Dairy cattle behavior classifications based on decision tree learning using 3‐axis neck‐mounted accelerometers

Demand has been increasing recently for an automated monitoring system of animal behavior as a tool for the management of livestock animals. This study investigated the association between the behavior of dairy cattle and the acceleration data collected using three‐axis neck‐mounted accelerometers, as well as the feasibility of improving the precision of behavior classifications through machine learning. In total 38 Holstein dairy cows were used, and kept in four different farms. A logger was mounted to each collar to obtain acceleration data for calculating the activity level and variations. At the same time the behavior of the cattle was observed visually. Characteristic acceleration waves were recorded for eating, rumination, and lying, respectively; and the activity level and variations were significantly different among these behaviors (p < 0.01). Decision tree learning was performed on the data set from Farm A and validated its precision; which proved to be 99.2% in cross‐validation, and 100% in test data sets from Farms B to D. This study showed that highly precise classifications for eating, rumination, and lying is possible by using decision tree learning to calculate the activity level and variations of cattle based on the data obtained by three‐axis accelerometers mounted to a collar.     

基于MODIS数据与机器学习的青藏高原草地地上生物量研究

青藏高原位于我国西部,又被称为“世界第三极”,对我国和世界的生态以及气候变化影响显著。为了评估2000-2020年青藏高原草地地上生物量（aboveground biomass,AGB）的变化情况,本研究采用多种机器学习方法结合MCD43A4产品数据模拟了草地地上生物量,并对该区域草地地上生物量的时空特征进行分析。结果表明：1）构建的机器学习模型中,Rborist模型精度最高,基于筛选后变量的R2达到0.6484。“prec＿05”、“prec＿06”、“tp＿12”、“NDPI”、“prec＿04”、“tmax＿01”、“prec＿08”、“prec＿12”这8个变量与生物量相关;2）青藏高原东南部的生物量要高于西北部,呈现由东南向西北递减趋势;3)2000-2020年间青藏高原草地生物量稳步增长,整体向好发展。青藏高原61.38%的草地变化趋势不具有可持续性,4.67%的草地持续性轻微恶化,持续性明显恶化的区域占比1.19%,呈稳定或恢复趋势的区域占比32.76%。     

Predicting likelihood of in vivo chemotherapy response in canine lymphoma using ex vivo drug sensitivity and immunophenotyping data in a machine learning model

We report a precision medicine platform that evaluates the probability of chemotherapy drug efficacy for canine lymphoma by combining ex vivo chemosensitivity and immunophenotyping assays with computational modelling. We isolated live cancer cells from fresh fine needle aspirates of affected lymph nodes and collected post‐treatment clinical responses in 261 canine lymphoma patients scheduled to receive at least 1 of 5 common chemotherapy agents (doxorubicin, vincristine, cyclophosphamide, lomustine and rabacfosadine). We used flow cytometry analysis for immunophenotyping and ex vivo chemosensitivity testing. For each drug, 70% of treated patients were randomly selected to train a random forest model to predict the probability of positive Veterinary Cooperative Oncology Group (VCOG) clinical response based on input variables including antigen expression profiles and treatment sensitivity readouts for each patient's cancer cells. The remaining 30% of patients were used to test model performance. Most models showed a test set ROC‐AUC > 0.65, and all models had overall ROC‐AUC > 0.95. Predicted response scores significantly distinguished (P < .001) positive responses from negative responses in B‐cell and T‐cell disease and newly diagnosed and relapsed patients. Patient groups with predicted response scores >50% showed a statistically significant reduction (log‐rank P < .05) in time to complete response when compared to the groups with scores <50%. The computational models developed in this study enabled the conversion of ex vivo cell‐based chemosensitivity assay results into a predicted probability of in vivo therapeutic efficacy, which may help improve treatment outcomes of individual canine lymphoma patients by providing predictive estimates of positive treatment response.     

Attribute selection and model evaluation for the maternal and paternal imprinted genes in bovine (Bos Taurus) using supervised machine learning algorithms

Imprinted genes display biased expression of paternal and maternal alleles in mammals. They are marked through epigenetic process during gametogenesis. Characterization of imprinted genes has expanded our understanding of the regulation and function of genes. In the current study, 22 experimentally validated imprinted genes in bovine (Bos Taurus) were analysed. Several supervised machine learning algorithms and attribute weighting methods were used to find characteristics of different types of imprinted genes and suggest a classification method for finding maternally and paternally expressed genes in bovine. For assessing the best model and comparing attributes in other organisms, we have also conducted a comparative analysis for human and sheep imprinted genes. According to the results of the present study, GC contents 10 and 100 kb upstream, Gly and Gln amino acids, Ile/ATC codon usage, LINE and SINE in 100kbup and length of first intron were significantly different between the maternal and paternal genes in cattle. Considering all species together, we found that GC content 100 kb up, LINE 100 kb up and the frequency of amino acids like Gly, Gln and Met were the most important attributes for identifying the paternal and maternal imprinted genes. These findings could imply conservation pattern in the attributes among these species.     

The effects of grazing and supplemental protein concentrations during the grazing period on subsequent finishing performance and carcass quality in Japanese Black cattle steers

The effects of grazing and supplemental protein concentrations, provided during the grazing period, on subsequent finishing performance and carcass quality were investigated. This experiment was carried out using 15 Japanese Black cattle (Wagyu) steers. The steers were fed as follows: (i) grazing supplemented with moderate protein concentrate (GMP) (18% crude protein (CP); dry matter (DM) basis) before finishing, followed by feeding in a barn until slaughter; (ii) grazing supplemented with low protein concentrate (GLP) (14% CP; DM basis) before finishing, followed by feeding in the barn until slaughter; and (iii) no grazing before finishing (NG). From the end of the grazing season to the end of the growing period, the GMP and GLP steers were managed in the same way as the NG steers. All of the animals were fed the same diet in the finishing period (9 months to 28 months). None of the three treatments affected the average daily gains. For all treatments, chilled carcass weights were more than 450 kg and did not differ significantly among the groups. The longissimus muscle areas in the grazed steers were numerically larger than in those receiving the NG treatment. Fat thickness was significantly greater (P < 0.05) in the NG steers than in the grazed steers. The intramuscular fat and marbling scores were not affected in the grazed steers. In conclusion, the carcass quality of grazed steers was similar to that of the NG steers at a similar final age, and the quantity of meat in the NG steers would be less than that of the GMP and GLP steers. Therefore, spring‐born Wagyu steers should be grazed using the GLP supplement before fattening.     

The grazing response of cattle to pasture contaminated with rabbit faeces and the implications for the transmission of paratuberculosis

Transmission of Mycobacterium avium subspecies paratuberculosis, the organism responsible for paratuberculosis (or Johne's disease) in ruminants, occurs through the faecal-oral route. As M. a. paratuberculosis has been isolated from rabbit faeces, cattle grazing rabbit faecal contaminated pasture may thus be at risk.A herd of 57 beef cattle was monitored on a farm in Perthshire, throughout the 1999 'grazing year', to investigate whether the cattle avoided rabbit faecal contaminated pasture and thus the potential for disease transmission. Grazing was measured every two days over eight rotations by sward heights on 40 marked treatment plots (0.5 m x 0.5 m) to which 0, 10, 50 and 250 rabbit faecal pellets were added. Cattle were also monitored by an active transponder system which enabled individual animals contacting two plots per field rotation (one control and one contaminated) to be recorded. During the monitored grazing year, grazing pressure was low with a net mean sward offtake of 18% of sward height per rotation. There were no significant differences between rabbit faecal treatments (0, 10, 50 and 250 pellets) with respect to the height or proportion of sward removed, or between the numbers of contacts made by cattle on contaminated and uncontaminated plots. Over 90% of all the cattle contacted contaminated plots, indicating that the potential for disease transmission was widespread among the herd.To our knowledge, this is the first reported instance of a lack of avoidance by grazing cattle towards swards contaminated with faeces, and implies that the potential for transmission of paratuberculosis from rabbit contaminated pasture is high.     

Effects of direct exposure to cold weather under grazing in winter on the physiological,immunological, and behavioral conditions of Japanese Black beef cattle in central Japan

This study aimed to reveal the effects of direct exposure to cold weather under grazing in winter (GW) on the health of Japanese Black beef cattle, as assessed using physiological, immunological, and behavioral parameters. Ten Japanese Black beef cattle (328 ± 45 kg, 7.6 ± 3.4 years of age) were used in this experiment. In winter, five of the 10 cattle grazed for 2 months in a 1.8 ha pasture (GW), and the remaining cattle were fed under confined conditions with tethering (control [CT]). The two groups were fed similar feed during the experiment, except for the grazing forage. Blood samples were collected approximately every 2 weeks. The numbers of neutrophils and monocytes and antioxidant enzyme activity were higher in the GW group than in the CT group (p < 0.05). The proportions of CD4‐single‐positive cells were lower in GW cattle than in CT cattle (p = 0.06). This study showed that direct exposure of beef cattle to cold weather under GW enhanced the levels of circulating neutrophils and monocytes and contributed to the kinetic homeostasis of lymphocytes but also activated antioxidant enzymes due to an increase in oxidative stress.