Establishment of computational biology in Greece and Cyprus: Past, present, and future.

We review the establishment of computational biology in Greece and Cyprus from its inception to date and issue recommendations for future development. We compare output to other countries of similar geography, economy, and size—based on publication counts recorded in the literature—and predict future growth based on those counts as well as national priority areas. Our analysis may be pertinent to wider national or regional communities with challenges and opportunities emerging from the rapid expansion of the field and related industries. Our recommendations suggest a 2-fold growth margin for the 2 countries, as a realistic expectation for further expansion of the field and the development of a credible roadmap of national priorities, both in terms of research and infrastructure funding

A Bio-Wicking System to Mitigate Capillary Water in Base Course

Water within pavement layers is the major cause of pavement deteriorations. High water content results in significant reduction in soil’s resilient behavior and increase in permanent deformation. Conventional drainage systems can only drain gravity water but not capillary water. Both preliminary lab and field tests have proven the drainage efficiency of a newly developed H2Ri geotextile with wicking fabrics. This bio-wicking system aims at resolving the potential issues that the original design may encounter: (1) H2Ri ultraviolet degradation, (2) H2Ri mechanical failure, (3) loss of drainage function under high suction, and (4) clogging and salt concentration. Both elemental level and full-scale test results indicated that the bio-wicking system is more effective in draining capillary water within the base courses compared with original design, in which the geotextile is directly exposed to the open air. However, a good drainage condition is required for the bio-wicking system to maintain its drainage efficiency. Accumulation of excess water will result in water re-entering the road embankment. Moreover, grass root and geotextile share the same working mechanism in transporting water. In the proposed bio-wicking system, the relatively smaller channels in the grass roots further ensures water moving from H2Ri geotextile, transporting through the stems of grass, and eventually evapo-transpiring into the air at the leaf-air interfaces. In sum, the bio-wicking system seemed to successfully address the concerns in the preliminary design and is a more efficient system to dehydrate the road embankment under unsaturated conditions.TenCate Geosynthetic

The ICT Component of Technological Diversification: Is there an underestimation of ICT capabilities among the world's largest companies?

This empirical paper analyses the importance of information and communications technologies (ICT) in the technological diversification trend among the world's large industrial firms. The objective of the research is twofold. First, to emphasise the emerging differences among technologies when companies from different industries patent outside their traditional technological competencies. Second, to investigate whether the tendency among large companies from all industries to patent in ICT is distinctive when compared with other technologies. We find that technological diversification in large companies has certainly occurred in ICTs. For other technologies the results are ambiguous. As could be expected there is considerable industry variation in the intensity and specific directions of ICT patenting. We conclude that the development of corporate capabilities in the key technologies of the emerging ICT paradigm is more widespread than previously emphasised in the literature. One implication is that the rise of multi-technology corporations can be related to the concept of long waves of techno-economic change and to studies characterising ICT as a general-purpose technology.ICT, technological diversification, patents, corporate capabilities, long waves

FluxSimulator: An R Package to Simulate Isotopomer Distributions in Metabolic Networks

The representation of biochemical knowledge in terms of fluxes (transformation rates) in a metabolic network is often a crucial step in the development of new drugs and efficient bioreactors. Mass spectroscopy (MS) and nuclear magnetic resonance spectroscopy (NMRS) in combination with ^13C labeled substrates are experimental techniques resulting in data that may be used to quantify fluxes in the metabolic network underlying a process. The massive amount of data generated by spectroscopic experiments increasingly requires software which models the dynamics of the underlying biological system. In this work we present an approach to handle isotopomer distributions in metabolic networks using an object-oriented programming approach, implemented using S4 classes in R. The developed package is called FluxSimulator and provides a user friendly interface to specify the topological information of the metabolic network as well as carbon atom transitions in plain text files. The package automatically derives the mathematical representation of the formulated network, and assembles a set of ordinary differential equations (ODEs) describing the change of each isotopomer pool over time. These ODEs are subsequently solved numerically. In a case study FluxSimulator was applied to an example network. Our results indicate that the package is able to reproduce exact changes in isotopomer compositions of the metabolite pools over time at given flux rates.

Traction force microscopy on soft elastic substrates: a guide to recent computational advances

The measurement of cellular traction forces on soft elastic substrates has become a standard tool for many labs working on mechanobiology. Here we review the basic principles and different variants of this approach. In general, the extraction of the substrate displacement field from image data and the reconstruction procedure for the forces are closely linked to each other and limited by the presence of experimental noise. We discuss different strategies to reconstruct cellular forces as they follow from the foundations of elasticity theory, including two- versus three-dimensional, inverse versus direct and linear versus non-linear approaches. We also discuss how biophysical models can improve force reconstruction and comment on practical issues like substrate preparation, image processing and the availability of software for traction force microscopy.Comment: Revtex, 29 pages, 3 PDF figures, 2 tables. BBA - Molecular Cell Research, online since 27 May 2015, special issue on mechanobiolog