VIPER may be downloaded free of charge at http://ncrr.pnl.gov/software/
Quantitative analysis of liquid chromatography (LC)-mass spectrometry (MS) and tandem mass spectrometry (MS/MS) data is essential to many proteomics studies. We have developed MASIC to accurately measure peptide abundances and LC elution times in LC-MS/MS analyses. This software program uses an efficient processing algorithm to quickly generate mass specific selected ion chromatograms from a dataset and provides an interactive browser that allows users to examine individual chromatograms with a variety of options.
We present a precursor ion independent top-down algorithm (PIITA) for use in automated assignment of protein identifications from tandem mass spectra of whole proteins. To acquire the data, we utilize data-dependent acquisition to select protein precursor ions eluting from a C4-based HPLC column for collision induced dissociation in the linear ion trap of an LTQ-Orbitrap mass spectrometer. Gas-phase fractionation is used to increase the number of acquired tandem mass spectra, all of which are recorded in the Orbitrap mass analyzer. To identify proteins, the PIITA algorithm compares deconvoluted, deisotoped, observed tandem mass spectra to all possible theoretical tandem mass spectra for each protein in a genomic sequence database without regard for measured parent ion mass. Only after a protein is identified, is any difference in measured and theoretical precursor mass used to identify and locate post-translation modifications. We demonstrate the application of PIITA to data generated via our wet-lab approach on a Salmonella typhimurium outer membrane extract and compare these results to bottom-up analysis. From these data, we identify 154 proteins by top-down analysis, 73 of which were not identified in a parallel bottom-up analysis. We also identify 201 unique isoforms of these 154 proteins at a false discovery rate (FDR) of Ͻ1%. (J Am Soc Mass
Introduction: Individuals after a transtibial amputation (TTA) are at risk to develop a hip flexion contracture, which may adversely affect future ambulation with a prosthesis. Although patients have traditionally been advised to lie prone to maintain or improve hip extension, compensatory pelvic tilting may occur in prone lying (PL). We sought to compare hip extension range of motion (ROM) in PL to the modified Thomas test (MTT) position, because research implies that, in the MTT, patients are better able to control for compensatory pelvic tilting. We hypothesized that individuals after a TTA would have a greater peak hip extension angle in the MTT position compared with the PL position. Methods: Ten individuals after a dysvascular TTA, mean age of 60 ± 8.42 years, participated in this study. The same physical therapist marked the femur and pelvis for goniometric measurement of peak hip extension angle by 12 raters blinded to each other's measurements. The markers remained unchanged as six raters measured all participants in PL and six different raters measured all participants in the MTT position.Results and Discussion: The intraclass correlation (ICC) indicated high interrater reliability between the raters for the PL and MTT positions (ICC = 0.985 for PL and 0.976 for MTT). The average peak hip extension angle in PL was −14.0°± 13.3°, standard error of mean = 4.3°; and in the MTT position was −8.6°± 15.3°, standard error of mean = 4.8°(the negative mean connotes that, on average, participants did not have hip extension to neutral for either condition). We found a mean of 5.4°± 6.6°more hip extension ROM for the MTT position compared with PL ( P = 0.028). Conclusions: Our findings show that, on average, patients after a TTA have significantly greater peak hip extension angle in the MTT position compared with the PL position. Thus, passive PL may not be as effective of a stretching position for preventing a hip flexion contracture after a TTA, because PL does not always extend the patient's hip to its maximum available ROM, due to the reduced ability to control the pelvis from tilting anteriorly. Clinical Relevance: Adequate hip flexor length is positively correlated with gait parameters, which include increased velocity and step length in people using a prosthesis after transtibial amputation. This study implies that the MTT position may be a better method for improving and maintaining hip flexor length over the traditional strategy of passive PL.
Background and Purpose: An accurate fall risk assessment is an important component of fall prevention, though a fall could occur during testing. To minimize this risk, different guarding methods are used, though there is disagreement regarding the optimal method. The purpose of this study was to compare the effect of 2 guarding methods, contact guarding (CG) and standby guarding (SG), on performance during the Functional Gait Assessment (FGA). We hypothesized that (1) there would not be a significant difference in FGA scores when comparing CG with SG, and (2) participants would not perceive a difference between the 2 guarding methods. Methods: Twenty-three community-dwelling older adults, mean age 73.6 (SD = 6.2) years, participated in this study. Each participant completed 2 trials of the FGA, one with CG and another with SG. Guarding for all trials was provided by the same experienced physical therapist (PT) for this within-subjects design. All trials were video recorded for review by 2 PT raters who were blinded to the purpose of the study. Results and Discussion: Functional Gait Assessment scores for the 2 PT raters indicated high internal agreement for both CG and SG conditions (CG: intraclass correlation coefficient [ICC] = 0.949; SG: ICC = 0.935), and CG FGA scores did not significantly differ from SG FGA scores (t 22 = 0.15, P = .882). Furthermore, none of the participants perceived a difference in guarding methods. Conclusions: The results of this study indicate that hands-on guarding does not significantly influence performance on the FGA when the guarding is provided by an experienced PT and the participant is a community-dwelling older adult.
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