A windows program for the derivation of steady-state equations in enzyme systems

Despite the number of computer-assisted methods described for the derivation of steady-state equations of enzyme systems, most of them are focused on strict steady-state conditions or are not able to solve complex reaction mechanisms. Moreover, many of them are based on computer programs that are either not readily available or have limitations. We present here a computer program called WinStes, which derives equations for both strict steady-state systems and those with the assumption of rapid equilibrium, for branched or unbranched mechanisms, containing both reversible and irreversible conversion steps. It solves reaction mechanisms involving up to 255 enzyme species, connected by up to 255 conversion steps. The program provides all the advantages of the Windows programs, such as a user-friendly graphical interface, and has a short computation time. WinStes is available free of charge on request from the authors. (c) 2006 Elsevier Inc. All rights reserved.

Visual-auditory integration during speech imitation in autism

Children with autistic spectrum disorder (ASD) may have poor audio-visual integration, possibly reflecting dysfunctional 'mirror neuron' systems which have been hypothesised to be at the core of the condition. In the present study, a computer program, utilizing speech synthesizer software and a 'virtual' head (Baldi), delivered speech stimuli for identification in auditory, visual or bimodal conditions. Children with ASD were poorer than controls at recognizing stimuli in the unimodal conditions, but once performance on this measure was controlled for, no group difference was found in the bimodal condition. A group of participants with ASD were also trained to develop their speech-reading ability. Training improved visual accuracy and this also improved the children's ability to utilize visual information in their processing of speech. Overall results were compared to predictions from mathematical models based on integration and non-integration, and were most consistent with the integration model. We conclude that, whilst they are less accurate in recognizing stimuli in the unimodal condition, children with ASD show normal integration of visual and auditory speech stimuli. Given that training in recognition of visual speech was effective, children with ASD may benefit from multi-modal approaches in imitative therapy and language training. (C) 2004 Elsevier Ltd. All rights reserved.

The abundance of short proteins in the mammalian proteome

Short proteins play key roles in cell signalling and other processes, but their abundance in the mammalian proteome is unknown. Current catalogues of mammalian proteins exhibit an artefactual discontinuity at a length of 100 aa, so that protein abundance peaks just above this length and falls off sharply below it. To clarify the abundance of short proteins, we identify proteins in the FANTOM collection of mouse cDNAs by analysing synonymous and nonsynonymous substitutions with the computer program CRITICA. This analysis confirms that there is no real discontinuity at length 100. Roughly 10% of mouse proteins are shorter than 100 aa, although the majority of these are variants of proteins longer than 100 aa. We identify many novel short proteins, including a dark matter'' subset containing ones that lack detectable homology to other known proteins. Translation assays confirm that some of these novel proteins can be translated and localised to the secretory pathway.

Extent and economic effect of heat loads on dairy cattle production in Australia

Objective To investigate the extent of heat load problems, caused by the combination of excessive temperature and humidity, in Holstein-Friesian cows in Australia. Also, to outline how milk production losses and consequent costs from this can be estimated and minimised. Procedures Long-term meteorological data for Australia were analysed to determine the distribution of hot conditions over space and time. Fifteen dairy production regions were identified for higher-resolution data analysis. Both the raw meteorological data and their integration into a temperature-humidity thermal index were compiled onto a computer program. This mapping software displays the distribution of climatic patterns, both Australia-wide and within the selected dairying regions. Graphical displays of the variation in historical records for 200 locations in the 15 dairying regions are also available. As a separate study, production data from research stations, on-farm trials and milk factory records were statistically analysed and correlated with the climatic indices, to estimate production losses due to hot conditions. Results Both milk yields and milk constituents declined with increases in the temperature-humidity index. The onset and rate of this decline are dependent on a number of factors, including location, level of production, adaptation, and management regime. These results have been integrated into a farm-level economic analysis for managers of dairy properties. Conclusion By considering the historical patterns of hot conditions over time and space, along with expected production losses, managers of dairy farms can now conduct an economic evaluation of investment strategies to alleviate heat loads. These strategies include the provision of sprinklers, shade structures, or combinations of these.

Simulating the effects of dominance and epistasis on selection response in the CIMMYT wheat breeding program using QuCim

Plant breeders use many different breeding methods to develop superior cultivars. However, it is difficult, cumbersome, and expensive to evaluate the performance of a breeding method or to compare the efficiencies of different breeding methods within an ongoing breeding program. To facilitate comparisons, we developed a QU-GENE module called QuCim that can simulate a large number of breeding strategies for self-pollinated species. The wheat breeding strategy Selected Bulk used by CIMMYT's wheat breeding program was defined in QuCim as an example of how this is done. This selection method was simulated in QuCim to investigate the effects of deviations from the additive genetic model, in the form of dominance and epistasis, on selection outcomes. The simulation results indicate that the partial dominance model does not greatly influence genetic advance compared with the pure additive model. Genetic advance in genetic systems with overdominance and epistasis are slower than when gene effects are purely additive or partially dominant. The additive gene effect is an appropriate indicator of the change in gene frequency following selection when epistasis is absent. In the absence of epistasis, the additive variance decreases rapidly with selection. However, after several cycles of selection it remains relatively fixed when epistasis is present. The variance from partial dominance is relatively small and therefore hard to detect by the covariance among half sibs and the covariance among full sibs. The dominance variance from the overdominance model can be identified successfully, but it does not change significantly, which confirms that overdominance cannot be utilized by an inbred breeding program. QuCim is an effective tool to compare selection strategies and to validate some theories in quantitative genetics.

Procedures and parameters in the real-time program refinement calculus

The real-time refinement calculus is a formal method for the systematic derivation of real-time programs from real-time specifications in a style similar to the non-real-time refinement calculi of Back and Morgan. In this paper we extend the real-time refinement calculus with procedures and provide refinement rules for refining real-time specifications to procedure calls. A real-time specification can include constraints on, not only what outputs are produced, but also when they are produced. The derived programs can also include time constraints oil when certain points in the program must be reached; these are expressed in the form of deadline commands. Such programs are machine independent. An important consequence of the approach taken is that, not only are the specifications machine independent, but the whole refinement process is machine independent. To implement the machine independent code on a target machine one has a separate task of showing that the compiled machine code will reach all its deadlines before they expire. For real-time programs, externally observable input and output variables are essential. These differ from local variables in that their values are observable over the duration of the execution of the program. Hence procedures require input and output parameter mechanisms that are references to the actual parameters so that changes to external inputs are observable within the procedure and changes to output parameters are externally observable. In addition, we allow value and result parameters. These may be auxiliary parameters, which are used for reasoning about the correctness of real-time programs as well as in the expression of timing deadlines, but do not lead to any code being generated for them by a compiler. (c) 2006 Elsevier B.V. All rights reserved.

Model checking Z specifications using SAL

The Symbolic Analysis Laboratory (SAL) is a suite of tools for analysis of state transition systems. Tools supported include a simulator and four temporal logic model checkers. The common input language to these tools was originally developed with translation from other languages, both programming and specification languages, in mind. It is, therefore, a rich language supporting a range of type definitions and expressions. In this paper, we investigate the translation of Z specifications into the SAL language as a means of providing model checking support for Z. This is facilitated by a library of SAL definitions encoding the Z mathematical toolkit.

UML approach to the generation of test sequences for Java-based concurrent systems

Starting with a UML specification that captures the underlying functionality of some given Java-based concurrent system, we describe a systematic way to construct, from this specification, test sequences for validating an implementation of the system. The approach is to first extend the specification to create UML state machines that directly address those aspects of the system we wish to test. To be specific, the extended UML state machines can capture state information about the number of waiting threads or the number of threads blocked on a given object. Using the SAL model checker we can generate from the extended UML state machines sequences that cover all the various possibilities of events and states. These sequences can then be directly transformed into test sequences suitable for input into a testing tool such as ConAn. As an illustration, the methodology is applied to generate sequences for testing a Java implementation of the producer-consumer system. © 2005 IEEE

A technique for modular logic program refinement

A refinement calculus provides a method for transforming specifications to executable code, maintaining the correctness of the code with respect to its specification. In this paper we introduce modules into a logic programming refinement calculus. Modules allow data types to be grouped together with sets of procedures that manipulate the data types. By placing restrictions on the way a program uses a module, we develop a technique for refining the module so that it uses a more efficient representation of the data type.

XSophe, a computer simulation software suite for the analysis of electron paramagnetic resonance spectra

The XSophe computer simulation software suite consisting of a daemon, the XSophe interface and the computational program Sophe is a state of the art package for the simulation of electron paramagnetic resonance spectra. The Sophe program performs the computer simulation and includes a number of new technologies including; the SOPHE partition and interpolation schemes, a field segmentation algorithm, homotopy, parallelisation and spectral optimisation. The SOPHE partition and interpolation scheme along with a field segmentation algorithm greatly increases the speed of simulations for most systems. Multidimensional homotopy provides an efficient method for accurately tracing energy levels and hence tracing transitions in the presence of energy level anticrossings and looping transitions and allowing computer simulations in frequency space. Recent enhancements to Sophe include the generalised treatment of distributions of orientational parameters, termed the mosaic misorientation linewidth model and a faster more efficient algorithm for the calculation of resonant field positions and transition probabilities. For complex systems the parallelisation enables the simulation of these systems on a parallel computer and the optimisation algorithms in the suite provide the experimentalist with the possibility of finding the spin Hamiltonian parameters in a systematic manner rather than a trial-and-error process. The XSophe software suite has been used to simulate multifrequency EPR spectra (200 MHz to 6 00 GHz) from isolated spin systems (S > ~½) and coupled centres (Si, Sj _> I/2). Griffin, M.; Muys, A.; Noble, C.; Wang, D.; Eldershaw, C.; Gates, K.E.; Burrage, K.; Hanson, G.R."XSophe, a Computer Simulation Software Suite for the Analysis of Electron Paramagnetic Resonance Spectra", 1999, Mol. Phys. Rep., 26, 60-84.

Computer-aided programming using formally specificed design templates

This paper describes a formal component language, used to support automated component-based program development. The components, referred to as templates, are machine processable, meaning that appropriate tool support, such as retrieval support, can be developed. The templates are highly adaptable, meaning that they can be applied to a wide range of problems. Some of the main features of the language are described, including: higher-order parameters; state variable declarations; specification statements and conditionals; applicability conditions and theories; meta-level place holders; and abstract data structures.