Addressing accuracy and precision issues in iTRAQ quantitation

iTRAQ (isobaric tags for relative or absolute quantitation) is a mass spectrometry technology that allows quantitative comparison of protein abundance by measuring peak intensities of reporter ions released from iTRAQ-tagged peptides by fragmentation during MS/MS. However, current data analysis techniques for iTRAQ struggle to report reliable relative protein abundance estimates and suffer with problems of precision and accuracy. The precision of the data is affected by variance heterogeneity: low signal data have higher relative variability; however, low abundance peptides dominate data sets. Accuracy is compromised as ratios are compressed toward 1, leading to underestimation of the ratio. This study investigated both issues and proposed a methodology that combines the peptide measurements to give a robust protein estimate even when the data for the protein are sparse or at low intensity. Our data indicated that ratio compression arises from contamination during precursor ion selection, which occurs at a consistent proportion within an experiment and thus results in a linear relationship between expected and observed ratios. We proposed that a correction factor can be calculated from spiked proteins at known ratios. Then we demonstrated that variance heterogeneity is present in iTRAQ data sets irrespective of the analytical packages, LC-MS/MS instrumentation, and iTRAQ labeling kit (4-plex or 8-plex) used. We proposed using an additive-multiplicative error model for peak intensities in MS/MS quantitation and demonstrated that a variance-stabilizing normalization is able to address the error structure and stabilize the variance across the entire intensity range. The resulting uniform variance structure simplifies the downstream analysis. Heterogeneity of variance consistent with an additive-multiplicative model has been reported in other MS-based quantitation including fields outside of proteomics; consequently the variance-stabilizing normalization methodology has the potential to increase the capabilities of MS in quantitation across diverse areas of biology and chemistry.

Measuring Nutrition Work Across Queensland

The public health and community nutrition workforce in Queensland has experienced significant change. These changes happened following a new government in 2012, and its response to the National Health and Hospitals Reform and budget constraints. This research documented and analysed current roles and activities of the preventative health nutrition workforce. An online survey was conducted with all positions known to be working in nutrition prevention (n=320). The sample population was generated using existing databases which were validated by comparisons with workforce data from the Queensland Health Department and sector consultation. Snowballing was also used. 128 practitioners responded to the survey (response rate =40%). This was made up of those whose job title included the words “nutritionist” or “dietitian” (n=64) and those whose job title did not (n=61). Three respondents did not supply a title. Ninety-four practitioners had a nutrition or dietetic qualification indicating that a number of the workforce have shifted to more generalist positions. Between 2009 and 2013 there has been a 90% reduction in the state-funded nutrition prevention workforce. The existing reduced workforce is now dispersed across a range of organisations. Areas of workforce growth such as Medicare Locals tend to attract less experienced practitioners (50% had ≤ 5years’ experience). These changes present challenges for the co-ordination and communication of nutrition work and equity and access of service delivery. This research highlights the need for adaptability of the public health and community nutrition workforce. These issues require consideration by the profession.

Keep ahead of the workforce development curve through the establishment of standardised training for rail incident investigators

The Australasian rail industry lacks a consistently accepted standard of minimal training necessary to perform rail incident investigations. Current Australasian courses do not offer the breadth of development required for a comprehensive career pathway in incident investigation (Biggs, Banks & Dovan, 2012; Short, Kains & Harris, 2010).

Local Commons : communicating local issues through place-based interventions

Due to the numerous possibilities of voicing concerns and the flood of data we are exposed to, local issues are at a risk of being overlooked. Following a research agenda proposed by Foth et al. (2013), this thesis explored the possible contributions of situated digital and tangible media for communicating local issues. Making use of the location of an issue could thereby not only allow to reach the targeted audience but also for a deeper involvement of citizens. Through the development of a design intervention in public space, called Local Commons, the benefits of this approach were investigated. Therefore, the intervention combined digital and tangible media in order to engage the public to contribute and debate different perspectives on a given local issue. The interaction with the intervention was thereby twofold. First, the intervention invited the audience to submit images of their perspectives on the issue, which were displayed on a public screen. Via tangible buttons in front of the screen, the audience then had the possibility to agree or disagree to the displayed perspectives, creating a space for deliberation. In a field study, the concept was subsequently tested and evaluated. The results of this study, although not generalisable, supported the chosen approach of this thesis.

Contemporary challenges in e-learning

Technology is impacting on most elements of organisations today and workforce development professionals have been some of the leading proponents of embracing technologies and the benefits they offer. E-learning has emerged as at least a complementary offering to face-to-face training, and in some cases has totally replaced more traditional forms of workforce development. This chapter explores the use of learning technologies and the benefits and drawbacks of their use. In particular it focuses on further exploring the issue of a perceived lack of interaction in some e-learning offerings; a factor identified as critical to address in order to ensure effective e-learning. The chapter discusses the issues of interaction and social presence to address feelings of isolation and offers some key considerations for those considering integrating technology into workforce development.

Health and safety for clean-up and recovery workers

This paper will identify and discuss the major occupational health and safety (OHS) hazards and risks for clean-up and recovery workers. The lessons learned from previous disasters including; the Exxon Valdez oil spill, World Trade Centre (WTC) terrorist attack, Hurricane Katrina and the Deepwater Horizon Gulf of Mexico oil spill will be discussed. The case for an increased level of preparation and planning to mitigate the health risks for clean-up and recovery workers will be presented, based on recurring themes identified in the peer reviewed literature. There are a number of important issues pertaining to the occupational health and safety of workers who are engaged in clean-up and recovery operations following natural and technological disasters. These workers are often exposed to a wide range of occupational health and safety hazards, some of which may be unknown at the time. It is well established that clean-up and recovery operations involve risks of physical injury, for example, from manual handling, mechanical equipment, extreme temperatures, slips, trips and falls. In addition to these well established physical injury risks there are now an increasing number of studies which highlight the risks of longer term or chronic health effects arising from clean-up and recovery work. In particular, follow up studies from the Exxon Valdez oil spill, Hurricane Katrina and the World Trade Centre (WTC) terrorism attack have documented the longer term health consequences of these events. These health effects include respiratory symptoms and musculoskeletal disorders, as well as post traumatic stress disorder (PTSD). In large scale operations many of those workers and supervisors involved have not had any specific occupational health and safety (OHS) training and may not have access to the necessary instruction, personal protective equipment or other appropriate equipment, this is especially true when volunteers are used to form part of the clean-up and recovery workforce. In general, first responders are better equipped and trained than clean-up and recovery workers and some of the training approaches used for the traditional first responders would be relevant for clean-up and recovery workers.

Selling new neighborhoods as good for walking : issues for measuring self-selection

Background: Self-selection-whether individuals inclined to walk more seek to live in walkable environments-must be accounted for when studying built environment influences on walking. The way neighborhoods are marketed to future residents has the potential to sway residential location choice, and may consequently affect measures of self-selection related to location preferences. We assessed how walking opportunities are promoted to potential buyers, by examining walkability attributes in marketing materials for housing developments. Methods: A content analysis of marketing materials for 32 new housing developments in Perth, Australia was undertaken, to assess how walking was promoted in the text and pictures. Housing developments designed to be pedestrian-friendly (LDs) were compared with conventional developments (CDs). Results: Compared with CDs, LD marketing materials had significantly more references to 'public transport,' small home sites,' walkable parks/open space,' ease of cycling,' safe environment,' and 'boardwalks.' Other walkability attributes approached significance. Conclusion: Findings suggest the way neighborhoods are marketed may contribute to self-reported reasons for choosing particular neighborhoods, especially when attributes are not present at the time of purchase. The marketing of housing developments may be an important factor to consider when measuring self-selection, and its influence on the built environment and walking relationship.

Major issues in business process management : an expert perspective

Study Approach The results presented in this report are part of a larger global study on the major issues in BPM. Only one part of the larger study is reported here, viz. interviews with BPM experts. Interviews of BPM tool vendors together with focus group studies involving user organizations were conducted in parallel and set the groundwork for the identification of BPM issues on a global scale. Through this multi-method approach, we identify four distinct sets of outcomes. First, as is the focus of this report, we identify the BPM issues as perceived by BPM experts. Second, the research design allows us to gain insight into the opinions of organizations deploying BPM solutions. Third, an understanding of organizations’ misconceptions of BPM technologies, as confronted by BPM tool vendors, is obtained. Last, we seek to gain an understanding of BPM issues on a global scale, together with knowledge of matters of concern. This final outcome is aimed to produce an industry-driven research agenda that will inform practitioners and, in particular, the research community worldwide on issues and challenges that are prevalent or emerging in BPM and related areas...

Can Business Continuity Management Create Reliability in Airports? (Issues from Theory into Practice)

The advances made within the aviation industry over the past several decades have significantly improved the availability, affordability and convenience of air travel and have been greatly beneficial in both social and economic terms. Air transport has developed into an irreplaceable service being relied on by millions of people each day and as such airports have become critical elements of national infrastructure to facilitate the movement of people and goods. As components of critical infrastructure (CI), airports are integral parts of a national economy supporting regional as well as national trade, commercial activity and employment. Therefore, any disruption or crisis which impacts the continuity of operations at airports can have significant negative consequences for the airport as a business, for the local economy and other nodes of transport infrastructure as well as for society. Due to the highly dynamic and volatile environment in which airports operate in, the aviation industry has faced many different challenges over the years ranging from terrorist attacks such as September 11, to health crises such as the SARS epidemic to system breakdowns such as the recent computer system outage at Virgin Blue Airlines in Australia. All these events have highlighted the vulnerability of airport systems to a range of disturbances as well as the gravity and widespread impact of any kind of discontinuity in airport functions. Such incidents thus emphasise the need for increasing resilience and reliability of airports and ensuring business continuity in the event of a crisis...

Scepticism and trust: two counterpoint essentials in science education for complex socio-scientific issues

In this response to Tom G. K. Bryce and Stephen P. Day’s (Cult Stud Sci Educ. doi:10.1007/s11422-013-9500-0, 2013) original article, I share with them their interest in the teaching of climate change in school science, but I widen it to include other contemporary complex socio-scientific issues that also need to be discussed. I use an alternative view of the relationship between science, technology and society, supported by evidence from both science and society, to suggest science-informed citizens as a more realistic outcome image of school science than the authors’ one of mini-scientists. The intellectual independence of students Bryce and Day assume, and intend for school science, is countered with an active intellectual dependence. It is only in relation to emerging and uncertain scientific contexts that students should be taught about scepticism, but they also need to learn when, and why to trust science as an antidote to the expressions of doubting it. Some suggestions for pedagogies that could lead to these new learnings are made. The very recent fifth report of the IPCC answers many of their concerns about climate change.