The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype–phenotype maps

Biological information is stored in DNA, RNA and protein sequences, which can be understood as genotypes that are translated into phenotypes. The properties of genotype–phenotype (GP) maps have been studied in great detail for RNA secondary structure. These include a highly biased distribution of genotypes per phenotype, negative correlation of genotypic robustness and evolvability, positive correlation of phenotypic robustness and evolvability, shape-space covering, and a roughly logarithmic scaling of phenotypic robustness with phenotypic frequency. More recently similar properties have been discovered in other GP maps, suggesting that they may be fundamental to biological GP maps, in general, rather than specific to the RNA secondary structure map. Here we propose that the above properties arise from the fundamental organization of biological information into ‘constrained'' and ‘unconstrained'' sequences, in the broadest possible sense. As ‘constrained'' we describe sequences that affect the phenotype more immediately, and are therefore more sensitive to mutations, such as, e.g. protein-coding DNA or the stems in RNA secondary structure. ‘Unconstrained'' sequences, on the other hand, can mutate more freely without affecting the phenotype, such as, e.g. intronic or intergenic DNA or the loops in RNA secondary structure. To test our hypothesis we consider a highly simplified GP map that has genotypes with ‘coding'' and ‘non-coding'' parts. We term this the Fibonacci GP map, as it is equivalent to the Fibonacci code in information theory. Despite its simplicity the Fibonacci GP map exhibits all the above properties of much more complex and biologically realistic GP maps. These properties are therefore likely to be fundamental to many biological GP maps.     

Suitability,efficiency and microbiological safety of novel physical technologies for the processing of ready‐to‐eat meals,meats and pumpable products

Consumer studies and market reports show an increase in consumption of ready‐to‐eat (RTE) foods. Although conventional processing technologies can in most cases produce safe products, they can also lead to the degradation of nutritional compounds and negatively affect quality characteristics. Consumers strongly prefer food that is minimally processed with the maximum amount of health‐promoting substances. Novel processing technologies as pre‐ or post‐treatment decontamination methods or as substitutes of conventional technologies have the potential to produce foods that are safe, rich in nutrient content and with superior organoleptic properties. Combining novel with conventional processes can eliminate potential drawbacks of novel technologies. This review examines available scientific information and critically evaluates the suitability and efficiency of various novel thermal and nonthermal technologies in terms of microbial safety, quality as well as nutrient content on the production of RTE meals, meats and pumpable products.     

On Application of Carbon-Containing Electrode Materials in Technology of Electrospark Alloying: Part 1. Peculiarities of Coating Formation Using Electrospark Treatment of Titanium Alloy OT4-1

Electrospark treatment of OT4-1 titanium alloy was performed sequentially with a STIM-20N hard-alloy electrode (TiC–20% Ni) and carbon-containing material (graphite and carbon-based composite materials). Kinetics of the mass transfer of the hard-alloy electrode was studied. The cathode mass loss during the first minute of the treatment was established. The kinetics results were processed using the methods of mathematical statistics. The erosion resistance of the applied carbon-containing materials was determined. Phase composition and relief of the coatings formed were analyzed. It was found that the application of the carbon-containing material increases the content of refractory phases in the coatings. Increase in the time of the treatment using the carbon-containing materials decreases the roughness of the coatings.     

Using decision analysis to determine optimal experimental design for monitoring sewer exfiltration with tracers.

The tracer methods developed to assess exfiltration from sewers in the European project APUSS (assessment of the performance of sewer systems) have a high degree of freedom with regard to the choice of tracer and the dosing strategy. These can lead to very different degrees of uncertainty in the measured exfiltration ratio. In this study, we demonstrate how to select an optimal experimental design using decision analysis, which accounts for this uncertainty and its associated costs. Although the results are site-specific, we can conclude generally that, when NaCl is used as the tracer, the accuracy of the exfiltration estimate is most sensitive to the amount of tracer used and the starting time of the experiment.     

One-dimensional GIS-based model compared with a two-dimensional model in urban floods simulation.

A GIS-based one-dimensional flood simulation model is presented and applied to the centre of the city of N?mes (Gard, France), for mapping flow depths or velocities in the streets network. The geometry of the one-dimensional elements is derived from the Digital Elevation Model (DEM). The flow is routed from one element to the next using the kinematic wave approximation. At the crossroads, the flows in the downstream branches are computed using a conceptual scheme. This scheme was previously designed to fit Y-shaped pipes junctions, and has been modified here to fit X-shaped crossroads. The results were compared with the results of a two-dimensional hydrodynamic model based on the full shallow water equations. The comparison shows that good agreements can be found in the steepest streets of the study zone, but differences may be important in the other streets. Some reasons that can explain the differences between the two models are given and some research possibilities are proposed.     

On the problem of hydrogen removal during heat treatment of large forgings

The solutions to a differential equation for the problem of heating of a cylinder in a medium with a fixed temperature are used to obtain equations for estimating the change in the hydrogen concentration in forgings from data on the hydrogen concentration at the cylinder axis or on the average bulk hydrogen concentration. Similar equations are also obtained for forgings having square cross sections. The calculation demonstrates that, for the case of a twofold decrease in the hydrogen concentration in a forging, the calculated times of annealing of a cylindrical forging differ by three times.     

An element-based displacement preconditioner for linear elasticity problems

Finite element analysis of problems in structural and geotechnical engineering results in linear systems where the unknowns are displacements and rotations at nodes. Although the solution of these systems can be carried out using either direct or iterative methods, in practice the matrices involved are usually very large and sparse (particularly for 3D problems) so an iterative approach is often advantageous in terms of both computational time and memory requirements. This memory saving can be further enhanced if the method used does not require assembly of the full coefficient matrix during the solution procedure. One disadvantage of iterative methods is the need to apply preconditioning to improve convergence. In this paper, we review a range of established element-based preconditioning methods for linear elastic problems and compare their performance with a new method based on preconditioning with element displacement components. This new method appears to offer a significant improvement in performance.     

On-line estimation of kinetic parameters in anaerobic digestion using observer-based estimators and multiwavelength fluorometry.

Observer-based estimators (OBE) were used for estimation of state variables and kinetic parameters in an anaerobic digestion (AD) process. A simplified first-order model with time-varying kinetic parameters was used to design an OBE for kinetic parameter estimation. This approach was validated on a laboratory-scale anaerobic reactor equipped with a multiwavelength fluorometer for on-line measurements of COD and VFA concentrations in the reactor effluent. The proposed estimators provide continuous adjustment of kinetic parameters and can be used for predictions of state variables between samples acquisition and during sensor failure.