An Iterative Procedure for Estimating Fixed Effects and Variance Components in Mixed Model Situations

Biometrics ◽  
1968 ◽  
Vol 24 (1) ◽  
pp. 13 ◽  
Author(s):  
E. P. Cunningham ◽  
C. R. Henderson
Keyword(s):  
Variance Components ◽  
Iterative Procedure ◽  
Fixed Effects ◽  
Mixed Model

scholarly journals Parámetros genéticos de crecimiento y producción de lana en ovinos usando la metodología de modelos mixtos

2009 ◽  
Vol 7 (1) ◽  
pp. 42
Author(s):  
Rodrigo Alfredo Martínez ◽  
Rodrigo Vásquez ◽  
Javier Vanegas ◽  
Marco Suárez
Keyword(s):  
Variance Components ◽  
Fixed Effects ◽  
Genetic Parameters ◽  
Mixed Model ◽  
Growth Characteristics ◽  
Random Component ◽  
Wool Production ◽  
Gibbs Sampling Algorithm ◽  
Calving Season ◽  
Number Of Births

<p>En este trabajo se estimaron los parámetros genéticos a partir de datos de campo registrados durante 26 años (1974 a 1999) en un núcleo de las razas ovinas Hampshire, Romney Marsh y Corriedale. Se estimaron los parámetros genéticos de las características de crecimiento, producción de lana y reproducción. Los modelos utilizados incluyeron efectos fijos, como ‘año de parto, ‘época de parto, ‘sexo, ‘número de parto; en el componente aleatorio también se incluyeron los efectos genéticos directo, materno y de ambiente permanente, dependiendo de la característica. Los análisis fueron hechos usando un modelo animal de característica simple mediante el programa MTGSAM® que emplea el algoritmo de muestreo de Gibbs para inferir los componentes de varianza. Se encontraron valores de heredabilidad directa que variaron entre 0,13 y 0,33 para peso al nacimiento y entre 0,16 y 0,35 para peso al destete corregido a 120 días y para caracteres de producción de lana, valores cercanos a 0,25. También se determinaron las tendencias anuales promedio de los valores genéticos y de los índices de consanguinidad para cada una de las razas, encontrando en términos generales valores promedio de consanguinidad de 3,47% para la raza Hampshire, 0,75% para Romney Marsh y 0,76% para Corriedale. Estos resultados sugieren una tendencia levemente creciente de los valores de consanguinidad, pero de acuerdo con lo que se espera para una población de conservación.  </p><p> </p><p><strong>Growth and wool production genetic parameters in sheep using mixed model methodology </strong></p><p>This work was aimed at estimating genetic parameters from field-data recorded over a 26-year period (1974 to 1999) in a flock of Hampshire, Romney Marsh and Corriedale sheep. Genetic parameters were estimated from growth characteristics, wool production and reproduction. The models used included fixed effects, such as birth year, calving season, gender and number of births. Direct, maternal and permanent environmental genetic effects were also included in the random component, depending on the characteristic. MTGSAM® software (using Gibbs’ sampling algorithm) was used on a simple animal model for inferring variance components. Direct heritability values were found, ranging form 0.13 to 0.33 for birth weight, 0.16 to 0.35 for weaning weight (corrected to 120 days) and values around 0.25 for wool production. Annual mean tendency of genetic values and consanguinity indices were also determined for each of the breeds, resulting in 3.47% mean consanguinity for the Hampshire, 0.75% for Romney Marsh and 0.76% for Corriedale breeds. These results suggested a slight tendency for increased consanguinity values, but remaining in line with those expected for a conservation population. </p>

HERITABILITY OF NONRETURN RATE OF CANADIAN HOLSTEIN-FRIESIAN BULLS

1983 ◽  
Vol 63 (1) ◽  
pp. 39-48 ◽  
Author(s):  
B. B. MURRAY ◽  
L. R. SCHAEFFER ◽  
E. B. BURNSIDE
Keyword(s):  
Maximum Likelihood ◽  
Artificial Insemination ◽  
Variance Components ◽  
Fixed Effects ◽  
Mixed Model ◽  
Factors Affecting ◽  
Holstein Friesian ◽  
Best Linear Unbiased ◽  
Dairy Bulls ◽  
One Year

Conception rates of Canadian Holstein-Friesian bulls in artificial insemination were recorded as percent 60- to 90-day nonreturns to first service. A total of 5, 923, 974 first services to 784 bulls by 207 sires were analyzed using a mixed model which included age of bull (1–14 yr), years (1956–1976), months and AI units as fixed effects. Bulls and sires of bulls were random. Significant differences were found in all classifications involving fixed effects. Nonreturn rates at one year of age were highest and significantly different from nonreturn rates at 9 yr of age and older. Lowest estimates of nonreturn rates were in January and December, and highest were in September and October. Differences were found among some AI units. Best linear unbiased predictions of differences among all service sires were obtained. Variance components were estimated iteratively by maximum likelihood. Heritability was 0.25 by regression of sire on son with 30 sires having four or more sons. Repeatability was 0.41. Many factors affecting nonreturn rates could not be identified, especially at the cow or herd level. Sire selection programs in AI units for high nonreturn rates in sires of young bulls should be successful. Key words: Fertility, dairy bulls, heritability

scholarly journals Professor Endrenyi’s Legacy: An Evaluation of the Regulatory Requirement “Fixed Effects, Rather Than Random Effects, Should Be Used for All Terms”

2021 ◽  
Vol 24 ◽  
pp. 413-420
Author(s):  
Anders Fuglsang
Keyword(s):  
Variance Components ◽  
Fixed Effects ◽  
Mixed Model ◽  
Linear Models ◽  
Regulatory Requirement ◽  
Subject Variability ◽  
Acceptance Range ◽  
Biased Estimates ◽  
True Values

Purpose: In the latest revision of the guideline for evaluation of bioequivalence (BE), European regulators introduced the requirement for using subjects as fixed factors in the underlying statistical models, even in replicate and semi-replicate studies. The implication was that estimates of within-subject variability were derived with a linear model rather than with a mixed model based on restricted maximum likelihood (REML). While REML-based methods are generally thought to give rise to less biased estimates of variance components, there have been no studies that compared the quality of REML-based estimates and estimates derived via linear models. Methods: A publication by Endrenyi and Tothfalusi from 1999 described simulations in a fashion that is useful for testing the European Medicines Agency’s (EMA) requirement.  This study defines 7 scenarios within which 10,000 individual 2-sequence, 2-treatment, 4-period trials are simulated and makes a comparison of the quality of estimates. Results: It is concluded that estimates based on REML are closer to the true values than estimates based on linear models, but significant differences are only shown in two of the seven scenarios tested.  REML-based estimators have less variability. Both types of estimates appear negatively biased and will therefore decrease the width of the acceptance range.  

scholarly journals Metabolic Adaptations to Dynamic Energy Requirements during Lactation and Pregnancy in Dairy Cows with Varying Proportions of Holstein and Simmental Breed

Proceedings ◽  
2020 ◽  
Vol 73 (1) ◽  
pp. 9
Author(s):  
Deise Aline Knob ◽  
André Thaler Neto ◽  
Helen Schweizer ◽  
Anna Weigand ◽  
Roberto Kappes ◽  
...  
Keyword(s):  
Energy Balance ◽  
Dairy Cows ◽  
Fixed Effects ◽  
Mixed Model ◽  
Negative Energy ◽  
Negative Energy Balance ◽  
Repeated Measure ◽  
Holstein Cows ◽  
Mixed Model Analysis ◽  
Genetic Groups

Depending on the breed or crossbreed line, cows have to cope with a more or less severe negative energy balance during the period of high milk yields in early lactation, which can be detected by beta-hydroxybutyrate (BHBA) and non-esterified fatty acids (NEFAs) in blood. Preventing cows from undergoing a severe negative energy balance by breeding and/or feeding measures is likely to be supported by the public and may help to improve the sustainability of milk production. The aim was to compare BHBA and NEFA concentrations in the blood of Holstein and Simmental cows and their crosses during the prepartum period until the end of lactation. In total, 164 cows formed five genetic groups according to their theoretic proportion of Holstein and Simmental genes as follows: Holstein (100% Holstein; n = 9), R1-Hol (51–99% Holstein; n = 30), F1 crossbreds (50% Holstein, 50% Simmental; n = 17), R1-Sim (1–49% Holstein; n = 81) and Simmental (100% Simmental; n = 27). NEFA and BHBA were evaluated once a week between April 2018 and August 2019. A mixed model analysis with fixed effects breed, week (relative to calving), the interaction of breed and week, parity, calving year, calving season, milking season, and the repeated measure effect on cows was used. Holstein cows had higher NEFAs (0.196 ± 0.013 mmol/L), and Simmental cows had the lowest NEFA concentrations (0.147 ± 0.008 mmol/L, p = 0.03). R1-Sim, F1 and R1-Hol cows had intermediate values (0.166 ± 0.005, 0.165 ± 0.010, 0.162 ± 0.008 mmol/L; respectively). The highest NEFA value was found in the first week after calving (0.49 ± 0.013 mmol/L). BHBA did not differ among genetic groups (p = 0.1007). There was, however, an interaction between the genetic group and week (p = 0.03). While Simmental, R1-Sim and F1 cows had the highest BHBA value, the second week after calving (0.92 ± 0.07 and 1.05 ± 0.04, and 1.10 ± 0.10 mmol/L, respectively), R1-Hol and Holstein cows showed the BHBA peak at the fourth week after calving (1.16 ± 0.07 and 1.36 ± 0.12 mmol/L, respectively). Unexpectedly, Holstein cows had a high BHBA peak again at week 34 after calving (1.68 ± 0.21 mmol/L). The genetic composition of the cows affects NEFA and BHBA. Simmental and R1-Sim cows mobilize fewer body reserves after calving. Therefore, dairy cows with higher degrees of Simmental origin might be more sustainable in comparison with Holstein genetics in the present study.

PSV-11 The effects of pelleting and extrusion on nutrient composition and protein quality measurements in a variety Canadian pulses

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 302-302
Author(s):  
Cara Cargo-Froom ◽  
Anna-Kate Shoveller ◽  
Daniel A Columbus ◽  
Chris Marinangeli ◽  
Elijah Kiarie ◽  
...  
Keyword(s):  
Protein Content ◽  
Faba Bean ◽  
Fixed Effects ◽  
Crude Protein ◽  
Mixed Model ◽  
Protein Quality ◽  
Positive Impact ◽  
Nutrient Composition ◽  
Crude Protein Content ◽  
Quality Measurements

Abstract Alternative forms of protein are an important focus in nutrition. This study sought to compare the effects of pelleting and extrusion on nutrient composition and protein quality measurements of Canadian pulses. Pulses used for the study included: 2 pea variety (Amarillo and dunn), lentils, chickpeas, and faba bean. Ingredients were ground through a 10/64” or a 2/64” screen to create a coarse and fine ground product, respectively. Both coarse and fine ground ingredients were pelleted at 60–65, 70–75, and 80–85 C0. Fine ground ingredients were extruded at three different temperatures (110, 130, 150 C0) and two moisture levels (18 and 22%). Samples were collected for all runs at the beginning, middle, and end of each run for both pelleted and extruded samples. Samples were analyzed for proximate analysis, amino acids including lysinoalanine, total and damaged starch, and total dietary fibre (including insoluble and soluble). Data were analyzed using a mixed model via proc glimmix in SAS, where ingredient, process, grind, temperature, and extrusion moisture were treated as fixed effects with different interactions selected based on model investigated. Crude protein content of whole pulses was highest in faba bean and lowest in the Amarillo pea, with faba bean protein content significantly higher than all other pulses, and lentil protein content significantly higher than Amarillo peas (P &lt; 0.05). All pelleting temperatures, nested within grind, significantly increased crude protein content of all pulses compared to whole pulses (P &lt; 0.05). All extrusion moistures significantly increased crude protein content of all pulses compared to whole pulses (P &lt; 0.05) and moisture/temperature interactions were significantly higher for all pulses compared to whole pulses (P &lt; 0.05). Amino acid comparisons produced similar significant results. This suggests that pelleting and extrusion processing can have a positive impact on protein content of pulses and protein quality measurements in pulses.

PSV-B-18 Characterization of the fecal microbiome of healthy adult beagle dogs supplemented with graded levels of bacillus coagulans GBI-30, 6086

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 337-338
Author(s):  
Heather L Acuff ◽  
Tara N Gaire ◽  
Tyler Doerksen ◽  
Andrea Lu ◽  
Michael P Hays ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Fixed Effects ◽  
Mixed Model ◽  
Healthy Adult ◽  
Random Effect ◽  
Bacillus Coagulans ◽  
Community Diversity ◽  
Rrna Gene ◽  
Beagle Dogs ◽  
Fecal Microbiome

Abstract This study aimed to evaluate the effect of Bacillus coagulans GBI-30, 6086 on the fecal microbiome of healthy adult dogs. Extruded diets containing graded levels of probiotic applied either to the base ration before extrusion or as a topical coating post-extrusion were randomly assigned to ten individually-housed Beagle dogs (7 castrated males, 3 spayed females) of similar age (5.75 ± 0.23 yr) and body weight (12.3 ± 1.5 kg) in a 5 x 5 replicated Latin square with 16-d adaptation and 5-d total fecal collection for each period. Five dietary treatments were formulated to deliver a dose of 0-, 6-, 7-, 8-, or 9-log10 CFU·dog-1·d-1. Fresh fecal samples (n=50) were analyzed by 16S rRNA gene pyrosequencing. Community diversity was evaluated in R (v4.0.3, R Core Team, 2019). Relative abundance data were analyzed using a mixed model (v9.4, SAS Institute, Inc., Cary, NC) with treatment and period as fixed effects and dog as a random effect. Results were considered significant at P &lt; 0.05. Predominant phyla were Firmicutes (mean 81.2% ± 5), Actinobacteria (mean 9.9% ± 4.4), Bacteroidetes (mean 4.5% ± 1.7), Proteobacteria (mean 1.3% ± 0.7), and Fusobacteria (mean 1.1% ± 0.6). No evidence of shifts in predominant phyla, class, family, or genus taxonomic levels were observed except for the Bacillus genus, which had a greater relative abundance (P = 0.0189) in the low probiotic coating and high probiotic coating treatment groups compared to the extruded probiotic group. Alpha-diversity indices (Richness, Chao1, ACE, Shannon, Simpson, Inverse Simpson, and Fisher) and beta-diversity metrics (principal coordinate analysis and multi-dimensional scaling) were similar for all treatments. This data indicates that supplementation with Bacillus coagulans GBI-30, 6086 at a dose of up to 9 log10 CFU·d-1 did not alter the overall diversity of the fecal microbiome of healthy adult dogs over a 21-d period.

Evaluation of genetic markers for litter size in Meishan synthetic and Large White pigs

1996 ◽  
Vol 1996 ◽  
pp. 18-18
Author(s):  
O.I. Southwood ◽  
S. Hoste ◽  
T.H. Short ◽  
A.J. Mileham ◽  
D. Cuthbert-Heavens
Keyword(s):  
Litter Size ◽  
Fixed Effects ◽  
Oestrogen Receptor ◽  
Mixed Model ◽  
Receptor Gene ◽  
Large White ◽  
Service Type ◽  
Sib Families ◽  
Natural Service ◽  
Size Data

A significant relationship between the oestrogen receptor gene (ESR) and litter size has been detected in USA populations of Large White and a synthetic comprising 50% Meishan (Rothschild et al., 1995). Animals carrying two copies of the favourable allele (B) had an extra pig born per litter than those that did not have the allele. This paper reports on results observed in a UK 50% Meishan synthetic and four UK Large White lines.Litter size data from 50% Meishan synthetic (L93) full-sib females where more than one ESR genotype was segregating. Data were analysed using a mixed model with full relationships and including the fixed effects of season of farrowing, parity, ESR genotype (AA, AB or BB) and service type (AI or natural service). Heritiability and permanent environmental effects for litter size were assumed as 0.09 and 0.11, repectively. A total of 27 full-sib families were represented and included 62 sows and 139 litter records. Hypothesis testing used the option in PEST under a mixed model (Groeneveld et al., 1991).

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