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- Anglart, D, et al.
(författare)
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Detecting and predicting changes in milk homogeneity using data from automatic milking systems.
- 2021
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Ingår i: Journal of Dairy Science. - : American Dairy Science Association. - 0022-0302 .- 1525-3198. ; 104:10, s. 11009-11017
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Tidskriftsartikel (refereegranskat)abstract
- To ensure milk quality and detect cows with signs of mastitis, visual inspection of milk by prestripping quarters before milking is recommended in many countries. An objective method to find milk changed in homogeneity (i.e., with clots) is to use commercially available inline filters to inspect the milk. Due to the required manual labor, this method is not applicable in automatic milking systems (AMS). We investigated the possibility of detecting and predicting changes in milk homogeneity using data generated by AMS. In total, 21,335 quarter-level milk inspections were performed on 5,424 milkings of 624 unique cows on 4 farms by applying visual inspection of inline filters that assembled clots from the separate quarters during milking. Images of the filters with clots were scored for density, resulting in 892 observations with signs of clots for analysis (77% traces or mild cases, 15% moderate cases, and 8% heavy cases). The quarter density scores were combined into 1 score indicating the presence of clots during a single cow milking and into 2 scores summarizing the density scores in cow milkings during a 30-h sampling period. Data generated from the AMS, such as milk yield, milk flow, conductivity, and online somatic cell counts, were used as input to 4 multilayer perceptron models to detect or predict single milkings with clots and to detect milking periods with clots. All models resulted in high specificity (98-100%), showing that the models correctly classified cow milkings or cow milking periods with no clots observed. The ability to successfully classify cow milkings or cow periods with observed clots had a low sensitivity. The highest sensitivity (26%) was obtained by the model that detected clots in a single milking. The prevalence of clots in the data was low (2.4%), which was reflected in the results. The positive predictive value depends on the prevalence and was relatively high, with the highest positive predictive value (72%) reached in the model that detected clots during the 30-h sampling periods. The misclassification rate for cow milkings that included higher-density scores was lower, indicating that the models that detected or predicted clots in a single milking could better distinguish the heavier cases of clots. Using data from AMS to detect and predict changes in milk homogeneity seems to be possible, although the prediction performance for the definitions of clots used in this study was poor.
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- Chozas, A., et al.
(författare)
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Family history of breast cancer is associated with elevated risk of prostate cancer : evidence for shared genetic risks
- 2022
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Ingår i: Human Heredity. - : S. Karger AG. - 0001-5652 .- 1423-0062. ; 87, s. 12-19
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Although breast and prostate cancers arise in different organs and are more frequent in the opposite sex, multiple studies have reported an association between their family history. Analysis of single nucleotide polymorphism data, based on distant relatives, has revealed a small positive genetic correlation between these cancers explained by common variants. The estimate of genetic correlation based on close relatives reveals the extent to which shared genetic risks are explained by both common and rare variants. This estimate is unknown for breast and prostate cancer. Method: We estimated the relative risks, heritability, and genetic correlation of breast cancer and prostate cancer, based on the Minnesota Breast and Prostate Cancer Study, a family study of 141 families ascertained for breast cancer. Results: Heritability of breast cancer was 0.34 (95% credible interval: 0.23-0.49) and 0.65 (95% credible interval: 0.36-0.97) for prostate cancer, and the genetic correlation was 0.23. In terms of odds ratios, these values correspond to a 1.3 times higher odds of breast cancer among probands, given that the brother has prostate cancer. Conclusion: This study shows the inherent relation between prostate cancer and breast cancer; an incident of one in a family increases the risk of developing the other. The large difference between estimates of genetic correlation from distant and close relatives, if replicated, suggests that rare variants contribute to the shared genetic risk of breast and prostate cancer. However, the difference could steam from genotype-by-family effects shared between the two types of cancers. ©; 2021 The Author(s).
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| 6. |
- Clouard, Camille
(författare)
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Computational statistical methods for genotyping biallelic DNA markers from pooled experiments
- 2022
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The information conveyed by genetic markers such as Single Nucleotide Polymorphisms (SNPs) has been widely used in biomedical research for studying human diseases, but also increasingly in agriculture by plant and animal breeders for selection purposes. Specific identified markers can act as a genetic signature that is correlated to certain characteristics in a living organism, e.g. a sensitivity to a disease or high-yield traits. Capturing these signatures with sufficient statistical power often requires large volumes of data, with thousands of samples to analyze and possibly millions of genetic markers to screen. Establishing statistical significance for effects from genetic variations is especially delicate when they occur at low frequencies.The production cost of such marker genotype data is thereforea critical part of the analysis. Despite recent technological advances, the production cost can still be prohibitive and genotype imputation strategies have been developed for addressing this issue. The genotype imputation methods have been widely investigated on human data and to a smaller extent on crop and animal species. In the case where only few reference genomes are available for imputation purposes, such as for non-model organisms, the imputation results can be less accurate. Group testing strategies, also called pooling strategies, can be well-suited for complementing imputation in large populations and decreasing the number of genotyping tests required compared to the single testing of every individual. Pooling is especially efficient for genotyping the low-frequency variants. However, because of the particular nature of genotype data and because of the limitations inherent to the genotype testing techniques, decoding pooled genotypes into unique data resolutions is a challenge. Overall, the decoding problem with pooled genotypes can be described as as an inference problem in Missing Not At Random data with nonmonotone missingness patterns.Specific inference methods such as variations of the Expectation-Maximization algorithm can be used for resolving the pooled data into estimates of the genotype probabilities for every individual. However, the non-randomness of the undecoded data impacts the outcomes of the inference process. This impact is propagated to imputation if the inferred genotype probabilities are to be devised as input into classical imputation methods for genotypes. In this work, we propose a study of the specific characteristics of a pooling scheme on genotype data, as well as how it affects the results of imputation methods such as tree-based haplotype clustering or coalescent models.
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| 7. |
- Hallén Sandgren, C, et al.
(författare)
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Homogeneity density scores of quarter milk in automatic milking systems.
- 2021
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Ingår i: Journal of Dairy Science. - : American Dairy Science Association. - 0022-0302 .- 1525-3198. ; 104:9, s. 10121-10130
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Tidskriftsartikel (refereegranskat)abstract
- Milk quality and clinical mastitis in dairy cows are monitored by detecting visually abnormal milk. A standardized method to evaluate clots in milk and studies of the incidence and dynamics of clots in milk at the quarter level are lacking. We validated a method to score clot density in quarter milk samples and describe the prevalence and dynamics of the density scores between consecutive samplings and periods in 4 farms with automatic milking systems. Using in-line filters, we collected quarter milk samples at each milking during 3 periods of 30 h each in each farm. Clot density was scored based on coverage of the filter area as 0 (negative), 1 (trace), 2 (mild), 3 (moderate), 4 (heavy), and 5 (very heavy). The score for a specific quarter and milking is referred to as the quarter milking score (QMS). Three assessors independently scored 902 images of filter samples with a Fleiss kappa value of 0.72. In total, 21,202 quarter milk samples from 5,398 milkings of 621 cows were collected. Of the quarter filter samples, 2.4% had visible clots, distributed as mild (1.4%), moderate (0.6%), heavy (0.3%), and very heavy (<0.1%, n = 8). Cases with a cow period sum of QMS ≥ 4, corresponding to 9.4% of all periods, harbored 86% and 94% of all QMS of 2 to 5 and 3 to 5, respectively. Of these cases, cows sampled in all 3 periods and clots in only 1 period had a quarter period sum score ≥ 1 in 1.8 different quarters in average. Corresponding numbers for the cows with clots or traces in 2 or 3 periods were 2.2 and 2.5 different quarters, respectively. A QMS of 2 to 5 in the preceding milking increased the chance of a QMS >1 in the following milking, with an average chance of 38%. The probability of a QMS > 1 increased with increasing previous QMS, a higher sum of QMS during the milking period, longer milking interval, and higher lactation number, but decreased with increasing days in milk. Our study showed that the method of clot-density scoring is feasible to perform and reproducible for investigating the occurrence and dynamics of clots in milk. Elevated clot-density scores clustered within certain cows and cow periods and appeared in new quarters of the cows over time. The low recurrence of QMS of 1 and 2 within quarters indicated that QMS 3 could be a reasonable threshold for detecting quarters with abnormal milk that require further attention.
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| 8. |
- Hansson, I, et al.
(författare)
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Cow characteristics associated with the variation in number of contacts between dairy cows
- 2023
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Ingår i: Journal of Dairy Science. - : Elsevier Inc.. - 0022-0302 .- 1525-3198. ; 106:4, s. 2685-
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Tidskriftsartikel (refereegranskat)abstract
- In modern freestall barns where large groups of cows are housed together, the behavior displayed by herd mates can influence the welfare and production of other individuals. Therefore, understanding social interactions in groups of dairy cows is important to enhance herd management and optimize the outcomes of both animal health and welfare in the future. Many factors can affect the number of social contacts in a group. This study aimed to identify which characteristics of a cow are associated with the number of contacts it has with other group members in 2 different functional areas (feeding and resting area) to increase our understanding of the social behavior of dairy cows. Inside 2 herds housed in freestall barns with around 200 lactating cows each, cow positions were recorded with an ultra-wideband real-time location system collecting all cows' positions every second over 2 wk. Using the positioning data of the cows, we quantified the number of contacts between them, assuming that cows spending time in proximity to one another (within a distance of 2.5 m for at least 10 min per day) were interacting socially. We documented in which barn areas these interactions occurred and used linear mixed models to investigate if lactation stage, parity, breed, pregnancy status, estrus, udder health, and claw health affect the number of contacts. We found variation in the number of contacts a cow had between individuals in both functional areas. Cows in later lactation had more contacts in the feeding area than cows in early lactation. Furthermore, in one herd, higher parity cows had fewer contacts in the feeding area than first parity cows, and in the other herd, cows in third parity or higher had more contacts in the resting area. This study indicates that cow characteristics such as parity and days in milk are associated with the number of contacts a cow has daily to its herd mates and provides useful information for further research on social interactions of dairy cows.
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| 10. |
- Marina, H., et al.
(författare)
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New insight into social relationships in dairy cows and how time of birth, parity, and relatedness affect spatial interactions later in life
- 2024
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Ingår i: Journal of Dairy Science. - 0022-0302 .- 1525-3198. ; 107:2, s. 1110-1123
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Tidskriftsartikel (refereegranskat)abstract
- Social interactions between cows play a fundamental role in the daily activities of dairy cattle. Real-time location systems provide on a continuous and automated basis information about the position of individual cows inside barns, offering a valuable opportunity to monitor dyadic social contacts. Understanding dyadic social interactions could be applied to enhance the stability of the social structure promoting animal welfare and to model disease transmission in dairy cattle. This study aimed to identify the effect of different cow characteristics on the likelihood of the formation and persistence of social contacts in dairy cattle. The individual position of the lactating cows was automatically collected once per second for 2 wk, using an ultra-wideband system on a Swedish commercial farm consisting of almost 200 dairy cows inside a freestall barn. Social networks were constructed using the position data of 149 cows with available information on all characteristics during the study period. Social contacts were considered as a binary variable indicating whether a cow pair was within 2.5 m of each other for at least 10 min per day. The role of cow characteristics in social networks was studied by applying separable temporal exponential random graph models. Our results revealed that cows of the same parity interacted more consistently, as well as those born within 7 d of each other or closely related by pedigree. The repeatability of the topological parameters indicated a consistent short-term stability of the individual animal roles within the social network structure. Additional research is required to elucidate the underlying mechanisms governing the long-term evolution of social contacts among dairy cattle and to investigate the relationship between these networks and the transmission of diseases in the dairy cattle population. .
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