Additional file 3: of Identification of key genes in human airway epithelial cells in response to respiratory pathogens using microarray analysis

The GSE48466 mRNA expression profile dataset. 12950 DEGs between normal and infected airway epithelial cells were identified. (XLSX 964 kb

Additional file 2: of Identification of key genes in human airway epithelial cells in response to respiratory pathogens using microarray analysis

The GSE6802 mRNA expression profile dataset. 1241 DEGs between normal and infected airway epithelial cells were identified. (XLSX 101 kb

Additional file 2: of Acute Penicillium marneffei infection stimulates host M1/M2a macrophages polarization in BALB/C mice

Title of data-raw data. Description of data- The raw data of Fig. 4, Fig. 5 and Fig. 6, please see Tables 1, 2, and 3, respectively. (DOCX 27 kb

The percentage of bacteria identified as definite (dark blue) and possible (light blue) causative agents in LRTI patients (for the full bacterial names see the legend of

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038743#pone-0038743-g002" target="_blank"><b>Figure 2</b></a><b>).</b> The patients are classified as: children, ≤14 yr; middle-aged adult, >14 yr but <70 yr; aged, ≥70 yr; AB, acute bronchitis; CAP, community acquired pneumonia; AECOPD, acute exacerbation of COPD; and AEBX, acute exacerbation of bronchiectasis.</p

Data Summary of qLAMP and culture assays.

<p>Note: The Abbreviations are: Ab, <i>A. baumannii</i>; Ec, <i>E. coli</i>; Hi, <i>H. influenzae</i>; Kp, <i>K. pneumoniae</i>; Pa, <i>P. aeruginosa</i>; Sa, <i>S. aureus</i>; Sm, <i>S. maltophilia</i>; and Sp, <i>S. pneumonia</i>.</p>*<p>indicates the number of patients whose positive culture was confirmed by one of the 4 culture-based tests.</p>**<p>indicate confirmation rate of the positive cultures by one of the 4 culture-based tests.</p>***<p>indicate the bacterial mortality due to refrigeration, storage, and transportation.</p

Relatedness between qLAMP and culture assays and cutoffs in different subgroups.

<p>Note: We only used the data from the three-time culture to test the consistency between qLAMP and culture assays. N and BX stand for not found and bronchiectasis, respectively.</p>*<p>In the piecewise linear regression of <i>S. pneumoniae</i> for child patients, all the detected titers were PCs (pathogen candidates), and no breakpoint was found. Therefore, the lowest titer detected in this subgroup is deemed as the upper cutoff.</p

qLAMP and culture result from LRTI patients.

<p>(A) The positive rates (the right vertical axis) of one-time culture (brown bar), three-time culture (blue bar), and quantitative LAMP (yellow bar) for the eight species in the panel (from the left: Ab, <i>A. baumannii</i>; <i>Ec, E. coli;</i> Hi, <i>H. influenzae;</i> Kp, <i>K. pneumoniae;</i> Pa, <i>P. aeruginosa;</i> Sa, <i>S. aureus</i>; Sm, <i>S. maltophilia;</i> and Sp, <i>S. pneumoniae</i>) detected from the number of patients (the left vertical axis). (B) The number of patients (the left vertical axis) who were tested positive for at least one bacterium in one-time culture, three-time culture, and qLAMP. Each bar is the sum of patient with single (blue bar) and multiple (yellow bar) species detected.</p

Examples of <i>S. pneumonia</i> showing the relationship between qLAMP and culture results (logistic regression) and cutoff determination based on competitive relationship (piece-wise linear regression).

<p>The horizontal axis displays the bacterial natural logarithmic titer in sputum sample. (A) Logistic regression curve (green line). Solid circles indicate patients; they are placed at the top of the chart when being test as positive and at the bottom of the chart when being tested as negative in the culture assays. The height and width of the bars display the frequency and the number of patients being tested positive in cultures, respectively. (B) Piecewise linear regression (black lines) of <i>S. pneumonia</i> in COPD patients. Open circles indicate patients; they are placed at the top of the chart when being PC (Pathogen Candidate) and at the bottom of the chart when NOT being PC.</p

The qLAMP-based diagnostic rates in LRTI patients and different subgroups.

<p>The qLAMP-based diagnostic rates in LRTI patients and different subgroups.</p

Comparison of demographic and clinical features of 17 fatal and 9 nonfatal H5N1 cases, China.

*<p>Medians were compared between fatal and survival cases with the Wilcoxon rank sum test. For categorical variables, percentages of cases in each category were compared with Fisher's exact test.</p>†<p>NA demotes not applicable.</p>‡<p>Two fatal H5N1 cases had underlying medical conditions, including a 24-year-old pregnant woman <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002985#pone.0002985-Shu1" target="_blank">[28]</a> and a 16-year-old male with a 10-year history of minimal change glomerulopathy. Two surviving H5N1 cases had underlying medical conditions, including a 26-year-old pregnant woman and a 44-year-old female with a ten-year history of chronic bronchitis [unpublished data, China CDC].</p>#<p>A higher proportion of cases survived that received any antiviral treatment compared to those that did not receive antivirals (67% [8/12 patients] vs 7% [1/14 patients], p = 0.003), and with a positive linear association: the Gamma coefficient equals 0.664 (p = 0.005) which indicate a positive correlation between antiviral therapy and disease outcome.</p>$<p>High-dose corticosteroid use was defined as ≥250 mg hydrocortisone or equivalent intravenous (IV) administration daily. For children <13 years old, high-dose corticosteroid use was defined as ≥5 mg hydrocortisone or equivalent IV/kg/day.</p>¶<p>[]: Indicates denominators for testing of fewer cases than full group.</p