Parameterized approximation schemes for steiner trees with small number of Steiner vertices

We study the Steiner Tree problem, in which a set of terminal vertices needs to be connected in the cheapest possible way in an edge-weighted graph. This problem has been extensively studied from the viewpoint of approximation and also parametrization. In particular, on one hand Steiner Tree is known to be APX-hard, and W[2]-hard on the other, if parameterized by the number of non-terminals (Steiner vertices) in the optimum solution. In contrast to this we give an efficient parameterized approximation scheme (EPAS), which circumvents both hardness results. Moreover, our methods imply the existence of a polynomial size approximate kernelization scheme (PSAKS) for the considered parameter. We further study the parameterized approximability of other variants of Steiner Tree, such as Directed Steiner Tree and Steiner Forest. For neither of these an EPAS is likely to exist for the studied parameter: For Steiner Forest an easy observation shows that the problem is APX-hard, even if the input graph contains no Steiner vertices. For Directed Steiner Tree we prove that computing a constant approximation for this parameter is W[1]-hard. Nevertheless, we show that an EPAS exists for Unweighted Directed Steiner Tree. Also we prove that there is an EPAS and a PSAKS for Steiner Forest if in addition to the number of Steiner vertices, the number of connected components of an optimal solution is considered to be a parameter

Effects of aerobic workout on the changes in the characteristics of dynamics of the center of gravity in different age categories

Introduction The quality and function of movements undergo deterioration due to weight gain. Aerobic training normalizes body weight, improves the health status, and in addition, it is expected to improve the dynamics of movements. The aims of this study were to prove the beneficial effects of recreational physical activities on the movements. Methods Participants were divided into five different age categories: second childhood, adolescence, mature age I, mature age II, and aging. Squatting and vertical jumping of the participants were measured at the beginning and at the end of a 5-month training program. These movements simulated ordinary daily movements. Changes in the body were determined by InBody230. APAS 3D system was used for movement analysis. Results The results showed significant improvements in body weight, fat mass, muscle mass, fat mass–body weight ratio, muscle mass–body weight ratio, body mass index, body fat percentage, and waist–hip ratio. During jumping, the lifting and sinking of the center of gravity’s (CG) position and its velocity and acceleration were improved. In case of squatting, the results showed significant improvements in the velocity and acceleration of dynamical characteristics of the CG. Other correlations were observed between changes in body composition and the dynamics of movements. Discussion The research proved that recreational training optimized body composition and improved the characteristics of CG’s dynamics. The study suggests considerable connection between body composition and the characteristics of the movements’ dynamics. From this point of view, our training program was the most effective in the working age groups

Comparison Criteria for Argumentation Semantics

Argumentation reasoning is a way for agents to evaluate a situation. Given a framework made of conflicting arguments, a semantics allows to evaluate the acceptability of the arguments. It may happen that the semantics associated to the framework has to be changed. In order to perform the most suitable change, the current and a potential new semantics have to be compared. Notions of difference measures between semantics have already been proposed, and application cases where they have to be minimized when a change of semantics has to be performed, have been highlighted. This paper develops these notions, it proposes an additional kind of difference measure, and shows application cases where measures may have to be maximized, and combined

Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies

The dramatic increase in heterogeneous types of biological data—in particular, the abundance of new protein sequences—requires fast and user-friendly methods for organizing this information in a way that enables functional inference. The most widely used strategy to link sequence or structure to function, homology-based function prediction, relies on the fundamental assumption that sequence or structural similarity implies functional similarity. New tools that extend this approach are still urgently needed to associate sequence data with biological information in ways that accommodate the real complexity of the problem, while being accessible to experimental as well as computational biologists. To address this, we have examined the application of sequence similarity networks for visualizing functional trends across protein superfamilies from the context of sequence similarity. Using three large groups of homologous proteins of varying types of structural and functional diversity—GPCRs and kinases from humans, and the crotonase superfamily of enzymes—we show that overlaying networks with orthogonal information is a powerful approach for observing functional themes and revealing outliers. In comparison to other primary methods, networks provide both a good representation of group-wise sequence similarity relationships and a strong visual and quantitative correlation with phylogenetic trees, while enabling analysis and visualization of much larger sets of sequences than trees or multiple sequence alignments can easily accommodate. We also define important limitations and caveats in the application of these networks. As a broadly accessible and effective tool for the exploration of protein superfamilies, sequence similarity networks show great potential for generating testable hypotheses about protein structure-function relationships

Pathways to cellular supremacy in biocomputing

Synthetic biology uses living cells as the substrate for performing human-defined computations. Many current implementations of cellular computing are based on the “genetic circuit” metaphor, an approximation of the operation of silicon-based computers. Although this conceptual mapping has been relatively successful, we argue that it fundamentally limits the types of computation that may be engineered inside the cell, and fails to exploit the rich and diverse functionality available in natural living systems. We propose the notion of “cellular supremacy” to focus attention on domains in which biocomputing might offer superior performance over traditional computers. We consider potential pathways toward cellular supremacy, and suggest application areas in which it may be found.A.G.-M. was supported by the SynBio3D project of the UK Engineering and Physical Sciences Research Council (EP/R019002/1) and the European CSA on biological standardization BIOROBOOST (EU grant number 820699). T.E.G. was supported by a Royal Society University Research Fellowship (grant UF160357) and BrisSynBio, a BBSRC/ EPSRC Synthetic Biology Research Centre (grant BB/L01386X/1). P.Z. was supported by the EPSRC Portabolomics project (grant EP/N031962/1). P.C. was supported by SynBioChem, a BBSRC/EPSRC Centre for Synthetic Biology of Fine and Specialty Chemicals (grant BB/M017702/1) and the ShikiFactory100 project of the European Union’s Horizon 2020 research and innovation programme under grant agreement 814408

A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes

BACKGROUND: Bread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines. RESULTS: A sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies. CONCLUSIONS: Evidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets