the online survey with 436 participants showed that for consumers with low K-Culture involvement, Perceived Usefulness and Perceived Ease-of-Use did not affect their Intention to Visit the island. Still, it had a significant impact on their Intention to Use the application. On the other hand, for the group with high K-Culture involvement, Perceived Usefulness had no effect on the Intention to Use and Intention to Visit. However, Perceived Ease-of-Use had a significant impact on their Intention to Use the application and Intention to Visit Jeju Island. Therefore, when user involvement in K-Culture is high, convenience of use has played a significant role in sensory media usage and the intention to visit, regardless of the usefulness of the mixed reality content. In contrast, users with low K-Culture involvement primarily focused on the functional aspects of the application. These findings open the path for follow-up studies on K-Culture involvement and immersive media tourism marketing, which will benefit digital tourism marketing and Korea's tourism industry.

A Study on Evaluating the Compressive Strength Development of Concrete Mixed with Non-sintered Hwangto Admixture by an Ultrasonic Method (비소성 황토 결합재를 혼합한 콘크리트의 강도 발현 평가를 위한 초음파 속도법의 검토)

  • Kim, Jeong-Wook;Kim, Won-Chang;Kim, Gyu-Yong;Lee, Tae-Gyu
    • Journal of the Korea Institute of Building Construction
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    • v.23 no.1
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    • pp.35-43
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    • 2023
  • In this study, the mechanical properties of concrete mixed with non-sintered hwangto(NHT) as an alternate material for cement were evaluated, and the compressive strength prediction equation of concrete based on ultrasonic pulse velocity analysis was proposed. Cement replacement rates for mixed NHT were set to 0, 15, and 30%, and design compressive strength was set to 30 and 45MPa to evaluate the effect on the amount of cement and NHT powder. The mechanical properties items analyzed were compressive strength, ultrasonic pulse velocity, and elastic modulus, and were measured on days 1, 3, 7, and 28. As the replacement rate of NHT increased, the mechanical properties tended to decrease. In addition, as a result of analyzing the correlation between compressive strength and ultrasonic pulse velocity, the correlation coefficient(R2) showed a high relationship(R2=0.95) on concrete mixed with NHT.

Effect of Replacing Corn and Wheat Bran With Soyhulls in Lactation Cow Diets on In Situ Digestion Characteristics of Dietary Dry Matter and Fiber and Lactation Performance

  • Meng, Qingxiang;Lu, Lin;Min, Xiaomei;McKinnon, P.J.;Xiong, Yiqiang
    • Asian-Australasian Journal of Animal Sciences
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    • v.13 no.12
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    • pp.1691-1698
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    • 2000
  • An in situ digestion trial (Experiment 1) and a lactation trial (Experiment 2) were conducted to determine the effects of replacing corn and wheat bran with soyhulls (SH) in lactating dairy cow diets on the extent and kinetics of digestion of DM and NDF, and lactation performance. In experiment 1, five mixed feeds consisting of mixed concentrate and roughages (50:50 on a DM basis) were formulated on isonitrogenous and isoenergetic bases to produce five levels (0, 25, 50, 75 and 100%) of SH replacement for corn and wheat bran. SH had high in situ digestion (92 and 89% for potentially digestible DM and NDF) and fairly fast digestion rate (7.2 and 6.3 %/h for DM and NDF). Increasing level of SH replacement resulted in increased NDF digestibility (linear, p=0.001-0.04) and similar DM digestibility (beyond 12 h incubation, p=0.10-0.41). As level of SH replacement increased, percentage of slowly digestible fraction (b) of DM increased (linear, p=0.03), percentage of rapidly digestible fraction (a) of DM tended to decrease (linear, p=0.14), and DM digestion lag time tended to be longer (linear, p=0.13). Percentage of potentially digestible fraction (a+b) and digestion rate (c) of slowly digestible fraction of dietary DM remained unaltered (p=0.36-0.90) with increasing SH in the diet. Increasing level of SH for replacing corn and wheat bran in the diet resulted in increases in percentages of b (quadratic, p<0.001), a (linear, p=0.08), a+b (quadratic, p=0.001) and a tendency to increase in c for NDF (linear, p<0.19). It was also observed that there was a satisfactory fit of a non-linear regression model to NDF digestion data ($R^2=0.986-0.998$), but a relatively poor fit of the model to DM digestion data ($R^2=0.915-0.968$). In experiment 2, 42 lactating Holstein cows were used in a randomized complete block design. SH replaced corn and wheat bran in mixed concentrates at 0, 25, and 50%, respectively. These mixed concentrates were mixed with roughages and fed ad libitum as complete diets. Replacing corn and wheat bran with SH at 0, 25 and 50% levels did not influence (p=0.56-0.95) DM intakes (18.4, 18.6, and 18.5 kg/d), milk yields (27.7, 28.4 and 27.6 kg/d), 4% fat-corrected-milk (FCM) yields (26.2, 27.6, and 27.3 kg/d) and percentages of milk protein (3.12, 3.17 and 3.18%), milk lactose (4.69, 4.76 and 4.68%) and SNF (8.50, 8.64, and 8.54%). On the other hand, milk fat percentges linearly increased (3.63, 3.85 and 3.90% for SH replacement rates of 0, 25 and 50% in the diet, p=0.08), while feed costs per kg FCM production were reduced.

A Study on the Effects of the Type of Mixed Manning and the Ratio of Foreign Crew, the Acceptance and Adaptation of Cross-Culture to the Group Cohesiveness, Job Satisfaction and Organizational Commitment in Ship Organizations (외국인 선원의 혼승 형태와 비율, 이문화 수용 및 적응에 따른 선박조직의 집단응집성과 직무만족 및 조직몰입에 관한 연구)

  • Heo, Ki-Young;Kim, Jin-Pil;Shin, Yong-John
    • Journal of Navigation and Port Research
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    • v.38 no.5
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    • pp.527-539
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    • 2014
  • This study establishes the research model and sets up the hypothesis in order to analyze the effect of the type of mixed manning and the ratio of foreign crew on the group cohesiveness, job satisfaction and organizational commitment in ship organizations and the moderating effect of the acceptance and adaptation of cross-culture. For statistical hypothesis testing, it conducts a questionnaire survey targeting mixed manning ships and examines empirically the inter-variables relation through the regression. The result of empirical research is that the group cohesiveness, job satisfaction and organizational commitment in the ship organization of Korean master(chief engineer) and foreign officers is higher than that of Korean master and officers. Moreover, it is found that the group cohesiveness of 31~50% foreign crew group is less than that of the others. However, There is no moderating effects of the acceptance and adaptation of cross-culture. Additionally, it demonstrates the higher job satisfaction and organizational commitment in the stronger cohesiveness groups. The finding suggests the rationale that shipping and ship management companies could raise the group cohesiveness, job satisfaction and organizational commitment by moderating the type of mixed manning and the ratio of foreign crew.