STAR: predicting recombination sites from amino acid sequence

Background: Designing novel proteins with site-directed recombination has enormous prospects. By locating effective recombination sites for swapping sequence parts, the probability that hybrid sequences have the desired properties is increased dramatically. The prohibitive requirements for applying current tools led us to investigate machine learning to assist in finding useful recombination sites from amino acid sequence alone. Results: We present STAR, Site Targeted Amino acid Recombination predictor, which produces a score indicating the structural disruption caused by recombination, for each position in an amino acid sequence. Example predictions contrasted with those of alternative tools, illustrate STAR'S utility to assist in determining useful recombination sites. Overall, the correlation coefficient between the output of the experimentally validated protein design algorithm SCHEMA and the prediction of STAR is very high (0.89). Conclusion: STAR allows the user to explore useful recombination sites in amino acid sequences with unknown structure and unknown evolutionary origin. The predictor service is available from http://pprowler.itee.uq.edu.au/star.

Structure and ultrastructure of the silk glands and spinneret of Helicoverpa armigera (Hubner) (Lepidoptera : Noctuidae)

This study provides comprehensive documentation of silk production in the pest moth Helicoverpa armigera from gland secretion to extrusion of silk thread. The structure of the silk glands, accessory structures and extrusion apparatus are reported. The general schema of the paired silk glands follows that found for Lepidoptera. Morphology of the duct, silk press, muscle attachments and spigot are presented as a three-dimensional reconstruction and the cuticular crescent-shaped profile of the silk press is demonstrated in both open and closed forms with attendant muscle blocks, allowing advances in our knowledge of how the silk press functions to regulate the extrusion of silk. Growth of the spigot across instars is documented showing a distinctive developmental pattern for this extrusion device. Its shape and structure are related to use and load-bearing activity. (c) 2005 Elsevier Ltd. All rights reserved.

Enabling change for corporate sustainability: An integrated perspective

This article explores the processes of change that enable corporations to move towards sustainable practices, focusing on the human resource and business strategies that support rather than diminish global ecology and human/social capabilities. We argue that this unified approach is necessary to bring about a change in the interpretation of corporate sustainability and to support the activities of change agents (managers, consultants, and community activists) in managing the massive corporate change needed to move corporations toward sustainable practices in a systematic way. We propose a schema in the form of an integrated phase model for understanding how corporations move from compliance modes to the attainment of strategic sustainability and beyond to the ‘ideal’ or sustaining corporation. We discuss the leadership of change and the roles and strategies that corporate change agents can employ to bring about both incremental and transformational change for sustainability.

Predicting structural disruption of proteins caused by crossover

We present a machine learning model that predicts a structural disruption score from a protein’s primary structure. SCHEMA was introduced by Frances Arnold and colleagues as a method for determining putative recombination sites of a protein on the basis of the full (PDB) description of its structure. The present method provides an alternative to SCHEMA that is able to determine the same score from sequence data only. Circumventing the need for resolving the full structure enables the exploration of yet unresolved and even hypothetical sequences for protein design efforts. Deriving the SCHEMA score from a primary structure is achieved using a two step approach: first predicting a secondary structure from the sequence and then predicting the SCHEMA score from the predicted secondary structure. The correlation coefficient for the prediction is 0.88 and indicates the feasibility of replacing SCHEMA with little loss of precision. ©2005 IEEE

Visualising collaboration via email: Finding the key players

Email is an important form of asynchronous communication. Visualizing analyses of email communication patterns during a collaborative activity help us better understand the nature of collaboration, and identify the key players. By analysing the contents of email communication and adding reflective comments on its perceived importance from the participants of a collaboration new information can be gleaned not immediately obvious in its original flat form. This paper outlines a proof-of-concept prototype collaborative email visualisation schema. Data from a collaboration case study is analysed and subsequently employed to construct a display of the relative impact of both key players and the types of email used.

Representing part-whole relationships in conceptual modeling: An empirical evaluation

The part-of or part-whole construct is a fundamental element of many conceptual modeling grammars that is used to associate one thing (a component) with another thing (a composite). Substantive theoretical issues surrounding the part-whole construct remain to be resolved, however. For instance, contrary to widespread claims, the relationship between components and composites is not always transitive. Moreover, how the partwhole construct should be represented in a conceptual schema diagram remains a contentious issue. Some analysts argue composites should be represented as a relationship or association. Others argue they should be represented as an entity. In this paper we use an ontological theory to support our arguments that composites should be represented as entities and not relationships or associations. We also describe an experiment that we undertook to test whether representing composites as relationships or entities enables users to understand a domain better. Our results support our arguments that using entities to represent composites enables users to better understand a domain.

Formal verification of type flaw attacks in security protocols

Security protocols are often modelled at a high level of abstraction, potentially overlooking implementation-dependent vulnerabilities. Here we use the Z specification language's rich set of data structures to formally model potentially ambiguous messages that may be exploited in a 'type flaw' attack. We then show how to formally verify whether or not such an attack is actually possible in a particular protocol using Z's schema calculus.

Feel it and deal with it: mental health practitioners' experiences of exposure to the trauma of survivor clients

Empathic engagement by the trauma therapist with another person's traumatic experiences is believed to create risks for the helping professional. Much attention has been focused upon the mental health professional experiencing symptoms of distress as a result of their exposure to the material of clients who survive traumatic incidents. This thesis contains the findings of a qualitative study that centres on a group of male mental health professionals and their experiences of exposure to the trauma material of survivor clients. The participants of the study practise within an internal Employee Assistance Program that provides, among other duties, a 24 hour, 7 day response to critical incidents to a heavy transport industry. Using semi-structured, in-depth interviews, the effects on the trauma therapists are explored by analysing their reactions to their survivor clients' accounts, the impact of these experiences upon their psychological schema, the organisational culture in which they practise and its influence upon their experiences and the methods participants use to cope with the psychological effects of exposure to trauma material. Participants' experiences are closely examined for critical comparisons with vicarious traumatization. Therapists' responses reveal their continued ability and motivation to empathically engage with the trauma material of survivor clients despite the potential risks.

Stratigrafia fisica ed analisi di facies dei depositi torbiditici della Formazione delle Arenarie del Monte Cervarola tra la Val Secchia e la Val Scoltenna (Aquitaniano-Burdigaliano, Appennino Settentrionale)

The Cervarola Sandstones Formation (CSF), Aquitanian-Burdigalian in age, was deposited in an elongate, NW-stretched foredeep basin formed in front of the growing Northern Apennines orogenic wedge. The stratigraphic succession of the CSF, in the same way of other Apennine foredeep deposits, records the progressive closure of the basin due to the propagation of thrust fronts toward north-east, i.e. toward the outer and shallower foreland ramp. This process produce a complex foredeep characterized by synsedimentary structural highs and depocenters that can strongly influence the lateral and vertical turbidite facies distribution. Of consequence the main aim of this work is to describe and discuss this influence on the basis of a new high-resolution stratigraphic framework performed by measuring ten stratigraphic logs, for a total thickness of about 2000m, between the Secchia and Scoltenna Valleys (30km apart). In particular, the relationship between the turbidite sedimentation and the ongoing tectonic activity during the foredeep evolution has been describe through various stratigraphic cross sections oriented parallel and perpendicular to the main tectonic structures. On the basis of the high resolution physical stratigraphy of the studied succession, we propose a facies tract and an evolutionary model for the Cervarola Sandstones in the studied area. Thanks to these results and the analogies with others foredeep deposits of the northern Apennines, such as the Marnoso-arenacea Formation, the Cervarola basin has been interpreted as a highly confined foredeep controlled by an intense synsedimentary tectonic activity. The most important evidences supporting this hypothesis are: 1) the upward increase, in the studied stratigraphic succession (about 1000m thick), of sandstone/mudstone ratio, grain sizes and Ophiomorpha-type trace fossils testifying the high degree of flow deceleration related to the progressive closure and uplift of the foredeep. 2) the occurrence in the upper part of the stratigraphic succession of coarse-grained massive sandstones overlain by tractive structures such as megaripples and traction carpets passing downcurrent into fine-grained laminated contained-reflected beds. This facies tract is interpreted as related to deceleration and decoupling of bipartite flows with the deposition of the basal dense flows and bypass of the upper turbulent flows. 3) the widespread occurrence of contained reflected beds related to morphological obstacles created by tectonic structures parallel and perpendicular to the basin axis (see for example the Pievepelago line). 4) occurrence of intra-formational slumps, constituted by highly deformed portion of fine-grained succession, indicating a syn-sedimentary tectonic activity of the tectonic structures able to destabilize the margins of the basin. These types of deposits increase towards the upper part of the stratigraphic succession (see points 1 and 2) 5) the impressive lateral facies changes between intrabasinal topographic highs characterized by fine-grained and thin sandstone beds and marlstones and depocenters characterized by thick to very thick coarse-grained massive sandstones. 6) the common occurrence of amalgamation surfaces, flow impact structures and mud-draped scours related to sudden deceleration of the turbidite flows induced by the structurally-controlled confinement and morphological irregularities. In conclusion, the CSF has many analogies with the facies associations occurring in other tectonically-controlled foredeeps such as those of Marnoso-arenacea Formation (northern Italy) and Annot Sandstones (southern France) showing how thrust fronts and transversal structures moving towards the foreland, were able to produce a segmented foredeep that can strongly influence the turbidity current deposition.

Contribution à un bilan méthodologique de la syntaxe de l'émergence diachronique du sujet obligatoire en français::e paramètre du sujet nul et le statut des clitiques

As any language French transformed over time. The evolution of French is marked by many phenomena at all organization levels. For syntax, these phenomena include from the medieval State to current state the assertive sentence of second verb schema change (where the verb should be preceded by a constituent, XVY) to SVO (where it is the subject that precedes the verb) and the passage of the optional expression required expression of the subject. The mandatory presence of the subject in current French is all the more remarkable that it distinguishes it from most other major contemporary romance languages that require explicit subject. This last group includes catalan, Spanish, Italian literary, some occitans, Portuguese, Romanian, and Sardinian, dialects French hugging with the florentin franco-provençal, some other occitans dialects Mediterranean Italian dialects and the ladin following Vanelli, Renzi and Beninca (1985/1985).

Meeting the challenge on the path to democracy: discursive strategies in governmental declarations

The communicative practice in the ex-GDR was complex and diverse, although public political discourse had been fairly ritualized. Text-types characteristic of the Communist Party discourse were full of general (superordinate) terms semantic specification was hardly possible (propositional reduction). Changes in the social world result in changes in the communicative practice as well. However, a systematic comparision of text-types across cultures and across ideological boundaries reveals both differences in the textual macro- and superstructures and overlapping as well as universal features, probably related to functional aspects (discourse of power). Six sample texts of the text-type `government declaration', two produced in the ex-GDR, four in the united Germany, are analysed. Special attention is paid to similarities and differences (i) in the textual superstructure (problem-solution schema), (ii) in the concepts that reflect the aims of political actions (simple worlds), (iii) in the agents who (are to) perform these actions (concrete vs abstract agents). Similarities are found mainly in the discursive strategies, e.g. legitimization text actions. Differences become obvious in the strategies used for legitimization, and also in the conceptual domains referred to by the problem-solution schema. The metaphors of construction, path and challenge are of particular interest in this respect.

Supporting interoperable interpolation: the INTAMAP approach

In many Environmental Information Systems the actual observations arise from a discrete monitoring network which might be rather heterogeneous in both location and types of measurements made. In this paper we describe the architecture and infrastructure for a system, developed as part of the EU FP6 funded INTAMAP project, to provide a service oriented solution that allows the construction of an interoperable, automatic, interpolation system. This system will be based on the Open Geospatial Consortium’s Web Feature Service (WFS) standard. The essence of our approach is to extend the GML3.1 observation feature to include information about the sensor using SensorML, and to further extend this to incorporate observation error characteristics. Our extended WFS will accept observations, and will store them in a database. The observations will be passed to our R-based interpolation server, which will use a range of methods, including a novel sparse, sequential kriging method (only briefly described here) to produce an internal representation of the interpolated field resulting from the observations currently uploaded to the system. The extended WFS will then accept queries, such as ‘What is the probability distribution of the desired variable at a given point’, ‘What is the mean value over a given region’, or ‘What is the probability of exceeding a certain threshold at a given location’. To support information-rich transfer of complex and uncertain predictions we are developing schema to represent probabilistic results in a GML3.1 (object-property) style. The system will also offer more easily accessible Web Map Service and Web Coverage Service interfaces to allow users to access the system at the level of complexity they require for their specific application. Such a system will offer a very valuable contribution to the next generation of Environmental Information Systems in the context of real time mapping for monitoring and security, particularly for systems that employ a service oriented architecture.

Capabilities for strategic flexibility:a cognitive content framework

Different forms of strategic flexibility allow for reactive adaptation to different changing environments and the proactive driving of change. It is therefore becoming increasingly important for decision makers to not only possess marketing capabilities, but also the capabilities for strategic flexibility in its various forms. However, our knowledge of the relationships between decision makers’ different ways of thinking and their capabilities for strategic flexibility is limited. This limitation is constraining research and understanding. In this article we develop a theoretical cognitive content framework that postulates relationships between different ways of thinking about strategy and different information-processing demands. We then outline how the contrasting beliefs of decision makers may influence their capabilities to generate different hybrid forms of strategic flexibility at the cognitive level. Theoretically, the framework is embedded in resource-based theory, personal construct theory and schema theory. The implications for research and theory are discussed.

The moderating role of individual differences in the relation between transformational/transactional leadership perceptions and organizational identification

In this study, we examined the relationship between transformational/transactional leadership perceptions and organizational identification and further explored the moderating role of individual difference variables, such as separateness–connectedness self-schema, and positive and negative affectivity. Data from 502 services employees indicated significant positive effects of transformational and transactional leadership perceptions on organizational identification. Regarding the moderating role of individual differences, our data showed that the positive relationship of transformational leadership and organizational identification was stronger for individuals of low positive affectivity as well as for employees of high negative affectivity. In addition, results indicated that transactional leadership had a stronger positive effect on organizational identification for individuals characterized by a connected self-schema.

Exchanging uncertainty: interoperable geostatistics?

Traditionally, geostatistical algorithms are contained within specialist GIS and spatial statistics software. Such packages are often expensive, with relatively complex user interfaces and steep learning curves, and cannot be easily integrated into more complex process chains. In contrast, Service Oriented Architectures (SOAs) promote interoperability and loose coupling within distributed systems, typically using XML (eXtensible Markup Language) and Web services. Web services provide a mechanism for a user to discover and consume a particular process, often as part of a larger process chain, with minimal knowledge of how it works. Wrapping current geostatistical algorithms with a Web service layer would thus increase their accessibility, but raises several complex issues. This paper discusses a solution to providing interoperable, automatic geostatistical processing through the use of Web services, developed in the INTAMAP project (INTeroperability and Automated MAPping). The project builds upon Open Geospatial Consortium standards for describing observations, typically used within sensor webs, and employs Geography Markup Language (GML) to describe the spatial aspect of the problem domain. Thus the interpolation service is extremely flexible, being able to support a range of observation types, and can cope with issues such as change of support and differing error characteristics of sensors (by utilising descriptions of the observation process provided by SensorML). XML is accepted as the de facto standard for describing Web services, due to its expressive capabilities which allow automatic discovery and consumption by ‘naive’ users. Any XML schema employed must therefore be capable of describing every aspect of a service and its processes. However, no schema currently exists that can define the complex uncertainties and modelling choices that are often present within geostatistical analysis. We show a solution to this problem, developing a family of XML schemata to enable the description of a full range of uncertainty types. These types will range from simple statistics, such as the kriging mean and variances, through to a range of probability distributions and non-parametric models, such as realisations from a conditional simulation. By employing these schemata within a Web Processing Service (WPS) we show a prototype moving towards a truly interoperable geostatistical software architecture.