Analysis of Dialogical Argumentation via Finite State Machines

Dialogical argumentation is an important cognitive activity by which agents exchange arguments and counterarguments as part of some process such as discussion, debate, persuasion and negotiation. Whilst numerous formal systems have been proposed, there is a lack of frameworks for implementing and evaluating these proposals. First-order executable logic has been proposed as a general framework for specifying and analysing dialogical argumentation. In this paper, we investigate how we can implement systems for dialogical argumentation using propositional executable logic. Our approach is to present and evaluate an algorithm that generates a finite state machine that reflects a propositional executable logic specification for a dialogical argumentation together with an initial state. We also consider how the finite state machines can be analysed, with the minimax strategy being used as an illustration of the kinds of empirical analysis that can be undertaken.Comment: 10 page

Systems analysis of bioenergetics and growth of the extreme halophile Halobacterium salinarum

Halobacterium salinarum is a bioenergetically flexible, halophilic microorganism that can generate energy by respiration, photosynthesis, and the fermentation of arginine. In a previous study, using a genome-scale metabolic model, we have shown that the archaeon unexpectedly degrades essential amino acids under aerobic conditions, a behavior that can lead to the termination of growth earlier than necessary. Here, we further integratively investigate energy generation, nutrient utilization, and biomass production using an extended methodology that accounts for dynamically changing transport patterns, including those that arise from interactions among the supplied metabolites. Moreover, we widen the scope of our analysis to include phototrophic conditions to explore the interplay between different bioenergetic modes. Surprisingly, we found that cells also degrade essential amino acids even during phototropy, when energy should already be abundant. We also found that under both conditions considerable amounts of nutrients that were taken up were neither incorporated into the biomass nor used as respiratory substrates, implying the considerable production and accumulation of several metabolites in the medium. Some of these are likely the products of forms of overflow metabolism. In addition, our results also show that arginine fermentation, contrary to what is typically assumed, occurs simultaneously with respiration and photosynthesis and can contribute energy in levels that are comparable to the primary bioenergetic modes, if not more. These findings portray a picture that the organism takes an approach toward growth that favors the here and now, even at the cost of longer-term concerns. We believe that the seemingly "greedy" behavior exhibited actually consists of adaptations by the organism to its natural environments, where nutrients are not only irregularly available but may altogether be absent for extended periods that may span several years. Such a setting probably predisposed the cells to grow as much as possible when the conditions become favorable

Chemical composition of processed bamboo for structural applications.

Natural materials are a focus for development of low carbon products for a variety of applications. To utilise these materials, processing is required to meet acceptable industry standards. Laminated bamboo is a commercial product that is currently being explored for structural applications, however there is a gap in knowledge about the effects of commercial processing on the chemical composition. The present study utilised interdisciplinary methods of analysis to investigate the effects of processing on the composition of bamboo. Two common commercial processing methods were investigated: bleaching (chemical treatment) and caramelisation (hygrothermal treatment). The study indicated that the bleaching process results in a more pronounced degradation of the lignin in comparison to the caramelised bamboo. This augments previous research, which has shown that the processing method (strip size) and treatment may affect the mechanical properties of the material in the form of overall strength, failure modes and crack propagation. The study provides additional understanding of the effects of processing on the properties of bamboo.This work was funded by a Leverhulme Trust Programme Grant, and EPSRC Grant EP/K023403/1

Differences in lateral gene transfer in hypersaline versus thermal environments

<p>Abstract</p> <p>Background</p> <p>The role of lateral gene transfer (LGT) in the evolution of microorganisms is only beginning to be understood. While most LGT events occur between closely related individuals, inter-phylum and inter-domain LGT events are not uncommon. These distant transfer events offer potentially greater fitness advantages and it is for this reason that these "long distance" LGT events may have significantly impacted the evolution of microbes. One mechanism driving distant LGT events is microbial transformation. Theoretically, transformative events can occur between any two species provided that the DNA of one enters the habitat of the other. Two categories of microorganisms that are well-known for LGT are the thermophiles and halophiles.</p> <p>Results</p> <p>We identified potential inter-class LGT events into both a thermophilic class of Archaea (Thermoprotei) and a halophilic class of Archaea (Halobacteria). We then categorized these LGT genes as originating in thermophiles and halophiles respectively. While more than 68% of transfer events into Thermoprotei taxa originated in other thermophiles, less than 11% of transfer events into Halobacteria taxa originated in other halophiles.</p> <p>Conclusions</p> <p>Our results suggest that there is a fundamental difference between LGT in thermophiles and halophiles. We theorize that the difference lies in the different natures of the environments. While DNA degrades rapidly in thermal environments due to temperature-driven denaturization, hypersaline environments are adept at preserving DNA. Furthermore, most hypersaline environments, as topographical minima, are natural collectors of cellular debris. Thus halophiles would in theory be exposed to a greater diversity and quantity of extracellular DNA than thermophiles.</p

Counting nodal domains on surfaces of revolution

We consider eigenfunctions of the Laplace-Beltrami operator on special surfaces of revolution. For this separable system, the nodal domains of the (real) eigenfunctions form a checker-board pattern, and their number $\nu_n$ is proportional to the product of the angular and the "surface" quantum numbers. Arranging the wave functions by increasing values of the Laplace-Beltrami spectrum, we obtain the nodal sequence, whose statistical properties we study. In particular we investigate the distribution of the normalized counts $\frac{\nu_n}{n}$ for sequences of eigenfunctions with $K \le n\le K + \Delta K$ where $K,\Delta K \in \mathbb{N}$. We show that the distribution approaches a limit as $K,\Delta K\to\infty$ (the classical limit), and study the leading corrections in the semi-classical limit. With this information, we derive the central result of this work: the nodal sequence of a mirror-symmetric surface is sufficient to uniquely determine its shape (modulo scaling).Comment: 36 pages, 8 figure

Biomimetic Supramolecular Fibers Exhibit Water-Induced Supercontraction.

Spider silk is a fascinating material, combining high strength and elasticity that outperforms most synthetic fibers. Another intriguing feature of spider silk is its ability to "supercontract," shrinking up to 50% when exposed to water. This is likely on account of the entropy-driven recoiling of secondary structured proteins when water penetrates the spider silk. In contrast, humidity-driven contraction in synthetic fibers is difficult to achieve. Here, inspired by the spider silk model, a supercontractile fiber (SCF), which contracts up to 50% of its original length at high humidity, comparable to spider silk, is reported. The fiber exhibits up to 300% uptake of water by volume, confirmed via environmental scanning electron microscopy. Interestingly, the SCF exhibits tunable mechanical properties by varying humidity, which is reflected by the prolonged failure strain and the reversible damping capacity. This smart supramolecular fiber material provides a new opportunity of fabricating biomimetic muscle for diverse applications

Stability of nodal structures in graph eigenfunctions and its relation to the nodal domain count

The nodal domains of eigenvectors of the discrete Schrodinger operator on simple, finite and connected graphs are considered. Courant's well known nodal domain theorem applies in the present case, and sets an upper bound to the number of nodal domains of eigenvectors: Arranging the spectrum as a non decreasing sequence, and denoting by $\nu_n$ the number of nodal domains of the $n$'th eigenvector, Courant's theorem guarantees that the nodal deficiency $n-\nu_n$ is non negative. (The above applies for generic eigenvectors. Special care should be exercised for eigenvectors with vanishing components.) The main result of the present work is that the nodal deficiency for generic eigenvectors equals to a Morse index of an energy functional whose value at its relevant critical points coincides with the eigenvalue. The association of the nodal deficiency to the stability of an energy functional at its critical points was recently discussed in the context of quantum graphs [arXiv:1103.1423] and Dirichlet Laplacian in bounded domains in $R^d$ [arXiv:1107.3489]. The present work adapts this result to the discrete case. The definition of the energy functional in the discrete case requires a special setting, substantially different from the one used in [arXiv:1103.1423,arXiv:1107.3489] and it is presented here in detail.Comment: 15 pages, 1 figur

Urochordate Histoincompatible Interactions Activate Vertebrate-Like Coagulation System Components

The colonial ascidian Botryllus schlosseri expresses a unique allorecognition system. When two histoincompatible Botryllus colonies come into direct contact, they develop an inflammatory-like rejection response. A surprising high number of vertebrates' coagulation genes and coagulation-related domains were disclosed in a cDNA library of differentially expressed sequence tags (ESTs), prepared for this allorejection process. Serine proteases, especially from the trypsin family, were highly represented among Botryllus library ortholgues and its “molecular function” gene ontology analysis. These, together with the built-up clot-like lesions in the interaction area, led us to further test whether a vertebrate-like clotting system participates in Botryllus innate immunity. Three morphologically distinct clot types (points of rejection; POR) were followed. We demonstrated the specific expression of nine coagulation orthologue transcripts in Botryllus rejection processes and effects of the anti-coagulant heparin on POR formation and heartbeats. In situ hybridization of fibrinogen and von Willebrand factor orthologues elucidated enhanced expression patterns specific to histoincompatible reactions as well as common expressions not augmented by innate immunity. Immunohistochemistry for fibrinogen revealed, in naïve and immune challenged colonies alike, specific antibody binding to a small population of Botryllus compartment cells. Altogether, molecular, physiological and morphological outcomes suggest the involvement of vertebrates-like coagulation elements in urochordate immunity, not assigned with vasculature injury

Gains and losses of coral skeletal porosity changes with ocean acidification acclimation

Ocean acidi\ufb01cation is predicted to impact ecosystems reliant on calcifying organisms, potentially reducing the socioeconomic bene\ufb01ts these habitats provide. Here we investigate the acclimation potential of stony corals living along a pH gradient caused by a Mediterranean CO2 vent that serves as a natural long-term experimental setting. We show that in response to reduced skeletal mineralization at lower pH, corals increase their skeletal macroporosity (features &gt;10 micrometers) in order to maintain constant linear extension rate, an important criterion for reproductive output. At the nanoscale, the coral skeleton\u2019s structural features are not altered. However, higher skeletal porosity, and reduced bulk density and stiffness may contribute to reduce population density and increase damage susceptibility under low pH conditions. Based on these observations, the almost universally employed measure of coral biomineralization, the rate of linear extension, might not be a reliable metric for assessing coral health and resilience in a warming and acidifying ocean