The Input Signal Step Function (ISSF), a Standard Method to Encode Input Signals in SBML Models with Software Support, Applied to Circadian Clock Models

LetterThis is the final version of the article. Available from SAGE Publications via the DOI in this record.Time-dependent light input is an important feature of computational models of the circadian clock. However, publicly available models encoded in standard representations such as the Systems Biology Markup Language (SBML) either do not encode this input or use different mechanisms to do so, which hinders reproducibility of published results as well as model reuse. The authors describe here a numerically continuous function suitable for use in SBML for models of circadian rhythms forced by periodic light-dark cycles. The Input Signal Step Function (ISSF) is broadly applicable to encoding experimental manipulations, such as drug treatments, temperature changes, or inducible transgene expression, which may be transient, periodic, or mixed. It is highly configurable and is able to reproduce a wide range of waveforms. The authors have implemented this function in SBML and demonstrated its ability to modify the behavior of publicly available models to accurately reproduce published results. The implementation of ISSF allows standard simulation software to reproduce specialized circadian protocols, such as the phase-response curve. To facilitate the reuse of this function in public models, the authors have developed software to configure its behavior without any specialist knowledge of SBML. A community-standard approach to represent the inputs that entrain circadian clock models could particularly facilitate research in chronobiology.K.S. was supported by the UK BBSRC grant BB/E015263/1. SynthSys Edinburgh is a Centre for Integrative Systems Biology (CISB) funded by BBSRC and EPSRC, reference BB/D019621/1

Modified sorting technique to mitigate the collateral mortality of trawled school prawns (Metapenaeus macleayi)

The potential for changes to onboard handling practices in order to improve the fate of juvenile school prawns (Metapenaeus macleayi) discarded during trawling were investigated in two Australian rivers (Clarence and Hunter) by comparing a purpose-built, water-filled sorting tray against a conventional dry tray across various conditions, including the range of typical delays before the start of sorting the catch (2 min vs. 15 min). Juvenile school prawns (n= 5760), caught during 32 and 16 deployments in each river, were caged and sacrificed at four times: immediately (T0), and at 24 (T24), 72 (T72), and 120 (T12 0) hours after having been discarded. In both rivers, most mortalities occurred between T0 and T24 and, after adjusting for control deaths (<12%), were greatest for the 15-min conventional treatment (up to 41% at T120). Mixed-effects logistic models revealed that in addition to the sampling time, method of sorting, and delay in sorting, the weight of the catch, salinity, and percentage cloud cover were significant predictors of mortality. Although trawling caused some mortalities and comparable stress (measured as L -lactate) in all school prawns, use of the water tray lessened the negative impacts of some of the above factors across both the 2-min and 15-min delays in sorting so that the overall discard mortality was reduced by more than a third. When used in conjunction with selective trawls, widespread application of the water tray should help to improve the sustainability of trawling for school prawns

Grid infrastructures for the electronics domain: requirements and early prototypes from an EPSRC pilot project

The fundamental challenges facing future electronics design is to address the decreasing – atomistic - scale of transistor devices and to understand and predict the impact and statistical variability these have on design of circuits and systems. The EPSRC pilot project “Meeting the Design Challenges of nanoCMOS Electronics” (nanoCMOS) which began in October 2006 has been funded to explore this space. This paper outlines the key requirements that need to be addressed for Grid technology to support the various research strands in this domain, and shows early prototypes demonstrating how these requirements are being addressed

Morphology of the recently re-classified Tasman masked booby (Sula dactylatra tasmani) breeding on the Kermadec Islands

Once thought to be extinct, the Tasman Booby Sula tasmani has recently been re-classified as a subspecies of the Masked Booby S. dactylatra on the basis of genetic data. This re-classification raises the issue of whether this novel clade has a distinct morphology. Morphological differences in size, as well as coloration of integuments, bill and iris have been found in other subspecies of the Masked Booby but have not yet been reported for live Kermadec Islands breeding individuals. Museum specimens from this breeding location have been separated from other Pacific breeding subspecies by their longer wings. We sampled a total of 21 individuals from North Meyer Islet, Kermadec Group, New Zealand, and applied molecular sexing to obtain sex-specific morphometric measurements. We matched dimorphism in vocalization with genetic sexing results and photographic documentation of human-assessed bill, foot and eye coloration. While culmen measurements were consistent with reports from museum specimens, wing chords from living specimens of Tasman Masked Boobies were 3% and 4% larger in males and females, respectively. Females had larger culmens and wings than males, consistent with the low extent of sexual dimorphism reported from museum skins. Adult Tasman Masked Boobies had yellow to buff-yellow feet, while fledglings, as in most sulids, had grey to greyish-yellow feet. Our findings confirm the distinctively long wing and particular iris coloration previously reported for the taxon and provide the first description of integument coloration of live specimens. This study highlights the importance of including in situ assessment in taxon descriptions

Meeting the design challenges of nano-CMOS electronics: an introduction to an upcoming EPSRC pilot project

The years of ‘happy scaling’ are over and the fundamental challenges that the semiconductor industry faces, at both technology and device level, will impinge deeply upon the design of future integrated circuits and systems. This paper provides an introduction to these challenges and gives an overview of the Grid infrastructure that will be developed as part of a recently funded EPSRC pilot project to address them, and we hope, which will revolutionise the electronics design industry

Diversity of vertebrate nicotinic acetylcholine receptors

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Rapid virological surveillance of community influenza infection in general practice

No abstract available