Seed-based biclustering of gene expression data

Background Accumulated biological research outcomes show that biological functions do not depend on individual genes, but on complex gene networks. Microarray data are widely used to cluster genes according to their expression levels across experimental conditions. However, functionally related genes generally do not show coherent expression across all conditions since any given cellular process is active only under a subset of conditions. Biclustering finds gene clusters that have similar expression levels across a subset of conditions. This paper proposes a seed-based algorithm that identifies coherent genes in an exhaustive, but efficient manner. Methods In order to find the biclusters in a gene expression dataset, we exhaustively select combinations of genes and conditions as seeds to create candidate bicluster tables. The tables have two columns: (a) a gene set, and (b) the conditions on which the gene set have dissimilar expression levels to the seed. First, the genes with less than the maximum number of dissimilar conditions are identified and a table of these genes is created. Second, the rows that have the same dissimilar conditions are grouped together. Third, the table is sorted in ascending order based on the number of dissimilar conditions. Finally, beginning with the first row of the table, a test is run repeatedly to determine whether the cardinality of the gene set in the row is greater than the minimum threshold number of genes in a bicluster. If so, a bicluster is outputted and the corresponding row is removed from the table. Repeating this process, all biclusters in the table are systematically identified until the table becomes empty. Conclusions This paper presents a novel biclustering algorithm for the identification of additive biclusters. Since it involves exhaustively testing combinations of genes and conditions, the additive biclusters can be found more readily.

Environmental incidents in a developing country and corporate environmental disclosures : a study of a multinational gas company

Purpose – The purpose of this paper is to examine the environmental disclosure initiatives of Niko Resources Ltd – a Canada-based multinational oil and gas company – following the two major environmental blowouts at a gas field in Bangladesh in 2005. As part of the examination, the authors particularly focus on whether Niko's disclosure strategy was associated with public concern pertaining to the blowouts. Design/methodology/approach – The authors reviewed news articles about Niko's environmental incidents in Bangladesh and Niko's communication media, including annual reports, press releases and stand-alone social responsibility report over the period 2004-2007, to understand whether news media attention as proxy for public concern has an impact on Niko's disclosure practices in relation to the affected local community in Bangladesh. Findings – The findings show that Niko did not provide any non-financial environmental information within its annual reports and press releases as a part of its responsibility to the local community which was affected by the blowouts, but it did produce a stand-alone report to address the issue. However, financial environmental disclosures, such as the environmental contingent liability disclosure, were adequately provided through annual reports to meet the regulatory requirements concerning environmental persecutions. The findings also suggest that Niko's non-financial disclosure within a stand-alone report was associated with the public pressures as measured by negative media coverage towards the Niko blowouts. Research limitations/implications – This paper concludes that the motive for Niko's non-financial environmental disclosure, via a stand-alone report, reflected survival considerations: the company's reaction did not suggest any real attempt to hold broader accountability for its activities in a developing country.

Optimisation of bio-oil extraction process from Beauty Leaf (Calophyllum inophyllum) oil seed as a second generation biodiesel source

The Beauty Leaf tree (Calophyllum inophyllum) is a potential source of non-edible vegetable oil for producing future generation biodiesel because of its ability to grow in a wide range of climate conditions, easy cultivation, high fruit production rate, and the high oil content in the seed. This plant naturally occurs in the coastal areas of Queensland and the Northern Territory in Australia, and is also widespread in south-east Asia, India and Sri Lanka. Although Beauty Leaf is traditionally used as a source of timber and orientation plant, its potential as a source of second generation biodiesel is yet to be exploited. In this study, the extraction process from the Beauty Leaf oil seed has been optimised in terms of seed preparation, moisture content and oil extraction methods. The two methods that have been considered to extract oil from the seed kernel are mechanical oil extraction using an electric powered screw press, and chemical oil extraction using n-hexane as an oil solvent. The study found that seed preparation has a significant impact on oil yields, especially in the screw press extraction method. Kernels prepared to 15% moisture content provided the highest oil yields for both extraction methods. Mechanical extraction using the screw press can produce oil from correctly prepared product at a low cost, however overall this method is ineffective with relatively low oil yields. Chemical extraction was found to be a very effective method for oil extraction for its consistence performance and high oil yield, but cost of production was relatively higher due to the high cost of solvent. However, a solvent recycle system can be implemented to reduce the production cost of Beauty Leaf biodiesel. The findings of this study are expected to serve as the basis from which industrial scale biodiesel production from Beauty Leaf can be made.

ICT to enhance the triangle of life : the soil, the seed, and the life-giver farmer

This paper reports on the outcomes of an ICT enabled social sustainability project “Green Lanka1” trialled in the Wilgamuwa village, which is situated in the Dambulla district of Sri Lanka. The main goals of the project were focused towards the provision of information about market prices, transportation options, agricultural decision support and modern agriculture practices of the farmer communities to improve their livelihood with the effective use of technologies. The project used Web and Mobile (SMS) enabled systems. The Green Lanka project was sponsored by the Information Communication Technology Agency (ICTA) of Sri Lanka under the Institutional Capacity Building Programme (ICBP) grant scheme which was sponsored by the World Bank. Six hundred families in Wilgamuwa village participated in the project activities. The project was designed, executed and studied through an Action Research approach. The lessons learned through the project activities provide an important understanding of the complex interaction between different stakeholders in the process of implementation of ICT enabled solutions within digitally divided societies. The paper analyses the processes used to reduce the resistance to change and improved involvement of farmer communities in ICT enabled projects. It also analyses the interaction between stakeholders involved in design and implementation of the project activities to improve the chances of project success.

“Would you; could you; on a boat?” Wait-time and travel-time activities during river ferry journeys and their relationship to overall satisfaction in Brisbane Queensland

This study investigates travel behaviour and wait-time activities as a component of passenger satisfaction with public transport in Brisbane, Australia. Australian transport planners recognise a variety of benefits to encouraging a mode shift away from automobile travel in favour of active and public transport use. Efforts to increase public transport ridership have included introducing state of the art passenger information systems, improving physical station access, and integrating system pricing, routes and scheduling for train, bus and ferry. Previous research regarding satisfaction with public transport emphasizes technical dimensions of service quality, including the timing and reliability of service. Those factors might be especially significant for frequent (commuting) travellers who look to balance the cost and efficiency of their travel options. In contrast, infrequent (leisure) passengers may be more concerned with way finding and the sensory experience of the journey. Perhaps due to the small relative proportion of trips made by river ferry compared to bus and rail, this mode of public transport has not received as much attention in travel-behaviour research. This case study of Brisbane’s river ferry system examines ferry passengers at selected terminals during peak and off-peak travel times to find out how travel behaviours and activities correlate to satisfaction with ferry travel. Data include 416 questionnaires completed by passengers intercepted during wait times at seven CityCat terminals in Brisbane. Descriptive statistical analysis revealed associations between specific wait time activities and satisfaction levels that could inform planners seeking to increase ridership and quality of life through ferry-oriented development.

Soiling the seed : microenvironment and epithelial mesenchymal plasticity

In the past decade we have come to appreciate that the microenvironment has the potential for major influence on the cancer cell. An extreme case for this occurs when the cancer cell changes its environment in the context of metastasis, where this may in part underpin the altered biology of cells in metasases. Increasing evidence suggests that changes in the cellular microenvironment contribute to tumourigenesis and metastasis, but the molecular basis of these alterations is not well understood. Reactive stroma provides oncogenic signals to facilitate tumourigenesis and metastasis—co-implantation of normal human epithelial cells in vivo with irradiated, carcinogen treated, or cancer derived fibroblasts leads to the enhancement or formation of malignant tumours.

Of Forrests and acrosn : philanthropic gift may seed other university giving

A$65 million pledge by Nicola and Andrew Forrest to all five West Australian univerisities alters the philanthropy landscape in Australia. The Forrest' donation comes less than a year after Louise and Graham Tuckwell's A$50 million donation to Australian national University.

Party to litigation insolvent company - costs order against non-party liquidator

In Kimtran Pty Ltd v Downie [2003] QDC 043 the court allowed in part an appeal from the refusal by the Queensland Building Tribunal to order the respondent liquidators pay the appellants' costs of proceedings in the Tribunal. The decision involved an examination of authorities which have considered the circumstances in which it is in the interests of justice to make an order for costs against a non-party.

Costs order against company in liquidation unlikely to be effective indemnity

In Kimtran v Downie [2003] QCA 424, the Queensland Court of Appeal allowed an appeal from the decision of a District Court judge who had ordered costs against a non-party liquidator. It held that the court's decision in relation to the awarding of costs against a liquidator was not constrained by the decision of the of the Court of Appeal in Mahaffey v Belar Pty Ltd [1999] QCA 2 in the manner stated in the District Court.

A review of Deeds of Company Arrangement

Deeds of company arrangement ('DOCAs') under Part 5.3A of the Corporations Act appear be something of a limited success. However, the use and outcomes of DOCAs raise legitimate questions as to whether the level of returns currently being achieved for creditors might be improved by legislative reform. The 2013 ARITA Terry Taylor Scholarship project entailed a review of a random sample of executed DOCAs effectuated between 1 August 2012 and 31 July 2013. This review was undertaken with the intention of producing a ‘snapshot’ of current trends and outcomes of the use of DOCAs in practice – ie, average (or typical) rates of dividends paid, what DOCAs customarily achieve, the profile of the companies executing DOCAs and the average duration of DOCAs. The purpose of this review was to empirically assess the use and effectiveness of DOCAs in order to inform the ongoing debate about the success or otherwise of Australia’s Part 5.3A voluntary administration regime (which recently marked its 20 year anniversary).

A sample review of Deeds of Company Arrangement under Part 5.3A of the Corporations Act

An empirical review of the operation of Part 5.3A of the Corporations Act 2001 (Cth) is timely given that Australia’s corporate rescue regime marked its 20 year anniversary in 2013. The research project culminating in this report was funded by the 2013 ARITA Terry Taylor Scholarship and entailed a review of a random sample of 72 executed DOCAs (and associated reports and returns) which were effectuated between 1 August 2012 and 31 July 2013. This sample review of DOCAs was undertaken with the intention of producing a ‘snapshot’ of current practices and trends pertaining to DOCAs – ie, average (or typical) rate of dividends paid, the outcomes or goals which DOCAs customarily achieve (eg, genuine company rescues, workouts, enhanced asset realisations or ‘quasi-liquidations’), the profile of the companies executing DOCAs and the average term/duration of DOCAs. The purpose and value of this sample review was to empirically assess the use and effectiveness of one important aspect of Part 5.3A and to further inform consideration and debate as to whether changes are warranted to Australia’s voluntary administration regime.