Journal: PLoS Neglected Tropical Diseases

Article Title: Multi-parameter approach to evaluate the timing of memory status after 17DD-YF primary vaccination

doi: 10.1371/journal.pntd.0006462

Figure Lengend Snippet: (A) Venn diagram analysis was carried out to identify the intersection of phenotypic/functional biomarkers amongst NV(day0), PV(day30-45), PV(year1-9) and PV(year10-11) and select those common attributes between PV(day30-45) and PV(year1-9), considered biomarkers of protection. Detailed Venn Diagram report is provided in the . (B) The performance indicators (cut-off, accuracy, sensitivity-Se and specificity-Sp) for the ten selected common biomarkers (eEfCD4, EMCD4, CMCD19, EMCD8, IFNCD4, IL-5CD8, TNFCD4, IFNCD8, TNFCD8 and IL-5CD4) are provided in the inserted table. (C) Heatmap analysis was carried out to illustrate the profile of phenotypic/functional biomarkers common at PV(day30-45) and PV(year1-9) as well as the mean index calculated considering all 10 phenotypic/functional biomarkers together and demonstrate the proportion (%) of volunteers presenting low (Green), median (Black) or high (Red) YF-Ag/CC index. Histograms were constructed to highlight the frequency of volunteers above the median YF-Ag/CC index (Red Curves). (D) Scatter plot were built to demonstrate the sensitivity (Red Circles) and specificity (Green Circles) of the mean index of 10 phenotypic/functional biomarkers, using the cut-off edge (Mean Index = 1.3) provided by the ROC curve analysis. (E) Memory diagram were constructed using the defined cut-off for phenotypic/functional biomarkers, the memory status was defined for each subject, considering the phenotypic/functional (Mean Index of 10 biomarkers >1.3) and PRNT (>2.9 Log mIU/mL, according to Simões et al., 2012). Column statistics were used to calculate the proportion of subjects displaying distinct status of resultant memory, referred as none, phenotypic/functional biomarkers—P&F, PRNT and both. (F) The resultant memory for the 10 phenotypic/functional biomarkers and PRNT was displayed on bar charts. Significant differences at p<0.05 (Chi-square test) of resultant status amongst study groups were represented by letters “a”, b”, “c” and “d” in comparison to NV(day0), PV(day30-45), PV(year1-9) and PV(year10-11), respectively.

Article Snippet: Additional analysis was carried out employing Venn diagram ( http://bioinformatics.psb.ugent.be/webtools/Venn/ ), ROC curve (MedCalc software package, Version 7.3.0.0), heatmap (R Project for Statistical Computing Version 3.0.1) and decision tree J48 algorithm (present in WEKA software version 3.6.11).

Techniques: Functional Assay, Construct, Comparison

Journal: PLoS Neglected Tropical Diseases

Article Title: Multi-parameter approach to evaluate the timing of memory status after 17DD-YF primary vaccination

doi: 10.1371/journal.pntd.0006462

Figure Lengend Snippet: (A) Decision tree analysis was carried out to identify root attributes [Ellipses] for phenotypic/functional (P&F) biomarkers amongst NV(day0)&PV(year10-11) [white rectangle] and PV(day30-45)&PV(year1-9) [black rectangle], considered biomarkers to discriminate unprotected from protected subjects. Leave-one-out-cross-validation analysis (LOOCV) was employed to minimize biased performance estimates by using all data set for decision tree model fitting. EMCD8 and IL-5CD4 were selected as major phenotypic and functional 17DD-YF Memory-related biomarkers, respectively. (B) Heatmaps were built, taking the mean index of the top-two phenotypic/functional biomarkers (EMCD8 & IL-5CD4) and demonstrating the proportion (%) of volunteers ranging from low (White) to high (Gray) YF-Ag/CC index. A scatter plot was constructed to show the sensitivity (Gray Circle) and specificity (White Circle) of the top-two biomarkers, employing the cut-off edge (Mean Index = 1.3) provided by the ROC curve analysis. (C) Resultant memory status was defined for each subject, considering the top-two biomarkers (Mean Index >1.3) and PRNT (>2.9 Log mIU/mL, according to Simões et al., 2012). Column statistics were used to calculate the proportion of subjects displaying differing categories of resultant memory, referred as none, top-two biomarkers—P&F, PRNT and both. (D) Pie charts illustrated the overall resultant memory status within each category, as determined by the top-two biomarkers and PRNT. Significant differences at p<0.05 (Chi-square test) of resultant memory status amongst study groups were represented by letters “a”, b”, “c” and “d” in comparison to NV(day0), PV(day30-45), PV(year1-9) and PV(year10-11), respectively.

Article Snippet: Additional analysis was carried out employing Venn diagram ( http://bioinformatics.psb.ugent.be/webtools/Venn/ ), ROC curve (MedCalc software package, Version 7.3.0.0), heatmap (R Project for Statistical Computing Version 3.0.1) and decision tree J48 algorithm (present in WEKA software version 3.6.11).

Techniques: Functional Assay, Biomarker Discovery, Construct, Comparison