CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions-1

<p><b>Copyright information:</b></p><p>Taken from "CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions"</p><p>http://www.biomedcentral.com/1471-2105/9/64</p><p>BMC Bioinformatics 2008;9():64-64.</p><p>Published online 29 Jan 2008</p><p>PMCID:PMC2253513.</p><p></p>des. The values for nodes , , , , , and are the same as node 's. Results for other nodes are not shown. Final identified clusters are delimited when the merging threshold 2.0 is used

CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions-0

<p><b>Copyright information:</b></p><p>Taken from "CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions"</p><p>http://www.biomedcentral.com/1471-2105/9/64</p><p>BMC Bioinformatics 2008;9():64-64.</p><p>Published online 29 Jan 2008</p><p>PMCID:PMC2253513.</p><p></p>des. The values for nodes , , , , , and are the same as node 's. Results for other nodes are not shown. Final identified clusters are delimited when the merging threshold 2.0 is used

Humoral Responses to Diverse Autoimmune Disease-Associated Antigens in Multiple Sclerosis

<div><p>To compare frequencies of autoreactive antibody responses to endogenous disease-associated antigens in healthy controls (HC), relapsing and progressive MS and to assess their associations with clinical and MRI measures of MS disease progression.</p><p>Methods</p><p>The study analyzed 969 serum samples from 315 HC, 411 relapsing remitting MS (RR-MS), 128 secondary progressive MS (SP-MS), 33 primary progressive MS (PP-MS) and 82 patients with other neurological diseases for autoantibodies against two putative MS antigens CSF114(Glc) and KIR4.1a and KIR4.1b and against 24 key endogenous antigens linked to diseases such as vasculitis, systemic sclerosis, rheumatoid arthritis, Sjogren’s syndrome, systemic lupus erythematosus, polymyositis, scleroderma, polymyositis, dermatomyositis, mixed connective tissue disease and primary biliary cirrhosis. Associations with disability and MRI measures of lesional injury and neurodegeneration were assessed.</p><p>Results</p><p>The frequencies of anti-KIR4.1a and anti-KIR4.1b peptide IgG positivity were 9.8% and 11.4% in HC compared to 4.9% and 7.5% in RR-MS, 8.6% for both peptides in SP-MS and 6.1% for both peptides in PP-MS (<i>p</i> = 0.13 for KIR4.1a and <i>p</i> = 0.34 for KIR4.1b), respectively. Antibodies against CSF114(Glc), KIR4.1a and KIR4.1b peptides were not associated with MS compared to HC, or with MS disease progression. <i>HLA DRB1</i>*15:01 positivity and anti-Epstein Barr virus antibodies, which are MS risk factors, were not associated with these putative MS antibodies.</p><p>Conclusions</p><p>Antibody responses to KIR4.1a and KIR4.1b peptides are not increased in MS compared to HC nor associated with MS disease progression. The frequencies of the diverse autoreactive antibodies investigated are similar in MS and HC.</p></div

Demographic, clinical, MRI characteristics and current disease-modifying therapies.

<p>* All continuous variables (age, disease duration, T2-LV, T1-LV) are mean ± standard deviation. For the ordinal EDSS, the median (inter-quartile range) are given.</p><p>^§ The remainder received other treatments.</p><p>Demographic, clinical, MRI characteristics and current disease-modifying therapies.</p

Frequency of positivity for different antibodies in healthy controls (HC), relapsing-remitting MS (RR-MS, includes CIS) and secondary progressive-MS (SP-MS includes secondary progressive MS, relapsing-remitting/secondary progressive MS), primary progressive MS (PP-MS includes primary relapsing MS) and Other Neurological Diseases (OND).

<p>* Pearson chi-square</p><p>Frequency of positivity for different antibodies in healthy controls (HC), relapsing-remitting MS (RR-MS, includes CIS) and secondary progressive-MS (SP-MS includes secondary progressive MS, relapsing-remitting/secondary progressive MS), primary progressive MS (PP-MS includes primary relapsing MS) and Other Neurological Diseases (OND).</p

Associations with MRI and clinical measures.

<p>EDSS: Expanded disability status scale; T2-LV: T2 lesion volume; T1-LV: T1 lesion volume; GMV: Normalized gray matter volume; WBV: Normalized whole brain volume. EDSS was analyzed with ordinal regression and the MRI variables were analyzed with linear regression. All analyses corrected for age, gender and type of MS. The Table entries summarize the unadjusted <i>p</i>-values from regression analyses. The <i>q</i>-values are shown in parentheses for cells with <i>p</i> ≤ 0.05</p><p>Associations with MRI and clinical measures.</p

Associations with <i>HLA DR*15</i>:<i>01</i>, anti-EBV-EBNA-1 quartiles and anti-EBV-VCA quartiles and anti-CMV positivity.

<p>* Anti-DNA positivity status was analyzed with logistic regression and the remaining titer variables were analyzed with linear regression. All analyses corrected for age, gender and type of MS.</p><p>The Table entries summarize the unadjusted <i>p</i>-values from regression analyses. The <i>q</i>-values are shown for cells with <i>p</i> ≤ 0.05.</p><p>Associations with <i>HLA DR*15</i>:<i>01</i>, anti-EBV-EBNA-1 quartiles and anti-EBV-VCA quartiles and anti-CMV positivity.</p

Antigenic targets and disease associations of antibodies assessed.

<p>SS: Sjogren’s Syndrome, SLE: Systemic lupus erythematosus, LDL: Low-density lipoprotein, MCTD: Mixed Connective Tissue Disease (MCTD), PBC: Primary biliary cirrhosis.</p><p>Antigenic targets and disease associations of antibodies assessed.</p

Additional file 1: Table S1. of Reserve-related activities and MRI metrics in multiple sclerosis patients and healthy controls: an observational study

Descriptive statistics of MRI measures. (XLS 10 kb

Additional file 2: Table S2. of Reserve-related activities and MRI metrics in multiple sclerosis patients and healthy controls: an observational study

Results of non-parametric tests comparing strenuous change groups in relapsing-remitting patients. (XLS 13 kb