Models for pattern formation in somitogenesis: a marriage of cellular and molecular biology

Somitogenesis, the process by which a bilaterally symmetric pattern of cell aggregations is laid down in a cranio-caudal sequence in early vertebrate development, provides an excellent model study for the coupling of interactions at the molecular and cellular level. Here, we review some of the key experimental results and theoretical models related to this process. We extend a recent chemical pre-pattern model based on the cell cycle Journal of Theoretical Biology 207 (2000) 305-316, by including cell movement and show that the resultant model exhibits the correct spatio-temporal dynamics of cell aggregation. We also postulate a model to account for the recently observed spatio-temporal dynamics at the molecular level

Numerical study of the stability of some explicit finite-difference methods for oscillatory advection

This paper is made available with the permission of the Australian Mathematical Society Inc. Copyright © 2005 Australian Mathematical SocietyThe basis for modelling unsteady transport in fluids is the one-dimensional advection equation. When high-order finite-difference methods for constant velocity advection are applied to the variable velocity case, they generally degenerate at least one order. For example, Crowley's formula, which is second order for constant velocity advection, is only first order when used with variable velocities. Modification of Crowley's formula has recently yielded three formulae which are second order in the variable velocity case. Two commonly used local stability analyses have been carried out on these formulae with conflicting results. The resulting stability regions have been studied by means of a series of numerical experiments using an oscillatory advection velocity to determine their applicability in tidal streams.John Noye and David McInerne

Sequestration of G3BP coupled with efficient translation inhibits stress granules in Semliki Forest virus infection

Dynamic, mRNA-containing stress granules (SGs) form in the cytoplasm of cells under environmental stresses, including viral infection. Many viruses appear to employ mechanisms to disrupt the formation of SGs on their mRNAs, suggesting that they represent a cellular defense against infection. Here, we report that early in Semliki Forest virus infection, the C-terminal domain of the viral nonstructural protein 3 (nsP3) forms a complex with Ras-GAP SH3-domain–binding protein (G3BP) and sequesters it into viral RNA replication complexes in a manner that inhibits the formation of SGs on viral mRNAs. A viral mutant carrying a C-terminal truncation of nsP3 induces more persistent SGs and is attenuated for propagation in cell culture. Of importance, we also show that the efficient translation of viral mRNAs containing a translation enhancer sequence also contributes to the disassembly of SGs in infected cells. Furthermore, we show that the nsP3/G3BP interaction also blocks SGs induced by other stresses than virus infection. This is one of few described viral mechanisms for SG disruption and underlines the role of SGs in antiviral defense

Low-frequency fluctuations in a semiconductor laser with phase conjugate feedback

We analyze the dynamics of a semiconductor laser with phase conjugate optical feedback, using numerical simulations based on rate equations for the complex amplitude of the electric field and the carrier density. From this analysis we observe the presence of low-frequency fluctuations which are similar to those observed in a semiconductor laser with conventional optical feedback. The similarities and differences between phase conjugate and conventional optical feedback are discussed, and a mechanism for the appearance of low-frequency fluctuations in a semiconductor laser with phase conjugate feedback is suggested

Toward Open Science at the European Scale: Geospatial Semantic Array Programming for Integrated Environmental Modelling

[Excerpt] Interfacing science and policy raises challenging issues when large spatial-scale (regional, continental, global) environmental problems need transdisciplinary integration within a context of modelling complexity and multiple sources of uncertainty. This is characteristic of science-based support for environmental policy at European scale, and key aspects have also long been investigated by European Commission transnational research. Approaches (either of computational science or of policy-making) suitable at a given domain-specific scale may not be appropriate for wide-scale transdisciplinary modelling for environment (WSTMe) and corresponding policy-making. In WSTMe, the characteristic heterogeneity of available spatial information and complexity of the required data-transformation modelling (D-TM) appeal for a paradigm shift in how computational science supports such peculiarly extensive integration processes. In particular, emerging wide-scale integration requirements of typical currently available domain-specific modelling strategies may include increased robustness and scalability along with enhanced transparency and reproducibility. This challenging shift toward open data and reproducible research (open science) is also strongly suggested by the potential - sometimes neglected - huge impact of cascading effects of errors within the impressively growing interconnection among domain-specific computational models and frameworks. Concise array-based mathematical formulation and implementation (with array programming tools) have proved helpful in supporting and mitigating the complexity of WSTMe when complemented with generalized modularization and terse array-oriented semantic constraints. This defines the paradigm of Semantic Array Programming (SemAP) where semantic transparency also implies free software use (although black-boxes - e.g. legacy code - might easily be semantically interfaced). A new approach for WSTMe has emerged by formalizing unorganized best practices and experience-driven informal patterns. The approach introduces a lightweight (non-intrusive) integration of SemAP and geospatial tools - called Geospatial Semantic Array Programming (GeoSemAP). GeoSemAP exploits the joint semantics provided by SemAP and geospatial tools to split a complex D-TM into logical blocks which are easier to check by means of mathematical array-based and geospatial constraints. Those constraints take the form of precondition, invariant and postcondition semantic checks. This way, even complex WSTMe may be described as the composition of simpler GeoSemAP blocks. GeoSemAP allows intermediate data and information layers to be more easily and formally semantically described so as to increase fault-tolerance, transparency and reproducibility of WSTMe. This might also help to better communicate part of the policy-relevant knowledge, often diffcult to transfer from technical WSTMe to the science-policy interface. [...

State updating and calibration period selection to improve dynamic monthly streamflow forecasts for an environmental flow management application

Monthly to seasonal streamflow forecasts provide useful information for a range of water resource management and planning applications. This work focuses on improving such forecasts by considering the following two aspects: (1) state updating to force the models to match observations from the start of the forecast period, and (2) selection of a shorter calibration period that is more representative of the forecast period, compared to a longer calibration period traditionally used. The analysis is undertaken in the context of using streamflow forecasts for environmental flow water management of an open channel drainage network in southern Australia. Forecasts of monthly streamflow are obtained using a conceptual rainfall–runoff model combined with a post-processor error model for uncertainty analysis. This model set-up is applied to two catchments, one with stronger evidence of non-stationarity than the other. A range of metrics are used to assess different aspects of predictive performance, including reliability, sharpness, bias and accuracy. The results indicate that, for most scenarios and metrics, state updating improves predictive performance for both observed rainfall and forecast rainfall sources. Using the shorter calibration period also improves predictive performance, particularly for the catchment with stronger evidence of non-stationarity. The results highlight that a traditional approach of using a long calibration period can degrade predictive performance when there is evidence of non-stationarity. The techniques presented can form the basis for operational monthly streamflow forecasting systems and provide support for environmental decision-making.Matthew S. Gibbs, David McInerney, Greer Humphrey, Mark A. Thyer, Holger R. Maier, Graeme C. Dandy and Dmitri Kavetsk

Free and Open Source Software underpinning the European Forest Data Centre

Worldwide, governments are growingly focusing on free and open source software (FOSS) as a move toward transparency and the freedom to run, copy, study, change and improve the software. The European Commission (EC) is also supporting the development of FOSS [...]. In addition to the financial savings, FOSS contributes to scientific knowledge freedom in computational science (CS) and is increasingly rewarded in the science-policy interface within the emerging paradigm of open science. Since complex computational science applications may be affected by software uncertainty, FOSS may help to mitigate part of the impact of software errors by CS community- driven open review, correction and evolution of scientific code. The continental scale of EC science-based policy support implies wide networks of scientific collaboration. Thematic information systems also may benefit from this approach within reproducible integrated modelling. This is supported by the EC strategy on FOSS: "for the development of new information systems, where deployment is foreseen by parties outside of the EC infrastructure, [F]OSS will be the preferred choice and in any case used whenever possible". The aim of this contribution is to highlight how a continental scale information system may exploit and integrate FOSS technologies within the transdisciplinary research underpinning such a complex system. A European example is discussed where FOSS innervates both the structure of the information system itself and the inherent transdisciplinary research for modelling the data and information which constitute the system content. [...

Treatment of Border Tax Rebates of Consumption Taxes under the Antidumping Law

This Article describes how Zenith Electronics Corp. v. United States ( Zenith ) made the treatment of export rebates of consumption taxes an issue under the U.S. antidumping law. It explains the position of the Department of Commerce ( Commerce ) that dumping margins should be calculated on a tax net basis (so that they equal the margins that would be found in the absence of taxes), and offers a general criticism of the argument in Zenith

Educational Computing: Some Policy Implications for Administrators

Administrators must also be sensitive to the potential dangers inherent in a thoughtless rush to incorporate computing in schools