The complexity of context: Guest editors' introduction

Cataloged from PDF version of article.As with other widely used notions that are commonly referred to in everyday activities without much hesitation, context is difficult to analyze scientifically and grasp in all its different demeanors. In our routine communicative activities, context is exploited both in production and in comprehension, and is strictly related to another problematic notion, viz. meaning. Thus Bateson (1979: 15): ‘‘Without context, words and actions have no meaning at all. This is true not only of human communication in words but also of all communication whatsoever, of all mental process, of all mind, including that which tells the sea anemone how to grow and the amoeba what he should do next.’’..

Complementary approaches to understanding the plant circadian clock

This is the final version of the article. Available from the Open Publishing Association via the DOI in this record.Proceedings - Third Workshop 'From Biology To Concurrency and back', Paphos, Cyprus, 27 March 2010Circadian clocks are oscillatory genetic networks that help organisms adapt to the 24-hour day/night cycle. The clock of the green alga Ostreococcus tauri is the simplest plant clock discovered so far. Its many advantages as an experimental system facilitate the testing of computational predictions. We present a model of the Ostreococcus clock in the stochastic process algebra Bio-PEPA and exploit its mapping to different analysis techniques, such as ordinary differential equations, stochastic simulation algorithms and model-checking. The small number of molecules reported for this system tests the limits of the continuous approximation underlying differential equations. We investigate the difference between continuous-deterministic and discrete-stochastic approaches. Stochastic simulation and model-checking allow us to formulate new hypotheses on the system behaviour, such as the presence of self-sustained oscillations in single cells under constant light conditions. We investigate how to model the timing of dawn and dusk in the context of model-checking, which we use to compute how the probability distributions of key biochemical species change over time. These show that the relative variation in expression level is smallest at the time of peak expression, making peak time an optimal experimental phase marker. Building on these analyses, we use approaches from evolutionary systems biology to investigate how changes in the rate of mRNA degradation impacts the phase of a key protein likely to affect fitness. We explore how robust this circadian clock is towards such potential mutational changes in its underlying biochemistry. Our work shows that multiple approaches lead to a more complete understanding of the clock.The authors thank Gerben van Ooijen for TopCount data and Jane Hillston and Andrew Millar for their helpful comments. The Centre for Systems Biology at Edinburgh is a Centre for Integrative Systems Biology (CISB) funded by BBSRC and EPSRC, ref. BB/D019621/1. CT is supported by The International Human Frontier Science Program Organization

Complementary approaches to understanding the plant circadian clock

Circadian clocks are oscillatory genetic networks that help organisms adapt to the 24-hour day/night cycle. The clock of the green alga Ostreococcus tauri is the simplest plant clock discovered so far. Its many advantages as an experimental system facilitate the testing of computational predictions. We present a model of the Ostreococcus clock in the stochastic process algebra Bio-PEPA and exploit its mapping to different analysis techniques, such as ordinary differential equations, stochastic simulation algorithms and model-checking. The small number of molecules reported for this system tests the limits of the continuous approximation underlying differential equations. We investigate the difference between continuous-deterministic and discrete-stochastic approaches. Stochastic simulation and model-checking allow us to formulate new hypotheses on the system behaviour, such as the presence of self-sustained oscillations in single cells under constant light conditions. We investigate how to model the timing of dawn and dusk in the context of model-checking, which we use to compute how the probability distributions of key biochemical species change over time. These show that the relative variation in expression level is smallest at the time of peak expression, making peak time an optimal experimental phase marker. Building on these analyses, we use approaches from evolutionary systems biology to investigate how changes in the rate of mRNA degradation impacts the phase of a key protein likely to affect fitness. We explore how robust this circadian clock is towards such potential mutational changes in its underlying biochemistry. Our work shows that multiple approaches lead to a more complete understanding of the clock

The complexity of context: Guest editors' introduction

[No abstract available

Hypoxia dictates metabolic rewiring of tumors: implications for chemoresistance

Hypoxia is a condition commonly observed in the core of solid tumors. The hypoxia-inducible factors (HIF) act as hypoxia sensors that orchestrate a coordinated response increasing the pro-survival and pro-invasive phenotype of cancer cells, and determine a broad metabolic rewiring. These events favor tumor progression and chemoresistance. The increase in glucose and amino acid uptake, glycolytic flux, and lactate production; the alterations in glutamine metabolism, tricarboxylic acid cycle, and oxidative phosphorylation; the high levels of mitochondrial reactive oxygen species; the modulation of both fatty acid synthesis and oxidation are hallmarks of the metabolic rewiring induced by hypoxia. This review discusses how metabolic-dependent factors (e.g., increased acidification of tumor microenvironment coupled with intracellular alkalinization, and reduced mitochondrial metabolism), and metabolic-independent factors (e.g., increased expression of drug efflux transporters, stemness maintenance, and epithelial-mesenchymal transition) cooperate in determining chemoresistance in hypoxia. Specific metabolic modifiers, however, can reverse the metabolic phenotype of hypoxic tumor areas that are more chemoresistant into the phenotype typical of chemosensitive cells. We propose these metabolic modifiers, able to reverse the hypoxia-induced metabolic rewiring, as potential chemosensitizer agents against hypoxic and refractory tumor cells

Shock tunnel studies of scramjet phenomena, supplement 5

A series of reports are presented on SCRAMjet studies, shock tunnel studies, and expansion tube studies. The SCRAMjet studies include: (1) Investigation of a Supersonic Combustion Layer; (2) Wall Injected SCRAMjet Experiments; (3) Supersonic Combustion with Transvers, Circular, Wall Jets; (4) Dissociated Test Gas Effects on SCRAMjet Combustors; (5) Use of Silane as a Fuel Additive for Hypersonic Thrust Production, (6) Pressure-length Correlations in Supersonic Combustion; (7) Hot Hydrogen Injection Technique for Shock Tunnels; (8) Heat Release - Wave Interaction Phenomena in Hypersonic Flows; (9) A Study of the Wave Drag in Hypersonic SCRAMjets; (10) Parametric Study of Thrust Production in the Two Dimensional SCRAMjet; (11) The Design of a Mass Spectrometer for use in Hypersonic Impulse Facilities; and (12) Development of a Skin Friction Gauge for use in an Impulse Facility. The shock tunnel studies include: (1) Hypervelocity flow in Axisymmetric Nozzles; (2) Shock Tunnel Development; and (3) Real Gas Efects in Hypervelocity Flows over an Inclined Cone. The expansion tube studies include: (1) Investigation of Flow Characteristics in TQ Expansion Tube; and (2) Disturbances in the Driver Gas of a Shock Tube

Atomic and electronic structures of doped silicon nanowires: A first-principles study

We have investigated the atomic and electronic structures of hydrogen saturated silicon nanowires doped with impurity atoms (such as Al, Ga, C, Si, Ge, N, P, As, Te, Pt) using a first-principles plane wave method. We considered adsorption and substitution of impurity atoms at the surface and also their substitution at the core of the nanowire. In the case of adsorption to the surface, we determined the most energetic adsorption geometry among various possible adsorption sites. All impurities studied lead to nonmagnetic ground state with a significant binding energy. Impurity bands formed at high impurity concentration are metallic for group IIIA and VA elements but are semiconductor and modify the band gap for group IVA and VIA elements. While low substitutional impurity concentration leads to usual n - and p -type behaviors reminiscent of bulk Si, this behavior is absent if the impurity atom is adsorbed on the surface. It is shown that the electronic properties of silicon nanowires can be modified by doping for optoelectronic applications. © 2007 The American Physical Society

Winds of change in accounting practices in an emerging market: Some observations and thoughts

In Turkey, publicly traded companies are required to comply with a new set of standards that are essentially similar to the International Financial Reporting Standards (IFRS) since 2005. In this study, we use the results of a survey carried out in Turkey with accounting or finance executives of publicly traded companies regarding their perceptions of the new set of standards and their expectations from the policy makers, compare the findings of global research with the survey results, and report our observations and opinion. The survey results suggest that there was lack of knowledge and experience for appropriate implementation - a common point raised globally as well. Early observations and findings reflect that, although a lot has been achieved on the way to convergence, more consensus and guidance from the national and international standard setters are necessary to fully realise the expected benefits of IFRS. Copyright © 2009, Inderscience Publishers

Geometric computing and uniform grid technique

If computational geometry should play an important role in the professional environment (e.g. graphics and robotics), the data structures it advocates should be readily implemented and the algorithms efficient. In the paper, the uniform grid and a diverse set of geometric algorithms that are all based on it, are reviewed. The technique, invented by the second author, is a flat, and thus non-hierarchical, grid whose resolution adapts to the data. It is especially suitable for telling efficiently which pairs of a large number of short edges intersect. Several of the algorithms presented here exist as working programs (among which is a visible surface program for polyhedra) and can handle large data sets (i.e. many thousands of geometric objects). Furthermore, the uniform grid is appropriate for parallel processing; the parallel implementation presented gives very good speed-up results. © 1989