• Title/Summary/Keyword: mixed effects regression model

Search Result 49, Processing Time 0.023 seconds

Longitudinal Analysis of Body Weight and Feed Intake in Selection Lines for Residual Feed Intake in Pigs

  • Cai, W.;Wu, H.;Dekkers, J.C.M.
    • Asian-Australasian Journal of Animal Sciences
    • /
    • v.24 no.1
    • /
    • pp.17-27
    • /
    • 2011
  • A selection experiment for reduced residual feed intake (RFI) in Yorkshire pigs consisted of a line selected for lower RFI (LRFI) and a random control line (CTRL). Longitudinal measurements of daily feed intake (DFI) and body weight (BW) from generation 5 of this experiment were used. The objectives of this study were to evaluate the use of random regression (RR) and nonlinear mixed models to predict DFI and BW for individual pigs, accounting for the substantial missing information that characterizes these data, and to evaluate the effect of selection for RFI on BW and DFI curves. Forty RR models with different-order polynomials of age as fixed and random effects, and with homogeneous or heterogeneous residual variance by month of age, were fitted for both DFI and BW. Based on predicted residual sum of squares (PRESS) and residual diagnostics, the quadratic polynomial RR model was identified to be best, but with heterogeneous residual variance for DFI and homogeneous residual variance for BW. Compared to the simple quadratic and linear regression models for individual pigs, these RR models decreased PRESS by 1% and 2% for DFI and by 42% and 36% for BW on boars and gilts, respectively. Given the same number of random effects as the polynomial RR models, i.e., two for BW and one for DFI, the non-linear Gompertz model predicted better than the polynomial RR models but not as good as higher order polynomial RR models. After five generations of selection for reduced RFI, the LRFI line had a lower population curve for DFI and BW than the CTRL line, especially towards the end of the growth period.

Patterns of consonant deletion in the word-internal onset position: Evidence from spontaneous Seoul Korean speech

  • Kim, Jungsun;Yun, Weonhee;Kang, Ducksoo
    • Phonetics and Speech Sciences
    • /
    • v.8 no.1
    • /
    • pp.45-51
    • /
    • 2016
  • This study examined the deletion of onset consonant in the word-internal structure in spontaneous Seoul Korean speech. It used the dataset of speakers in their 20s extracted from the Korean Corpus of Spontaneous Speech (Yun et al., 2015). The proportion of deletion of word-internal onset consonants was analyzed using the linear mixed-effects regression model. The factors that promoted the deletion of onsets were primarily the types of consonants and their phonetic contexts. The results showed that onset deletion was more likely to occur for a lenis velar stop [k] than the other consonants, and in the phonetic contexts, when the preceding vowel was a low central vowel [a]. Moreover, some speakers tended to more frequently delete onset consonants (e.g., [k] and [n]) than other speakers, which reflected individual differences. This study implies that word-internal onsets undergo a process of gradient reduction within individuals' articulatory strategies.

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
    • /
    • v.38 no.5
    • /
    • pp.527-539
    • /
    • 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.

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
    • /
    • v.13 no.12
    • /
    • pp.1691-1698
    • /
    • 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.

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
    • /
    • v.33 no.10
    • /
    • pp.1558-1565
    • /
    • 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.

The wage determinants of the vocational high school graduates using mixed effects mode (혼합모형을 이용한 특성화고 졸업생의 임금결정요인 분석)

  • Ryu, Jangsoo;Cho, Jangsik
    • Journal of the Korean Data and Information Science Society
    • /
    • v.27 no.4
    • /
    • pp.935-946
    • /
    • 2016
  • In this paper, we analyzed wage determinants of the vocational high school graduates utilizing both individual-level and work region-level variables. We formulate the models in the way wage determination has multi-level structure in the sense that individual wage is influenced by individual-level variables (level-1) and work region-level (level-2) variables. To incorporate dependency between individual wages into the model, we utilize hierarchical linear model (HLM). The major results are as follows. First, it is shown that the HLM model is better than the OLS regression models which do not take level-1 and level-2 variables simultaneously into account. Second, random effects on sex, maester dummy and engineering dummy variables are statistically significant. Third, the fixed effects on business hours and mean wage of regular job for level-2 variables are statistically significant effect individual-level wages. Finally, parental education level, parental income, number of licenses and high school grade are statistically significant for higher individual-level wages.

A Study on the Survival Characteristics of the Restaurant Business in Major and Side-Street Trade Areas, Seoul (서울시 발달상권과 골목상권의 일반음식점 생존특성 연구)

  • Kim, Dongjun;Yi, Changhyo;Lee, Seungil
    • Journal of Korea Planning Association
    • /
    • v.54 no.5
    • /
    • pp.76-90
    • /
    • 2019
  • The purpose of this study is to analyze the survival characteristics of the restaurant business by trade area type (major and side street). By the increase of the unemployment rate, the new foundation of selt-employment type is increasing. However, due to high competition and economic recession, the sustainability of new foundation is not high. Therefore, in this study, survival analysis was performed considering the individual and commercial characteristics focused on the ordinary restaurants. The major findings are as follow. First, the characteristics of parcel unit and adjacent area have a significant effect on the survival. This means the micro-scopic spatial characteristics should be considered for survival in the location choice. Second, the regional economic characteristics in trade area have a significant effect on survival. Furthermore, these characteristics are different by the trade area type. Third. the development characteristics have a different effect on survival by the building usage and trade area type. Finally, regional economic characteristics have a significant effect on survival. These results are expected to be used as basic data for commercial location selection and trade area analysis system in the private and public sectors.

Variance Components and Genetic Parameters for Milk Production and Lactation Pattern in an Ethiopian Multibreed Dairy Cattle Population

  • Gebreyohannes, Gebregziabher;Koonawootrittriron, Skorn;Elzo, Mauricio A.;Suwanasopee, Thanathip
    • Asian-Australasian Journal of Animal Sciences
    • /
    • v.26 no.9
    • /
    • pp.1237-1246
    • /
    • 2013
  • The objective of this study was to estimate variance components and genetic parameters for lactation milk yield (LY), lactation length (LL), average milk yield per day (YD), initial milk yield (IY), peak milk yield (PY), days to peak (DP) and parameters (ln(a) and c) of the modified incomplete gamma function (MIG) in an Ethiopian multibreed dairy cattle population. The dataset was composed of 5,507 lactation records collected from 1,639 cows in three locations (Bako, Debre Zeit and Holetta) in Ethiopia from 1977 to 2010. Parameters for MIG were obtained from regression analysis of monthly test-day milk data on days in milk. The cows were purebred (Bos indicus) Boran (B) and Horro (H) and their crosses with different fractions of Friesian (F), Jersey (J) and Simmental (S). There were 23 breed groups (B, H, and their crossbreds with F, J, and S) in the population. Fixed and mixed models were used to analyse the data. The fixed model considered herd-year-season, parity and breed group as fixed effects, and residual as random. The single and two-traits mixed animal repeatability models, considered the fixed effects of herd-year-season and parity subclasses, breed as a function of cow H, F, J, and S breed fractions and general heterosis as a function of heterozygosity, and the random additive animal, permanent environment, and residual effects. For the analysis of LY, LL was added as a fixed covariate to all models. Variance components and genetic parameters were estimated using average information restricted maximum likelihood procedures. The results indicated that all traits were affected (p<0.001) by the considered fixed effects. High grade $B{\times}F$ cows (3/16B 13/16F) had the highest least squares means (LSM) for LY ($2,490{\pm}178.9kg$), IY ($10.5{\pm}0.8kg$), PY ($12.7{\pm}0.9kg$), YD ($7.6{\pm}0.55kg$) and LL ($361.4{\pm}31.2d$), while B cows had the lowest LSM values for these traits. The LSM of LY, IY, YD, and PY tended to increase from the first to the fifth parity. Single-trait analyses yielded low heritability ($0.03{\pm}0.03$ and $0.08{\pm}0.02$) and repeatability ($0.14{\pm}0.01$ to $0.24{\pm}0.02$) estimates for LL, DP and parameter c. Medium heritability ($0.21{\pm}0.03$ to $0.33{\pm}0.04$) and repeatability ($0.27{\pm}0.02$ to $0.53{\pm}0.01$) estimates were obtained for LY, IY, PY, YD and ln(a). Genetic correlations between LY, IY, PY, YD, ln(a), and LL ranged from 0.59 to 0.99. Spearman's rank correlations between sire estimated breeding values for LY, LL, IY, PY, YD, ln(a) and c were positive (0.67 to 0.99, p<0.001). These results suggested that selection for IY, PY, YD, or LY would genetically improve lactation milk yield in this Ethiopian dairy cattle population.

Convergence Study on the Optimization for Suppression of Starch Hydrolysis using Rutin, Quercetin and Dietary Fiber Mixture Design (루틴, 퀘르세틴, 식이섬유 혼합물 설계를 이용한 전분소화 지연 효과의 최적화에 대한 융합 연구)

  • Oh, Imkyung;Bae, In Young
    • Journal of the Korea Convergence Society
    • /
    • v.11 no.5
    • /
    • pp.35-41
    • /
    • 2020
  • This study was conducted to develop the efficient system for starch hydrolysis suppression using rutin, quercetin and dietary fiber through the statistical mixture design. The three components were replaced with wheat flour at the level of 10% and the mixed gel with three components was characterized by in vitro starch digestion. The mixture design was applied by simplex-centroid experimental model. The quadratic model (R2=0.86) was well fitted and the obtained regression equation indicated that the significant positive effects was observed in the quercetin and fiber mixture. Based on the statistical results, the best mixing ratio of quercetin and fiber was 72: 28 that led to the lowest predicted glycemic index (pGI). Their interactions on the pGI of starch digestibility were clearly visualized in the 3D surface plot. These results suggested that the mixture of quercetin and fiber interact strongly with wheat flour, consequently retarding starch hydrolysis by 15%.

Potential influence of κ-casein and β-lactoglobulin genes in genetic association studies of milk quality traits

  • Zepeda-Batista, Jose Luis;Saavedra-Jimenez, Luis Antonio;Ruiz-Flores, Agustin;Nunez-Dominguez, Rafael;Ramirez-Valverde, Rodolfo
    • Asian-Australasian Journal of Animal Sciences
    • /
    • v.30 no.12
    • /
    • pp.1684-1688
    • /
    • 2017
  • Objective: From a review of published information on genetic association studies, a meta-analysis was conducted to determine the influence of the genes ${\kappa}-casein$ (CSN3) and ${\beta}-lactoglobulin$ (LGB) on milk yield traits in Holstein, Jersey, Brown Swiss, and Fleckvieh. Methods: The GLIMMIX procedure was used to analyze milk production and percentage of protein and fat in milk. Models included the main effects and all their possible two-way interactions; not estimable effects and non-significant (p>0.05) two-way interactions were dropped from the models. The three traits analyzed used Poisson distribution and a log link function and were determined with the Interactive Data Analysis of SAS software. Least square means and multiple mean comparisons were obtained and performed for significant main effects and their interactions (p<0.0255). Results: Interaction of breed by gene showed that Holstein and Fleckvieh were the breeds on which CSN3 ($6.01%{\pm}0.19%$ and $5.98%{\pm}0.22%$), and LGB ($6.02%{\pm}0.19%$ and $5.70%{\pm}0.22%$) have the greatest influence. Interaction of breed by genotype nested in the analyzed gene indicated that Holstein and Jersey showed greater influence of the CSN3 AA genotype, $6.04%{\pm}0.22%$ and $5.59%{\pm}0.31%$ than the other genotypes, while LGB AA genotype had the largest influence on the traits analyzed, $6.05%{\pm}0.20%$ and $5.60%{\pm}0.19%$, respectively. Furthermore, interaction of type of statistical model by genotype nested in the analyzed gene indicated that CSN3 and LGB genes had similar behavior, maintaining a difference of more than 7% across analyzed genotypes. These results could indicate that both Holstein and Jersey have had lower substitution allele effect in selection programs that include CSN3 and LGB genes than Brown Swiss and Fleckvieh. Conclusion: Breed determined which genotypes had the greatest association with analyzed traits. The mixed model based in Bayesian or Ridge Regression was the best alternative to analyze CSN3 and LGB gene effects on milk yield and protein and fat percentages.