| 1. |
- Svensson, Catarina, et al.
(author)
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Dairy farmer and farm staff attitudes and perceptions regarding daily milk allowance to calves
- 2023
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In: Journal of Dairy Science. - : Elsevier. - 0022-0302 .- 1525-3198. ; 106:10, s. 7220-7239
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Journal article (peer-reviewed)abstract
- The benefits of feeding calves more milk are increasingly being recognized by dairy farmers. However, most producers have still not implemented higher feeding plans. The aim of the present study was to gain a deeper understanding of farmer and farm staff attitudes, and the perceptions and factors considered in their decision-making regarding daily milk allowances. We collected data through focus group interviews with dairy farmers, farm managers, and calf-care workers who were selected using purposive and snowball sampling. In total, 40 persons (24 women and 16 men) joined a focus group interview (6 in all, each with 5–8 participants). Interviews were recorded, and recordings were transcribed and analyzed thematically. Participants had contrasting opinions about the minimum, maximum, and recommended daily milk allowances to their calves. Their suggested lowest daily milk allowance to sustain animal welfare ranged from 4 to 8–10 L and the maximum allowance from 6 to 15 L. We found that farmers' and farm staff's choices and recommendations of milk-feeding protocols were influenced by a large number of factors that could be grouped into 4 themes: (1) Life beyond work, (2) Farm facilities and equipment, (3) Care of the calves, and (4) Profitability and production. Participants' considerations were similar and aimed to maximize daily milk allowance based on farm conditions. However, the allowances they described as optimal for their calves often differed from what they considered practically feasible. We found that the care of the calves and the well-being of the owners and the staff was central in the participants' decision-making, but that this care perspective was challenged by the social and economic sustainability of the farm. Most participants fed their calves twice daily and did not think that increasing that number would be practically feasible. Our results indicate that the participants' viewpoints regarding calves were important for their decision-making about milk allowances. We suggest that a more holistic perspective should be used when advising farmers about milk allowances, putting particular emphasis on the caring and social sustainability aspects of the individual farm.
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| 2. |
- Rönnegård, Lars, et al.
(author)
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Genetic heterogeneity of residual variance - estimation of variance components using double hierarchical generalized linear models
- 2010
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In: Genetics Selection Evolution. - : Springer Science and Business Media LLC. - 0999-193X .- 1297-9686. ; 42
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Journal article (peer-reviewed)abstract
- Background: The sensitivity to microenvironmental changes varies among animals and may be under genetic control. It is essential to take this element into account when aiming at breeding robust farm animals. Here, linear mixed models with genetic effects in the residual variance part of the model can be used. Such models have previously been fitted using EM and MCMC algorithms.Results: We propose the use of double hierarchical generalized linear models (DHGLM), where the squared residuals are assumed to be gamma distributed and the residual variance is fitted using a generalized linear model. The algorithm iterates between two sets of mixed model equations, one on the level of observations and one on the level of variances. The method was validated using simulations and also by re-analyzing a data set on pig litter size that was previously analyzed using a Bayesian approach. The pig litter size data contained 10,060 records from 4,149 sows. The DHGLM was implemented using the ASReml software and the algorithm converged within three minutes on a Linux server. The estimates were similar to those previously obtained using Bayesian methodology, especially the variance components in the residual variance part of the model.Conclusions: We have shown that variance components in the residual variance part of a linear mixed model can be estimated using a DHGLM approach. The method enables analyses of animal models with large numbers of observations. An important future development of the DHGLM methodology is to include the genetic correlation between the random effects in the mean and residual variance parts of the model as a parameter of the DHGLM.
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| 3. |
- Rönnegård, Lars, et al.
(author)
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Modelling dominance in a flexible intercross analysis
- 2009
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In: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 10
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Journal article (peer-reviewed)abstract
- Conclusion: We have extended FIA to include QTL dominance effects. The power of FIA was superior, or similar, to standard regression methods for QTL effects with dominance. The difference in power for FIA with or without dominance is expected to be small as long as the QTL effects are not overdominant. We suggest that FIA with only additive effects should be the standard model to be used, especially since it is more computationally efficient.
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| 4. |
- Gardella, Eusebio, et al.
(author)
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Zero-product balanced algebras
- 2023
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In: Linear Algebra and Its Applications. - 0024-3795. ; 670, s. 121-153
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Journal article (peer-reviewed)abstract
- We say that an algebra is zero-product balanced if ab 0 c and a 0 bc agree modulo tensors of elements with zero-product. This is closely related to but more general than the notion of a zero-product determined algebra introduced and developed by Bresar, Villena and others. Every surjective, zero-product preserving map from a zero-product balanced algebra is automatically a weighted epimorphism, and this implies that zero-product balanced algebras are determined by their linear and zero-product structure. Further, the commutator subspace of a zero-product balanced algebra can be described in terms of square-zero elements. We show that a commutative, reduced algebra is zero-product balanced if and only if it is generated by idempotents. It follows that every commutative, zero-product balanced algebra is spanned by nilpotent and idempotent elements. (c) 2023 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http:// creativecommons .org /licenses /by /4 .0/).
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| 5. |
- Nilsson, Mikael, et al.
(author)
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Learning Based Image Segmentation of Pigs in a Pen
- 2014
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In: ; , s. 1-4
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Conference paper (peer-reviewed)abstract
- As farms are getting bigger with more animals, less manual supervision and attention can be given the animals on both group and individual level. In order not to jeopardize animal welfare, automated supervision is in some way already in use. Function and control of ventilation is already in use in modern pig stables, e.g. by the use of sensors for temperature, relative humidity and malfunction connected to alarm. However, by measuring continuously directly on the pigs, more information and more possibilities to adjust production inputs would be possible. In this work, the focus is on a key image processing algorithm aiding such a continuous system - segmentation of pigs in images from video. The proposed solution utilizes extended state-of-the-art features in combination with a structured prediction framework based on a logistic regression solver using elastic net regularization. Objective results on manually segmented images indicate that the proposed solution, based on learning, performs better than approaches suggested in recent publications addressing pig segmentation in video.
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| 6. |
- Crooks, Lucy, et al.
(author)
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An Improved Method for Estimating Chromosomal Line Origin in QTL Analysis of Crosses Between Outbred Lines
- 2011
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In: G3. - : Oxford University Press (OUP). - 2160-1836. ; 1, s. 57-64
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Journal article (peer-reviewed)abstract
- Estimating the line origin of chromosomal sections from marker genotypes is a vital step in quantitative trait loci analyses of outbred line crosses. The original, and most commonly used, algorithm can only handle moderate numbers of partially informative markers. The advent of high-density genotyping with SNP chips motivates a new method because the generic sets of markers on SNP chips typically result in long stretches of partially informative markers. We validated a new method for inferring line origin, triM (tracing inheritance with Markov models), with simulated data. A realistic pattern of marker information was achieved by replicating the linkage disequilibrium from an existing chicken intercross. There were approximately 1500 SNP markers and 800 F-2 individuals. The performance of triM was compared to GridQTL, which uses a variant of the original algorithm but modified for larger datasets. triM estimated the line origin with an average error of 2%, was 10% more accurate than GridQTL, considerably faster, and better at inferring positions of recombination. GridQTL could not analyze all simulated replicates and did not estimate line origin for around a third of individuals at many positions. The study shows that triM has computational benefits and improved estimation over available algorithms and is valuable for analyzing the large datasets that will be standard in future.
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| 7. |
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| 8. |
- Besnier, Francois, et al.
(author)
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Fine mapping and replication of QTL in outbred chicken advanced intercross lines
- 2011
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In: Genetics Selection Evolution. - Paris : Springer Science and Business Media LLC. - 0999-193X .- 1297-9686. ; 43, s. 3-
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Journal article (peer-reviewed)abstract
- BACKGROUND: Linkage mapping is used to identify genomic regions affecting the expression of complex traits. However, when experimental crosses such as F2 populations or backcrosses are used to map regions containing a Quantitative Trait Locus (QTL), the size of the regions identified remains quite large, i.e. 10 or more Mb. Thus, other experimental strategies are needed to refine the QTL locations. Advanced Intercross Lines (AIL) are produced by repeated intercrossing of F2 animals and successive generations, which decrease linkage disequilibrium in a controlled manner. Although this approach is seen as promising, both to replicate QTL analyses and fine-map QTL, only a few AIL datasets, all originating from inbred founders, have been reported in the literature.METHODS: We have produced a nine-generation AIL pedigree (n = 1529) from two outbred chicken lines divergently selected for body weight at eight weeks of age. All animals were weighed at eight weeks of age and genotyped for SNP located in nine genomic regions where significant or suggestive QTL had previously been detected in the F2 population. In parallel, we have developed a novel strategy to analyse the data that uses both genotype and pedigree information of all AIL individuals to replicate the detection of and fine-map QTL affecting juvenile body weight.RESULTS: Five of the nine QTL detected with the original F2 population were confirmed and fine-mapped with the AIL, while for the remaining four, only suggestive evidence of their existence was obtained. All original QTL were confirmed as a single locus, except for one, which split into two linked QTL.CONCLUSIONS: Our results indicate that many of the QTL, which are genome-wide significant or suggestive in the analyses of large intercross populations, are true effects that can be replicated and fine-mapped using AIL. Key factors for success are the use of large populations and powerful statistical tools. Moreover, we believe that the statistical methods we have developed to efficiently study outbred AIL populations will increase the number of organisms for which in-depth complex traits can be analyzed.
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| 9. |
- Boqvist, Sofia, et al.
(author)
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Sources of sporadic Yersinia enterocilitica infection in children in Sweden, 2004 : a case-control study
- 2009
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In: Epidemiology and Infection. - 0950-2688 .- 1469-4409. ; 137, s. 897-905
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Journal article (peer-reviewed)abstract
- Young children account for a large proportion of reported Yersinia enterocolitica infections in Sweden with a high incidence compared with other gastrointestinal infections, such as salmonellosis and campylobacteriosis. A case-control study was conducted to investigate selected risk factors for domestic sporadic yersiniosis in children aged 0–6 years in Sweden. In total, 117 cases and 339 controls were included in the study. To minimize exclusion of observations due to missing data a multiple non-parametric imputation technique was used. The following risk factors were identified in the multivariate analysis : eating food prepared from raw pork products (OR 3.0, 95% CI 1.8–5.1) or treated sausage (OR 1.9, 95% CI 1.1–3.3), use of a baby’s dummy (OR 1.9, 95% CI 1.1–3.2) and contact with domestic animals (OR 2.0, 95% CI 1.2–3.4). We believe that the importance of Y. enterocolitica infection in children has been neglected and that results from this study can be used to develop preventive recommendations.
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| 10. |
- Rönnegård, Lars, et al.
(author)
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Hglm: A package for fitting hierarchical generalized linear models
- 2010
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In: The R Journal. - 2073-4859. ; 2:2, s. 20-28
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Journal article (peer-reviewed)abstract
- We present the hglm package for fitting hierarchical generalized linear models. It can be used for linear mixed models and generalized linear mixed models with random effects for a variety of links and a variety of distributions for both the outcomes and the random effects. Fixed effects can also be fitted in the dispersion part of the model.
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