Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models

<p>Abstract</p> <p>Background</p> <p>Design of newly engineered microbial strains for biotechnological purposes would greatly benefit from the development of realistic mathematical models for the processes to be optimized. Such models can then be analyzed and, with the development and application of appropriate optimization techniques, one could identify the modifications that need to be made to the organism in order to achieve the desired biotechnological goal. As appropriate models to perform such an analysis are necessarily non-linear and typically non-convex, finding their global optimum is a challenging task. Canonical modeling techniques, such as Generalized Mass Action (GMA) models based on the power-law formalism, offer a possible solution to this problem because they have a mathematical structure that enables the development of specific algorithms for global optimization.</p> <p>Results</p> <p>Based on the GMA canonical representation, we have developed in previous works a highly efficient optimization algorithm and a set of related strategies for understanding the evolution of adaptive responses in cellular metabolism. Here, we explore the possibility of recasting kinetic non-linear models into an equivalent GMA model, so that global optimization on the recast GMA model can be performed. With this technique, optimization is greatly facilitated and the results are transposable to the original non-linear problem. This procedure is straightforward for a particular class of non-linear models known as Saturable and Cooperative (SC) models that extend the power-law formalism to deal with saturation and cooperativity.</p> <p>Conclusions</p> <p>Our results show that recasting non-linear kinetic models into GMA models is indeed an appropriate strategy that helps overcoming some of the numerical difficulties that arise during the global optimization task.</p

GRB 050509b: the elusive optical/nIR/mm afterglow of a short-duration GRB

We present multiwavelength (optical/near infrared/millimetre) observations of a short duration gamma-ray burst detected by Swift (GRB 050509b) collected between 0 seconds and ~18.8 days after the event. No optical, near infrared or millimetre emission has been detected in spite of the well localised X-ray afterglow, confirming the elusiveness of the short duration events. We also discuss the possibility of the burst being located in a cluster of galaxies at z= 0.225 or beyond. In the former case, the spectral energy distribution of the neighbouring, potential host galaxy, favours a system harbouring an evolved dominant stellar population (age ~360 Myr), unlike most long duration GRB host galaxies observed so far, i.e. thus giving support to a compact binary merger origin. Any underlying supernova that could be associated with this particular event should have been at least 3 magnitudes fainter than the type Ib/c SN 1998bw and 2.3 magnitudes fainter than a typical type Ia SN

The human remains from Axlor (Dima, Biscay, northern Iberian Peninsula)

OBJECTIVES We provide the description and comparative analysis of all the human fossil remains found at Axlor during the excavations carried out by J. M. de Barandiarán from 1967 to 1974: a cranial vault fragment and eight teeth, five of which likely belonged to the same individual, although two are currently lost. Our goal is to describe in detail all these human remains and discuss both their taxonomic attribution and their stratigraphic context. MATERIALS AND METHODS We describe external and internal anatomy, and use classic and geometric morphometrics. The teeth from Axlor are compared to Neandertals, Upper Paleolithic, and recent modern humans. RESULTS Three teeth (a left dm2, a left di1, and a right I1) and the parietal fragment show morphological features consistent with a Neandertal classification, and were found in an undisturbed Mousterian context. The remaining three teeth (plus the two lost ones), initially classified as Neandertals, show morphological features and a general size that are more compatible with their classification as modern humans. DISCUSSION The combined anatomical and stratigraphic study suggest that the remains of two different adult Neandertals have been recovered during the old excavations performed by Barandiarán: a left parietal fragment (Level VIII) and a right I1 (Level V). Additionally, two different Neandertal children lost deciduous teeth during the formations of levels V (left di1) and IV (right dm2). In addition, a modern human individual is represented by five remains (two currently lost) from a complex stratigraphic setting. Some of the morphological features of these remains suggest that they may represent one of the scarce examples of Upper Paleolithic modern human remains in the northern Iberian Peninsula, which should be confirmed by direct dating