A comparison of methods for classifying clinical samples based on proteomics data : a case study for statistical and machine learning approaches

The discovery of protein variation is an important strategy in disease diagnosis within the biological sciences. The current benchmark for elucidating information from multiple biological variables is the so called “omics” disciplines of the biological sciences. Such variability is uncovered by implementation of multivariable data mining techniques which come under two primary categories, machine learning strategies and statistical based approaches. Typically proteomic studies can produce hundreds or thousands of variables, p, per observation, n, depending on the analytical platform or method employed to generate the data. Many classification methods are limited by an n≪p constraint, and as such, require pre-treatment to reduce the dimensionality prior to classification. Recently machine learning techniques have gained popularity in the field for their ability to successfully classify unknown samples. One limitation of such methods is the lack of a functional model allowing meaningful interpretation of results in terms of the features used for classification. This is a problem that might be solved using a statistical model-based approach where not only is the importance of the individual protein explicit, they are combined into a readily interpretable classification rule without relying on a black box approach. Here we incorporate statistical dimension reduction techniques Partial Least Squares (PLS) and Principal Components Analysis (PCA) followed by both statistical and machine learning classification methods, and compared them to a popular machine learning technique, Support Vector Machines (SVM). Both PLS and SVM demonstrate strong utility for proteomic classification problems.

Is the iPhone a useful clinical tool to monitor spinal deformity patients?

The progression of spinal deformity is traditionally monitored on hard copy radiographs using the Cobb method with a protractor and pencil. The rotation of the spine and ribcage (rib hump) in scoliosis is measured with a hand-held inclinometer/Scoliometer. The iPhone and other smart phones, can accurately sense inclination, and can therefore be used to measure Cobb angles and rib hump angulation. The purpose of this study was to quantify the performance of the iPhone compared to the standard protractor (Cobb angles) and the Scoliometer (rib hump).

A survey to evaluate the implementation of a national clinical assessment form

Purpose: The Australian Universities Radiation Therapy Student Clinical Assessment Form (AURTSCAF) was designed to assess the clinical skills of radiation therapy (RT) students from the six universities that offer entry level RT programs. Given the AURTSCAF has now been in use for over two years, the Radiation Therapy Program Coordinators (RTPC) group initiated a post implementation evaluation survey. This formed the final phase of the AURTSCAF project and was funded by the Radiation Oncology Division of the Department of Health and Ageing. Methods: A cross-sectional designed survey using purposive sampling was distributed via email to all RT clinical sites. The survey asked questions about the requirements of a pass grade for students at different stages of their program, and the addition of a new category of assessment related to fitness to practise. Response types included both forced choice closed ended responses and open ended responses. There was also a section for open comments about the AURTSCAF. Results: There were 100 responses (55%) from clinicians who had utilised the assessment form over the previous 12 month period. Responses highlighted several positives with regard to the utility and implementation of the form. Comments regarding areas for improvement with the standardisation of the grading of students and consensus for the addition of a new domain in fitness for practise have informed the recommended changes proposed for 2012. Conclusion: This evaluation has provided a representative sample of the views of clinicians involved in assessing students on clinical placement. Recommendations include the addition of the sixth domain of assessment: Fitness for practise, the addition of descriptors and prompts for this domain in the user guide, the addition of a consensus statement about the use of the rating scale and dissemination of the proposed changes nationally.

Evaluation of coronary angiographic projections to balance the clinical yield with the radiation risk

Objective: Radiation safety principles dictate that imaging procedures should minimise the radiation risks involved, without compromising diagnostic performance. This study aims to define a core set of views that maximises clinical information yield for minimum radiation risk. Angiographers would supplement these views as clinically indicated. Methods: An algorithm was developed to combine published data detailing the quality of information derived for the major coronary artery segments through the use of a common set of views in angiography with data relating to the dose–area product and scatter radiation associated with these views. Results: The optimum view set for the left coronary system comprised four views: left anterior oblique (LAO) with cranial (Cr) tilt, shallow right anterior oblique (AP-RAO) with caudal (Ca) tilt, RAO with Ca tilt and AP-RAO with Cr tilt. For the right coronary system three views were identified: LAO with Cr tilt, RAO and AP-RAO with Cr tilt. An alternative left coronary view set including a left lateral achieved minimally superior efficiency (,5%), but with an ,8% higher radiation dose to the patient and 40% higher cardiologist dose. Conclusion: This algorithm identifies a core set of angiographic views that optimises the information yield and minimises radiation risk. This basic data set would be supplemented by additional clinically determined views selected by the angiographer for each case. The decision to use additional views for diagnostic angiography and interventions would be assisted by referencing a table of relative radiation doses for the views being considered.

Proteomics science & society : the role of knowledge translation in moving towards clinical applications

Background: Outside the mass-spectrometer, proteomics research does not take place in a vacuum. It is affected by policies on funding and research infrastructure. Proteomics research both impacts and is impacted by potential clinical applications. It provides new techniques & clinically relevant findings, but the possibilities for such innovations (and thus the perception of the potential for the field by funders) are also impacted by regulatory practices and the readiness of the health sector to incorporate proteomics-related tools & findings. Key to this process is how knowledge is translated. Methods: We present preliminary results from a multi-year social science project, funded by the Canadian Institutes of Health Research, on the processes and motivations for knowledge translation in the health sciences. The proteomics case within this wider study uses qualitative methods to examine the interplay between proteomics science and regulatory and policy makers regarding clinical applications of proteomics. Results: Adopting an interactive format to encourage conference attendees’ feedback, our poster focuses on deficits in effective knowledge translation strategies from the laboratory to policy, clinical, & regulatory arenas. An analysis of the interviews conducted to date suggests five significant choke points: the changing priorities of funding agencies; the complexity of proteomics research; the organisation of proteomics research; the relationship of proteomics to genomics and other omics sciences; and conflict over the appropriate role of standardisation. Conclusion: We suggest that engagement with aspects of knowledge translation, such as those mentioned above, is crucially important for the eventual clinical application ofproteomics science on any meaningful scale.

Perceptions of clinical safety climate of the multicultural nursing workforce in Saudi Arabia : a cross-sectional survey

Purpose The purpose of this study is to explore the safety climate perceptions of the multicultural nursing workforce, and to investigate the influence of diversity of the multicultural nursing workforce on clinical safety in a large tertiary hospital in Saudi Arabia. Background Working in a multicultural environment is challenging. Each culture has its own unique characteristics and dimensions that shape the language, lifestyle, beliefs, values, customs, traditions, and patterns of behaviour, which expatriate nurses must come to terms with. However, cultural diversity in the health care environment can potentially affect the quality of care and patient safety. Method A mixed-method case study (survey, interview and document analysis) was employed. A primary study phase entailed the administration of the Safety Climate Survey (SCS). A population sampling strategy was used and 319 nurses participated, yielding a 76.8% response rate. Descriptive and inferential statistics (Kruskal–Wallis test) were used to analyse survey data. Results The data revealed the nurses’ perceptions of the clinical safety climate in this multicultural environment was unsafe, with a mean score of 3.9 out of 5. No significant difference was found between the age groups, years of nursing experience and their perceptions of the safety climate in this context. A significant difference was observed between the national background categories of nurses and perceptions of safety climate. Conclusion Cultural diversity within the nursing workforce could have a significant influence on perceptions of clinical safety. These findings have the potential to inform policy and practice related to cultural diversity in Saudi Arabia.

National Institute for Clinical Studies Report for Phase 1, Evidence Uptake Network : Best Practice Community Care for Clients with Chronic Venous Leg Ulcers

Chronic leg ulcers cause significant pain, cost, decreased quality of life and morbidity for a considerable segment of the older population (Graham et al., 2003a). At any given time the prevalence of patients with open leg ulcers receiving treatment is between 0.11% - 0.18% (Briggs & Closs 2003). Chronic leg ulcers occur in approximately 1 - 2% of the over 60 population in the US, UK, Europe and Australia (Baker & Stacey 1994; Johnson 1995; Lees & Lambert 1992; Margolis et al. 2002). Considerable research has been undertaken to determine the best treatment practices that will aid in the management and the healing of these ulcers, and practical and effective strategies and techniques for healing venous leg ulcers have been trialled to demonstrate their beneficial effects (Nelson et al. 2004; Cullum et al. 2001)...