412 research outputs found

    Computation in Physical Systems: A Normative Mapping Account

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    The relationship between abstract formal procedures and the activities of actual physical systems has proved to be surprisingly subtle and controversial, and there are a number of competing accounts of when a physical system can be properly said to implement a mathematical formalism and hence perform a computation. I defend an account wherein computational descriptions of physical systems are high-level normative interpretations motivated by our pragmatic concerns. Furthermore, the criteria of utility and success vary according to our diverse purposes and pragmatic goals. Hence there is no independent or uniform fact to the matter, and I advance the ‘anti-realist’ conclusion that computational descriptions of physical systems are not founded upon deep ontological distinctions, but rather upon interest-relative human conventions. Hence physical computation is a ‘conventional’ rather than a ‘natural’ kind

    Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli.

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    Fast and accurate identification and typing of pathogens are essential for effective surveillance and outbreak detection. The current routine procedure is based on a variety of techniques, making the procedure laborious, time-consuming, and expensive. With whole-genome sequencing (WGS) becoming cheaper, it has huge potential in both diagnostics and routine surveillance. The aim of this study was to perform a real-time evaluation of WGS for routine typing and surveillance of verocytotoxin-producing Escherichia coli (VTEC). In Denmark, the Statens Serum Institut (SSI) routinely receives all suspected VTEC isolates. During a 7-week period in the fall of 2012, all incoming isolates were concurrently subjected to WGS using IonTorrent PGM. Real-time bioinformatics analysis was performed using web-tools (www.genomicepidemiology.org) for species determination, multilocus sequence type (MLST) typing, and determination of phylogenetic relationship, and a specific VirulenceFinder for detection of E. coli virulence genes was developed as part of this study. In total, 46 suspected VTEC isolates were characterized in parallel during the study. VirulenceFinder proved successful in detecting virulence genes included in routine typing, explicitly verocytotoxin 1 (vtx1), verocytotoxin 2 (vtx2), and intimin (eae), and also detected additional virulence genes. VirulenceFinder is also a robust method for assigning verocytotoxin (vtx) subtypes. A real-time clustering of isolates in agreement with the epidemiology was established from WGS, enabling discrimination between sporadic and outbreak isolates. Overall, WGS typing produced results faster and at a lower cost than the current routine. Therefore, WGS typing is a superior alternative to conventional typing strategies. This approach may also be applied to typing and surveillance of other pathogens

    Synthesis of poly(1-vinylimidazole)-block-poly(9-vinylcarbazole) copolymers via RAFT and their use in chemically responsive graphitic composites

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    This study reports the synthesis of novel poly(1-vinylimidazole)-b-poly(9-vinylcarbazole) (PVI-b-PVK) block copolymers with varying monomer ratios using reversible addition-fragmentation chain-transfer (RAFT) polymerization and their incorporation in responsive composite materials. Specifically, non-covalent exfoliation of two different conductive fillers, multi-walled carbon nanotubes (MWCNTs) or reduced graphene oxide (rGO), was studied. The percolation threshold of the synthesized nanocomposites was dependent on the polymer used for dispersion, showing a better affinity of the fillers for block copolymers with higher relative carbazole content. Resistivity measurements showed selective variation in the resistance signal when the materials were exposed to various organic solvents and acids, providing a good basis for the design of sensing devices

    Is Evolution Algorithmic?

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    In Darwin’s Dangerous Idea, Daniel Dennett claims that evolution is algorithmic. On Dennett’s analysis, evolutionary processes are trivially algorithmic because he assumes that all natural processes are algorithmic. I will argue that there are more robust ways to understand algorithmic processes that make the claim that evolution is algorithmic empirical and not conceptual. While laws of nature can be seen as compression algorithms of information about the world, it does not follow logically that they are implemented as algorithms by physical processes. For that to be true, the processes have to be part of computational systems. The basic difference between mere simulation and real computing is having proper causal structure. I will show what kind of requirements this poses for natural evolutionary processes if they are to be computational

    Harnessing Higher-Order (Meta-)Logic to Represent and Reason with Complex Ethical Theories

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    The computer-mechanization of an ambitious explicit ethical theory, Gewirth's Principle of Generic Consistency, is used to showcase an approach for representing and reasoning with ethical theories exhibiting complex logical features like alethic and deontic modalities, indexicals, higher-order quantification, among others. Harnessing the high expressive power of Church's type theory as a meta-logic to semantically embed a combination of quantified non-classical logics, our work pushes existing boundaries in knowledge representation and reasoning. We demonstrate that intuitive encodings of complex ethical theories and their automation on the computer are no longer antipodes.Comment: 14 page

    Combining intention and emotional state inference in a dynamic neural field architecture for human-robot joint action

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    We report on our approach towards creating socially intelligent robots, which is heavily inspired by recent experimental findings about the neurocognitive mechanisms underlying action and emotion understanding in humans. Our approach uses neuro-dynamics as a theoretical language to model cognition, emotional states, decision making and action. The control architecture is formalized by a coupled system of dynamic neural fields representing a distributed network of local but connected neural populations. Different pools of neurons encode relevant information in the form of self-sustained activation patterns, which are triggered by input from connected populations and evolve continuously in time. The architecture implements a dynamic and flexible context-dependent mapping from observed hand and facial actions of the human onto adequate complementary behaviors of the robot that take into account the inferred goal and inferred emotional state of the co-actor. The dynamic control architecture was validated in multiple scenarios in which an anthropomorphic robot and a human operator assemble a toy object from its components. The scenarios focus on the robot’s capacity to understand the human’s actions, and emotional states, detect errors and adapt its behavior accordingly by adjusting its decisions and movements during the execution of the task.The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This work was possible in part by the funding of research grants from the Portuguese Foundation for Science and Technology (grant numbers SFRH/BD/48527/2008, SFRH/BPD/71874/2010, SFRH/BD/81334/2011), and with funding from FP6-IST2 EU-IP Project JAST (project number 003747) and FP7 Marie Curie ITN Neural Engineering Transformative Technologies NETT (project number 289146).info:eu-repo/semantics/publishedVersio

    Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data

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    Accurate and rapid typing of pathogens is essential for effective surveillance and outbreak detection. Conventional serotyping of Escherichia coli is a delicate, laborious, time-consuming, and expensive procedure. With whole-genome sequencing (WGS) becoming cheaper, it has vast potential in routine typing and surveillance. The aim of this study was to establish a valid and publicly available tool for WGS-based in silico serotyping of E. coli applicable for routine typing and surveillance. A FASTA database of specific O-antigen processing system genes for O typing and flagellin genes for H typing was created as a component of the publicly available Web tools hosted by the Center for Genomic Epidemiology (CGE) (www.genomicepidemiology.org). All E. coli isolates available with WGS data and conventional serotype information were subjected to WGS-based serotyping employing this specific SerotypeFinder CGE tool. SerotypeFinder was evaluated on 682 E. coli genomes, 108 of which were sequenced for this study, where both the whole genome and the serotype were available. In total, 601 and 509 isolates were included for O and H typing, respectively. The O-antigen genes wzx, wzy, wzm, and wzt and the flagellin genes fliC, flkA, fllA, flmA, and flnA were detected in 569 and 508 genome sequences, respectively. SerotypeFinder for WGS-based O and H typing predicted 560 of 569 O types and 504 of 508 H types, consistent with conventional serotyping. In combination with other available WGS typing tools, E. coli serotyping can be performed solely from WGS data, providing faster and cheaper typing than current routine procedures and making WGS typing a superior alternative to conventional typing strategies
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