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  • 1. Anglart, D
    et al.
    Emanuelson, U
    Rönnegård, Lars
    Dalarna University, School of Information and Engineering, Statistics.
    Sandgren, C Hallén
    Detecting and predicting changes in milk homogeneity using data from automatic milking systems.2021In: Journal of Dairy Science, ISSN 0022-0302, E-ISSN 1525-3198, Vol. 104, no 10, p. 11009-11017Article in journal (Refereed)
    Abstract [en]

    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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  • 2. Anglart, D.
    et al.
    Hallén-Sandgren, C.
    Emanuelson, U.
    Rönnegård, Lars
    Dalarna University, School of Technology and Business Studies, Statistics. SLU.
    Comparison of methods for predicting cow composite somatic cell counts2020In: Journal of Dairy Science, ISSN 0022-0302, E-ISSN 1525-3198, Vol. 103, no 9, p. 8433-8442Article in journal (Refereed)
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  • 3. Hallén Sandgren, C
    et al.
    Anglart, D
    Klaas, I C
    Rönnegård, Lars
    Dalarna University, School of Information and Engineering, Statistics.
    Emanuelson, U
    Homogeneity density scores of quarter milk in automatic milking systems.2021In: Journal of Dairy Science, ISSN 0022-0302, E-ISSN 1525-3198, Vol. 104, no 9, p. 10121-10130Article in journal (Refereed)
    Abstract [en]

    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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  • 4.
    Hansson, I
    et al.
    Swedish University of Agricultural Sciences, Uppsala.
    Silvera, A
    Swedish University of Agricultural Sciences, Uppsala.
    Ren, K
    Swedish University of Agricultural Sciences, Uppsala.
    Woudstra, S
    University of Copenhagen, Frederiksberg, Denmark.
    Skarin, A
    Swedish University of Agricultural Sciences, Uppsala.
    Fikse, W F
    Swedish University of Agricultural Sciences, Uppsala.
    Nielsen, P P
    RISE Research Institute of Sweden, Lund.
    Rönnegård, Lars
    Dalarna University, School of Information and Engineering, Statistics. Swedish University of Agricultural Sciences, Uppsala.
    Cow characteristics associated with the variation in number of contacts between dairy cows2023In: Journal of Dairy Science, ISSN 0022-0302, E-ISSN 1525-3198, Vol. 106, no 4, p. 2685-2699Article in journal (Refereed)
    Abstract [en]

    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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  • 5.
    Kroese, Adrien
    et al.
    Swedish University of Agricultural sciences, Uppsala.
    Alam, Moudud
    Dalarna University, School of Information and Engineering, Statistics.
    Hernlund, Elin
    Swedish University of Agricultural sciences, Uppsala.
    Berthet, David
    Sony Nordic, Lund.
    Tamminen, Lena-Mari
    Swedish University of Agricultural sciences, Uppsala.
    Fall, Nils
    Swedish University of Agricultural sciences, Uppsala.
    Högberg, Niclas
    Swedish University of Agricultural sciences, Uppsala.
    3D pose estimation to detect posture transition in free-stall housed dairy cows2024In: Journal of Dairy Science, ISSN 0022-0302, E-ISSN 1525-3198Article in journal (Refereed)
    Abstract [en]

    Free stall comfort is reflected in various indicators, including the ability for dairy cattle to display unhindered posture transition movements in the cubicles. To ensure farm animal welfare, it is instrumental for the farm management to be able to continuously monitor occurrences of abnormal motions. Advances in computer vision have enabled accurate kinematic measurements in several fields such as human, equine and bovine biomechanics. An important step upstream to measuring displacement during posture transitions is to determine that the behavior is accurately detected. In this study, we propose a framework for detecting lying to standing posture transitions from 3D pose estimation data. A multi-view computer vision system recorded posture transitions between Dec. 2021 and Apr. 2022 in a Swedish stall housing 183 individual cows. The output data consisted of the 3D coordinates of specific anatomical landmarks. Sensitivity of posture transition detection was 88.2% while precision reached 99.5%. Analyzing those transition movements, breakpoints detected the timestamp of onset of the rising motion, which was compared with that annotated by observers. Agreement between observers, measured by intra-class correlation, was 0.85 between 3 human observers and 0.81 when adding the automated detection. The intra-observer mean absolute difference in annotated timestamps ranged from 0.4s to 0.7s. The mean absolute difference between each observer and the automated detection ranged from 1.0s to 1.3s. There was a significant difference in annotated timestamp between all observer pairs but not between the observers and the automated detection, leading to the conclusion that the automated detection does not introduce a distinct bias. We conclude that the model is able to accurately detect the phenomenon of interest and that it is equatable to an observer.

  • 6.
    Marina, Héctor
    et al.
    Swedish University of Agricultural Sciences, Uppsala.
    Ren, Keni
    Swedish University of Agricultural Sciences, Uppsala.
    Hansson, Ida
    Swedish University of Agricultural Sciences, Uppsala.
    Fikse, Freddy
    Swedish University of Agricultural Sciences, Uppsala.
    Nielsen, Per Peetz
    RISE Research Institute of Sweden; RISE Ideon, Lund.
    Rönnegård, Lars
    Dalarna University, School of Information and Engineering, Statistics. Swedish University of Agricultural Sciences, Uppsala.
    New insight into social relationships in dairy cows, and how time of birth, parity and relatedness affect spatial interactions later in life2024In: Journal of Dairy Science, ISSN 0022-0302, E-ISSN 1525-3198, Vol. 107, no 2, p. 1110-1123Article in journal (Refereed)
    Abstract [en]

    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 impact 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 weeks, using an ultra-wideband system on a Swedish commercial farm consisting of nearly 200 dairy cows inside a free-stall 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 are 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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  • 7.
    Rönnegård, Lars
    et al.
    Dalarna University, School of Technology and Business Studies, Statistics. Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden.
    Felleki, Majbritt
    Dalarna University, School of Technology and Business Studies, Statistics. Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden.
    Fikse, W. F.
    Mulder, H. A.
    Strandberg, E.
    Variance component and breeding value estimation for genetic heterogeneity of residual variance in Swedish Holstein dairy cattle2013In: Journal of Dairy Science, ISSN 0022-0302, E-ISSN 1525-3198, Vol. 96, no 4, p. 2627-2636Article in journal (Refereed)
    Abstract [en]

    Trait uniformity, or micro-environmental sensitivity, may be studied through individual differences in residual variance. These differences appear to be heritable, and the need exists, therefore, to fit models to predict breeding values explaining differences in residual variance. The aim of this paper is to estimate breeding values for micro-environmental sensitivity (vEBV) in milk yield and somatic cell score, and their associated variance components, on a large dairy cattle data set having more than 1.6 million records. Estimation of variance components, ordinary breeding values, and vEBV was performed using standard variance component estimation software (ASReml), applying the methodology for double hierarchical generalized linear models. Estimation using ASReml took less than 7 d on a Linux server. The genetic standard deviations for residual variance were 0.21 and 0.22 for somatic cell score and milk yield, respectively, which indicate moderate genetic variance for residual variance and imply that a standard deviation change in vEBV for one of these traits would alter the residual variance by 20%. This study shows that estimation of variance components, estimated breeding values and vEBV, is feasible for large dairy cattle data sets using standard variance component estimation software. The possibility to select for uniformity in Holstein dairy cattle based on these estimates is discussed.

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