Finding microRNA regulatory modules in human genome using rule induction

Background: MicroRNAs (miRNAs) are a class of small non-coding RNA molecules (20-24 nt), which are believed to participate in repression of gene expression. They play important roles in several biological processes (e.g. cell death and cell growth). Both experimental and computational approaches have been used to determine the function of miRNAs in cellular processes. Most efforts have concentrated on identification of miRNAs and their target genes. However, understanding the regulatory mechanism of miRNAs in the gene regulatory network is also essential to the discovery of functions of miRNAs in complex cellular systems. To understand the regulatory mechanism of miRNAs in complex cellular systems, we need to identify the functional modules involved in complex interactions between miRNAs and their target genes. Results: We propose a rule-based learning method to identify groups of miRNAs and target genes that are believed to participate cooperatively in the post-transcriptional gene regulation, so-called miRNA regulatory modules (MRMs). Applying our method to human genes and miRNAs, we found 79 MRMs. The MRMs are produced from multiple information sources, including miRNA-target binding information, gene expression and miRNA expression profiles. Analysis of two first MRMs shows that these MRMs consist of highly-related miRNAs and their target genes with respect to biological processes. Conclusion: The MRMs found by our method have high correlation in expression patterns of miRNAs as well as mRNAs. The mRNAs included in the same module shared similar biological functions, indicating the ability of our method to detect functionality-related genes. Moreover, review of the literature reveals that miRNAs in a module are involved in several types of human cancer

Use of a Generalized Additive Model to Investigate Key Abiotic Factors Affecting Microcystin Cellular Quotas in Heavy Bloom Areas of Lake Taihu

Lake Taihu is the third largest freshwater lake in China and is suffering from serious cyanobacterial blooms with the associated drinking water contamination by microcystin (MC) for millions of citizens. So far, most studies on MCs have been limited to two small bays, while systematic research on the whole lake is lacking. To explain the variations in MC concentrations during cyanobacterial bloom, a large-scale survey at 30 sites across the lake was conducted monthly in 2008. The health risks of MC exposure were high, especially in the northern area. Both Microcystis abundance and MC cellular quotas presented positive correlations with MC concentration in the bloom seasons, suggesting that the toxic risks during Microcystis proliferations were affected by variations in both Microcystis density and MC production per Microcystis cell. Use of a powerful predictive modeling tool named generalized additive model (GAM) helped visualize significant effects of abiotic factors related to carbon fixation and proliferation of Microcystis (conductivity, dissolved inorganic carbon (DIC), water temperature and pH) on MC cellular quotas from recruitment period of Microcystis to the bloom seasons, suggesting the possible use of these factors, in addition to Microcystis abundance, as warning signs to predict toxic events in the future. The interesting relationship between macrophytes and MC cellular quotas of Microcystis (i.e., high MC cellular quotas in the presence of macrophytes) needs further investigation

Sustainability Assessment of Environmentally Conscious Manufacturing Companies

Sustainable manufacturing is becoming increasingly important with substantial social, environmental and economic benefits, thus companies show more tendency to adopt this concept. Recognizing the benefits of sustainability, manufacturing companies need to measure how sustainable they perform. However, sustainability can be thought as an abstract issue which is difficult to measure and also assess. Measuring sustainability is a continuously evolving research area which generates various sustainability indicators to assess companies' production activities. Practically, while evaluating the sustainability performance of a manufacturing system, various indicators should be considered simultaneously. This study focuses on the usage of sustainability indicators to assess the sustainability of a production company from a multi-criteria decision making point of view. As a case study, the sustainability performances of an international beverage company which produces non-alcoholic drinks were evaluated. TOPSIS method was adopted as an assessment method with the use of several conflicting indicators simultaneously

Sustainability assessment of manufacturing organizations based on indicator sets: A formal concept analysis

International audienceOrganizations are struggling to survive in today's competitive market. They are mostly obliged to meet customers' expectations and demand for sustainable products from one side and comply with governmental rules and regulations regarding energy, resources, materials, etc. on the other side. Therefore, measuring their sustainability performance and trying to keep up with the competitors is essential for their future development. Consequently, organizations' perception of operational sustainability can reveal their strategies on how to be sustainable, endeavouring the three pillars of economic, environmental and social. The present work investigates the role of indicators' choice and their meaning for sustainability assessment of manufacturing organizations. To this point, an analysis is conducted on the sustainability assessment of 100 manufacturing organizations using GRI indicators for assessing their sustainability state. A Formal Concept Analysis was run to look over the indicators and their interpretations to reach a given degree of sustainability of the organization

Integrating Joint Behaviour and Dialogue Description

. Agents are becoming increasingly common as a means of structuring interactive systems, due to the highly complex and concurrent nature of modern systems. The manner in which interaction between these agents is specified is of fundamental importance, and must pay heed to expressivity and reuse concerns. There are also concerns specific to interactive systems, and in particular the need to specify and reason about user-system dialogue. We have shown previously that the standard model of object interaction is inadequate with respect to these concerns, and that the action model performs better with respect to these criteria. In this paper these results are drawn together with approaches previously taken in interactive systems. From this basis a schema calculus with interleaving semantics is proposed, which better addresses the concerns of expressivity and reuse in the interactive systems context. 1 Introduction Modern interactive systems are large, complex entities comprisin..