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Application of the more stringent statistical tests applied to the normalized 2D DIGE data decreased the number of potentially differentially expressed proteins from the number obtained from DeCyder and increased the confidence in detecting differential expression in human clinical studies.

No abstract

The complexity of human plasma presents a number of challenges to the efficient and reproducible proteomic analysis of differential expression in response to disease. Before individual variation and disease-specific protein biomarkers can be identified from human plasma, the experimental variability inherent in the protein separation and detection techniques must be quantified. We report on the variation found in two-dimensional difference gel electrophoresis (2-D DIGE) analysis of human plasma. Eight aliquots of a human plasma sample were subjected to top-6 highest abundant protein depletion and were subsequently analyzed in triplicate for a total of 24 DIGE samples on 12 gels. Spot-wise standard deviation estimates indicated that fold changes greater than 2 can be detected with a manageable number of replicates in simple ANOVA experiments with human plasma. Mixed-effects statistical modeling quantified the effect of the dyes, and segregated the spot-wise variance into components of sample preparation, gel-to-gel differences, and random error. The gel-to-gel component was found to be the largest source of variation, followed by the sample preparation step. An improved protocol for the depletion of the top-6 high-abundance proteins is suggested, which, along with the use of statistical modeling and future improvements in gel quality and image processing, can further reduce the variation and increase the efficiency of 2-D DIGE proteomic analysis of human plasma.

Quantifying the variation in the human plasma proteome is an essential prerequisite for disease-specific biomarker detection. We report here on the longitudinal and individual variation in human plasma characterized by two-dimensional difference gel electrophoresis (2-D DIGE) using plasma samples from eleven healthy subjects collected three times over a two week period. Fixed-effects modeling was used to remove dye and gel variability. Mixed-effects modeling was then used to quantitate the sources of proteomic variation. The subject-to-subject variation represented the largest variance component, while the time-within-subject variation was comparable to the experimental variation found in a previous technical variability study where one human plasma sample was processed eight times in parallel and each was then analyzed by 2-D DIGE in triplicate. Here, 21 protein spots had larger than 50% CV, suggesting that these proteins may not be appropriate as biomarkers and should be carefully scrutinized in future studies. Seventy-eight protein spots showing differential protein levels between different individuals or individual collections were identified by mass spectrometry and further characterized using hierarchical clustering. The results present a first step toward understanding the complexity of longitudinal and individual variation in the human plasma proteome, and provide a baseline for improved biomarker discovery.

A few different approaches exist for computing undecimated wavelet transform. In this work we construct three undecimated schemes and evaluate their performance for image noise reduction. We use standard wavelet based de-noising techniques and compare the performance of our algorithms with the original undecimated wavelet transform, as well as with the decimated wavelet transform. The experiments we have made show that our algorithms have better noise removal/blurring ratio.

No abstract

The apparent warming of Earth's surface during the 20 th century may be biased by large changes in the coverage of surface temperature measurements since 1900. We investigate this issue using climate model simulations. By imposing observed coverage changes on simulated surface temperatures, we obtain estimates of 20 th-century temperature-change for both full global coverage and for actual historical coverage. In 10 of 16 simulations including human climate perturbations, the temperature change from globally complete model output is significantly larger than that derived from historically-masked model output. The remaining 6 simulations show no significant difference between complete and masked model output. Thus, our results do not support the hypothesis that the increase in Earth's surface temperature has been overestimated due to incomplete observational data. Rather, if the simulations we analyzed are realistic, the true temperature increase over the last century is slightly larger than that estimated from available observations. We also analyzed 8 simulations of natural internal climate variability which omit human climate perturbations. In none of these simulations does the temperature change during 100 years-whether obtained from globally complete or masked model output-come close to the observed 20 th century temperature increase.