Relationship of neurological impairment to intrathecal humoral response (Ig_LOC) and cytokine responses.

<p>Note: All data are median (IQR). Significant difference to response in normal GCS cases (Dunns post hoc test) indicated in bold and.</p>**<p>p<0.01.</p>***<p>p<0.001.</p

Details of potential “intermediate-stage” cases.

a<p>: CSF DC: Detection of trypanosomes after double centrifugation of the CSF.</p

CSF cytokine concentrations in HAT.

<p>IL-10 (a), IFN-γ (b), TNF-α (c), TGF-β (d) and IL-6 (e) concentrations in control, early and late stage HAT patients. Boxes indicate median and interquartile range, and whiskers represent 10^th and 90^th percentiles. ***p<0.001; *p<0.05 Mann-Whitney U test. BLD = below limit of detection. ND: Not analysed due to insufficient material.</p

Characteristics of study population.

<p>Characteristics of study population.</p

A. Principle Component Analysis of isolates collected in 2003.

<p>Coordinate 1 accounts for 70% of the variation observed and separates the Malawi population from those in Uganda. Principal coordinate 2 accounts for 12% of the total variation, partially separating the two Ugandan populations, in addition to highlighting the diversity within Malawi. B. Principal Component Analysis of the isolates collected in Uganda. Coordinate 1 accounts for 58% of the observed variation and separates the majority of the Ug/Ke 61–97 isolates from those collected in 2003. Principal coordinate 2 accounts for 18% of the variation and partially separates the Tororo and Soroti isolates collected in 2003. While principal coordinates 1 and 2 account for 76% of the observed variation within the sample set the three populations are not completely separated.</p

eBURST analysis of the Ugandan samples.

<p>The putative founder genotype (SER002) is at the centre of the star-shaped radial lineage. Each node differs from its immediate neighbour by a single locus (i.e. the isolates are identical to each other at 6/7 loci), and is labelled with a representative isolate name.</p

Pairwise values of Wright's fixation index (F_ST; above diagonal) and Nei's genetic distance (<i>D</i>; below diagonal) between populations of <i>T. b. rhodesiense</i> as defined by focus and time.

<p>Pairwise values of Wright's fixation index (F_ST; above diagonal) and Nei's genetic distance (<i>D</i>; below diagonal) between populations of <i>T. b. rhodesiense</i> as defined by focus and time.</p

Basic population genetic parameters of the four <i>T. b. rhodesiense</i> populations.

<p>n = ‘all samples/unique MLGs (n)’, respectively, p = proportion of polymorphic loci, A = mean allele number per locus, He = Expected heterozygosity, Ho = Observed heterozygosity, F_IS = fixation index; the first number in each cell is measurement with all samples, the second number is after removal of repeated genotypes.</p

Linkage equilibrium/disequilibrium in <i>T. b. rhodesiense</i> populations and the frequency of repeated genotypes.

<p>nd = not done, as analysis not appropriate.</p

Neighbour joining tree of isolates included in study, constructed using Nei's genetic distance.

<p>Significant separation of the Malawi population from those in Uganda is shown (bootstrap values are labelled for significant nodes) while within Uganda the three populations cannot be significantly resolved. Populations: Malawi = blue, Ug/Ke 61–97 = green, Soroti = yellow, Tororo = red.</p