Informed baseline subtraction of proteomic mass spectrometry data aided by a novel sliding window algorithm

Proteomic matrix-assisted laser desorption/ionisation (MALDI) linear time-of-flight (TOF) mass spectrometry (MS) may be used to produce protein profiles from biological samples with the aim of discovering biomarkers for disease. However, the raw protein profiles suffer from several sources of bias or systematic variation which need to be removed via pre-processing before meaningful downstream analysis of the data can be undertaken. Baseline subtraction, an early pre-processing step that removes the non-peptide signal from the spectra, is complicated by the following: (i) each spectrum has, on average, wider peaks for peptides with higher mass-to-charge ratios (m/z), and (ii) the time-consuming and error-prone trial-and-error process for optimising the baseline subtraction input arguments. With reference to the aforementioned complications, we present an automated pipeline that includes (i) a novel `continuous' line segment algorithm that efficiently operates over data with a transformed m/z-axis to remove the relationship between peptide mass and peak width, and (ii) an input-free algorithm to estimate peak widths on the transformed m/z scale. The automated baseline subtraction method was deployed on six publicly available proteomic MS datasets using six different m/z-axis transformations. Optimality of the automated baseline subtraction pipeline was assessed quantitatively using the mean absolute scaled error (MASE) when compared to a gold-standard baseline subtracted signal. Near-optimal baseline subtraction was achieved using the automated pipeline. The advantages of the proposed pipeline include informed and data specific input arguments for baseline subtraction methods, the avoidance of time-intensive and subjective piecewise baseline subtraction, and the ability to automate baseline subtraction completely. Moreover, individual steps can be adopted as stand-alone routines.Comment: 50 pages, 19 figure

A Review Of Australia's Compulsory Superannuation Scheme After A Decade

The Australian superannuation system places trustees in the key role of managing superannuation assets and we subject the role of trustee to close scrutiny while identifying the very substantial principal-and-agent problems that exist in the industry. We consider two policy issues: member choice of fund and portability of accumulated balances in the light of how they would improve the ability of individual members to maximise retirement benefits and the efficiency of the system. We argue that the award superannuation scheme which requires, by conditions in industrial awards, contributions of three per cent of wage or salary of an employee continues along side the SG scheme is due for review.

TESTING THE INCOMPLETE ARBITRATE HYPOTHESIS: EVIDENCE FROM AUSTRALIAN WHOLESALE SUPERANNUATION FUNDS

This paper tests the efficiency of capital markets when information is costly to obtain by analysing the performance of Australian wholesale superannuation funds specialising in the management of domestic equity portfolios from 1991 through 1999. Using a fund regression approach, the paper finds evidence that is consistent with an incomplete arbitrage function, with investment managers generating returns sufficiently high to compensate them for the increased costs of active asset selection. Risk-adjusted returns in the Australian superannuation fund industry, net of management fees and expenses, are comparable to the returns from a passive asset selection policy.Superannuation funds, Australia

A survey to determine how the media affected operational security of the 1st Armored Division in Bosnia

The purpose of this study is to survey the commanders and public affairs officers who were mobilized and deployed to Bosnia in 1995 with the U.S. Army’s 1st Armored Division as part of Operation Joint Endeavor, for their views about how they think the media affected their units’ operational security. Many articles have been written concerning the adversarial relationship between the military and the media, but little scientific research has been published on the effects of the media on military operational security during times of conflict. This study will build on the research previously conducted by Capt. John B. Snyder and Capt. Kenneth D. Payne, as part of a survey and analysis of Military Public Affairs Officers who served in Operation Desert Shield/Desert Storm. They found that six of ten public affairs officers were aware of reports published by the media that may have compromised military operations. Such reports can add to the fears and myths of commanders that media personnel cannot be trusted and if given the opportunity will sacrifice the lives of Americans troops to publish a “hot” story (Snyder and Payne, 42)