Median Coefficient Of Variation Research Articles

Model based prediction of plateau pressure in mechanically ventilated patients

Abstract The risk of ventilator induced lung injury in mechanically ventilated (MV) critically ill patients can be mitigated by patient-specific optimisation of ventilator settings. Recent studies have shown that driving pressure, i.e. the difference between plateau pressure (Pplat ) and PEEP, is a strong indicator for survival in MV patients suffering from ARDS. However, to measure Pplat , an extended end-inspiratory pause (EIP) has to be applied, possibly interrupting ventilation therapy. This study presents a method for predicting Pplat from normal breaths in MV patients. A total of 859 MV breaths with a 5 second EIP were recorded in 27 MV patients with ARDS. Two methods for determining Pplat were tested, one using an exponential fit of the pressure data and the other using a four-parameter viscoelastic model (VEM). Each method was identified using various lengths of data after the peak inspiratory pressure (PIP). Using the identified parameters, both methods were then used to predict the Pplat recorded at 5 seconds. The exponential method showed a median coefficient of variation (CV) from the real Pplat of 42.9% using data from PIP to 0.5 seconds after PIP, 24.9% using 1 second of data and 15.2% using 1.5 seconds of data. The respective VEM prediction median CVs were of 17.2%, 9.7% and 8.4%. Therefore, the VEM showed a better prediction than the non-physiological exponential model, allowing it to be used to reduce the clinical burden of determining Pplat by reducing the required length of the EIP to 1.5 seconds.

Determinants and Regulation of Protein Turnover in Yeast.

Protein turnover maintains the recycling needs of theproteome, and its malfunction has been linked to aging and age-related diseases. However, not allproteins turnover equally, and the factors that contribute to accelerate or slow down turnover are mostly unknown. We measured turnover rates for 3,160 proteins in exponentially growing yeast and analyzed their dependence on physical, functional, and genetic properties. We found that functional characteristics, including protein localization, complex membership, and connectivity, have greater effect on turnover than sequence elements. We also found that protein turnover and mRNA turnover are correlated. Analysis under nutrient perturbation and osmotic stress revealed that protein turnover highly depends on cellular state and is faster when proteinsare being actively used. Finally, stress-induced changes in protein and transcript abundance correlated with changes in protein turnover. This study provides a resource of protein turnover rates and principles to understand the recycling needs of the proteome under basal conditions and perturbation.

Beat-to-beat variability of fetal myocardial performance index.

To determine whether there is beat-to-beat (BTB) variability in the fetal left myocardial performance index (MPI), as evaluated by an automated system, and whether there is a correlation between MPI and fetal heart rate (FHR). This was a prospective cross-sectional study of uncomplicated, morphologically normal, singleton pregnancies at 20-38 weeks' gestation. Multiple cineloops for left MPI measurement were acquired during a single examination of each fetus. Raw cineloop data were analyzed by our automated MPI system (intraclass correlation coefficient of 1.0 for any given waveform) to produce a set of MPIs. The corresponding instantaneous FHR was measured for each individual cardiac cycle for which MPI was calculated. Data from 29 fetuses were analyzed; mean MPI was 0.52, mean FHR was 150 beats per min and the median number of cardiac cycles examined per fetus was 70 (interquartile range, 31-115). Marked BTB variability was noted; median coefficient of variation was 10% (range, 5.5-13.9%). FHR was weakly correlated with absolute MPI (r = 0.22; P < 0.05). BTB variation in MPI as a percentage of the mean MPI was not significantly correlated with FHR (r = 0.031; P = 0.146). When standard error of the mean of all MPI values was divided by the mean for each case, it showed that at least four cardiac cycles should be averaged to reduce MPI variability to approximately ± 5%. There is significant BTB variability in fetal left MPI, which has an overall weak correlation with FHR. This could be a factor affecting the consistency of MPI values reported by different research groups. Variability would be reduced by averaging 4-5 cardiac cycles per fetus. Copyright © 2016 ISUOG. Published by John Wiley & Sons Ltd.

Variability in measures of mineral metabolism in children on hemodialysis: impact on clinical decision-making.

Variability in measures of mineral metabolism has not been studied in pediatric end stage kidney disease. We sought to determine the intra-individual variability in measures of mineral metabolism in children on hemodialysis (HD) and its impact on clinical decision-making. We conducted a prospective single-center study of children (3.6-17.3 years old) on chronic HD. Serial twice weekly measures of serum calcium, phosphate and intact parathyroid hormone (PTH), as well as weekly measures of fibroblast growth factor 23 (FGF23) and vitamin D metabolites, were obtained over a 12-week period in 10 children. Samples (n = 226) were assayed in a single batch at the end of the study. The median intra-individual coefficient of variation (CV) calculated by 4-week blocks was 5.1-6.5% for calcium, 9.5-14.9% for phosphate and 32.7-33.4% for PTH. The median overall CV for FGF23 was 44.4%. Using the first value of each block as a reference, subsequent values would dictate a discrepant management decision 33-56%, 19-28%, and 30-33% of the time for calcium, phosphate, and PTH, respectively. Adjusting for sex and age, most of the variability in phosphate and PTH was attributable to within-participant variability. For calcium, 49% of the variability was attributable to day of blood collection (Monday vs. Friday). The median (range) of an individual participant's values within clinical target ranges was 55% (26-86%) for calcium, 58% (0-96%) for phosphate, and 21% (0-64%) for PTH. There is considerable intra-individual variability in measures of mineral metabolism that serve as surrogate markers for bone health in children on HD. Within a 4-week period, at least 20-30% of measures would dictate a discrepant decision from the referent measure of that month. These findings have important implications for clinical decision-making and underscore the need to base therapeutic decisions on trends rather than single measurements.

Towards standardization of 18F-FET PET imaging: do we need a consistent method of background activity assessment?

BackgroundPET with O-(2-18F-fluoroethyl)-L-tyrosine (18F-FET) has reached increasing clinical significance for patients with brain neoplasms. For quantification of standard PET-derived parameters such as the tumor-to-background ratio, the background activity is assessed using a region of interest (ROI) or volume of interest (VOI) in unaffected brain tissue. However, there is no standardized approach regarding the assessment of the background reference. Therefore, we evaluated the intra- and inter-reader variability of commonly applied approaches for clinical 18F-FET PET reading.The background activity of 20 18F-FET PET scans was independently evaluated by 6 readers using a (i) simple 2D-ROI, (ii) spherical VOI with 3.0 cm diameter, and (iii) VOI consisting of crescent-shaped ROIs; each in the contralateral, non-affected hemisphere including white and gray matter in line with the European Association of Nuclear Medicine (EANM) and German guidelines. To assess intra-reader variability, each scan was evaluated 10 times by each reader. The coefficient of variation (CoV) was assessed for determination of intra- and inter-reader variability. In a second step, the best method was refined by instructions for a guided background activity assessment and validated by 10 further scans.ResultsCompared to the other approaches, the crescent-shaped VOIs revealed most stable results with the lowest intra-reader variabilities (median CoV 1.52%, spherical VOI 4.20%, 2D-ROI 3.69%; p < 0.001) and inter-reader variabilities (median CoV 2.14%, spherical VOI 4.02%, 2D-ROI 3.83%; p = 0.001). Using the guided background assessment, both intra-reader variabilities (median CoV 1.10%) and inter-reader variabilities (median CoV 1.19%) could be reduced even more.ConclusionsThe commonly applied methods for background activity assessment show different variability which might hamper 18F-FET PET quantification and comparability in multicenter settings. The proposed background activity assessment using a (guided) crescent-shaped VOI allows minimization of both intra- and inter-reader variability and might facilitate comprehensive methodological standardization of amino acid PET which is of interest in the light of the anticipated EANM technical guidelines.

Super-SILAC mix coupled with SIM/AIMS assays for targeted verification of phosphopeptides discovered in a large-scale phosphoproteome analysis of hepatocellular carcinoma

Plentiful studies have established a close association between aberrant phosphorylation and hepatocellular carcinoma (HCC). Here, we applied a quantitative phosphoproteomics platform combining dimethylation labeling and online 3D strong cation exchange chromatography (SCX)-titanium oxide (TiO2)/RP-LTQ-Orbitrap to compare phosphoproteomes between three pairs of HCC tissues and non-tumor counterparts. This analysis yielded 7868 quantifiable phosphopeptides and numerous up- or down-regulated candidates. Increased phosphorylation of LMNA and NIPA was confirmed using specific antibodies. To expand our verification capability, we evaluated the use of LTQ-Orbitrap run in SIM/Accurate inclusion mass screening (AIMS) mode with a super-SILAC mixture as an internal standard to quantify a subset of phosphopeptide candidates in HCC tissue samples. In sample I used for discovery experiment, we successfully quantified 32 (in SIM mode) and 30 (in AIMS mode) phosphopeptides with median coefficients of variation (CVs) of 7.5% and 8.3%, respectively. When the assay was applied to other three pairs of HCC specimens for verification experiment, 40 target phosphopeptides were quantified reliably (~7.5% CV), and more than half of them were differentially expressed between tumor and adjacent non-tumor tissues. Collectively, these results indicate the feasibility of using super-SILAC mix-SIM/AIMS assays for targeted verification of phosphopeptides discovered by large-scale phosphoproteome analyses of HCC specimens. SignificanceIn this study, we developed a strategy for conducting both discovery and targeted verification of deregulated phosphoproteins in HCC tissue specimens on LTQ-Orbitrap. This strategy allowed us to generate a quantitative HCC tissue phosphoproteome dataset containing significantly deregulated phosphoproteins that represents a valuable resource for the identification of potential HCC biomarkers and/or therapeutic targets. Furthermore, our proof-of-concept experiments demonstrated the feasibility of applying LTQ-Orbitrap, operated in SIM/AIMS mode, to multiplex and targeted verification of phosphopeptides in individual tissue specimens using a super-SILAC mix as an internal phosphopeptide standard. This method could be readily applied to verify dozens of phosphopeptide candidates in a larger HCC sample set.

Plasma protein absolute quantification by nano-LC Q-TOF UDMSE for clinical biomarker verification.

Background and aimsProteome-based biomarker studies are targeting proteins that could serve as diagnostic, prognosis, and prediction molecules. In the clinical routine, immunoassays are currently used for the absolute quantification of such biomarkers, with the major limitation that only one molecule can be targeted per assay. The aim of our study was to test a mass spectrometry based absolute quantification method for the verification of plasma protein sets which might serve as reliable biomarker panels for the clinical practice.MethodsSix EDTA plasma samples were analyzed after tryptic digestion using a high throughput data independent acquisition nano-LC Q-TOF UDMSE proteomics approach. Synthetic Escherichia coli standard peptides were spiked in each sample for the absolute quantification. Data analysis was performed using ProgenesisQI v2.0 software (Waters Corporation).ResultsOur method ensured absolute quantification of 242 non redundant plasma proteins in a single run analysis. The dynamic range covered was 105. 86% were represented by classical plasma proteins. The overall median coefficient of variation was 0.36, while a set of 63 proteins was found to be highly stable. Absolute protein concentrations strongly correlated with values reviewed in the literature.ConclusionsNano-LC Q-TOF UDMSE proteomic analysis can be used for a simple and rapid determination of absolute amounts of plasma proteins. A large number of plasma proteins could be analyzed, while a wide dynamic range was covered with low coefficient of variation at protein level. The method proved to be a reliable tool for the quantification of protein panel for biomarker verification in the clinical practice.

Interlaboratory Reproducibility of a Targeted Metabolomics Platform for Analysis of Human Serum and Plasma.

A critical question facing the field of metabolomics is whether data obtained from different centers can be effectively compared and combined. An important aspect of this is the interlaboratory precision (reproducibility) of the analytical protocols used. We analyzed human samples in six laboratories using different instrumentation but a common protocol (the AbsoluteIDQ p180 kit) for the measurement of 189 metabolites via liquid chromatography (LC) or flow injection analysis (FIA) coupled to tandem mass spectrometry (MS/MS). In spiked quality control (QC) samples 82% of metabolite measurements had an interlaboratory precision of <20%, while 83% of averaged individual laboratory measurements were accurate to within 20%. For 20 typical biological samples (serum and plasma from healthy individuals) the median interlaboratory coefficient of variation (CV) was 7.6%, with 85% of metabolites exhibiting a median interlaboratory CV of <20%. Precision was largely independent of the type of sample (serum or plasma) or the anticoagulant used but was reduced in a sample from a patient with dyslipidaemia. The median interlaboratory accuracy and precision of the assay for standard reference plasma (NIST SRM 1950) were 107% and 6.7%, respectively. Likely sources of irreproducibility were the near limit of detection (LOD) typical abundance of some metabolites and the degree of manual review and optimization of peak integration in the LC-MS/MS data after acquisition. Normalization to a reference material was crucial for the semi-quantitative FIA measurements. This is the first interlaboratory assessment of a widely used, targeted metabolomics assay illustrating the reproducibility of the protocol and how data generated on different instruments could be directly integrated in large-scale epidemiological studies.

Surface anatomical landmarks for the location of posterior sacral foramina in sacral nerve stimulation.

Sacral nerve stimulation is a common treatment for various pelvic floor disorders. It consists of the percutaneous introduction of electrodes through the posterior sacral foramina for therapeutic stimulation of the target sacral spinal nerve. The aim of our study was to determine the surface anatomical landmarks of the sacrum to facilitate identification of the posterior sacral foramina. This study was conducted on 20 human cadavers. The cadavers were placed in a prone position, and all the soft tissues of the sacral region were removed to allow exposure of the osseous structures. Different measurements were taken in relation to the posterior sacral foramina, the posterior superior iliac spine (PSIS) and the median sacral crest (MSC). A median coefficient of variation (CV) was determined. The diameter of the second sacral foramen showed the greatest variability. The distances between each individual foramen and the MSC had an acceptable variability (CV<20%). In contrast, the distance between foramina had a high variability. The distance between PSIS and the second posterior sacral foramen was also found to have an acceptable variability (CV<20%). However, the angle formed by an horizontal line between PSIS and a line between PSIS and S2 foramina had high variability. We found that the distance between sacral foramina and MSC is relatively constant while the distance between foramina and the relations between foramina and PSIS is highly variable. Detailed knowledge of the anatomy may facilitate electrode placement and is complementary to the regular use of fluoroscopy.

Potential Primary Endpoint for Exploratory Clinical Trial in Patients with Overactive Bladder: A Systematic Literature Review.

To identify a potential primary endpoint in an early-phase exploratory trial among key overactive bladder (OAB) symptoms. Placebo-controlled double-blinding trials in patients with OAB were extracted for systematic literature review. The correlation between key OAB symptoms recorded in bladder diaries and coefficient of variation (CV) in each study were assessed. Forty-one controlled trials were extracted for the present review. Mean number of urgency episodes in 24 h was substantially associated with mean number of urgency incontinence episodes in 24 h, mean volume voided per micturition, and mean number of micturitions in 24 h (Spearman's r = 0.725, -0.661, and 0.657, respectively). Mean number of micturitions in 24 h was also substantially associated with mean volume voided per micturition (Spearman's r = -0.674). Mean number of incontinence episodes in 24 h was substantially associated with mean number of urgency incontinence episodes in 24 h and mean volume voided per micturition (Spearman's r = 0.840 and -0.628, respectively). The median CV of mean volume voided per micturition in each trial was the smallest among all endpoints. Our findings suggest that volume voided per micturition is a useful symptom for evaluating OAB candidate compounds in a small sample size and represents an effective primary endpoint, especially in exploratory clinical trials.

Impact of volunteer-related and methodology-related factors on the reproducibility of brachial artery flow-mediated vasodilation

Brachial artery flow-mediated dilation (FMD) is a popular technique to examine endothelial function in humans. Identifying volunteer and methodological factors related to variation in FMD is important to improve measurement accuracy and applicability. Volunteer-related and methodology-related parameters were collected in 672 volunteers from eight affiliated centres worldwide who underwent repeated measures of FMD. All centres adopted contemporary expert-consensus guidelines for FMD assessment. After calculating the coefficient of variation (%) of the FMD for each individual, we constructed quartiles (n = 168 per quartile). Based on two regression models (volunteer-related factors and methodology-related factors), statistically significant components of these two models were added to a final regression model (calculated as β-coefficient and R). This allowed us to identify factors that independently contributed to the variation in FMD%. Median coefficient of variation was 17.5%, with healthy volunteers demonstrating a coefficient of variation 9.3%. Regression models revealed age (β = 0.248, P < 0.001), hypertension (β = 0.104, P < 0.001), dyslipidemia (β = 0.331, P < 0.001), time between measurements (β = 0.318, P < 0.001), lab experience (β = -0.133, P < 0.001) and baseline FMD% (β = 0.082, P < 0.05) as contributors to the coefficient of variation. After including all significant factors in the final model, we found that time between measurements, hypertension, baseline FMD% and lab experience with FMD independently predicted brachial artery variability (total R = 0.202). Although FMD% showed good reproducibility, larger variation was observed in conditions with longer time between measurements, hypertension, less experience and lower baseline FMD%. Accounting for these factors may improve FMD% variability.

Fifteen years of Belgian experience with external quality assessment of semen analysis.

Semen analysis is difficult to standardize, quality control and quality assurance are necessary to ensure that results are accurate and precise. This Belgian EQA survey over a 15-year period, involving 121 laboratories, attempted to reduce interlaboratory variability and at the same time, encouraged participating laboratories to implement correct techniques as advised by the WHO. Over the total period, the median coefficient of variation (CV) for sperm count, irrespective of the method used was 19.2%, while using improved Neubauer chamber resulted in a significantly (p<0.001) lower median CV (14.4%). The overall median CV for rapid progressive motility was high (37.1%), but progressive motility (15.1%) and total motility (13.8%) were acceptable. Sperm morphology revealed a large variability in 79.4% irrespective of the staining procedures or evaluation criteria used. Participation in the Belgian EQA is on voluntary basis. Both, participation and implementation of the correct techniques should be made mandatory for accreditation and benefit of patient treatment. The existing Belgian EQA program should now be harmonized with other existing EQA schemes in Europe.

Regional Flood Frequency Analysis using Support Vector Regression under historical and future climate

Summary Regional Flood Frequency Analysis (RFFA) is a statistical method widely used to estimate flood quantiles of catchments with limited streamflow data. In addition, to estimate the flood quantile of ungauged sites, there could be only a limited number of stations with complete dataset are available from hydrologically similar, surrounding catchments. Besides traditional regression based RFFA methods, recent applications of machine learning algorithms such as the artificial neural network (ANN) have shown encouraging results in regional flood quantile estimations. Another novel machine learning technique that is becoming widely applicable in the hydrologic community is the Support Vector Regression (SVR). In this study, an RFFA model based on SVR was developed to estimate regional flood quantiles for two study areas, one with 26 catchments located in southeastern British Columbia (BC) and another with 23 catchments located in southern Ontario (ON), Canada. The SVR-RFFA model for both study sites was developed from 13 sets of physiographic and climatic predictors for the historical period. The Ef (Nash Sutcliffe coefficient) and R2 of the SVR-RFFA model was about 0.7 when estimating flood quantiles of 10, 25, 50 and 100 year return periods which indicate satisfactory model performance in both study areas. In addition, the SVR-RFFA model also performed well based on other goodness-of-fit statistics such as BIAS (mean bias) and BIASr (relative BIAS). If the amount of data available for training RFFA models is limited, the SVR-RFFA model was found to perform better than an ANN based RFFA model, and with significantly lower median CV (coefficient of variation) of the estimated flood quantiles. The SVR-RFFA model was then used to project changes in flood quantiles over the two study areas under the impact of climate change using the RCP4.5 and RCP8.5 climate projections of five Coupled Model Intercomparison Project (CMIP5) GCMs (Global Climate Models) for the 2041–2100 period. The results suggest that due to a projected increase in the mean annual precipitation, and rainfall of a given return period, the flood quantile is projected to increase by about 7% for the southeastern BC and 29% for southern ON region in the mid- and late 21st century.

T1-weighted Dynamic Contrast-enhanced MR Imaging of the Lung in Asthma: Semiquantitative Analysis for the Assessment of Contrast Agent Kinetic Characteristics

To evaluate the contrast agent kinetics of dynamic contrast material-enhanced (DCE) magnetic resonance (MR) imaging in healthy lungs and asthmatic lungs by using non-model-based semiquantitative parameters and to explore the relationships with pulmonary function testing and eosinophil level. The study was approved by the National Research Ethical Committee (reference no. 11/NW/0387), and written informed consent was obtained from all individuals. Ten healthy subjects and 30 patients with asthma underwent pulmonary function tests, blood and sputum eosinophil counts, and 1.5-T DCE MR imaging within 7 days. Semiquantitative parameters of contrast agent kinetics were calculated from the relative signal intensity-time course curves on a pixel-by-pixel basis and were summarized by using whole-lung median values. The distribution heterogeneity was assessed by using the regional coefficient of variation. DCE MR imaging readouts were compared between groups by using one-way analysis of variance, and the relationships with pulmonary function testing and eosinophil counts were assessed by using Pearson correlation analysis. Asthmatic patients showed significantly lower peak enhancement (P < .001) and initial areas under the relative signal intensity curve in the first 60 seconds (P = .002) and significantly reduced late-phase washout slope (P = .002) when compared with healthy control subjects. The distribution heterogeneity of bolus arrival time (P = .029), time to peak (P = .008), upslope of the first-pass peak (P = .011), and late-phase washout slope (P = .032), estimated by using the median coefficient of variation, were significantly higher in asthmatic patients than in healthy control subjects. These imaging readouts also showed significant linear correlations with measurements of pulmonary function testing but not with eosinophil level in patients with asthma. The contrast agent kinetic characteristics of T1-weighted DCE MR images of asthmatic lungs are different from those of healthy lungs and are related to measurements of pulmonary function testing but not to eosinophil level.

The use of dried blood spot sampling for the measurement of HbA1c: a cross-sectional study.

BackgroundThe use of dried blood spot (DBS) sampling is an alternative to traditional venous blood collection, and particularly useful for people living in rural and remote areas, and for those who are infirm, house-bound or time-poor. The objective of this study was to assess whether the measurement of glycated haemoglobin A1c (HbA1c) in DBS samples provided comparative and acceptably precise results.MethodsVenous and capillary blood samples were collected from 115 adult participants. After proper instruction, each participant punctured his/her own finger and collected capillary blood samples on pieces of a proprietary cellulose filter paper. Each filter paper was subsequently placed inside a breathable envelope, stored at room temperature, and processed on the same day (D0), four (D4), seven (D7) and fourteen (D14) days after collection. HbA1c was measured in duplicates/triplicates in whole venous blood (WB), capillary blood (capDBS) and venous blood placed on the matrix paper (venDBS), by turbidimetric inhibition immunoassay. Intra-assay coefficients of variation (CV) were calculated. DBS values were compared to WB results using linear regression, Bland-Altman plots and cross-validation models.ResultsEleven and 56 patients had type 1 and type 2 diabetes mellitus, respectively. Mean HbA1c levels were 6.22 ± 1.11 % for WB samples (n = 115). The median intra-assay CV was lower than 3 % for WB and capDBS on all days. Results from capDBS and venDBS showed high correlation and agreement to WB results, with narrow 95 % limits of agreement (except for results from D14 samples), as observed in Bland-Altman plots. When capDBS values were applied to equations derived from regression analyses, results approached those of WB values. A cross-validation model showed that capDBS results on D0, D4 and D7 were close to the WB results, with prediction intervals that were narrow enough to be clinically acceptable.ConclusionsThe measurement of HbA1c from DBS samples provided results that were comparable to results from WB samples, if measured up to seven days after collection. Intra-assay coefficients of variation were low, results were in agreement with the gold-standard, and prediction intervals were clinically acceptable. The measurement of HbA1c through DBS sampling may be considered in situations where traditional venipuncture is not available.Trial registrationAustralian New Zealand Clinical Trials Registry ID ACTRN12613000769785.

Quantitative Assessment of Intra-Patient Variation in CD4+ T Cell Counts in Stable, Virologically-Suppressed, HIV-Infected Subjects.

ObjectivesCounts of absolute CD4+ T lymphocytes (CD4+ T cells) are known to be highly variable in untreated HIV-infected individuals, but there are no data in virologically-suppressed individuals. We investigated CD4+ T cell variability in stable, virologically-suppressed, HIV-1 infected adults on combination antiretroviral therapy (cART).MethodsFrom a large hospital database we selected patients with stable virological suppression on cART for >3 years with >10 CD4+ T cell measurements performed over a further >2 years; and a control group of 95 patients not on cART.ResultsWe identified 161 HIV-infected patients on cART without active HCV or HBV infection, with stable virological suppression for a median of 6.4 years. Over the study period 88 patients had reached a plateau in their absolute CD4+ T cell counts, while 65 patients had increasing and 8 patients had decreasing absolute CD4+ T cell counts. In patients with plateaued CD4+ T cell counts, variability in absolute CD4+ T cell counts was greater than in percent CD4+ T cells (median coefficient of variation (CV) 16.6% [IQR 13.8-20.1%] and CV 9.6% [IQR 7.4-13.0%], respectively). Patients with increasing CD4+ T cell counts had greater variability in absolute CD4+ T cell counts than those with plateaued CD4 T cell counts (CV 19.5% [IQR 16.1-23.8%], p<0.001) while there was no difference in percent CD4+ T cell variability between the two groups. As previously reported, untreated patients had CVs significantly higher than patients on cART (CVs of 21.1% [IQR 17.2-32.0%], p<0.001 and 15.2% (IQR 10.7-20.0%), p<0.001, respectively). Age or sex did not affect the degree of CD4+ variation.ConclusionsAdults with stable, virologically-suppressed HIV infection continue to have significant variations in individual absolute CD4+ T cell and percent CD4+ T cell counts; this variation can be of clinical relevance especially around CD4+ thresholds. However, the variation seen in individuals on cART is substantially less than in untreated subjects.

High within-day variability of fecal calprotectin levels in patients with active ulcerative colitis: what is the best timing for stool sampling?

Fecal calprotectin (FC) is considered the best noninvasive way to assess disease activity in ulcerative colitis (UC). However, it is not known which is the more suitable moment for stool sampling in patients with increased stool frequency. The aims of this study were to assess the intraindividual variation of FC within day and to evaluate if the first bowel movement in the morning is the more suitable sample for FC measurement in patients with acute flares of UC. Patients admitted because of active UC were invited to collect samples from several bowel movements (including the first in the morning) during the same day providing their ordinal chronology. FC was measured by means of a quantitative rapid point-of-care test based on lateral flow assay immunochromatography. Eighteen patients were included for a total of 56 stool samples. Most patients had extensive UC and severe disease activity. Within-day FC values varied widely, and the median coefficient of variation was 40% (5%-114%) with a median range of variation of FC values of 3887 mg/kg (69-9946). The sample from the first stool in the morning obtained the highest individual FC within-day value in 33.3% of cases and the lowest in 38.9%. FC values widely vary between motions in patients with active UC. Stool sample collection from the first bowel movement in the morning does not ensure the highest or lowest within-day FC value. In patients with overt active UC, a single FC determination should not be used as the basis for therapeutic strategies.

Quantifying reversible oxidation of protein thiols in photosynthetic organisms.

Photosynthetic organisms use dynamic post-translational modifications to survive and adapt, which include reversible oxidative modifications of protein thiols that regulate protein structure, function, and activity. Efforts to quantify thiol modifications on a global scale have relied upon peptide derivatization, typically using isobaric tags such as TMT, ICAT, or iTRAQ that are more expensive, less accurate, and provide less proteome coverage than label-free approaches--suggesting the need for improved experimental designs for studies requiring maximal coverage and precision. Herein, we present the coverage and precision of resin-assisted thiol enrichment coupled to label-free quantitation for the characterization of reversible oxidative modifications on protein thiols. Using C. reinhardtii and Arabidopsis as model systems for algae and plants, we quantified 3662 and 1641 unique cysteinyl peptides, respectively, with median coefficient of variation (CV) of 13% and 16%. Further, our method is extendable for the detection of protein abundance changes and stoichiometries of cysteine oxidation. Finally, we demonstrate proof-of-principle for our method, and reveal that exogenous hydrogen peroxide treatment regulates the C. reinhardtii redox proteome by increasing or decreasing the level of oxidation of 501 or 67 peptides, respectively. As protein activity and function is controlled by oxidative modifications on protein thiols, resin-assisted thiol enrichment coupled to label-free quantitation can reveal how intracellular and environmental stimuli affect plant survival and fitness through oxidative stress.

An integrated quantification method to increase the precision, robustness, and resolution of protein measurement in human plasma samples.

BackgroundCurrent quantification methods for mass spectrometry (MS)-based proteomics either do not provide sufficient control of variability or are difficult to implement for routine clinical testing.ResultsWe present here an integrated quantification (InteQuan) method that better controls pre-analytical and analytical variability than the popular quantification method using stable isotope-labeled standard peptides (SISQuan). We quantified 16 lung cancer biomarker candidates in human plasma samples in three assessment studies, using immunoaffinity depletion coupled with multiple reaction monitoring (MRM) MS. InteQuan outperformed SISQuan in precision in all three studies and tolerated a two-fold difference in sample loading. The three studies lasted over six months and encountered major changes in experimental settings. Nevertheless, plasma proteins in low ng/ml to low μg/ml concentrations were measured with a median technical coefficient of variation (CV) of 11.9% using InteQuan. The corresponding median CV using SISQuan was 15.3% after linear fitting. Furthermore, InteQuan surpassed SISQuan in measuring biological difference among clinical samples and in distinguishing benign versus cancer plasma samples.ConclusionsWe demonstrated that InteQuan is a simple yet robust quantification method for MS-based quantitative proteomics, especially for applications in biomarker research and in routine clinical testing.Electronic supplementary materialThe online version of this article (doi:10.1186/1559-0275-12-3) contains supplementary material, which is available to authorized users.

Point-of-care testing and INR within-subject variation in patients receiving a constant dose of vitamin K antagonist.

Many patients treated with vitamin K antagonists (VKA) determine their INR using point-of-care (POC) whole blood coagulation monitors. The primary aim of the present study was to assess the INR within-subject variation in self-testing patients receiving a constant dose of VKA. The second aim of the study was to derive INR imprecision goals for whole blood coagulation monitors. Analytical performance goals for INR measurement can be derived from the average biological within-subject variation. Fifty-six Thrombosis Centres in the Netherlands were invited to select self-testing patients who were receiving a constant dose of either acenocoumarol or phenprocoumon for at least six consecutive INR measurements. In each patient, the coefficient of variation (CV) of INRs was calculated. One Thrombosis Centre selected regular patients being monitored with a POC device by professional staff. Sixteen Dutch Thrombosis Centres provided results for 322 selected patients, all using the CoaguChek XS. The median within-subject CV in patients receiving acenocoumarol (10.2 %) was significantly higher than the median CV in patients receiving phenprocoumon (8.6 %) (p = 0.001). The median CV in low-target intensity acenocoumarol self-testing patients (10.4 %) was similar to the median CV in regular patients monitored by professional staff (10.2 %). Desirable INR analytical imprecision goals for POC monitoring with CoaguChek XS in patients receiving either low-target intensity acenocoumarol or phenprocoumon were 5.1 % and 4.3 %, respectively. The approximate average value for the imprecision of the CoaguChek XS, i. e. 4 %, is in agreement with these goals.