Browsing by Author "Yang DA"

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    Design-Based Approach for Analysing Survey Data in Veterinary Research
    (MDPI (Basel, Switzerland), 2021-06-08) Yang DA; Laven RA; Bertelloni F
    Sample surveys are an essential approach used in veterinary research and investigation. A sample obtained from a well-designed sampling process along with robust data analysis can provide valuable insight into the attributes of the target population. Two approaches, design-based or model-based, can be used as inferential frameworks for analysing survey data. Compared to the model-based approach, the design-based approach is usually more straightforward and directly makes inferences about the finite target population (such as the dairy cows in a herd or dogs in a region) rather than an infinite superpopulation. In this paper, the concept of probability sampling and the design-based approach is briefly reviewed, followed by a discussion of the estimations and their justifications in the context of several different elementary sampling methods, including simple random sampling, stratified random sampling, and one-stage cluster sampling. Finally, a concrete example of a complex survey design (involving multistage sampling and stratification) is demonstrated, illustrating how finding unbiased estimators and their corresponding variance formulas for a complex survey builds on the techniques used in elementary sampling methods.
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    Evaluating Alternatives to Locomotion Scoring for Detecting Lameness in Pasture-Based Dairy Cattle in New Zealand: In-Parlour Scoring
    (MDPI (Basel, Switzerland), 2022-03-11) Werema CW; Yang DA; Laven LJ; Mueller KR; Laven RA; Kofler J
    Earlier detection followed by efficient treatment can reduce the impact of lameness. Currently, locomotion scoring (LS) is the most widely used method of early detection but has significant limitations in pasture-based cattle and is not commonly used routinely in New Zealand. Scoring in the milking parlour may be more achievable, so this study compared an in-parlour scoring (IPS) technique with LS in pasture-based dairy cows. For nine months on two dairy farms, whole herd LS (4-point 0−3 scale) was followed 24 h later by IPS, with cows being milked. Observed for shifting weight, abnormal weight distribution, swollen heel or hock joint, and overgrown hoof. Every third cow was scored. Sensitivity and specificity of individual IPS indicators and one or more, two or more or three positive indicators for detecting cows with locomotion scores ≥ 2 were calculated. Using a threshold of two or more positive indicators were optimal (sensitivity > 92% and specificity > 98%). Utilising the IPS indicators, a decision tree machine learning procedure classified cows with locomotion score class ≥2 with a true positive rate of 75% and a false positive rate of 0.2%. IPS has the potential to be an alternative to LS on pasture-based dairy farms.
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    First report of the within-farm prevalence of bovine digital dermatitis in Chinese Holstein dairy cows in Jiangsu, China: A Bayesian modelling approach
    (Elsevier Ltd, 2024-06) Ma X; Laven RA; Jiang P; Yang DA
    Digital dermatitis is one of the most important causes of lameness in dairy cattle, particularly in housed, intensively-managed cattle. The number of modern intensive dairy farms in China has increased markedly in recent years; however, we lack research on digital dermatitis in Chinese dairy cattle. This preliminary study aimed to estimate the prevalence of digital dermatitis on three conveniently selected farms in Jiangsu, China. The washed hind feet of all lactating cows on all three farms were examined during milking with the aid of a mobile phone light source. True prevalence was then estimated from the apparent prevalence using a Bayesian superpopulation approach to account for the imperfect nature of identifying digital dermatitis in cows during milking. Despite none of the farms having thought it necessary to implement routine digital dermatitis monitoring or control, the disease was found on all three sampled farms. All lesions observed were either chronic M4 or M4.1 type-lesions, with no M2 lesions (i.e. acute ulcerated lesions) observed. The estimated true prevalences on the farms were 7.3% (95% credible interval [CrI]: 5.4%-9.6%), 8.3% (95%CrI: 6.3%-10.8%), and 29.8% (95%CrI: 22.9%-37.2%).
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    Identification of risk factors for ewe mortality during the pregnancy and lambing period in extensively managed flocks
    (BioMed Central Ltd, 2023-12-06) Flay KJ; Chen AS; Yang DA; Kenyon PR; Ridler AL
    BACKGROUND: Ewe mortality during pregnancy and lambing is an issue for sheep producers globally, resulting in reduced productivity and profitability, compromised ewe welfare, and poor consumer perception. Despite these negative consequences, there was little investigation into factors associated with ewe death during this time. Therefore, this study aimed to assess associations between ewe body condition score (BCS), weight, reproductive parameters, and risk of mortality during pregnancy and lambing. METHODS: Four cohorts from three commercial New Zealand farms participated, with 13,142 ewe lambs enrolled and followed over time. Data were collected for five consecutive lambings. Visits aligned with key on-farm management times, specifically: prior to breeding, at pregnancy diagnosis (PD), prior to lambing (set-stocking), and, at weaning of their lambs. At each visit, ewes were weighed, BCS assessed and reproductive status was recorded when relevant (litter size at PD and lactation status after lambing). Ewes that died or were culled were recorded, and any ewes that were absent from consecutive visits were presumed dead. Logistic regressions were developed to assess the relationship between weight and BCS at each visit, PD result (single or multiple-bearing) and lactation status (wet or dry) in each year, and, risk of mortality during the pregnancy and lambing period in each year. RESULTS: In the PD to weaning period, mortality incidence ranged from 6.3 to 6.9% for two-tooth (18-months-old at breeding) to mixed-age (54-months-old at breeding) ewes. For ewe lambs (7 to 8-months-old at breeding), mortality was 7.3% from set-stocking to weaning. Heavier ewe lambs at PD were less likely to die during lambing (OR: 0.978, p = 0.013), as were those with greater set-stocking BCS. In subsequent years, BCS was a predictor of ewe death, with odds of mortality greatest for ewes < BCS 2.5. Additionally, for poorer BCS ewes, increasing weight reduced risk of mortality, but there was no impact of increasing weight in greater BCS ewes. CONCLUSIONS: This study identified risk factors associated with ewe mortality during the pregnancy and lambing period. Flock owners can use these to either cull at-risk ewes or proactively intervene to reduce likelihood of mortality, thereby improving flock productivity, profitability and welfare.
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    Performance of the StaphGold ELISA test in determining subclinical Staphylococcus aureus infections in dairy cows using a Gaussian mixture model
    (John Wiley and Sons Ltd, 2022-07-20) Yang DA; Laven RA
    BACKGROUND: A novel ELISA test has been developed to detect antigen-specific IgG in early and late lactation cows in New Zealand. OBJECTIVES: This study was to evaluate the discriminatory ability of the ELISA based on the detection of S. aureus-specific IgG as a screening test. METHODS: The ELISA was used for the composite milk samples taken during routine herd testing in 2018-2019 milking season in New Zealand. In the absence of a gold standard test, the diagnostic specificity and sensitivity was estimated using a Gaussian mixture model. RESULTS: The ELISA test had a high accuracy (AUC = 0.98) to detect antigen-specific IgG in early and late lactation cows with high somatic cell count due to either subsequent to or contemporaneous with the S. aureus invasion. Using an S/P ratio = 0.3 as the cut-off value, the ELISA test has sensitivity of 0.9 and specificity of 0.95, while the sensitivity increased to 0.94 at a cost of a decreased specificity of 0.9 at a lower cut-off value 0.26. CONCLUSIONS: The integration of the ELISA test as a screening tool into specific control programs may be useful to reduce the spread of S. aureus infections, to aid with treatment decisions, and to establish a correct milking order.
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    Prevalence and genetic diversity of Theileria equi from horses in Xinjiang Uygur Autonomous region, China.
    (Elsevier B.V., 2023-07-01) Zhang Y; Shi Q; Laven R; Li C; He W; Zheng H; Liu S; Lu M; Yang DA; Guo Q; Chahan B
    Theileria equi is a tick-borne intracellular apicomplexan protozoan parasite that causes equine theileriosis (ET). ET is an economically important disease with a worldwide distribution that significantly impacts international horse movement. Horses are an essential part of the economy in Xinjiang which is home to ∼10% of all the horses in China. However, there is very limited information on the prevalence and genetic complexity of T. equi in this region. Blood samples from 302 horses were collected from May to September 2021 in Ili, Xinjiang, and subjected to PCR examination for the presence of T. equi. In addition, a Bayesian latent class model was employed to estimate the true prevalence of T. equi, and a phylogenetic analysis was carried out based on the 18S rRNA gene of T. equi isolates. Seventy-two horses (23.8%) were PCR positive. After accounting for the imperfect PCR test using a Bayesian latent class model, the estimated true prevalence differed considerably between age groups, being 10.8% (95%CrI: 5.8% - 17.9%) in ≤ 3-year-old horses and 35.7% (95%CrI: 28.1% - 44.5%) in horses that were > 3 year-old. All T. equi isolates had their 18S rRNA gene (430bp) sequenced and analyzed in order to identify whether there were multiple genotypes of T. equi in the Xinjiang horse population. All of the 18S rRNA genes clustered into one phylogenetic group, clade E, which is thus probably the dominant genotype of T. equi in Xinjiang, China. To summarize, we monitored the prevalence of T. equi in horses of Xinjiang, China, with a focus on the association between age and the occurrence of T. equi by Bayesian modelling, accompanied by the genotyping of T. equi isolates. Obtaining the information on genotypes and age structure is significant in monitoring the spread of T. equi and studying the factors responsible for the distribution.