Biomathematics and Statistics Scotland

for the three treatment groups. Shaded areas are ± 1 standard error of the mean. 17 Figure 5. Model-based probabilities of obtaining walking scores of ‘Immobile’, ‘With difficulty’ and ‘Normal’ across the six study days, for the three treatment groups. Posted on Authorea 16 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160029789.93744641 — This a preprint and has not been peer reviewed. Data may be preliminary. Figure 6. Model-based probabilities of cattle being on pasture across the six study days, for the three treatment groups. Shaded areas are ± 1 standard error of the mean (where available). Figure 7 . Model-based probabilities of cattle salivating across the six study days, for the three treatment groups. Hosted file FMD Cameroon Tables 140920.docx available at https://authorea.com/users/359354/articles/ 481409-efficacy-and-application-of-a-novel-topical-anaesthetic-wound-formulation-for- treating-cattle-with-foot-and-mouth-disease-a-field-trial-in-cameroon Hosted file FMD Cameroon Figures 140920.docx available at https://authorea.com/users/359354/articles/ 481409-efficacy-and-application-of-a-novel-topical-anaesthetic-wound-formulation-for- treating-cattle-with-foot-and-mouth-disease-a-field-trial-in-cameroon 18

…9JY, UK; smetcalfe@knoell.com 5 Biomathematics and Statistics Scotland, Edinburgh EH9 3FD, Scotland, UK; giles.innocent@bioss.ac.uk 6 Department of Microbiology and Infectious Diseases, NSW Health Pathology, Nepean Hospital…

…9JY, UK; smetcalfe@knoell.com 5 Biomathematics and Statistics Scotland, Edinburgh EH9 3FD, Scotland, UK; giles.innocent@bioss.ac.uk 6 Department of Microbiology and Infectious Diseases, NSW Health Pathology, Nepean Hospital…

…Data is presented as cumulative odds ratios with the statistical probabilities of calves in each treatment group displaying response score Y = 0, 1, 2 and 3. For all statistical calculations, P values…

lable, pre-treatment data were included as a co-variate. Baseline data were defined as the latest measurement of a given variable before treatment was administered. The statistical model included treatment, sex (except for parameters only measured in one sex), and treatment-by-sex interactions as fixed effects, while the repeated measures ANOVA model included treatment, sex and time (and their 2-way and 3-way interac- tions) as fixed effects. Data were compared either within or across sex depending on observed interactions. Models were selected using backwards elimination where 3-way and 2-way interaction terms with the highest p-Value were sequentially dropped from the model. The process was performed hierarchically starting with the 3-way interaction terms using a threshold p-Value of 0.1, as required by regulatory guidelines. Model selection was stopped when any of the following occurred: (i) all interaction terms at the highest level had a p-Value < 0.1; (ii) no interaction terms remained in the model. The statistical model was therefore: Parameter = Baseline_variables + Treatment + Sex + Time + Treatment:Sex + Treat- ment:Time + Sex:Time + Treatment:Sex:Time + Residual_Error Least squares means were compared at a significance level of p < 0.1 in the first instance apart from treatment by sex by time point, which was compared at p < 0.05 in the first instance. For the repeated measures models, most residual error patterns were selected based on a comparison of Akaike Information Criteria (AIC) output for models containing an unstructured (UN), autoregressive (AR; 1), variance components (VC) and independent residual error pattern (with the lowest AIC preferred among the possible covariance matrices). The denominator degrees of freedom in the covariance pattern

…9JY, UK; smetcalfe@knoell.com 5 Biomathematics and Statistics Scotland, Edinburgh EH9 3FD, Scotland, UK; giles.innocent@bioss.ac.uk 6 Department of Microbiology and Infectious Diseases, NSW Health Pathology, Nepean Hospital…

nt of pain sensitivity in calves follow- elled using two separate mixed effects negative bino- ing disbudding. The black ovals indicate the position of the mial regression models, where calf was treated as horn bud wound and the numbers indicate the location for pla- random effects, and the natural logarithm of length cement of the pressure algometer. of video recorded at each time period was added as an offset term. For head shakes, a mixed effects Poisson regression model with a robust standard Half of the calves were tested on the right horn first, error was adopted, which also included calf as a followed by the left horn, with the remainder tested in random effect and the same offset term. Initial explana- the opposite order. All calves returned to typical farm tory variables included in the multivariable models management (in one group) following the completion were farm, treatment group and time, and the inter- of the trial at 24 hours. All animal health events were action between treatment group and time. This inter- recorded and any animals that were suffering illnesses action term was included as it was possible that the were removed from the trial. Any calves that expressed treatments had a different duration of action. Starting an unusually high aversion to pain sensitivity testing with a full model that included the interaction term, (struggling, vocalisation) were removed from further fixed effects were dropped from the model if Akaike assessments on welfare grounds. information criteria from the simpler model was In addition to the algometer measurements, the smaller. Results are reported as incidence rate ratios person applying the algometer also subjectively (IRR), which can be interpreted as the increase, or graded the calf’s pain response

I. Zootechnical Description..........................................................................................................13 II. Veterinary Inventory................................................................................................................. 15 Biological Outcomes........................................................................................................ 16 Affective Experiences............................................................................................................17 Association Between Circumstances, Biological Outcomes, and Affective Experiences.20 III. Affective Quantification.......................................................................................................... 20 (A) Temporal Description Using Notation Systems.............................................................21 (B) Calculation of Cumulative Affect....................................................................................27 IV. Epidemiological Investigation................................................................................................ 29 V. Econometric Calculation......................................................................................................... 29 Cumulative Pain and Pleasure for Each Life-Fate................................................................30 Cumulative Pain and Pleasure for the Average Individual in a System.............................. 30 Welfare Footprint: Cumulative Pain and Pleasure per Unit of Product.............................. 30 Interspecific Scaling...............................................................................................................31 Welfare Footprint Expression and

…using R statistical software version 3.6.1 and IBM SPSS Statistics for Windows, Version 26.0 (IBM Corp, Mean arterial blood pressure (MAP) Armonk). For the statistical analysis metric variables and…

…using R statistical software version 3.6.1 and IBM SPSS Statistics for Windows, Version 26.0 (IBM Corp, Mean arterial blood pressure (MAP) Armonk). For the statistical analysis metric variables and…