A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation

Background: A Java™ application is presented, which compares large numbers (n > 100) of raw FTICR mass spectra from patients and controls. Two peptide profile matrices can be produced simultaneously, one with occurrences of peptide masses in samples and another with the intensity of common peak masses in all the measured samples, using the peak- and background intensities of the raw data. In latter way, more significantly differentially expressed peptides are found between groups than just using the presence or absence in samples of common peak masses. The software application is tested by searching angiogenesis related proteins in glioma by comparing laser capture micro dissected- and enzymatic by trypsin digested tissue sections. Results: By hierarchical clustering of the presence-absence matrix, it appears that proteins, such as hemoglobin alpha and delta subunit, fibrinogen beta and gamma chain precursor, tubulin specific chaperone A, epidermal fatty acid binding protein, neutrophil gelatinase-associated lipocalin prec

Hoffa's fat pad resection during total knee arthroplasty does not affect functioning and gait:a double-blind randomized clinical trial

INTRODUCTION: Hoffa's fat pad is considered a source of anterior knee pain and may limit prosthetic knee function. Resection of Hoffa's fat pad in total knee arthroplasty (TKA), however, is controversial, and little is known about the functional outcomes including gait quality. This double-blind randomized controlled trial (i) compared functional recovery between TKAs where Hoffa was resected or preserved, and (ii) compared recovery of self-reported function with objective (gait-related) outcomes.MATERIALS AND METHODS: Eighty-five patients (age 66.4 ± 8.0 years, 47% women) scheduled to undergo TKA for primary osteoarthritis were randomly assigned to either fat pad resection or preservation. Subjective measures of functioning were assessed at baseline, 6 weeks, 3 months, and 12 months postoperatively and included the Knee Injury and Osteoarthritis Outcome Score (KOOS), Kujala, and visual analog scale (VAS) for pain. Objective measures of functioning were assessed at baseline, 3 months, and 12 months postoperatively and included instrumented range-of-motion and gait analysis. Longitudinal analyses (generalized estimating equations) were used to compare recovery between groups, and chi-square tests compared attainment of minimal clinical important difference (MCID) and patient acceptable symptom state (PASS). Finally, correlation analyses explored associations between subjective and objective recovery in function.RESULTS: Resection patients showed poorer improvement in KOOS quality of life in the first 6 weeks (B=-10.02, 95% confidence interval (CI) [-18.91, -1.12], p = .027), but stronger improvement in knee extension after 3 months (B = 3.02, 95%CI [0.45, 5.60], p = .021) compared to preservation patients. Regarding MCID or PASS, no differences were noted between groups at 3 and 12 months (all p &gt; .05). Subjective function substantially improved in the first 3 months, while objective outcomes improved only between 3 and 12 months. Moderate to strong correlations were identified between changes in knee flexion and gait with Kujala and KOOS in the resection but not in the preservation group.CONCLUSIONS: Similar functional outcomes were achieved after TKA with or without resection of Hoffa's fat pad. Hence, removing the fat pad to promote surgical exposure will not affect functional outcomes including gait quality. Functional recovery of objective outcomes was not always consistent with subjective recovery, suggesting that both self-reported as well as objective, gait-related outcomes may provide meaningful information on functional recovery following TKA.TRIAL REGISTRATION: This clinical trial was prospectively registered under the Netherlands Trial Registry (# NL3638). This registry has recently been replaced by the Dutch Trial Registry where this study can be accessed via https://onderzoekmetmensen.nl/en/trial/20994 .</p

A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation-3

<p><b>Copyright information:</b></p><p>Taken from "A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation"</p><p>http://www.biomedcentral.com/1471-2105/9/133</p><p>BMC Bioinformatics 2008;9():133-133.</p><p>Published online 1 Mar 2008</p><p>PMCID:PMC2323386.</p><p></p

A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation-2

1154.7128 Da, represented by the grey lines, is as expected not present in Glioma vessels.<p><b>Copyright information:</b></p><p>Taken from "A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation"</p><p>http://www.biomedcentral.com/1471-2105/9/133</p><p>BMC Bioinformatics 2008;9():133-133.</p><p>Published online 1 Mar 2008</p><p>PMCID:PMC2323386.</p><p></p

A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation-0

Ioma vessels with codes TH1 to TH10, 10 spectra of normal vessels with codes S1 to S10, and 10 spectra of tissue surrounding the normal vessels with codes TS1 to TS10 are included. Two "normal vessels" samples, S5 and TS5, were excluded because they could not be calibrated. The highlighted box in Figure 3 represents the hierarchical clustering order 490 with mass 1037.5355 Da to 789 with mass 1665.7891 Da as presented (see Additional file ).<p><b>Copyright information:</b></p><p>Taken from "A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation"</p><p>http://www.biomedcentral.com/1471-2105/9/133</p><p>BMC Bioinformatics 2008;9():133-133.</p><p>Published online 1 Mar 2008</p><p>PMCID:PMC2323386.</p><p></p

A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation-1

Phodiesterase at 1508.8739 Da represented by the grey lines is as expected not present in glioma vessels).<p><b>Copyright information:</b></p><p>Taken from "A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation"</p><p>http://www.biomedcentral.com/1471-2105/9/133</p><p>BMC Bioinformatics 2008;9():133-133.</p><p>Published online 1 Mar 2008</p><p>PMCID:PMC2323386.</p><p></p