Parameters for CRFs in training and testing.

<p>We use Stanford CRFs with the following settings in the experiment.</p

Testing results on GENIA data by four approaches.

<p>SVM-CRFs¹ refers to the SVM-CRFs without amending and SVM-CRFs² is SVM-CRFs with amending. P, R and F1 are precision, recall, and F1 respectively.</p

Fold change in the expression profiles of some important immune function related genes induced by <i>S</i>. <i>aureus</i> and <i>S</i>. <i>aureus</i> + PG treatments.

<p>Fold change in the expression profiles of some important immune function related genes induced by <i>S</i>. <i>aureus</i> and <i>S</i>. <i>aureus</i> + PG treatments.</p

Transmission electron microscopy (TEM) analysis of RAW264.7 cells infected with <i>S</i>. <i>aureus</i>.

<p>The RAW264.7 cells were either not infected or infected with <i>S</i>. <i>aureus</i> alone or in combination with PG for two different time points. The upper panel shows the pictures by TEM after 1 h of <i>S</i>. <i>aureus</i> infection, while lower panel depicts the same after 24 h. Bar = 2 μm. Black arrow indicated the internalized <i>S</i>. <i>aureus</i>.</p

Testing results on JNLPBA04 data by four approaches.

<p>SVM- CRFs¹ refers to the SVM-CRFs without amending and SVM-CRFs2 is SVM-CRFs with amending. P, R and F1 are precision, recall, and F₁ respectively.</p

The gene expression profile microarray analysis.

<p>The gene expression profile analysis was performed using mouse DNA microarray chip using RNA isolated from RAW264.7 cells either treated with <i>S</i>. <i>aureus</i> or <i>S</i>. <i>aureus</i> + PG. Non-treated RAW264.7 cells were used as a control. Red signal indicates up-regulation of gene expression, while green signal depicts down-regulation.</p

Fold change in the expression profiles of the Toll pathway related genes induced by <i>S</i>. <i>aureus</i> and <i>S</i>. <i>aureus</i> +PG treatments.

<p>Fold change in the expression profiles of the Toll pathway related genes induced by <i>S</i>. <i>aureus</i> and <i>S</i>. <i>aureus</i> +PG treatments.</p

The expression profiles of immune genes in <i>Mus musculus</i> macrophages during <i>Staphylococcus aureus</i> infection

<div><p><i>Staphylococcus aureus</i> is an important pathogen which is often the cause of major morbidity and mortality in both hospital and community settings. For this reason, we investigated the host cell early immune resoponse to <i>S</i>. <i>aureus</i> infection using genome-wide analysis. To do this, we infected <i>Mus musculus</i> RAW264.7 cells with <i>S</i>. <i>aureus</i> alone or in the presence of free peptidoglycan (PG), which appears in the <i>S</i>. <i>aureus</i> cell wall. Post infection, we performed a genome-wide analysis of RAW246.7 cells to identify significant changes in the gene expression profile. Further, we analyzed the infected RAW246.7 cells with transmission electron microscopy looking for the presence of bacterial cells inside the host cell. We also used flow cytometry to determine whether cells had induced apoptosis. The results showed that <i>S</i>. <i>aureus</i> induced apoptosis in the RAW246.7 cells but did not effectively clear away intracellular bacteria cells. However, <i>S</i>. <i>aureus</i> + PG treatment inhibited the apoptosis and activated the host cell inflammation response, possibly involving NF-κB and JAK-STAT pathways, as identified by genome-wide analysis, in RAW246.7 cells. Our study demonstrated for the first time that an independent application of free PG was capable of activating immune responses the host cells.</p></div

Forward and backward probability squeezing takes the product of the probability obtained by forward inference and the probability obtained by backword inference.

<p>Here and are the transfer probability, while is the probability of taking .</p

Parameters for SVM in training and testing.

<p>We use LIB SVM with the following settings in the experiment. The basis function is exp(-gamma*|u-v|²).</p