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Additional file 6: Table S3. Abundances of taxa in responders vs nonresponders. Relative abundances of significantly different taxa (only < 0.9 or > 1.1 fold shown) between responders and nonresponders at baseline. Median relative abundance (percentage) is shown, also the ratio between the medians of responders and nonresponders and the p-value are given

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Additional file 4: Table S2. Characteristics of successful FMTs vs unsuccessful FMTs. Characteristics of successful FMTs vs unsuccessful FMTs

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Additional file 5: Figure S1. Heat map of change in responders vs nonresponders. Heatmap showing fold change in microbiota abundance of significantly different species between responders and non-responders before versus after FMT. FMTs are shown, therefore patients who have received 2 FMTs are shown twice. Faecalibacterium 1 and 2 are both subgroups of the Faecalibacterium genus. Faecalibacterium 1 is the genus in the strict sense, whereas the Faecalibacterium 2 group includes uncultured bacteria related to the phylotypes Eldhufec289, Eldhufec276 and Eldhufec259

Role of Tumor Necrosis Factor-α in the Human Systemic Endotoxin-Induced Transcriptome

<div><p>TNFα has been implicated in the pathogenesis of various inflammatory diseases. Different strategies to inhibit TNFα in patients with sepsis and chronic inflammatory conditions have shown contrasting outcomes. Although TNFα inhibitors are widely used in clinical practice, the impact of TNFα antagonism on white blood cell gene expression profiles during acute inflammation in humans <i>in vivo</i> has not been assessed. We here leveraged the established model of human endotoxemia to examine the effect of the TNFα antagonist, etanercept, on the genome-wide transcriptional responses in circulating leukocytes induced by intravenous LPS administration in male subjects. Etanercept pre-treatment resulted in a markedly dampened transcriptional response to LPS. Gene co-expression network analysis revealed this LPS-induced transcriptome can be categorized as TNFα responsive and non-responsive modules. Highly significant TNFα responsive modules include NF-kB signaling, antiviral responses and T-cell mediated responses. Within these TNFα responsive modules we delineate fundamental genes involved in epigenetic modifications, transcriptional initiation and elongation. Thus, we provide comprehensive information about molecular pathways that might be targeted by therapeutic interventions that seek to inhibit TNFα activity during human inflammatory diseases.</p></div

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Additional file 3: Table S1. Characteristics of responders vs nonresponders. Characteristics of responders vs nonresponders

Additional file 1: Table S1. of Carotid arterial wall inflammation in peripheral artery disease is augmented by type 2 diabetes: a cross-sectional study

Fontaine classification of PAD. Table S2. Linear regression analysis for insulin in diabetic subjects. Table S3. Medication use in PAD subjects. Table S4. Linear regression analysis for insulin in diabetic subjects. Figure S1. Target to Background ratio (TBRmean) did not correlate to plasma C-peptide levels. (PDF 53 kb

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Additional file 2: Table S4. Culture results in decolonized subjects. Rectal and urine cultures at follow-up (baseline, 1, 2 and 4 weeks after FMT)

Pulmonary tumor foci formation in syndencan-1 −/− versus wild type mice with and without treatment with LMWH.

<p>Syndecan-1 −/− and wild type mice were administered 2.0×10⁵ B16F10 melanoma cells into the lateral tail vein. One group of mice was treated with LMWH (15 mg/kg enoxaparin ) prior to the administration of B16F10 melanoma cells and LMWH treatment was repeated after 6, 12 and 24 h. Mice were sacrificed 14 days after cancer cell injection and the number of tumor foci at the surface of the lungs was determined. Error bars represent medians ± interquartile range (n = 8), * p<0.05; *** p<0.001.</p

TNFα responsive module hub (driver) genes and co-expression network visualization.

<p>Genes within transcriptional modules can be categorized as peripheral or hubs on the basis of how correlated a gene is with all other genes in the network, defined as the genes' connectivity measure, <b>k</b>. High intramodulr connectivities denote highly important module genes oftentimes possessing transcriptional factor activity. <b>A</b>. Unsupervised hierarchical clustering heatmap plot of the TNFα responsive module hub genes. Red denotes high expression; blue denotes low expression. The relative importance of each module within the co-expression network can be highlighted by unsupervised visualizations of each genes' weighted correlation coefficient. This was implemented in the Cytoscape® platform <b>B</b>. TNFα responsive co-expression modules were visualized by an organic layout considering weighted correlation coefficients >0.1 (equivalent to correlation coefficient >0.9).</p

Functional annotation and hub genes for the LPS-induced co-expression modules.

<p>LPS-induced transcriptome is organized into 38 co-expression network modules. Each module was analyzed for enrichment of biological pathways by IPA (Ingenuity® systems, <a href="http://www.ingenuity.com" target="_blank">www.ingenuity.com</a>).</p