A clear correlation between the difference and the mean magnitude can be noticed for both groups.

<p>Dashed line y = 0 represents the line of equality, which stands for perfect agreement. (a) Regression based mean difference (bias) and 95% limits of agreement for the differences of the CD68⁺/CD3⁺ cell density ratios as determined by the 2D nucleus and 3D approaches in the non-smoker group. All values lie within the interval between the calculated 95% limits of agreement; (b) Regression based mean difference (bias) with 95% C.I. of the regression line (dotted) for the differences of the CD68⁺/CD3⁺ cell density ratios in the smoker group. The 95% C.I. includes several horizontal lines (slope = 0) so that the fitted linear model does not achieve the desired statistical significance. Two large outliers encircled; (c) Regression based mean difference (bias) and 95% limits of agreement for the differences of the CD68⁺/CD3⁺ cell density ratios as determined by the 2D nucleus and 3D approaches in the smoker group after removing the two large outliers. All values lie within the interval between the calculated 95% limits of agreement. Notice the similar slope to the fitted model in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092510#pone-0092510-g007" target="_blank">Figure 7a</a> (non-smoker group).</p

Schematic SUR sampling of the sections of a biopsy.

<p>After exhaustive sectioning, every three sections were mounted on numbered glass slides (1 to 28 in this example). With a random outset between the 1^st and the 9^th slide, nine slide samples, each consisting of every 9^th glass slide, were collected and stained.</p

2D profiles per unit area <i>versus</i> 3D numerical density.

<p>(a) T-lymphocytes, non-smokers, r = 0.84, <i>p</i> = 0.017; (b) T-lymphocytes, smokers, r = 0.96, <i>p</i><0.001; (c) macrophages, non-smokers, r_nucleus = 0.95, <i>p</i> = 0.001; r_cell = 0.76, <i>p</i> = 0.046; (d) macrophages, smokers, r_nucleus = 0.98, <i>p</i><0.001; r_cell = 0.89, <i>p</i> = 0.007</p

CD68⁺/CD3⁺ Cell Ratios by Group and Counting Design.

<p><i>Definition of abbreviations</i>: 3D  =  physical disector, 2D nucleus  =  counts of nuclear profiles, 2D cell  =  counts of cell profiles (with and without nucleus),  =  coefficient of error of the mean ratio estimate.</p

Physical disector (3D) and profile counting (2D) within a consecutive reference and look-up section.

<p>Red triangles mark cell profiles seen in the reference section which are not present in the look-up section (bidirectional counting); green circles mark all cell profiles seen in the right section; yellow squares mark each assessed counting frame/field of view. The cell profile cutting the lower exclusion (red) line is not counted either in 3D or in 2D.</p

Mean CD68⁺/CD3⁺ cell density ratios (mean ± SEM) for each design and study group.

<p>Mean CD68⁺/CD3⁺ cell density ratios (mean ± SEM) for each design and study group.</p

Quantitative Morphological Data by Group and Cell Type.

<p><i>Definition of abbreviations</i>: N_V  =  numerical density, N_{A nucleus}  =  nuclear profile per unit area, N_{A cell}  =  cell profile per unit area,  =  coefficient of error of the mean estimate, N. A.  =  not analysed</p

Mean counts per unit volume and area (mean + SD) by group and cell population.

<p>Mean counts per unit volume and area (mean + SD) by group and cell population.</p

Subject Demographics.

<p>Subject Demographics.</p

Study design.

<p>Blood refers to the sample that was used for hematology and blood chemistry. Serum refers to the sample that was used for biomarker analysis. d = day.</p