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

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

Computation in Physical Systems: A Normative Mapping Account

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

Is Evolution Algorithmic?

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

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

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