The Complexity of Repairing, Adjusting, and Aggregating of Extensions in Abstract Argumentation

We study the computational complexity of problems that arise in abstract argumentation in the context of dynamic argumentation, minimal change, and aggregation. In particular, we consider the following problems where always an argumentation framework F and a small positive integer k are given. - The Repair problem asks whether a given set of arguments can be modified into an extension by at most k elementary changes (i.e., the extension is of distance k from the given set). - The Adjust problem asks whether a given extension can be modified by at most k elementary changes into an extension that contains a specified argument. - The Center problem asks whether, given two extensions of distance k, whether there is a "center" extension that is a distance at most (k-1) from both given extensions. We study these problems in the framework of parameterized complexity, and take the distance k as the parameter. Our results covers several different semantics, including admissible, complete, preferred, semi-stable and stable semantics

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

Raman scattering investigation and symmetry analysis of ferroelectric/ferroelastic Sb5O7I polytype 2MA

The polytype 2MA (beta-Sb5O7I) has the simplest acentric structure of the antimony oxideiodide family. It undergoes an antiferrodistortive phase transition at 438K and is both ferroelectric and ferroelastic below that temperature. The complete polarized Raman spectra in the ferroic phase have been measured and compared with those of the ferroelastic, centric polytype 2MC (agr-Sb5O7I). Several lines could be attributed to Sb—0 and Sb—I vibrations. A factor group analysis has been performed and compatibility relations have been established connecting phonon species in the low and high temperature phase. As a function of temperature the spectra revealed a strongly temperature dependent central line and several phonon lines whose intensities vanish aboveT c . Using these phonon line intensities the temperature variation of the order parameter could be determined. The experimental results indicate that the phase transition is of first order