A clustering based hybrid system for mass spectrometry data analysis

Recently, much attention has been given to the mass spectrometry (MS) technology based disease classification, diagnosis, and protein-based biomarker identification. Similar to microarray based investigation, proteomic data generated by such kind of high-throughput experiments are often with high feature-to-sample ratio. Moreover, biological information and pattern are compounded with data noise, redundancy and outliers. Thus, the development of algorithms and procedures for the analysis and interpretation of such kind of data is of paramount importance. In this paper, we propose a hybrid system for analyzing such high dimensional data. The proposed method uses the k-mean clustering algorithm based feature extraction and selection procedure to bridge the filter selection and wrapper selection methods. The potential informative mass/charge (m/z) markers selected by filters are subject to the k-mean clustering algorithm for correlation and redundancy reduction, and a multi-objective Genetic Algorithm selector is then employed to identify discriminative m/z markers generated by k-mean clustering algorithm. Experimental results obtained by using the proposed method indicate that it is suitable for m/z biomarker selection and MS based sample classification.

Markers and risk factors for HCV, HBV and HIV in a network of injecting drug users in Melbourne

Background and aims: Current injecting drug users (IDU) in major street drug markets within greater Melbourne were recruited to a longitudinal study on blood borne viruses. Here we investigated risk factors for hepatitis C virus (HCV), hepatitis B virus (HBV) and HIV infection in these IDU at the time of their recruitment.

Methods : Three hundred and eighty-two IDU completed detailed questionnaires on their drug use and risk behaviours, and provided blood samples for serology testing. These data were analysed using univariate and multivariate techniques.

Results : The overall prevalence of exposure to HCV, HBV and HIV was estimated at 70%, 34% and <1%, respectively. Independent predictors of HCV exposure were history of imprisonment (RR 1.34, 95% CI 1.19–1.52), use of someone else's needle or syringe (RR 1.23, 95% CI 1.07–1.42), >7.6 years length of time injecting (RR 1.21, 95% CI 1.07–1.37), and originating from Vietnam (RR 1.12, 95% CI 1.07–1.18). Independent predictors of HBV exposure were HCV exposure (RR 2.15, 95% CI 1.35–3.43), >7.6 years length of time injecting (RR 1.57, 95% CI 1.17–2.13) and originating from outside Australia (RR 1.60, 95% CI 1.22–2.10). Neither prison- nor community-applied tattoos predicted HCV or HBV exposure. Up to 31% of IDU who injected for 1 year or less were HCV antibody positive, as were 53% of those who injected for 2 years or less.

Conclusions : Ongoing engagement with young IDU, through the provision of harm reduction education and resources, is critical if we are to address blood borne viral infections and other health and social harms associated with injecting drug use.

Effect of vitamin D supplementation on vitamin D status and bone turnover markers in young adults

Objective: To assess the vitamin D status of healthy young people living in Northern Ireland and the effect of vitamin D supplementation on vitamin D status and bone turnover.

Design: Double-blinded randomised controlled intervention study.

Setting: University of Ulster, Coleraine, Northern Ireland.

Subjects: In total, 30 apparently healthy students (15 male and 15 female subjects), aged 18–27 years, were recruited from the university, with 27 completing the intervention.

Interventions: Subjects were randomly assigned, to receive either 15 mug (600 IU) vitamin D3 and 1500 mg calcium/day (vitamin D group), or 1500 mg calcium/day (control group) for 8 weeks between January and March. Vitamin D status, bone turnover markers, serum calcium and parathyroid hormone concentrations were measured at baseline and post intervention.

Results: At baseline, vitamin D status was low in both the vitamin D group (47.9 (s.d. 16.0)) and the control group (55.5 (s.d. 18.6) nmol/l 25(OH)D). Post intervention vitamin D status was significantly higher in the vitamin D-treated group (86.5 (s.d. 24.5)) compared to the control group (48.3 (s.d. 16.8) nmol/l) (P<0.0001). There was no significant effect of supplementation on bone turnover markers or PTH concentrations.

Conclusions: This study suggests that young adults in Northern Ireland do not consume an adequate daily dietary intake of vitamin D to maintain plasma vitamin D concentrations in the wintertime. A daily supplement of 15 mug vitamin D3 significantly increased vitamin D status in these individuals to levels of sufficiency. Achievement of an optimum vitamin D status among young adults may have future positive health implications.

Population structure in the highly fragmented range of Tor douronensis (Cyprinidae) in Sarawak, Malaysia revealed by microsatellite DNA markers

1. Understanding the structure of threatened populations, particularly those that exist in degraded or fragmented habitats is crucial for their effective management and conservation. Recently developed methods of individual-based analysis of genetic data provide an unprecedented opportunity to understand the relationships amongst fragmented populations.

2. In the present study, population structure of an important cyprinid species (Tor douronensis), which is indigenous to Sarawak, Malaysia, is investigated as part of an ongoing conservation effort to restore threatened wild populations of the species. The population structure inferred using data from seven autosomal microsatellite loci was generally consistent with geography and habitat fragmentation.

3. The results indicate that there are two well-defined clusters of T. douronensis in Sarawak, namely the 'northeastern' and the 'southwestern' clusters. In addition, a further subdivision was observed in each of the clusters distributed between river systems. Low levels of gene flow were also observed and migrants between habitat fragments were identified, possibly resulting from human-mediated translocations.

4. Implications of the findings for management and conservation of T. douronensis are discussed.

Characterization of microsatellite DNA markers for a mahseer species, Tor tambroides (Cyprinidae) and cross-amplification in four congeners

This study reports the isolation and characterization of microsatellite DNA markers in a mahseer species, Tor tambroides (Pisces, Cyprinidae). Of a total of 14 loci evaluated, 10 were polymorphic in T. tambroides samples, with an average of 2.86 alleles per locus. Deviations from Hardy–Weinberg equilibrium were observed at one locus and there was no indication of linkage disequilibrium among loci. A high level of cross-amplification among four congeners was achieved, with 12 loci successfully amplifying and 11 loci showing polymorphism in at least one other species. These markers will be a useful resource for population genetic studies and broodstock management of closely related mahseer species.

Does the inclusion of moderate amounts of red meat in the diet of exercising older women impact on faecal markers of bowel health, including faecal lactoferrin?

Background: High intakes of red meat may be associated with increased risk of colorectal cancer (CRC), however, to determine CRC risk, it is important to assess faecal changes related to protein and carbohydrate metabolism.

Objective: To determine the influence of three weekly meals rich in red meat as opposed to a carbohydrate control diet on faecal markers which are involved in the aetiology of CRC.

Design: Twenty post-menopausal women (aged 60-75) undertook, 3 times a week for 12 weeks, a 30 minute exercise session followed immediately by a cooked meal that was high in lean red meat, low in carbohydrate (n= 10) or low in lean red meat, high in carbohydrate (n=10). Dietary fibre intake and macronutrients were kept constant. At the beginning and end of the study, three-day faecal samples were collected and by-products of protein fermentation and carbohydrate metabolism, undigested fibre residues, and faecal output and colonic bacterial microbiota changes measured.

Outcomes: No significant differences were observed in subjects on either diet when comparing faecal output, faecal pH, other faecal markers, nor faecal lactoferrin. There was a trend observed in changes in the population of colonic microbiota using FISH analysis. Bacteroides spp. and Prevotella spp. appeared to decrease in women consuming a high red meat diet compared with an increase in women consuming a high carbohydrate diet.

Conclusions: In this pilot study the trend in colonic microbiota change is interesting and suggests that dietary influence of colonic microbiota, especially changes in Bacteroidetes, may be indicative of risk of gut damage and disease compared to other faecal markers.

More than a mere story : social and political markers in Australian short fiction of the 1980's

This thesis is a literary history which argues that much of the short fiction published in Australia during the 1980s was deeply influenced by the rapid social and political changes during that decade. My argument concentrates on links between the short stones of the period and the socio/political environment into which they were written. The decade was marked by massive changes in technology, the workplace, and in all other areas of social life. In general terms, the ideology of the 'market' predominated over notions of small 'l' liberalism and the last vestiges of state intervention in the economy. The Australian short story benefited from the social 'experiments' of the 1970s in that its concerns became broader - encompassing the onslaught of feminism, the foregrounding of 'multicultural' concerns, and a move away from the bush into the city as a primary site for narratives. The decade was a rich period for the genre. Why was there a tolerance for a new diversity, in literary terms, when the social and political environment was turning to the right? This is a central question of the thesis. I argue that instead of the 'base' determining the 'superstructure' (i.e. culture) the superstructural changes were essential to the deconstruction of the social and political landscape. This thesis contends that a relationship always exists between the 'literary' and 'the social'. I argue, among other things, that many of the short fictions were influenced by 'postmodern' theory to the extent that they became a form of traumatic note-taking, which masked a late romanticism beneath a fear of the sovereign subject. The fear of 'closure' which insinuated itself into many of the texts, besides being a form of academic corrective, was also a flight from emotional candor. I argue that storytelling was, in many cases, the loser.

Molecular genetic markers for abalone aquaculture

Describes the development and mapping of molecular markers in the blacklip and greenlip abalones. By means of a genome scan using a novel selective DNA pooling strategy, markers associated with growth were discovered that could potentially be applied to increase genetic gain in abalone aquaculture, whilst minimising inbreeding.

Indicative markers of leadership provided by ICT professional bodies in the promotion and support of ethical conduct

Most countries with a mature Information and Communications Technology (ICT industry have at least one professional body (PB) that claims to represent its members working with such technology. Other ICT PBs operate in the international arena. These PBs may differ in membership criteria, jurisdiction and even objectives but all profess to promote high ethical and professional standards. This study seeks to determine the common indicative markers that demonstrate that an ICT PB is offering leadership in identifying, promoting and supporting ethical conduct amongst a variety of constituencies including its own members and beyond. An extensive literature review identified over 200 prospective markers covering a broad range of potential activities of an ICT PB. These were grouped into nine major areas: ethical professional practice; continuous professional development; research and publication; education of future professionals; members’ career development; social obligations; professional engagement; preserving professional dignity/ reputation and regulation of the profession. These markers were arranged hierarchically in a word processing document referred to as a “marker template”. An analysis of selected ICT PBs websites was undertaken to confirm and refine the template. It will be used in the future for a comparative study of how professional bodies offer leadership to their various constituencies in the area of ethical conduct.

Antioxidant vitamin supplements and markers of bone turnover in a community sample of nonsmoking women

Background: Whereas several epidemiological studies suggest that low dietary intake of vitamins C and E is linked to increased hip fracture in smokers and antioxidants (dietary and endogenous) are reduced in elderly osteoporotic women, none has demonstrated an effect of supplemental antioxidants on bone turnover.

Methods: In an observational study of 533 randomly selected women, we investigated the associations among the use of antioxidant supplements, vitamins C and E, serum levels of biochemical markers of bone turnover (C-telopeptide [CTx] and bone-specific alkaline phosphatase [BSAP]), and whole body bone mineral density (BMD).

Results: Twenty-two women were identified as current users of supplemental vitamin C or E. Duration of antioxidant supplement use was negatively associated with age-adjusted and weight-adjusted serum CTx, such that mean CTx levels (natural log transformed) were 0.022 units lower for each year of exposure. No significant differences were detected for adjusted serum BSAP or whole body BMD.

Conclusions: Our results suggest that antioxidant vitamin E or C supplements may suppress bone resorption in nonsmoking postmenopausal women. Coupling of bone formation and resorption may explain the absence of an effect on bone formation markers, given evidence of enhanced effects of antioxidants on osteoblast differentiation; this warrants further investigation. This work adds to the growing body of evidence that antioxidants may play a role in preventing osteoporosis.