Efficiency of 3 classifier proteins; haptoglobin, apolipoprotein A-I and retinol-binding protein for prediction of malaria (FM and VM) and leptospirosis (febrile control) was analyzed using receiver operating characteristic (ROC) curves [plot of true positives (sensitivity) vs false positives (1-specificity) for each possible cutoff] using GraphPad Prism software package (version 5.02). ROC curve analysis was performed for only those 3 classifier proteins (out of 6) for which absolute serum concentration values (immunoturbidimetric assay/ELISA) were measured. Sensitivity and specificity values for the marker proteins were calculated at different threshold points. Two-sided p-values less than 0.05 were considered statistically significant. Figure S1 Evaluation of the depletion efficiency for albumin and IgG from human serum. Two major highabundance serum proteins; albumin and IgG were removed using Albumin & IgG Depletion SpinTrap (GE Healthcare) to reduce the dynamic range of serum protein concentration. (A) Levels of albumin and IgG in CBB stained 2D gel before and after depletion. 600 mg of total serum proteins were focused on linear pH 4-7 IPG strips (18 cm) and then separated on 12.5% polyacrylamide gels. Depletion of the top two high-abundance proteins (albumin and IgG) introduced nearly two-fold increase in overall spot number in 2D gels. (B) Levels of albumin and IgG in CBB stained 1D-SDS-PAGE gel before and after depletion showing the efficiency of the depletion process. 10 mg of total crude [C] and depleted [D] serum proteins were loaded onto each lane and separated on 10% polyacrylamide gels. (C) Densitometric analysis of the 1D-SDS-PAGE gels revealed around 85% and 80% depletion of albumin and IgG respectively. (PDF) Figure S2 Trends of differentially expressed proteins in falciparum malaria patients visualized in 2DE gels. (A) Representative 2D gels of serum from healthy controls and FM patients. 600 mg of total serum proteins were focused on linear pH 4-7 IPG strips (18 cm) and then separated on 12.5% polyacrylamide gels, which were stained with Gel Code Blue Stain. Protein spots exhibiting significantly altered expression levels are marked on the gels. Down (B) and up (C) -regulation of protein expression levels in FM patients. The 3D images of statistically significant (p,0.05) differentially expressed spots were analyzed using IMP7 software. Data is represented as mean 6 SEM (where n = 20). (PDF) Figure S6 IPA defined interaction networks associated with the differentially expressed proteins in falciparum malaria. Differentially expressed serum proteins identified in FM patients were entered as focus molecules in the analytical software to generate biological processes, pathways and molecular networks associated with the identified proteins. (A) The top-scoring network (score 35); cell signaling, molecular transport, vitamin and mineral metabolism. This network incorporated 14 out of the 27 differentially expressed proteins (focus molecules), (B) The second net-work; lipid metabolism, molecular transport, small molecule biochemistry (score 23). This network incorporated 10 focus molecules. Green and red symbols represent proteins that were down and up-regulated in falciparum malaria, respectively (identified in this study). White symbols represent associated proteins identified in the functional analysis for which the difference in expression level did not achieve statistical significance in our study. (PDF) Figure S7 Gene Ontology (GO) terms for molecular functions, cellular components and biological processes associated with the differentially expressed serum proteins identified in falciparum malaria. A total of 1394 Gene Ontology (GO) terms were identified, of which the distribution of second level of GO terms that were enriched in two or more proteins is shown as molecular functions (A) and cellular components (B) and biological processes (C). (PDF) Figure S8 Biological process regulated by differentially expressed serum proteins identified in falciparum and vivax malaria patients. Regulations were based on Natural Language Processing performed on MEDLINE abstracts as available in GeneSpring software package (version 11.5, Agilent Technologies). Identified process (A) common in both the plasmodial infections (B) specific for P. falciparum (C) specific for P. vivax infection. Red triangles and blue squares represent positive and negative regulations, respectively. (PDF) Figure S9 Discrimination of falciparum and vivax malaria from healthy controls on the basis of differential expressions of selected serum proteins. PLS-DA scores plot for (A) FM (red spheres, n = 10) and HC (green spheres, n = 10) samples, based on 5 differentially expressed proteins (Table  S8 .1A) identified using 2DE, (B) FM (red spheres, n = 6), VM (blue spheres, n = 5) and HC (green spheres, n = 5) samples based on 7 differentially expressed proteins (Table S8.  Novel Method for Isolation of Murine Clara Cell Secretory Protein-Expressing Cells with Traces of Stemness Clara cells are non-ciliated, secretory bronchiolar epithelial cells that serve to detoxify harmful inhaled substances. Clara cells also function as stem/progenitor cells for repair in the bronchioles. Clara cell secretory protein (CCSP) is specifically expressed in pulmonary Clara cells and is widely used as a Clara cell marker. In addition CCSP promoter is commonly used to direct gene expression into the lung in transgenic models. The discovery of CCSP immunoreactivity in plasma membranes of airway lining cells prompted us to explore the possibility of enriching Clara cells by flow cytometry. We established a novel and simple method for the isolation of CCSP-expressing cell Clara cells using a combination of mechanical and enzymatic dissociation followed by flow cytometry sorting technology. We showed that ∼25% of dissociated cells from whole lung expressed CCSP. In the resulting preparation, up to 98% of cells expressed CCSP. Notably, we found that several common stem cell markers including CD44, CD133, Sca-1 and Sox2 were expressed in CCSP(+) cells. Moreover, CCSP(+) cells were able to form spheroid colonies in vitro with 0.97‰ efficiency. Parallel studies in vivo confirmed that a small population of CCSP(−)expressing cells in mouse airways also demonstrates stem cell-like properties such as label retention and harboring rare bronchioalveolar stem cells (BASCs) in terminal bronchioles (TBs). We conclude that CCSP(+) cells exhibit a number of stem cell-like features including stem cell marker expression, bronchosphere colony formation and self-renewal ability. Clara cell isolation by flow cytometry sorting is a useful method for investigating the function of primary Clara cells in stem cell research and mouse models. Human lungs are composed of three functional and morphological compartments: proximal and distal airways and the alveolar compartment. Proximal airways are lined by a pseudostratified epithelium with a number of cell types with important protective functions such as ciliated cells, goblet cells, and basal cells. More distally, the lining is a simplified columnar epithelium largely made up of non-ciliated secretory cells called Clara cells, and a few ciliated and basal cells. [1, 2] . Further down, the respiratory bronchioles are lined by cuboidal epithelium comprised entirely of ciliated and Clara cells, whereas, the epithelium of the alveolar compartment is comprised of type I and type II cells. In mouse, the pseudostratified epithelium is limited to trachea and extrapulmonary main bronchi while Clara cells make up over 80% of the epithelium, with few interspersed ciliated cells, that line intrapulmonary conducting airways [3] . These features make mouse an excellent tool for studying the functions of Clara cells.