Plan of the testing apparatus.

<p>Each of the eight pens (1–8; 2.375 m×9.6 m each) was divided by a sheeted hurdle attached to a gate that could be closed behind the sheep after it chose one of the two stimuli (s) placed at the far end of the pen. The sheep would move out of the start pen (A, B) and move towards the stimuli (dashed arrow). When it reached the gate it would have to choose to go down one or other side of the pen to reach one of the stimuli. The sheep was allowed to self-correct if it turned around before it had reached point b (B, C). Point a is the point beyond which the tallest sheep might be able to see into the bucket.</p

Order of Discriminations.

<p>C1 =  blue, C2 =  yellow, C3 =  purple, C4 =  green, S1 =  cone, S2 =  trapezoid.</p

Performance of sheep in the two choice discrimination task.

<p>Each point represents the mean (± SEM) number of correct choices made in each set of 8 discriminations. Where points are joined by solid lines, the sets of discriminations were tested on the same day. Where points are joined by dotted lines, testing was conducted on a different day. SD =  simple discrimination, SR  =  simple discrimination reversal, Ret1 =  first retention trial, CD =  compound discrimination IDS = intradimensional shift, IDR  =  intradimensional shift reversal, EDS =  extradimensional shift, EDR = extradimensional shift reversal.</p

Aggregate appearance in CA1 and dentate gyrus (DG).

<p>In R6/2 hippocampus, Htt aggregates visualised by staining with the MW8 antibody could not be seen at 18 days of age but could be found in many neurons at 19 days in the CA1 (B, black arrowheads) and increased in number with time (C, black arrowheads). Cell distribution in this region is shown in a parallel section showed with a cresyl violet stain (A”–C”). In the DG, MW8-positive aggregates were absent up to 24 days, but were present at 26 days (F, black arrowheads). Staining with ubiquitin antibody did not reveal the presence of inclusions in any region at these time points (A’–F’). Cell distribution in both regions was visualised with a cresyl violet (CV) stain (D”–F”). Scale bar  = 50 µm.</p

An example of high-resolution positional data collected through GPS technology.

<p>This example illustrates the movement patterns of a single sheep from a flock of Merino sheep. The data is split into the period in the holding pen, the period in the race (between the holding pen and the field) and the period in the field. The holding pen and the field are illustrated in the figure on the left, while the tracks of the animal are illustrated (in blue) in the figure on the right. The data set for an entire flock consists of such a trajectory sequence for each individual in the flock. More details of this data set can be found in the data collection section of the paper. Given such a set of movement patterns, the aim of this paper is to provide tools to infer the affiliation network of the group.</p

An example of constructing a movement model with respect to a given partition.

<p>The partition is the same as given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0132417#pone.0132417.g002" target="_blank">Fig 2</a>. The animal’s trajectory is given in (a), while the observation counts of the animal into the subregions of the partition is given in (b). Using these observation counts the maximum likelihood estimate of the movement model is given in (c). The animal’s movements have been modelled with a categorical model.</p

A snapshot of the movement patterns of the flock in the genuine mixing experiment.

<p>Members of one of sub-flock are depicted using red circles, whiles members of the other sub-flock are depicted using blue squares. (a) The position of the flock in relation to the field at an instant during the data collection period. The boundary of the field is denoted with a solid black line. (b) A close-up image of the flock during the same instant as in (a).</p

The positional error of linearly interpolated data.

<p>The table shows the results of reducing sampling rate from 1 sample/s, linearly interpolating to reconstruct the missing values, and comparing against the original data. The results support the assumption that a GPS data sampling rate of 1 sample/s is likely to be more than adequate as a means of establishing sheep positions for this study, and that little would be gained by increasing it.</p

Results of the artificial mixing experiment.

<p>The plot shows the proportion of connections within the two sub-flocks, <i>SG</i>1 ↔ <i>SG</i>1 and <i>SG</i>2 ↔ <i>SG</i>2, and between the two sub-flocks <i>SG</i>1 ↔ <i>SG</i>2. The plots show the results of the significance test using a regular partition (a) and an irregular partition (b).</p

Comparison of MW8 and ubiquitin staining patterns.

<p>Higher magnification microscopy analysis was used in order to compare MW8 and ubiquitin staining patterns in single R6/2 neurons. In CA1, CA3 and cortex, MW8 labelling could be observed in cells before any aggregates were visible, a phenomenon that was not apparent with ubiquitin staining. The initial morphologies of MW8-positive aggregates were different from ubiquitin-positive inclusions, in that only nucleation centres of the aggregates were ubiquitinated and the MW8-immunolabelled Htt protein that was not localised to the nucleation centre did not appear to be ubiquitinated. In contrast, aggregates with clear nucleation centres were visible by 25 days in the striatum. And at the same time, larger punctate ubiquitin-labelled inclusions were already visible in STR neurones. Ubiquitinated inclusions were much bigger than MW8-positive aggregates and did not change much in size, even though Htt aggregates got bigger with time.</p