SCORPION2: A database for structure-function analysis of scorpion toxins

Scorpion toxins are important experimental tools for characterization of vast array of ion channels and serve as scaffolds for drug design. General public database entries contain limited annotation whereby rich structure-function information from mutation studies is typically not available. SCORPION2 contains more than 800 records of native and mutant toxin sequences enriched with binding affinity and toxicity information, 624 three-dimensional structures and some 500 references. SCORPION2 has a set of search and prediction tools that allow users to extract and perform specific queries: text searches of scorpion toxin records, sequence similarity search, extraction of sequences, visualization of scorpion toxin structures, analysis of toxic activity, and functional annotation of previously uncharacterized scorpion toxins. The SCORPION2 database is available at http://sdmc.i2r.a-star.edu.sg/scorpion/. (c) 2006 Elsevier Ltd. All rights reserved.

Transcriptome analysis of Neotyphodium and Epichloë grass endophytes

Large-scale gene discovery has been performed for the grass fungal endophytes Neotyphodium coenophialum, Neotyphodium lolii, and Epichloe festucae. The resulting sequences have been annotated by comparison with public DNA and protein sequence databases and using intermediate gene ontology annotation tools. Endophyte sequences have also been analysed for the presence of simple sequence repeat and single nucleotide polymorphism molecular genetic markers. Sequences and annotation are maintained within a MySQL database that may be queried using a custom web interface. Two cDNA-based microarrays have been generated from this genome resource, They permit the interrogation of 3806 Neotyphodium genes (Nchip (TM) rnicroarray), and 4195 Neotyphodium and 920 Epichloe genes (EndoChip (TM) microarray), respectively. These microarrays provide tools for high-throughput transcriptome analysis, including genome-specific gene expression studies, profiling of novel endophyte genes, and investigation of the host grass-symbiont interaction. Comparative transcriptome analysis in Neotyphodium and Epichloe was performed. (c) 2006 Elsevier

Biodiversity conservation planning tools: Present status and challenges for the future

Species extinctions and the deterioration of other biodiversity features worldwide have led to the adoption of systematic conservation planning in many regions of the world. As a consequence, various software tools for conservation planning have been developed over the past twenty years. These, tools implement algorithms designed to identify conservation area networks for the representation and persistence of biodiversity features. Budgetary, ethical, and other sociopolitical constraints dictate that the prioritized sites represent biodiversity with minimum impact on human interests. Planning tools are typically also used to satisfy these criteria. This chapter reviews both the concepts and technical choices that underlie the development of these tools. Conservation planning problems can be formulated as optimization problems, and we evaluate the suitability of different algorithms for their solution. Finally, we also review some key issues associated with the use of these tools, such as computational efficiency, the effectiveness of taxa and abiotic parameters at choosing surrogates for biodiversity, the process of setting explicit targets of representation for biodiversity surrogates, and

The communication rights in the information society (CRIS) campaign: Applying social movement theories to an analysis of global media reform

Social movement theories offer useful conceptual and analytical tools to the study and research of global media reform movements. This article is a critical analysis of the Communication Rights in the Information Society (CRIS) campaign. It explores its successes and blind-spots in the light of social movement theory, in particular resource mobilization theory (RMT), and offers practical directions for the movement to move on from where it is to where it ought to be.

Playing in continuous spaces: Some analysis and extension of population-based incremental learning

As an alternative to traditional evolutionary algorithms (EAs), population-based incremental learning (PBIL) maintains a probabilistic model of the best individual(s). Originally, PBIL was applied in binary search spaces. Recently, some work has been done to extend it to continuous spaces. In this paper, we review two such extensions of PBIL. An improved version of the PBIL based on Gaussian model is proposed that combines two main features: a new updating rule that takes into account all the individuals and their fitness values and a self-adaptive learning rate parameter. Furthermore, a new continuous PBIL employing a histogram probabilistic model is proposed. Some experiments results are presented that highlight the features of the new algorithms.

Applying a Systems Approach to the Analysis of the Benefits of Conversion to Organic Production

Although the current level of organic production in industrialised countries amounts to little more than 1-2 percent, it is recognised that one of the major issues shaping agricultural output over the next several decades will be the demand for organic produce (Dixon et al. 2001). In Australia, the issues of healthy food and environmental concern contribute to increasing demand and market volumes for organic produce. However, in Indonesia, using more economical inputs for organic production is a supply-side factor driving organic production. For individual growers and processors, conversion from conventional to organic agriculture is often a challenging step, entailing a thorough revision of established practices and heightened market insecurity. This paper examines the potential for a systems approach to the analysis of the conversion process, to yield insights for household and community decisions. A framework for applying farming systems research to investigate the benefits of organic production in both Australia and Indonesia is discussed. The framework incorporates scope for farmer participation, crucial to the understanding of farming systems; analysis of production; and relationships to resources, technologies, markets, services, policies and institutions in their local cultural context. A systems approach offers the potential to internalise the external effects that may be constraining decisions to convert to organic production, and for the design of decision-making tools to assist households and the community. Systems models can guide policy design and serve as a mechanism for predicting the impact of changes to the policy and market environments. The increasing emphasis of farming systems research on community and environment in recent years is in keeping with the proposed application to organic production, processing and marketing issues. The approach will also facilitate the analysis of critical aspects of the Australian production, marketing and policy environment, and the investigation of these same features in an Indonesian context.

Spectroscopic analysis of terrestrial analogues for the interpretation of surface composition of rocky bodies in the solar system. Effects of mineral mixing and particle size. Applications to moon, mars and implications for mercury.

Among the Solar System’s bodies, Moon, Mercury and Mars are at present, or have been in the recent years, object of space missions aimed, among other topics, also at improving our knowledge about surface composition. Between the techniques to detect planet’s mineralogical composition, both from remote and close range platforms, visible and near-infrared reflectance (VNIR) spectroscopy is a powerful tool, because crystal field absorption bands are related to particular transitional metals in well-defined crystal structures, e.g., Fe2+ in M1 and M2 sites of olivine or pyroxene (Burns, 1993). Thanks to the improvements in the spectrometers onboard the recent missions, a more detailed interpretation of the planetary surfaces can now be delineated. However, quantitative interpretation of planetary surface mineralogy could not always be a simple task. In fact, several factors such as the mineral chemistry, the presence of different minerals that absorb in a narrow spectral range, the regolith with a variable particle size range, the space weathering, the atmosphere composition etc., act in unpredictable ways on the reflectance spectra on a planetary surface (Serventi et al., 2014). One method for the interpretation of reflectance spectra of unknown materials involves the study of a number of spectra acquired in the laboratory under different conditions, such as different mineral abundances or different particle sizes, in order to derive empirical trends. This is the methodology that has been followed in this PhD thesis: the single factors previously listed have been analyzed, creating, in the laboratory, a set of terrestrial analogues with well-defined composition and size. The aim of this work is to provide new tools and criteria to improve the knowledge of the composition of planetary surfaces. In particular, mixtures composed with different content and chemistry of plagioclase and mafic minerals have been spectroscopically analyzed at different particle sizes and with different mineral relative percentages. The reflectance spectra of each mixture have been analyzed both qualitatively (using the software ORIGIN®) and quantitatively applying the Modified Gaussian Model (MGM, Sunshine et al., 1990) algorithm. In particular, the spectral parameter variations of each absorption band have been evaluated versus the volumetric FeO% content in the PL phase and versus the PL modal abundance. This delineated calibration curves of composition vs. spectral parameters and allow implementation of spectral libraries. Furthermore, the trends derived from terrestrial analogues here analyzed and from analogues in the literature have been applied for the interpretation of hyperspectral images of both plagioclase-rich (Moon) and plagioclase-poor (Mars) bodies.

Investigation of healthy and infected newborn saliva: the role of proteins and lipids as potential inflammatory diagnostic tools

We have carried out a discovery proteomics investigation aimed at identifying disease biomarkers present in saliva, and, more specifically, early biomarkers of inflammation. The proteomic characterization of saliva is possible due to the straightforward and non-invasive sample collection that allows repetitive analyses for pharmacokinetic studies. These advantages are particularly relevant in the case of newborn patients. The study was carried out with samples collected during the first 48 hours of life of the newborns according to an approved Ethic Committee procedure. In particular, the salivary samples were collected from healthy and infected (n=1) newborns. Proteins were extracted through cycles of sonication, precipitated in ice cold acetone, resuspended and resolved by 2D-electrophoresis. MALDI TOF/TOF mass spectrometry analysis was performed for each spot obtaining the proteins’ identifications. Then we compared healthy newborn salivary proteome and an infected newborn salivary proteome in order to investigate proteins differently expressed in inflammatory condition. In particular the protein alpha-1-antitrypsin (A1AT), correlated with inflammation, was detected differently expressed in the infected newborn saliva. Therefore, in the second part of the project we aimed to develop a robust LC-MS based method that identifies and quantifies this inflammatory protein within saliva that might represent the first relevant step to diagnose a condition of inflammation with a no-invasive assay. The same LC-MS method is also useful to investigate the presence of the F allelic variant of the A1AT in biological samples, which is correlated with the onset of pulmonary diseases. In the last part of the work we analysed newborn saliva samples in order to investigate how phospholipids and mediators of inflammation (eicosanoids) are subject to variations under inflammatory conditions and a trend was observed in lysophosphatidylcholines composition according to the inflammatory conditions.

Ontology ranking based on the analysis of concept structures

In view of the need to provide tools to facilitate the re-use of existing knowledge structures such as ontologies, we present in this paper a system, AKTiveRank, for the ranking of ontologies. AKTiveRank uses as input the search terms provided by a knowledge engineer and, using the output of an ontology search engine, ranks the ontologies. We apply a number of metrics in an attempt to investigate their appropriateness for ranking ontologies, and compare the results with a questionnaire-based human study. Our results show that AKTiveRank will have great utility although there is potential for improvement.

A novel neural network technique for exploratory data analysis

This paper surveys the context of feature extraction by neural network approaches, and compares and contrasts their behaviour as prospective data visualisation tools in a real world problem. We also introduce and discuss a hybrid approach which allows us to control the degree of discriminatory and topographic information in the extracted feature space.

Managing healthcare quality using logical framework analysis

Purpose - The purpose of this paper is to develop an integrated quality management model that identifies problems, suggests solutions, develops a framework for implementation and helps to evaluate dynamically healthcare service performance. Design/methodology/approach - This study used the logical framework analysis (LFA) to improve the performance of healthcare service processes. LFA has three major steps - problems identification, solution derivation, and formation of a planning matrix for implementation. LFA has been applied in a case-study environment to three acute healthcare services (Operating Room utilisation, Accident and Emergency, and Intensive Care) in order to demonstrate its effectiveness. Findings - The paper finds that LFA is an effective method of quality management of hospital-based healthcare services. Research limitations/implications - This study shows LFA application in three service processes in one hospital. This very limited population sample needs to be extended. Practical implications - The proposed model can be implemented in hospital-based healthcare services in order to improve performance. It may also be applied to other services. Originality/value - Quality improvement in healthcare services is a complex and multi-dimensional task. Although various quality management tools are routinely deployed for identifying quality issues in healthcare delivery, they are not without flaws. There is an absence of an integrated approach, which can identify and analyse issues, provide solutions to resolve those issues, develop a project management framework to implement those solutions. This study introduces an integrated and uniform quality management tool for healthcare services. © Emerald Group Publishing Limited.

Strategy tools as boundary objects: a strategy-as-practice perspective

This review is structured in three sections and provides a conceptual framework for the empirical analysis of strategy tools as they are used in practice. Examples of strategy tools are SWOT analysis or Porter’s Five Forces, among others. Section one reviews empirical research into the use of strategy tools, classifying them according to variations in their use. Section two explains the concept of boundary objects as the basis for our argument that strategy tools may be understood as boundary objects. Boundary objects are artefacts that are meaningfully and usefully incorporated to enable sharing of information and transfer of knowledge across intra-organizational boundaries, such as laterally across different strategic business units or vertically across hierarchical levels. Section three draws the two bodies of literature together, conceptualizing strategy tools in practice as boundary objects. This review contributes to knowledge on using strategy tools in practice.

An evaluation of task analysis techniques for industrial process control

The concept of a task is fundamental to the discipline of ergonomics. Approaches to the analysis of tasks began in the early 1900's. These approaches have evolved and developed to the present day, when there is a vast array of methods available. Some of these methods are specific to particular contexts or applications, others more general. However, whilst many of these analyses allow tasks to be examined in detail, they do not act as tools to aid the design process or the designer. The present thesis examines the use of task analysis in a process control context, and in particular the use of task analysis to specify operator information and display requirements in such systems. The first part of the thesis examines the theoretical aspect of task analysis and presents a review of the methods, issues and concepts relating to task analysis. A review of over 80 methods of task analysis was carried out to form a basis for the development of a task analysis method to specify operator information requirements in industrial process control contexts. Of the methods reviewed Hierarchical Task Analysis was selected to provide such a basis and developed to meet the criteria outlined for such a method of task analysis. The second section outlines the practical application and evolution of the developed task analysis method. Four case studies were used to examine the method in an empirical context. The case studies represent a range of plant contexts and types, both complex and more simple, batch and continuous and high risk and low risk processes. The theoretical and empirical issues are drawn together and a method developed to provide a task analysis technique to specify operator information requirements and to provide the first stages of a tool to aid the design of VDU displays for process control.

The influence of tool geometry on the performance of drilling tools

The main objective of the work presented in this thesis is to investigate the two sides of the flute, the face and the heel of a twist drill. The flute face was designed to yield straight diametral lips which could be extended to eliminate the chisel edge, and consequently a single cutting edge will be obtained. Since drill rigidity and space for chip conveyance have to be a compromise a theoretical expression is deduced which enables optimum chip disposal capacity to be described in terms of drill parameters. This expression is used to describe the flute heel side. Another main objective is to study the effect on drill performance of changing the conventional drill flute. Drills were manufactured according to the new flute design. Tests were run in order to compare the performance of a conventional flute drill and non conventional design put forward. The results showed that 50% reduction in thrust force and approximately 18% reduction in torque were attained for the new design. The flank wear was measured at the outer corner and found to be less for the new design drill than for the conventional one in the majority of cases. Hole quality, roundness, size and roughness were also considered as a further aspect of drill performance. Improvement in hole quality is shown to arise under certain cutting conditions. Accordingly it might be possible to use a hole which is produced in one pass of the new drill which previously would have required a drilled and reamed hole. A subsidiary objective is to design the form milling cutter that should be employed for milling the foregoing special flute from drill blank allowing for the interference effect. A mathematical analysis in conjunction with computing technique and computers is used. To control the grinding parameter, a prototype drill grinder was designed and built upon the framework of an existing cincinnati cutter grinder. The design and build of the new grinder is based on a computer aided drill point geometry analysis. In addition to the conical grinding concept, the new grinder is also used to produce spherical point utilizing a computer aided drill point geometry analysis.