Now showing 1 - 10 of 19
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Joint Spatio-Temporal Modeling of Mycobacterium bovis Infections in Badgers and Cattle - Results from the Irish Four Area Project

2013-06, Kelly, Gabrielle E.

In Ireland and in the UK, bovine tuberculosis(bTB) infects cattle and wildlife badgers (Meles meleslinnaeus) and badgers contribute to the spread of the disease in cattle. Isotropic and anisotropic spatio-temporalmodels are fitted to cattle herd and badger settbTB incidence data from the Four Area Project using sequences of linear geostatistical models. An association was found between the spatial distribution of the disease in cattle and badgers in two of three areas. The limited association may be due to irregularity of sett territories,fragmentation of farms, TB-test insensitivity, temporal lags associated with transmission or non-spatial transmission. A statistical methodology is outlined whereby hypotheses related to spatial correlation structure may be tested.

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A comparison of sampling grids, cut off distance and type of residuals in parametric variogram estimation

2016-11-16, Jin, Renhao, Kelly, Gabrielle E.

In spatial statistics, the correct identification of a variogram model when fitted to an empirical variogram depends on many factors. Here, simulation experiments show fitting based on the variogram cloud is preferable to that based on Matheron's and Cressie–Hawkins empirical variogram estimators. For correct model specification, a number of models should be fitted to the empirical variogram using a grid of cut-off values, and recommendations are given for best choice. A design where roughly half the maximum distance between points equals the practical range works well for correct variogram identification of any model, with varying nugget sizes and sample sizes.

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Spatio-Temporal Modelling of TB in Cattle Herds

2012-08, Kelly, Gabrielle E.

We examine spatial association of bovine TB in cattle herds using data from Ireland. Badgers (Meles meles), a protected species under the Wildlife Act 1976 (OAG 2012), have been implicated in the spread of the disease in cattle. Current disease control policies include reactive culling (in response to TB outbreaks) of badgers in the index and neighbouring farms. Kelly and More (2011) using generalized linear geostatistical models, established that TB clusters in cattle herds and estimated the practical spatial ranges at which this occurs. Here this work is extended by taking into account possible anisotropy. Changes in spatial association over two time periods are also examined. The results have direct implications for establishing scale and direction in reactive culling. They are also of import regarding the evaluation of vaccines for badgers and cattle.

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A simulation comparison of estimators of spatial covariance parameters and associated bootstrap percentiles

2018-09, Kelly, Gabrielle E., Menezes, Raquel

A simulation study is implemented to study estimators of the covariance structure of a stationary Gaussian spatial process and a spatial process with t-distributed margins. The estimators compared are Gaussian restricted maximum likelihood (REML) and curve-fitting by ordinary least squares and by the nonparametric Shapiro-Botha approach. Processes with Matérn covariance functions are considered and the parameters estimated are the nugget, partial sill and practical range. Both parametric and nonparametric bootstrap distributions of the estimators are computed and compared to the true marginal distributions of the estimators. Gaussian REML is the estimator of choice for both Gaussian and t-distributed data and all choices of the Matérn covariance structure. However, accurate estimation of the Matérn shape parameter is critical to achieving a good fit while this does not affect the Shapiro-Botha estimator. The parametric bootstrap performed well for all estimators although it tended to be biased downward. It was slightly better than the nonparametric bootstrap for Gaussian data, equivalent to it for t-distributed data and worse overall for the Shapiro-Botha estimates. A numerical example, obtained from environmental monitoring, is included to illustrate the application of the methods and the bootstrap.

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A neural network analysis of Lifeways cross-generation imputed data

2018-12-14, Kelly, Gabrielle E.

Objectives: Neural networks are a powerful statistical tool that use nonlinear regression type models to obtain predictions. Their use in the Lifeways cross-generation study that examined body mass index (BMI) of children, among other measures, is explored here. Our aim is to predict the BMI of children from that of their parents and maternal and paternal grandparents. For comparison purposes, linear models will also be used for prediction. A complicating factor is the large amount of missing data. The missing data may be imputed and we examine the effects of different imputation methods on prediction. An analysis using neural networks (and also linear models) that uses all available data without imputation is also carried out, and is the gold standard by which the analyses with imputed data sets are compared. Results: Neural network models performed better than linear models and can be used as a data analytic tool to detect nonlinear and interaction effects. Using neural networks the BMI of a child can be predicted from family members to within roughly 2.84 units. Results between the imputation methods were similar in terms of mean squared error, as were results based on imputed data compared to un-imputed data.

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A long term observational study of the impact of badger removal on herd restrictions due to bovine TB in the Irish midlands during 1989-2004

2008-10, Kelly, Gabrielle E., Condon, J., More, Simon John, Dolan, Leonard A., Higgins, Isabella M., Eves, John A.

An observational study was carried out, using data collected from four areas in the Irish midlands, between 1989 and 2004, to critically evaluate the long-term effects of proactive badger culling and to provide insights into reactive badger culling tuberculosis (TB) prevalence in cattle. Confirmed cattle herd TB incidence is the outcome measure used throughout. Relative to reactive culling, proactive badger culling was associated with a decrease in incidence in each of the 16 years of observation, which encompassed periods of both intensive and less-intensive badger removal. By 2004, we observed a decrease of 22% [95% confidence interval (CI) 15-29, P<0.001] in the entire proactive and 37% (95% CI 25–47, P<0.001), in the inner proactive removal areas. The size of the decrease increased with time (P=0.055). There was a decrease (constant over time) of at least 14% (95% CI 76–97, P=0.013) in incidence in the inner compared to the outer control area (herds ≤2 km, >2 km, from proactive removal area boundaries, respectively). Incidence in the outer proactive removal area (herds <1.6 km from the proactive removal boundary) was similar to the inner control area (P=0.890). Incidence in the outer control area and total control area, compared to a neighbouring area some distance away, increased over the course of the study. Differences with the total control area were not statistically significant but the outer control area was 11% higher than the neighbouring area by 2004 (borderline significance P=0.057).

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Epithelium-on Corneal Cross-linking for Progressive Keratoconus: Two-year Outcomes

2018-12, Cummings, Arthur B., Shaw, Parker J., Kelly, Gabrielle E.

Corneal cross-linking (CXL) has been established as a successful treatment tool for the treatment of progressive keratoconus in terms of slowing or halting progressive corneal steepening and thinning and even on some occasions, reversing the steepening. To date the Dresden epithelium-off protocol is regarded as the gold standard and the epithelium-on (epi-on) approaches have met with less success. Both doctors and patients would welcome an epi-on CXL procedure that provided good outcomes as the morbidity with epi-on CXL is so much less and the safety is enhanced. Patient comfort is greater with the epi-on techniques when compared to epi-off. This study looked at 82 eyes that had documented progression of keratoconus and then underwent epi-on CXL using the CXLO system. The results show that corneal steepening can be halted and even reversed over a 2-year follow-up period with no complications noted. Over the 24 months post treatment on average there was a decrease in all keratometry values, BAD and ISV when compared to before treatment with IHD being marginally increased. Further studies over a longer follow-up period are required but recent publications using the same approach are validating the findings seen in this study.

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Spatial clustering of TB-infected cattle herds prior to and following proactive badger removal

2011-08, Kelly, Gabrielle E., More, Simon John

Bovine tuberculosis (TB) is primarily a disease of cattle. In both Ireland and the UK, badgers (Meles meles) are an important wildlife reservoir of infection. This paper examined the hypothesis that TB is spatially correlated in cattle herds, established the range of correlation and the effect, if any, of proactive badger removal on this. We also re-analysed data from the Four Area Project in Ireland, a large-scale intervention study aimed at assessing the effect of proactive badger culling on bovine TB incidence in cattle herds, taking possible spatial correlation into account. We established that infected herds are spatially correlated (the scale of spatial correlation is presented), but at a scale that varies with time and in different areas. Spatial correlation persists following proactive badger removal.

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Body mass index and height over three generations: evidence from the Lifeways cross-generational cohort study

2012-01, Murrin, Celine, Kelly, Gabrielle E., Tremblay, Richard Ernest, Kelleher, Cecily

Background: Obesity and its measure of body mass index are strongly determined by parental body size. Debate continues as to whether both parents contribute equally to offspring body mass which is key to understanding the aetiology of the disease. The aim of this study was to use cohort data from three generations of one family to examine the relative maternal and paternal associations with offspring body mass index and how these associations compare with family height to demonstrate evidence of genetic or environmental cross-generational transmission. Methods: 669 of 1082 families were followed up in 2007/8 as part of the Lifeways study, a prospective observational cross-generation linkage cohort. Height and weight were measured in 529 Irish children aged 5 to 7 years and were self-reported by parents and grandparents. All adults provided information on self-rated health, education status, and indicators of income, diet and physical activity. Associations between the weight, height, and body mass index of family members were examined with mixed models and heritability estimates computed using linear regression analysis. Results: Self-rated health was associated with lower BMI for all family members, as was age for children. When these effects were accounted for evidence of familial associations of BMI from one generation to the next was more apparent in the maternal line. Heritability estimates were higher (h2 = 0.40) for mother-offspring pairs compared to father-offspring pairs (h2 = 0.22). In the previous generation, estimates were higher between mothersparents (h2 = 0.54-0.60) but not between fathers-parents (h2 = -0.04-0.17). Correlations between mother and offspring across two generations remained significant when modelled with fixed variables of socioeconomic status, health, and lifestyle. A similar analysis of height showed strong familial associations from maternal and paternal lines across each generation. Conclusions: This is the first family cohort study to report an enduring association between mother and offspring BMI over three generations. The evidence of BMI transmission over three generations through the maternal line in an observational study corroborates the findings of animal studies. A more detailed analysis of geno and phenotypic data over three generations is warranted to understand the nature of this maternal-offspring relationship.

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Towards reliable spatial prediction

2018-12-16, Kelly, Gabrielle E., Menezes, Raquel

Estimation of the variogram and associated parameters in spatial analysis is important for assessing spatial dependence and in predicting values of the measured variable at unsampled locations i.e. kriging. A simulation study is implemented to compare the performance of (i) Gaussian restricted maximum likelihood (REML) estimation, (ii) curve-fitting by ordinary least squares and (iii) nonparametric Shapiro-Botha estimation for estimating the covariance structure of a stationary Gaussian spatial process and a spatial process with t-distributed margins. Processes with Matern covariance functions are considered and the parameters estimated are the nugget, partial sill and practical range. Both parametric and nonparametric bootstrap distributions of the estimators are computed and compared to the true marginal distributions of the estimators. Gaussian REML is the estimator of choice for both Gaussian and t-distributed data and all choices of Matern variogram. However, accurate estimation of the Matern shape parameter is critical to achieving a good fit while this does not affect the Shapiro-Botha estimator. The parametric and nonparametric bootstrap both performed well, the latter being better for the Shapiro-Botha estimates. A numerical example, obtained from environmental monitoring, is included to illustrate the application of the methods and the bootstrap.