Additional file 2: Table S2. of The addition of a sagittal image fusion improves the prostate cancer detection in a sensor-based MRI /ultrasound fusion guided targeted biopsy

Cancer Detection Rate and Gleason pattern in Group A and B excluding men with abnormal DRE and including only men with prior negative biopsy. (DOCX 19 kb

Effects of different normalization approaches on the expression of miR-200a and miR-20a.

<p>The relative expression of (A) miR-200a and (B) miR-20a as highly and moderately differentially expressed miRNAs, respectively was calculated using the following normalization strategies recommended by geNorm (a–c), NormFinder (d–f), BestKeeper (g), and RNU6B (h). The geNorm approaches were: (a) the four-reference-miRNA combination recommended as necessary number of reference miRNAs (miR-101, miR-125a-5p, miR-148b, miR-151-5p); (b) the three best ranked miRNAs according to their M values (miR-125a-5p, miR-148b, and miR-151-5p) and (c) the best two-gene-reference combination (miR-125a-5p, miR-151-5p). NormFinder normalization approaches were: (d) the best two reference gene combination (miR-125a-5p, Z30); (e) the three best ranked reference genes (miR-148b, miR-181b, miR-874); (f) the best single miRNA, miR-148b. BestKeeper normalization approach was (g) RNU48; (j) RNU6B as the most frequently recommended normalizer in bladder cancer studies. Values are given as arbitrary units; boxes (blank, nonmalignant tissue; black, malignant tissue) represent lower and upper quartiles with medians as horizontal line; whiskers depict the 10–90 percentiles. Significances are illustrated as <i>P</i> values of the Mann-Whitney <i>U</i> test.</p

Ranking of candidate reference miRNAs and small RNAs in human nonmalignant and malignant bladder tissues according to their stability value using geNorm, NormFinder, and BestKeeper algorithms.

&<p>High expression stability is indicated by low stability value.</p>#<p>SD [±x-fold]: standard deviation of the absolute regulation coefficients. SD >1 can be considered inconsistent.</p

geNorm analysis of RT-qPCR-based candidate reference genes.

<p>(A) The geNorm analysis shows the calculation of the average expression stability value M of all candidate reference genes determined by RT-qPCR. Genes with the highest M value have the least stable expression, while the genes with the lowest M value have the most stable expression. The x-axis presents the ranking of reference genes in order of increasing stability from left to the right. (B) Calculation of the optimal number of reference genes for normalization. geNorm calculates a normalization factor assessing the optimal number of reference genes for generating that factor. The normalization factor is calculated from at least two genes taking into account the variable V as the average pairwise variation (V_NF) between two sequential normalization factors. The thin broken line illustrates the cut-off value V_NF <0.15. In this experiment, the optimal number of reference genes was four (V4/5). geNorm shows the variation of the normalization factor of four genes as the best combination (miR-101, miR-148b; miR-125a-5p, and miR-151-5p) in relation to five genes as shown in (A) and in the following order. All the results are presented according to the output files of the geNorm program.</p

Expression of candidate reference genes in human nonmalignant and malignant bladder tissue samples.

<p>RT-qPCR analyses were performed from 17 nonmalignant bladder tissue samples and 41 samples from low-grade and high-grade papillary urothelial carcinoma. Expression levels of the candidate reference genes are given as arbitrary units. Boxes (blank, nonmalignant samples; black, malignant samples) represent lower and upper quartiles with median as horizontal line; whiskers depict the 10 and 90 percentiles. Significances are illustrated as <i>P</i> values of the Mann-Whitney <i>U</i> test.</p

Candidate reference miRNAs selected from microarray analysis.^†

†<p>The TaqMan MicroRNA Assay ID, miRBase accession number, and the sequence for each miRNA are compiled in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039309#pone.0039309.s002" target="_blank">Table S2</a>.</p>&<p>miRNAs marked in Italics were not included in further analyses because their low expression level was beyond the dynamic range of the assay (>35Cq) (further details see text).</p>#<p>The miRNA ID from the miRBase version 10.1 and 18, respectively.</p>§<p>Symbols “N” and “R” indicate the selection of the candidate reference miRNAs based on normalized or raw microarray data as described in the text.</p

Association between (A) the maximum urinary calprotectin increase and ischaemic time and (B) the maximum urinary NGAL increase and ischaemic time in Group 1 (NSS with renal ischaemia) in a linear regression model, as assessed by Spearman’s correlation test.

<p>Regression lines are plotted. Linear regression model: A: R = 0.16, B = 103.61 (95% CI -219.96–427.19), p = 0.51; B: R = 0.09, B = 1.71 (95% CI -7.88–11.31), p = 0.71. Spearman’s correlation: A: R = 0.29 (95% CI -0.19–0.66), p = 0.21; B: R = 0.26 (95% CI -0.22–0.64), p = 0.26. NSS, nephron sparing surgery for kidney tumours; B, regression co-efficient, slope of the regression line; R, correlation co-efficient; CI, confidence interval.</p

Concentrations of (A) urinary calprotectin, (B) urinary neutrophil gelatinase—associated lipocalin (NGAL), (C) plasma creatinine, and (D) the estimated glomerular filtration rate (eGFR) in patients undergoing nephron sparing surgery (NSS) for kidney tumours with renal pedicle clamping (renal ischaemia, Group 1) or without renal ischaemia (Group 2), and in patients undergoing radical nephrectomy for living kidney donation (Group 3).

<p>Data are presented as median and interquartile range. Asterisks indicate significant changes from baseline in a non-parametric analysis of variance (Kruskal-Wallis test, corrected for multiple comparisons by Dunn’s test as a post hoc pairwise multiple comparison). p.o., post-operative. * p < 0.05, ** p < 0.01, *** p < 0.001.</p