[Show abstract][Hide abstract] ABSTRACT: Frailty models can be fit as mixed-effects Poisson models after transforming time-to-event data to the Poisson model framework. We assess, through simulations, the robustness of Poisson likelihood estimation for Cox proportional hazards models with log-normal frailties under misspecified frailty distribution. The log-gamma and Laplace distributions were used as true distributions for frailties on natural log scale. Factors such as the magnitude of heterogeneity, censoring rate, number and sizes of groups were explored. In the simulations, the Poisson modeling approach that assumes log-normally distributed frailties provided accurate estimates of within- and between-group fixed effects even under a misspecified frailty distribution. Non-robust estimation of variance components was observed in the situations of substantial heterogeneity, large event rates, or high data dimensions.
Communication in Statistics- Simulation and Computation 08/2015; · 0.29 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The emergence of pathogens resistant to antimicrobials has prompted political initiatives targeting a reduction in the use of veterinary antimicrobials in Denmark, especially for pigs. This study elucidates the tendency of pig farms with a significantly higher antimicrobial use to remain in clusters in certain geographical regions of Denmark. Animal Daily Doses/100 pigs/day were calculated for all three age groups of pigs (weaners, finishers and sows) for each quarter during 2012–13 in 6,143 commercial indoor pig producing farms. The data were split into four time periods of six months. Repeated spatial cluster analyses were performed to identify persistent clusters, i.e. areas included in a significant cluster throughout all four time periods. Antimicrobials prescribed for weaners did not result in any persistent clusters. In contrast, antimicrobial use in finishers clustered persistently in two areas (157 farms), while those issued for sows clustered in one area (51 farms). A multivariate analysis including data on antimicrobial use for weaners, finishers and sows as three separate outcomes resulted in three persistent clusters (551 farms). Compared to farms outside the clusters during this period, weaners, finishers and sows on farms within these clusters had 19%, 104% and 4% higher use of antimicrobials, respectively. Production type, farm type and farm size seemed to have some bearing on the clustering effect. Adding these factors as categorical covariates one at a time in the multivariate analysis reduced the persistent clusters by 24.3%, 30.5% and 34.1%, respectively.
PLoS ONE 08/2015; 10(8). DOI:10.1371/journal.pone.0136834 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The objectives of this study were to use non-equilibrium gravitational field-flow fractionation (GrFFF), an immunotag-less method of sorting mesenchymal stem cells (MSCs), to sort equine muscle tissue-derived mesenchymal stem cells (MMSCs) and bone marrow-derived mesenchymal stem cells (BMSC) into subpopulations and to carry out assays in order to compare their osteogenic capabilities. Cells from 1 young adult horse were isolated from left semitendinosus muscle tissue and from bone marrow aspirates of the fourth and fifth sternebrae. Aliquots of 800 × 10(3) MSCs from each tissue source were sorted into 5 fractions using non-equilibrium GrFFF (GrFFF proprietary system). Pooled fractions were cultured and expanded for use in osteogenic assays, including flow cytometry, histochemistry, bone nodule assays, and real-time quantitative polymerase chain reaction (qPCR) for gene expression of osteocalcin (OCN), RUNX2, and osterix. Equine MMSCs and BMSCs were consistently sorted into 5 fractions that remained viable for use in further osteogenic assays. Statistical analysis confirmed strongly significant upregulation of OCN, RUNX2, and osterix for the BMSC fraction 4 with P < 0.00001. Flow cytometry revealed different cell size and granularity for BMSC fraction 4 and MMSC fraction 2 compared to unsorted controls and other fractions. Histochemisty and bone nodule assays revealed positive staining nodules without differences in average nodule area, perimeter, or stain intensity between tissues or fractions. As there are different subpopulations of MSCs with different osteogenic capacities within equine muscle- and bone marrow-derived sources, these differences must be taken into account when using equine stem cell therapy to induce bone healing in veterinary medicine.
Canadian journal of veterinary research = Revue canadienne de recherche vétérinaire 04/2015; 79(2):101-8. · 1.02 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In Eastern Canada, an increasing number of pests, predators and pathogens in downriver areas (close to the ocean) have led the aquaculture industry to consider growing oysters in upriver areas (close to the river source). In this study, oyster growth performance was compared between downriver and upriver environments by means of stock transfer experiments within the Richibucto estuary. In May 2009, seed oysters (~26 mm shell height) originating from two downriver sites (salinity ~20–30 ‰) were transferred upriver (salinity ~5–20 ‰). Follow-up measurements in October 2009 revealed that the seed transferred upriver grew and survived as well as seed that remained downriver, while the mortality rates of adult oysters (shell height ~66 mm) were lower at the upriver site. Meat content was unaffected in adult oysters transferred upriver. However, there were indications that the upriver environment promoted shell growth (mm) in adult oysters. Oysters transferred upriver had a gain in shell height (LSM ± SE) over the oysters that remained downriver (2.7 ± 0.5 vs. 1.8 ± 0.5 mm) and in shell width [Median (95 % CI); 2.8 mm (1.9, 3.6) vs. 1.0 mm (0.3, 1.2)]. Therefore, the holding of adult oysters upriver during the spring–summer period confers productivity advantages on top of protection from diseases and predation. By contrast, productivity losses were recorded when relocating adult oysters originating from the upriver environment. More specifically, final organic meat content were approximately 35 % less in adult oysters transferred downriver compared to those that remained upriver (0.48 ± 0.04 vs. 0.74 ± 0.04 g). Results suggest that transfers along the river impact physiological processes such as gametogenesis and shell formation in adult oysters.
Aquaculture International 12/2014; 23(4). DOI:10.1007/s10499-014-9866-3 · 0.98 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Mastitis is a complex disease affecting dairy cows and is considered to be the most costly disease of dairy herds. The hazard of mastitis is a function of many factors, both managerial and environmental, making its control a difficult issue to milk producers. Observational studies of clinical mastitis (CM) often generate datasets with a number of characteristics which influence the analysis of those data: the outcome of interest may be the time to occurrence of a case of mastitis, predictors may change over time (time-dependent predictors), the effects of factors may change over time (time-dependent effects), there are usually multiple hierarchical levels, and datasets may be very large. Analysis of such data often requires expansion of the data into the counting-process format – leading to larger datasets – thus complicating the analysis and requiring excessive computing time.
Preventive Veterinary Medicine 12/2014; 117(3-4). DOI:10.1016/j.prevetmed.2014.09.013 · 2.17 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Repeated multivariate scanning statistics revealed three persistent clusters (551 farms) in the amount of consumed antimicrobials. Production type, herd type and herd size were found to explain some of the clustering. Emergence of antimicrobial resistance has increased the public awareness of the use of veterinary antimicrobials. It is hypothesized that farms with a persistently high antimicrobial use are spatially clustered, due to the clustering of disease, demographic characteristics, management and medication practices. The objective of this study was to identify the geographical distribution of Danish indoor commercial pig farms prescribing significantly more antimicrobials throughout the two years study period. A register based cross-sectional study with repeated measurements on antimicrobial use from 6,143 Danish indoor commercial pig producing farms was executed.
[Show abstract][Hide abstract] ABSTRACT: Piscirickettsiosis (SRS) is an endemic bacterial disease of high economic importance and is the primary reason for antibiotic usage in the aquaculture industry in Chile. Understanding the epidemiology of this disease is important in order to develop better control strategies for the Chilean aquaculture industry. The objectives of this project were to 1) describe the epidemiology of SRS on Atlantic salmon and rainbow trout farms, and 2) to identify factors that impact the severity of SRS outbreaks. Special attention was given to vaccine strategies currently used by the industry. Production data from 14 Atlantic salmon farms (252 cages) and 11 rainbow trout farms (216 cages) that had completed their production cycles between 2010 and 2012 were investigated. Regression models were used to evaluate time-to-first outbreak of SRS and total mortality attributed to SRS mortality. The factors evaluated in our models were: vaccine type (control and 5 vaccines), smolt weight and cumulative mortality within the first 4 weeks in saltwater, season of smolt introduction, infection with other pathogens during the production cycle, SRS treatments, and total number of sea lice treatments. The prevalence of SRS-affected cages on infected farms was high for both species; however, outbreaks appeared more severe (i.e. higher mortalities) on rainbow trout farms. Onset of SRS outbreaks was, on average, for fish in different vaccine groups, between 2480 degree-days (dd) and 3829 dd for Atlantic salmon, and between 1696 dd and 2241 dd for rainbow trout. For both species, none of the vaccines evaluated completely prevented SRS, although there were significant variations in the time-to-first outbreak and the severity of SRS outbreaks associated with vaccines after controlling for farm effect and other predictors. Specifically, a booster vaccine strategy in Atlantic salmon had significantly lower mortalities associated with SRS and a delay in the onset of disease compared to several of the other vaccines evaluated. Whether the differences observed between vaccines are economically significant is unknown. In rainbow trout, time-to-first outbreak was significantly delayed for vaccinated fish compared to the unvaccinated fish after we controlled for other factors in our model; however, total SRS mortality of vaccinated rainbow trout was not significantly different than unvaccinated rainbow trout. Consistent for both species was that mortality during the first 4 weeks post-salt water entry was associated with time-to-outbreak of SRS, and this effect was dependent on the vaccine used.
[Show abstract][Hide abstract] ABSTRACT: A cross-classified and multiple membership Cox model was applied to calf mortality data from Western Canada, where 23,409 calves from 174 herds were followed for up to 180 days after calving. The herds were cross-classified by 49 veterinary clinics and 9 ecological regions and in a multiple membership relation to the veterinary clinics, resulting in a 3-level cross-classified and multiple membership data structure. The model was formulated in a mixed-effects Poisson model framework with normally distributed random effects, and was fitted to the data by Bayesian Markov Chain Monte Carlo (MCMC) estimation. Important fixed effects included whether the calf was a twin, calf gender, assistance at calving, cow age, average temperature the first week after calving, the percentage of the herd that had already calved, whether calf shelters were provided, whether cow-calf pairs were moved to a nursery area, and whether any animals were purchased into the herd at or near the time of calving. The analysis demonstrated a greater variation among herds than among both ecological regions and veterinary clinics. Further, a simulation study for a setting similar to the real data gave evidence that the used approach provides valid estimates.
Preventive Veterinary Medicine 07/2014; 115(1-2). DOI:10.1016/j.prevetmed.2014.03.012 · 2.17 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Control of sea lice in Chile is largely based on antiparasitic treatments, synthetic pyrethroids being the most used drugs. In recent years, farmers in Chile have reported decreased performance of pyrethroid-based treatments. The aim of this study was to assess the performance of two deltamethrin-based (Alphamax® and a generic product) and one cypermethrin-based (Betamax®) product on the different life stages of Caligus rogercresseyi, while controlling potential confounders. We found that both deltamethrin products and the cypermethrin product had a significant effect on the reduction of juvenile, mobile adult, and gravid female lice, compared with untreated pens; however, the effect on juvenile lice was less than on mobile stages. There was no evidence that pyrethroids performed better on certain mobile life stages, such as gravid females. When the three products were compared, no significant differences were observed in the numbers of juvenile, adult male, and non-gravid female lice after we controlled for potential confounders; however, cypermethrin exhibited a small, yet significantly greater effect on the gravid female group when compared with one of the deltamethrin-based products. We also confirmed that other factors besides the product choice, such as the pre-treatment sea lice abundance, water temperature and salinity, and time elapsed to the post-treatment sample, affect the post-treatment sea lice level as well, and therefore, they should be taken into consideration when assessing the effect of immersion treatments.
Aquaculture 04/2014; s 426–427:231–237. DOI:10.1016/j.aquaculture.2014.02.007 · 1.88 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: This study was designed to assess the physiological impact of transferring oysters between upriver and downriver aquaculture sites, a common practice in North America that is primarily aimed at reducing disease infections and predation on cultured stocks. In May 2009, oysters (Crassostrea virginica) were reciprocally transferred between an upriver and a downriver site in the Richibucto estuary in eastern Canada. Mortality, tissue and cellular stress responses were subsequently evaluated in August and October 2009. Overall, oyster mortality remained low (~5%) throughout the 5-month study period with no significant difference between sites or oyster sources. However, by October oysters reared at the upriver site, regardless of their origin, had significantly higher levels of lysosomal membrane destabilization (63.6%, SE = 1.9) and digestive tubule atrophy (33.3–42.4%, SE = 3.6) than oysters reared at the downriver site (47.5%, SE = 1.8; 15.6–19.1%, SE = 3.8 respectively). They also exhibited a greater salinity differential between their mantle/haemolymph fluids and the ambient seawater, possibly indicating more restricted exchange with the environment. In general, the transfer of upriver oysters to a downriver site had a positive impact, i.e. lower levels of lysosomal destabilization and tubule atrophy, whereas transfer of downriver oysters upriver had the opposite effect. These results suggest that upriver environmental conditions negatively impact cellular and tissue integrity in oysters without leading to mortality during the summer–autumn period.
Aquaculture Research 03/2014; 46(12). DOI:10.1111/are.12436 · 1.38 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: This study assessed the standard urinalysis technique and sediment stain techniques as predictors of bacterial culture results for canine and feline urine. Canine (n = 111) and feline (n = 79) urine samples were evaluated using unstained wet-mount and air-dried Gram and Wright-Giemsa stained sediment; results were compared to aerobic bacterial culture. Eleven canine and 7 feline urine samples were culture positive. Unstained wet-mount and stained sediment had sensitivities of 89% and 83% and specificities of 91% and 99%, respectively. The specificity of using either stain was higher (P < 0.01) than wet-mount examination for detecting bacteriuria. There were significant differences among 3 technologists in detecting true positives (P < 0.01). Association of sediment and culture results used 112 canine and 81 feline samples. There was a negative association (P < 0.01) between lipid detection and wet-mount identification of bacteria.
The Canadian veterinary journal. La revue veterinaire canadienne 11/2013; 54(11):1061-6. · 0.52 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: This paper discusses statistical modelling for data with a hierarchical structure, and distinguishes in this context between three different meanings of the term hierarchical model: to account for clustering, to investigate variability and separate predictive equations at different hierarchical levels (multi-level analysis), and in a Bayesian framework to involve multiple layers of data or prior information. Within each of these areas, the paper reviews both past developments and the present state, and offers indications of future directions. In a worked example, previously reported data on piglet lameness are reanalyzed with multi-level methodology for survival analysis, leading to new insights into the data structure and predictor effects. In our view, hierarchical models of all three types discussed have much to offer for data analysis in veterinary epidemiology and other disciplines.
Preventive Veterinary Medicine 10/2013; 113(3). DOI:10.1016/j.prevetmed.2013.10.001 · 2.17 Impact Factor