Modular fulltext search for MySQL

An objective of the project is to develop a modular fulltext search engine using MySQL database server. The search engine should operate with the Czech language's specific attributes. There is no endeavor to develop high quality modules solving linguistic problems. Project should provide interface and ability to plug-in (plug-out) next modules. Project's software platform is Unix, programming language C++

Additional file 3: Table S2. of Allelic imbalance of multiple sclerosis susceptibility genes IKZF3 and IQGAP1 in human peripheral blood

Details of excluded measurements per investigated gene. (PDF 82 kb

Additional file 4: Figure S2. of Allelic imbalance of multiple sclerosis susceptibility genes IKZF3 and IQGAP1 in human peripheral blood

Allele-specific expression analyses of IKZF3 and IQGAP1 in samples from healthy controls. Allele-specific expression of the genes was normalised to the mean of all genomic DNA for (a) rs907091 in IKZF3 and (b) rs11609 in IQGAP1. Each bar represents five replicate measurements. Data are presented as the normalized change in Ct between the two alleles (nΔCt). nΔCt values above zero represent lower expression of the MS risk allele, whereas nΔCt values below zero represents higher expression of the MS risk allele. Error bars represent the standard error of the mean. A two-tailed unpaired Student’s t-test was used to compare each column with the gDNA measurement, P-values <0.05 are indicated with *. A > B = allele A expressed higher than B, A < B = allele A expressed lower than B. (TIF 84 kb

NOGO-A - MTR correlation parameters.

<p>NOGO-A - MTR correlation parameters.</p

NOGO-A count correlated to MTR value.

<p>Correlation between oligodendrocyte density, estimated from NOGO-A stained tissue, and MTR values. Dots represent animals, with MTR measurement taken imediately before the animal was sacrificed for histological staining.</p

Flow chart of the rostro-caudal gradient study.

<p>In the rostro-caudal gradient (RCG) study, we examined the seven following points of the RCG from a PSP patient: 1-2^nd, 10-11^th, 16-17^th, 24-25^th, 31-32^nd, 38-39^th and 44-45^th mL CSF, referred to as RCG point 1-7, respectively. Twelve samples were digested and iTRAQ labeled (114-117). A reference, (labeled with iTRAQ reagent 114) containing the same amount of each RCG point, was included in each experiment. The RCG points 1 and 7 were included twice. After digestion and iTRAQ-labeling, samples were combined as follows: Exp. 1 (reference, 44-45^th mL, 24-25^th mL and 1-2^nd mL), Exp. 2 (reference, 1-2^nd mL, 38-39^th mL and 16-17^th mL), and Exp. 3 (reference, 10-11^th mL, 44-45^th mL and the 31-32^nd mL). The three experiments were fractionated by mixed mode reversed phase-anion chromatography (MM (RP-AX)) and analyzed on an Orbitrap Velos Pro. The protein abundances were averaged for each protein in the duplicate samples.</p

PLP area correlated to MTR value.

<p>Correlation between myelin content, estimated from PLP stained tissue, and MTR values. Dots represent animals, with MTR measurement taken imediately before being sacrificed for histological staining.</p

Longitudinal PLP area.

<p>Progression of myelin content over time, estimated from PLP stained tissue. Lateral in the corpus callosum (red ), medial in the corpus callosum (green ), in the deep gray matter (blue ) and in the cerebral cortex (black ).</p

LMER model parameters.

<p>LMER model parameters.</p

Categorization of proteins based on fold change, R-squared values and major expected contributing source of origin.

<p>In order to explore how different proteins were affected by the rostro-caudal gradient, we used the fold change and R-squared values of the proteins quantified with SID-MRM and iTRAQ to categorize the proteins into the three categories: affected by the RCG, unaffected by the RCG and uncertain. The fold change was calculated between the 1-2^nd and 44-45^th mL of CSF (referred to as RCG point 1 and 7), and the classification was based on the criteria from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090429#pone-0090429-t001" target="_blank">Table 1</a>.The proteins are also categorized into groups based on the major expected contributing source of origin, with Uniprot as the primary reference unless otherwise stated. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090429#pone.0090429.s006" target="_blank">Table S5</a> for details. The asterisk (*) marks conflicting results: affected + unaffected  =  uncertain; affected + uncertain  =  affected; unaffected + uncertain  =  unaffected. Proteins only quantified in the SID-MRM study is marked with ^a.</p