Interpolation Methods to Improve Data Quality of Indoor Positioning Data for Dairy Cattle

Position data from real-time indoor positioning systems are increasingly used for studying individual cow behavior and social behavior in dairy herds. However, missing data challenges achieving reliable continuous activity monitoring and behavior studies. This study investigates the pattern of missing data and alternative interpolation methods in ultra-wideband based real-time indoor positioning systems in a free-stall barn. We collected 3 months of position data from a Swedish farm with around 200 cows. Data sampled for 6 days from 69 cows were used in subsequent analyzes to determine the location and duration of missing data. Data from 20 cows with the most reliable tags were selected to compare the effects of four different interpolation methods (previous, linear interpolation, cubic spline data interpolation and modified Akima interpolation). By comparing the observed data with the interpolations of the simulated missing data, the mean error distance varied from around 55 cm, using the previously last observed position, to around 17 cm for modified Akima. Modified Akima interpolation has the lowest error distance for all investigated activities (rest, walking, standing, feeding). Larger error distances were found in areas where the cows walk and turn, such as the corner between feeding and cubicles. Modified Akima interpolation is expected to be useful in the subsequent analyses of data gathered using real-time indoor positioning systems

Genetic response to selection on reindeer calf weights

Selection response was investigated after 11 years of selection in the herding district of Ruvhten Sijte in Sweden (63°N,12°E) by comparing the weights of calves owned by herders applying selection with the weights of calves owned by herders not applying selection. Three owner groups in Ruvhten Sijte have selected calves at the autumn slaughter every year since 1986 by retaining heavy calves. They own approximately 45% of the reindeer in Ruvhten Sijte. The other owners do not select on recorded weights, and all animals mix during the mating season. The recorded data on calf weights (1986 to 1997) consisted of 12 484 observations, with mean selection differentials of 2.9 kg and 4.6 kg for female and male calves, respectively (phenotypic standard deviation equal to 4.4 kg). The female generation interval was 6.4 years. In 1996 and 1997, autumn live weights of calves owned by herders applying selection (n = 971) were compared with the weights of calves owned by herders not applying selection (n = 1125). The observed difference was 0.67 kg (total mean = 42.6 kg), of which 0.32 kg was due to differences in dam age structure between the two types of herds, therefore the estimated difference in selection response was 0.35 kg. The realized heritability was 0.2. The potential response that would have been realized if the selected part of the herd had been isolated from gene flow was predicted to be 2.0 kg. In conclusion, the introduction of a selection programme applied by all owners in a herding district would result in an increase in calf weights of approximately 2 kg after two generations of selection.&nbsp

Is Firm Interdependence within Industries Important for Portfolio Credit Risk?

A drawback of available portfolio credit risk models is that they fail to allow for default risk dependency across loans other than through common risk factors. Thereby, thesemodels ignore that close ties can exist between companies due to legal, financial and business relations. In this paper, we integrate the insights from theoretical models of default correlation into a commonly used model of default and portfolio credit risk by allowing for dependency between firm default risk through both common factors and industry specific errors in a duration model. An application using pooled data from two Swedish banks business loan portfolios over the period 1996-2000 shows that estimates of individual default risk are little affected by including industry specific errors. However, accounting for these industry effects increases VaR estimates by 50-200 percent. A traditional model with only systematic factors, although able to fit the broad trends in credit losses, cannot match these fluctuations because it fails to capture credit losses in bad times, when banks are typically hit by large unexpected credit losses. The model we propose manages to follow both the trend in credit losses and produce industry driven, time-varying, fluctuations in losses around that trend. Consequently, this model will better aid banks and regulators in determining the appropriate size of economic capital requirements. Capital buffers derived from our model will be larger for periods with large aggregate disturbances and smaller in better times, and avoid both overcapitalization in good times and undercapitalization in bad times

Family History of Breast Cancer Is Associated with Elevated Risk of Prostate Cancer: Evidence for Shared Genetic Risks

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 stem from genotype-by-family effects shared between the two types of cancers

Breeding schemes in reindeer husbandry

The objective of the paper was to investigate annual genetic gain from selection (G), and the influence of selection on the inbreeding effective population size (Ne), for different possible breeding schemes within a reindeer herding district. The breeding schemes were analysed for different proportions of the population within a herding district included in the selection programme. Two different breeding schemes were analysed: an open nucleus scheme where males mix and mate between owner flocks, and a closed nucleus scheme where the males in non-selected owner flocks are culled to maximise G in the whole population. The theory of expected long-term genetic contributions was used and maternal effects were included in the analyses. Realistic parameter values were used for the population, modelled with 5000 reindeer in the population and a sex ratio of 14 adult females per male. The standard deviation of calf weights was 4.1 kg. Four different situations were explored and the results showed: 1. When the population was randomly culled, Ne equalled 2400. 2. When the whole population was selected on calf weights, Ne equalled 1700 and the total annual genetic gain (direct + maternal) in calf weight was 0.42 kg. 3. For the open nucleus scheme, G increased monotonically from 0 to 0.42 kg as the proportion of the population included in the selection programme increased from 0 to 1.0, and Ne decreased correspondingly from 2400 to 1700. 4. In the closed nucleus scheme the lowest value of Ne was 1300. For a given proportion of the population included in the selection programme, the difference in G between a closed nucleus scheme and an open one was up to 0.13 kg. We conclude that for mass selection based on calf weights in herding districts with 2000 animals or more, there are no risks of inbreeding effects caused by selection

New insight into social relationships in dairy cows and how time of birth, parity, and relatedness affect spatial interactions later in life

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 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 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 applying separable temporal exponential random graph ity interacted more consistently, as well as those born contacts among dairy cattle and to investigate the relaof diseases in the dairy cattle population

Detecting and predicting changes in milk homogeneity using data from automatic milking systems

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

Detecting Major Genetic Loci Controlling Phenotypic Variability in Experimental Crosses

Traditional methods for detecting genes that affect complex diseases in humans or animal models, milk production in livestock, or other traits of interest, have asked whether variation in genotype produces a change in that trait’s average value. But focusing on differences in the mean ignores differences in variability about that mean. The robustness, or uniformity, of an individual’s character is not only of great practical importance in medical genetics and food production but is also of scientific and evolutionary interest (e.g., blood pressure in animal models of heart disease, litter size in pigs, flowering time in plants). We describe a method for detecting major genes controlling the phenotypic variance, referring to these as vQTL. Our method uses a double generalized linear model with linear predictors based on probabilities of line origin. We evaluate our method on simulated F2 and collaborative cross data, and on a real F2 intercross, demonstrating its accuracy and robustness to the presence of ordinary mean-controlling QTL. We also illustrate the connection between vQTL and QTL involved in epistasis, explaining how these concepts overlap. Our method can be applied to a wide range of commonly used experimental crosses and may be extended to genetic association more generally

Современные подходы в формировании прогнозов у больных артериальной гипертензией

ГИПЕРТЕНЗИЯ /ДИАГНКРОВЕНОСНЫХ СОСУДОВ БОЛЕЗНИПРОГНОЗАЛГОРИТМ