Bayesian Modeling in Genetics and Genomicsvvv

This chapter provides a critical review of statistical methods applied in animal and plant breeding programs, especially Bayesian methods. Classical and Bayesian procedures are presented in pedigree-based and marker-based models. The flexibility of the Bayesian approaches and their high accuracy of prediction of the breeding values are illustrated. We show a tendency of the superiority of Bayesian methods over best linear unbiased prediction (BLUP) in accuracy of selection, but some difficulties on elicitation of some complex prior distributions are investigated. Genetic models including marker and pedigree information are more accurate than statistical models based on markers or pedigree alone

Fitting lactation curves of dairy cattle in different types of herds in Tunisia

peer reviewedThe incomplete gamma function was used to fit lactation curves of Holstein-Friesian cows in four types of herds in Tunisia. A total of 8640 records were used in the analysis. These included 1269, 637, 239, and 498 first lactation and 2986, 1441, 650, and 920 second and later lactation records in four herd groups namely investors, state, cooperative, and farmers' herds, respectively. The effects of environmental variables, production sector, herd, parity, first test-day date, calving year, and calving season on the main lactation curve traits were analysed. The factors associated with milk yield at the beginning of lactation and the decreasing phase of the curve, persistency, and peak yield varied significantly (P<0.01) with all variables. The ascending phase of the lactation curve was not affected by parity and calving year, while days in milk until peak depended only on the rank of lactation. The state herds had the lowest peak and total yields. The summer season was unfavourable for milk production. In contrast to first lactation cows, third lactation cows had the highest peak and total yields. Milk yield was highly correlated with peak yield (r = 0.79) and was not related to persistency measure. (C) 2003 Elsevier B.V. All rights reserved

Genetic analysis of milk production traits of Tunisian Holsteins using random regression test-day model with Legendre polynomials

Objective The objective of this study was to estimate genetic parameters of milk, fat, and protein yields within and across lactations in Tunisian Holsteins using a random regression test-day (TD) model. Methods A random regression multiple trait multiple lactation TD model was used to estimate genetic parameters in the Tunisian dairy cattle population. Data were TD yields of milk, fat, and protein from the first three lactations. Random regressions were modeled with third-order Legendre polynomials for the additive genetic, and permanent environment effects. Heritabilities, and genetic correlations were estimated by Bayesian techniques using the Gibbs sampler. Results All variance components tended to be high in the beginning and the end of lactations. Additive genetic variances for milk, fat, and protein yields were the lowest and were the least variable compared to permanent variances. Heritability values tended to increase with parity. Estimates of heritabilities for 305-d yield-traits were low to moderate, 0.14 to 0.2, 0.12 to 0.17, and 0.13 to 0.18 for milk, fat, and protein yields, respectively. Within-parity, genetic correlations among traits were up to 0.74. Genetic correlations among lactations for the yield traits were relatively high and ranged from 0.78±0.01 to 0.82±0.03, between the first and second parities, from 0.73±0.03 to 0.8±0.04 between the first and third parities, and from 0.82±0.02 to 0.84±0.04 between the second and third parities. Conclusion These results are comparable to previously reported estimates on the same population, indicating that the adoption of a random regression TD model as the official genetic evaluation for production traits in Tunisia, as developed by most Interbull countries, is possible in the Tunisian Holsteins

Genotypic study of Tunisian Arabian stallions

Diversity of Arabian stallions distributed throughout the territory of Tunisia has been evaluated. Seventeen microsatellite markers were used for the determination of genetic variation. A total of 95 alleles were detected in the 50 stallions studied. The number of alleles per locus ranged from 2 to 9 with an average of 5.6. The observed mean number of genetically diverse alleles (Na) was 5.6 (0.44). The mean number of expected alleles (Ne) was 3.42 (0.28). The average expected and observed heterozygosity was approximately 0.675 (0.026) and 0.593 (0.044), respectively. Principal component analysis showed the presence of 2 subpopulations in the studied sample set. These findings demonstrate the potential of microsatellites as a tool for designing and controlling animal breeds. Results show that the population under study has sufficient levels of genetic variations, which can be used as a foundation for developing plans for species conservation and long-term sustainability

Comparison of different adjustment models of the growth curve of Barbarin lambs under two bioclimatic zones in Tunisia

L’objectif de cette étude est d’analyser les performances de croissance de la race ovine Barbarine avec ses deux principaux écotypes (Barbarine à tête rousse et la Barbarine à tête noire) sous deux différents étages bioclimatiques (aride et semi-aride) ainsi que d’ajuster la courbe de croissance de cette race. On a utilisé les données de contrôle de croissance de vingt troupeaux de race ovine Barbarine, collectées durant 4 années, concernant 12&nbsp;919 agneaux pesés à 21 jours d’intervalle. Les poids aux âges types ainsi que les Gains moyens Quotidiens (GMQ) 10-30, 30-50, 50-70 et 70-90 de la race Barbarine à tête rousse sont supérieurs à ceux de la Barbarine à tête noire. Les poids aux âges types de la Barbarine à tête rousse sont de 5,33 Kg, 8,50 Kg, 11,5 Kg, 15,2 Kg et 17,7 Kg respectivement pour les poids à 10, 30, 50, 70 et 90 jours. Celles des gains moyens sont de 160,3 g, 163,4g, 219,2 g et 157,5 g respectivement pour les GMQ10-30, GMQ30-50, GMQ30-70 et GMQ30-90. De même, les performances de croissance enregistrées sous l’étage bioclimatique aride sont supérieures à celles de l’étage semi-aride. L’ajustement des courbes de croissance a été effectué selon quatre modèles mathématiques non linéaires (Brody, Logistique, Gompertz et Von Bertalanffy). Ces modèles ont été évalués en fonction du coefficient de détermination (R²) et de la somme des carrées des écarts résiduels (SCER). Les résultats ont indiqué que le modèle Logistique, ayant les valeurs de R² les plus élevées et les SCER les plus faibles,&nbsp;a montré le meilleur ajustement de la croissance des agneaux barbarins, alors que le modèle de Brody a donné les valeurs de R² les plus basses et les SCER les plus élevées. Les paramètres de la fonction Logistique (A, B et C) sont respectivement de 17,9&nbsp;; 4,1 et 0,0381 pour la Barbarine à tête noire et de 18,8, 4,00 et 0,0406 pour la Barbarine à tête rousse. Les paramètres des courbes de croissance ont varié avec l’interaction écotype – étage bioclimatique, la ferme, l’interaction troupeau – année d’agnelage, l’âge de la mère, l’interaction&nbsp; sexe – mode de naissance et le mois de naissance. Mots clés: Courbe de croissance, modèle non linéaire, race BarbarineThe objective of this study is to analyze the growth performance of the Barbarine sheep breed with its two main ecotypes (Red-headed Barbarine and Black-headed Barbarine) under two different bioclimatic zones (arid and semi-arid) as well as to adjust the growth curve of this breed. Growth monitoring data from twenty flocks of Barbarine sheep were used, collected over 4 years on 12 919 lambs weighed regularly at 21-day intervals. The weights at the standard ages as well as Averge&nbsp;Daily Gains (ADG) 10-30, 30-50, 50-70 and 70-90 of the Red-headed Barbarine are higher than that of the Black-headed Barbarine. The average weights at typical ages of the Red-headed Barbarine were 5.33 Kg, 8.50 Kg, 11.5 Kg, 15.2 Kg and 17.7 Kg respectively at 10, 30, 50, 70 and 90 days. Those of the ADG were 160.3 g, 163.4 g, 219.2 g and 157.5 g respectively for the ADG10-30, ADG 30-50, ADG 30-70 and ADG 30-90. Similarly, the growth performances recorded under the arid bioclimatic zone were higher than those of the semi-arid zone. The adjustment of the growth curves was carried out according to four nonlinear mathematical models (Brody, Logistics, Gompertz and Von Bertalanffy). These models were evaluated based on the coefficient of determination (R²) and the sum of squares of residual deviations (SCER). The results indicated that the Logistic model, having the highest R² values ??and the lowest SCERs, showed the best fit for Barbarin lamb growth while Brody's model gave the lowest R² values ??and the highest SCERs. The Logistic function parameters (A, B and C) were respectively 17.9, 4.08 and 0.0381 for the black-headed barbarine and 18.8, 4.00 and 0.0406 for the Red-headed Barbarine. These parameters varied with the interaction ecotype – bioclimatic zone, the farm, the interaction herd – year of lambing, the age of the mother, the interaction sex – mode of birth and the month of birth. Keywords: growth curve, nonlinear model, Barbary breed

Adjustment of the lactation curve of Holstein cows according to Wood's model

Les deux objectifs de cette étude ont été d’ajuster les courbes de lactation des vaches Holstein en Tunisie et d’étudier les facteurs de variations des paramètres de ces dernières. L’ajustement a été réalisé selon le modèle de Wood pour les 9 premières lactations. Les données proviennent de 190&nbsp;905 contrôles journaliers de la quantité de lait, de la matière grasse (MG) et de la matière protéique (MP), collectés entre 1995 et 2011 et répartis sur 10 troupeaux issus de 4 différents secteurs de production. La fonction de Wood a servi pour modéliser les courbes de lactations par la régression non linéaire. Les paramètres de la courbe de lactation «a», MG et MP les plus élevées ont été enregistrés à la 3ème, 4èmeet 5ème lactation, contrairement au paramètre «b». Le paramètre «c» et la persistance la plus élevée de la courbe de lactation ont été enregistrés à la 1ère lactation. Pour les paramètres des courbes de lactation et ses traits (lait, MG et MP), ils ont tous été affectés par les facteurs inclus dans le modèle d’analyse à savoir le secteur, le troupeau, l’interaction année de vêlage-saison de vêlage et le numéro de lactation. Mots clés: Contrôles journaliers, ajustement, Wood, courbe de lactationThe two objectives of this study were to adjust the lactation curves of Holstein cows in Tunisia and to study the factors of variation of the parameters of the latter. The adjustment was made according to the Wood model for the first 9 lactations. The data comes from 190,905 daily checks of the quantity of milk, fat (MG) and protein (MP), collected between 1995 and 2011 and distributed over 10 herds from 4 different production sectors. Wood's function was used to model the lactation curves by nonlinear regression. The highest “a”, MG and MP lactation curve parameters were recorded at the 3rd, 4th and 5th lactation, unlike the “b” parameter. The “c” parameter and the highest persistence of the lactation curve were recorded in the 1st lactation. For the parameters of the lactation curves and its traits (milk, fat and protein), they were all affected by the factors included in the analysis model, namely the sector, the herd, the interaction year of calving - calving season and lactation number. Keywords: Daily checks, adjustment, Wood, lactation curv

Assessment of growth hormone gene polymorphism effects on reproductive traits in Holstein dairy cattle in Tunisia

Research to assess the effect of single genes on reproductive traits in bovine species is imperative to elucidate genes' functions and acquire a better perspective of quantitative traits. The present study was undertaken to characterize genetic diversity in the bovine growth hormone (GH) gene in a population of 410 Holstein dairy cows in Tunisia. The analyses were based on single nucleotide polymorphisms, and GH-AluI and GH-MspI detections and genotyping were carried out using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Data were analyzed using a mixed linear model with the MIXED procedure to reveal the possible effect of GH genotypes on reproductive traits. The frequency data of AluI(L//V) and MspI(+//−) alleles were 87.04//12.96 and 70.06//29.94, respectively. The distribution of the frequency of GH genotypes for LL/LV/VV and (−/−)//(+/−)//(+/+) were 77.75//18.59//3.66 and 15.37//29.13//55.50, respectively. The results of the statistical analyses proved that GH-AluI showed a substantial favorable effect on exanimate traits except for the age at first calving; however, only a suggestive effect of GH-MspI on the calving interval (CI) and the days open (DI) was found. The homozygous LL genotype seemed to be advantageous with respect to the CI and the DI compared with LV and VV genotypes. Heterozygous MspI(+/−) cows tended to have a longer CI and DI than MspI(+/+) and MspI(−/−) cows, but the difference was not statistically significant. A significant effect of different GH-AluI–MspI combined genotypes was found on the number of inseminations per conception, the CI and the DI, and the LL/– combined genotype seemed to be associated with better reproductive performance. Based on these results, the LL genotype of the GH locus can be considered to be a favorable genotype for reproductive traits in Holstein dairy cattle, although these findings need to be confirmed by further research before polymorphisms can be used in a marker-assisted selection program.</p

Cost-effectiveness of non-invasive methods for assessment and monitoring of liver fibrosis and cirrhosis in patients with chronic liver disease: systematic review and economic evaluation

BACKGROUND: Liver biopsy is the reference standard for diagnosing the extent of fibrosis in chronic liver disease; however, it is invasive, with the potential for serious complications. Alternatives to biopsy include non-invasive liver tests (NILTs); however, the cost-effectiveness of these needs to be established. OBJECTIVE: To assess the diagnostic accuracy and cost-effectiveness of NILTs in patients with chronic liver disease. DATA SOURCES: We searched various databases from 1998 to April 2012, recent conference proceedings and reference lists. METHODS: We included studies that assessed the diagnostic accuracy of NILTs using liver biopsy as the reference standard. Diagnostic studies were assessed using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. Meta-analysis was conducted using the bivariate random-effects model with correlation between sensitivity and specificity (whenever possible). Decision models were used to evaluate the cost-effectiveness of the NILTs. Expected costs were estimated using a NHS perspective and health outcomes were measured as quality-adjusted life-years (QALYs). Markov models were developed to estimate long-term costs and QALYs following testing, and antiviral treatment where indicated, for chronic hepatitis B (HBV) and chronic hepatitis C (HCV). NILTs were compared with each other, sequential testing strategies, biopsy and strategies including no testing. For alcoholic liver disease (ALD), we assessed the cost-effectiveness of NILTs in the context of potentially increasing abstinence from alcohol. Owing to a lack of data and treatments specifically for fibrosis in patients with non-alcoholic fatty liver disease (NAFLD), the analysis was limited to an incremental cost per correct diagnosis. An analysis of NILTs to identify patients with cirrhosis for increased monitoring was also conducted. RESULTS: Given a cost-effectiveness threshold of £20,000 per QALY, treating everyone with HCV without prior testing was cost-effective with an incremental cost-effectiveness ratio (ICER) of £9204. This was robust in most sensitivity analyses but sensitive to the extent of treatment benefit for patients with mild fibrosis. For HBV [hepatitis B e antigen (HBeAg)-negative)] this strategy had an ICER of £28,137, which was cost-effective only if the upper bound of the standard UK cost-effectiveness threshold range (£30,000) is acceptable. For HBeAg-positive disease, two NILTs applied sequentially (hyaluronic acid and magnetic resonance elastography) were cost-effective at a £20,000 threshold (ICER: £19,612); however, the results were highly uncertain, with several test strategies having similar expected outcomes and costs. For patients with ALD, liver biopsy was the cost-effective strategy, with an ICER of £822. LIMITATIONS: A substantial number of tests had only one study from which diagnostic accuracy was derived; therefore, there is a high risk of bias. Most NILTs did not have validated cut-offs for diagnosis of specific fibrosis stages. The findings of the ALD model were dependent on assuptions about abstinence rates assumptions and the modelling approach for NAFLD was hindered by the lack of evidence on clinically effective treatments. CONCLUSIONS: Treating everyone without NILTs is cost-effective for patients with HCV, but only for HBeAg-negative if the higher cost-effectiveness threshold is appropriate. For HBeAg-positive, two NILTs applied sequentially were cost-effective but highly uncertain. Further evidence for treatment effectiveness is required for ALD and NAFLD. STUDY REGISTRATION: This study is registered as PROSPERO CRD42011001561. FUNDING: The National Institute for Health Research Health Technology Assessment programme

Performance of the ATLAS Electromagnetic Calorimeter End-cap Module 0

The construction and beam test results of the ATLAS electromagnetic end-cap calorimeter pre-production module 0 are presented. The stochastic term of the energy resolution is between 10% GeV^1/2 and 12.5% GeV^1/2 over the full pseudorapidity range. Position and angular resolutions are found to be in agreement with simulation. A global constant term of 0.6% is obtained in the pseudorapidity range 2.5 < eta < 3.2 (inner wheel)