Additional file 2: Table S1. of Pan-cancer analysis of systematic batch effects on somatic sequence variations

List of the MAFs used in the analysis. Table S2. List of 999 batch-biased variants in TCGA data. Table S3. List of batch-biased genes among the SMGs. (XLSX 111 kb

gtReport.txt

We conducted extreme-phenotype GWAS comparing CHB patients who achieved functional cure before age of 60 years and those who maintained high serum levels of HBsAg even after age of 60 years

Development and Validation of a Smartphone Addiction Scale (SAS)

<div><p>Objective</p><p>The aim of this study was to develop a self-diagnostic scale that could distinguish smartphone addicts based on the Korean self-diagnostic program for Internet addiction (K-scale) and the smartphone's own features. In addition, the reliability and validity of the smartphone addiction scale (SAS) was demonstrated.</p> <p>Methods</p><p>A total of 197 participants were selected from Nov. 2011 to Jan. 2012 to accomplish a set of questionnaires, including SAS, K-scale, modified Kimberly Young Internet addiction test (Y-scale), visual analogue scale (VAS), and substance dependence and abuse diagnosis of DSM-IV. There were 64 males and 133 females, with ages ranging from 18 to 53 years (M = 26.06; SD = 5.96). Factor analysis, internal-consistency test, t-test, ANOVA, and correlation analysis were conducted to verify the reliability and validity of SAS.</p> <p>Results</p><p>Based on the factor analysis results, the subscale “disturbance of reality testing” was removed, and six factors were left. The internal consistency and concurrent validity of SAS were verified (Cronbach's alpha = 0.967). SAS and its subscales were significantly correlated with K-scale and Y-scale. The VAS of each factor also showed a significant correlation with each subscale. In addition, differences were found in the job (p<0.05), education (p<0.05), and self-reported smartphone addiction scores (p<0.001) in SAS.</p> <p>Conclusions</p><p>This study developed the first scale of the smartphone addiction aspect of the diagnostic manual. This scale was proven to be relatively reliable and valid.</p> </div

Factor analysis of SAS.

*<p>A cutoff of 0.40 was used for inclusion.</p

Concurrent validity of SAS: Partial correlation analysis by controlling the level of education between the subscales of the SAS, K-scale, Y-scale, and VAS (N = 197).

**<p>p<.01</p

<em>Orientia tsutsugamushi</em> Subverts Dendritic Cell Functions by Escaping from Autophagy and Impairing Their Migration

<div><h3>Background</h3><p>Dendritic cells (DCs) are the most potent antigen-presenting cells that link innate and adaptive immune responses, playing a pivotal role in triggering antigen-specific immunity. Antigen uptake by DCs induces maturational changes that include increased surface expression of major histocompatibility complex (MHC) and costimulatory molecules. In addition, DCs actively migrate to regional lymph nodes and activate antigen-specific naive T cells after capturing antigens. We characterize the functional changes of DCs infected with <em>Orientia tsutsugamushi</em>, the causative agent of scrub typhus, since there is limited knowledge of the role played by DCs in <em>O. tsutsugamushi</em> infection.</p> <h3>Methodology/Principal Finding</h3><p><em>O. tsutsugamushi</em> efficiently infected bone marrow-derived DCs and induced surface expression of MHC II and costimulatory molecules. In addition, <em>O. tsutsugamushi</em> induced autophagy activation, but actively escaped from this innate defense system. Infected DCs also secreted cytokines and chemokines such as IL-6, IL-12, MCP5, MIP-1α, and RANTES. Furthermore, <em>in vitro</em> migration of DCs in the presence of a CCL19 gradient within a 3D collagen matrix was drastically impaired when infected with <em>O. tsutsugamushi</em>. The infected cells migrated much less efficiently into lymphatic vessels of ear dermis <em>ex vivo</em> when compared to LPS-stimulated DCs. <em>In vivo</em> migration of <em>O. tsutsugamushi</em>-infected DCs to regional lymph nodes was significantly impaired and similar to that of immature DCs. Finally, we found that MAP kinases involved in chemotactic signaling were differentially activated in <em>O. tsutsugamushi</em>-infected DCs.</p> <h3>Conclusion/Significance</h3><p>These results suggest that <em>O. tsutsugamushi</em> can target DCs to exploit these sentinel cells as replication reservoirs and delay or impair the functional maturation of DCs during the bacterial infection in mammals.</p> </div

Induction of autophagy in DCs infected with <i>O. tsutsugamushi</i>.

<p>A and B. DCs were infected with <i>O. tsutsugamushi</i> for indicated time periods and subjected to immunoblot analysis for LC3 and β-actin as a loading control. LC3 II/LC3 I ratios were determined by densitometry of the immunoblot results from three independent experiments. Error bar: mean+S.D. C. DCs were infected with live <i>O. tsutsugamushi</i> (OT) or UV-inactivated bacteria (UV-OT) for 2 h and stained with scrub typhus patients' sera and anti-LC3 antibody. Colocalization of <i>O. tsutsugamushi</i> (green) with autophagosomes (red) was analyzed by confocal microscopy. CNT: immature DC, DIC: differential interference contrast.</p

Differential activation of MAP kinases in <i>O. tsutsugamushi</i>-infected DCs upon exposure to CCL19.

<p>DCs were stimulated with <i>O. tsutsugamushi</i> (OT), or LPS for 18 h and then further incubated with CCL19 (200 ng/ml) for the indicated times. The activation of ERK and p38 MAP kinases was assessed by immunoblot using specific anti-phospho-ERK1/2 or phospho-p38 MAP kinases antibodies. ERK1/2, p38, and GAPDH were used as loading controls. CNT: immature DCs.</p

<i>In vitro</i> migration of DCs infected with <i>O. tsutsugamushi</i> in a 3D collagen matrix.

<p>A. Single cell tracking was performed using Manual Tracking Plugin with Image J software. Thirty cells were randomly selected and tracked for 4 h. B. Speed, directionality, and Euclidean distance parameters were calculated by analyzing the acquired data from the Chemotaxis and Migration Tool Plugin software. The graphs represent velocity, directionality, and Euclidean distance, respectively. Red bars represent mean values. *: <i>p</i><0.05, **: <i>p</i><0.01, CNT: immature DCs, OT: DCs infected with <i>O. tsutsugamushi</i>, UV-OT: DCs infected with UV-inactivated <i>O. tsutsugamushi</i>, LPS: DCs stimulated with LPS, OT/LPS: DCs stimulated with <i>O. tsutsugamushi</i> and LPS.</p