Citation and peer review of data: moving towards formal data publication

This paper discusses many of the issues associated with formally publishing data in academia, focusing primarily on the structures that need to be put in place for peer review and formal citation of datasets. Data publication is becoming increasingly important to the scientific community, as it will provide a mechanism for those who create data to receive academic credit for their work and will allow the conclusions arising from an analysis to be more readily verifiable, thus promoting transparency in the scientific process. Peer review of data will also provide a mechanism for ensuring the quality of datasets, and we provide suggestions on the types of activities one expects to see in the peer review of data. A simple taxonomy of data publication methodologies is presented and evaluated, and the paper concludes with a discussion of dataset granularity, transience and semantics, along with a recommended human-readable citation syntax.

Smoking and symbolism: children, communication and cigarettes

Health promotion, with its concern with empowerment and autonomy, must recognize the agency of its target population. Based on 85 in-depth interviews with 10- to 11-year-old children throughout Northern Ireland, this paper argues that it is necessary to focus on the social relations of children if we are to understand and prevent childhood smoking. Addressing the complex issue of childhood agency, it is argued that regardless of various restrictions to their choices, children can act intentionally in constructing their identities. Instead of viewing the smoking children as communicating with the adult world, we focus on smoking as negotiation of status within the children's culture. Such negotiations utilize symbolism derived from and shared with the `adult world'. It is important that those analyzing children's lives understand children's ideas and behaviour on their own terms. We must make sure that the very concepts in which the children's experiences are put are appropriate ones. It is suggested that the metaphor `rite of passage' and terminology such as peer `pressure' versus adult `influence', commonly used to analyse the children's smoking behaviour, may actually conceal important aspects of childhood agency.

An experimental investigation of peer influences on hostile attributions in adolescents

Aggression in young people has been associated with a bias towards attributing hostile intent to others; however, little is known about the origin of biased social information processing. The current study explored the potential role of peer contagion in the emergence of hostile attribution in adolescents. 134 adolescents were assigned to one of two manipulated ‘chat-room’ conditions, where they believed they were communicating with online peers (e-confederates) who endorsed either hostile or benign intent attributions. Adolescents showed increased hostile attributions following exposure to hostile e-confederates and reduced hostility in the benign condition. Further analyses demonstrated that social anxiety was associated with a reduced tendency to take on hostile peer attitudes. Neither gender nor levels of aggression influenced individual susceptibility to peer influence, but aggressive adolescents reported greater affinity with hostile e-confederates.

Virtual landmarking for locality aware peer IDs

In Peer-to-Peer (P2P) networks, it is often desirable to assign node IDs which preserve locality relationships in the underlying topology. Node locality can be embedded into node IDs by utilizing a one dimensional mapping by a Hilbert space filling curve on a vector of network distances from each node to a subset of reference landmark nodes within the network. However this approach is fundamentally limited because while robustness and accuracy might be expected to improve with the number of landmarks, the effectiveness of 1 dimensional Hilbert Curve mapping falls for the curse of dimensionality. This work proposes an approach to solve this issue using Landmark Multidimensional Scaling (LMDS) to reduce a large set of landmarks to a smaller set of virtual landmarks. This smaller set of landmarks has been postulated to represent the intrinsic dimensionality of the network space and therefore a space filling curve applied to these virtual landmarks is expected to produce a better mapping of the node ID space. The proposed approach, the Virtual Landmarks Hilbert Curve (VLHC), is particularly suitable for decentralised systems like P2P networks. In the experimental simulations the effectiveness of the methods is measured by means of the locality preservation derived from node IDs in terms of latency to nearest neighbours. A variety of realistic network topologies are simulated and this work provides strong evidence to suggest that VLHC performs better than either Hilbert Curves or LMDS use independently of each other.

Response theory for equilibrium and non-equilibrium statistical mechanics: causality and generalized Kramers-Kronig relations

We consider the general response theory recently proposed by Ruelle for describing the impact of small perturbations to the non-equilibrium steady states resulting from Axiom A dynamical systems. We show that the causality of the response functions entails the possibility of writing a set of Kramers-Kronig (K-K) relations for the corresponding susceptibilities at all orders of nonlinearity. Nonetheless, only a special class of directly observable susceptibilities obey K-K relations. Specific results are provided for the case of arbitrary order harmonic response, which allows for a very comprehensive K-K analysis and the establishment of sum rules connecting the asymptotic behavior of the harmonic generation susceptibility to the short-time response of the perturbed system. These results set in a more general theoretical framework previous findings obtained for optical systems and simple mechanical models, and shed light on the very general impact of considering the principle of causality for testing self-consistency: the described dispersion relations constitute unavoidable benchmarks that any experimental and model generated dataset must obey. The theory exposed in the present paper is dual to the time-dependent theory of perturbations to equilibrium states and to non-equilibrium steady states, and has in principle similar range of applicability and limitations. In order to connect the equilibrium and the non equilibrium steady state case, we show how to rewrite the classical response theory by Kubo so that response functions formally identical to those proposed by Ruelle, apart from the measure involved in the phase space integration, are obtained. These results, taking into account the chaotic hypothesis by Gallavotti and Cohen, might be relevant in several fields, including climate research. In particular, whereas the fluctuation-dissipation theorem does not work for non-equilibrium systems, because of the non-equivalence between internal and external fluctuations, K-K relations might be robust tools for the definition of a self-consistent theory of climate change.

Evidence of dispersion relations for the nonlinear response of the Lorenz 63 system

Along the lines of the nonlinear response theory developed by Ruelle, in a previous paper we have proved under rather general conditions that Kramers-Kronig dispersion relations and sum rules apply for a class of susceptibilities describing at any order of perturbation the response of Axiom A non equilibrium steady state systems to weak monochromatic forcings. We present here the first evidence of the validity of these integral relations for the linear and the second harmonic response for the perturbed Lorenz 63 system, by showing that numerical simulations agree up to high degree of accuracy with the theoretical predictions. Some new theoretical results, showing how to derive asymptotic behaviors and how to obtain recursively harmonic generation susceptibilities for general observables, are also presented. Our findings confirm the conceptual validity of the nonlinear response theory, suggest that the theory can be extended for more general non equilibrium steady state systems, and shed new light on the applicability of very general tools, based only upon the principle of causality, for diagnosing the behavior of perturbed chaotic systems and reconstructing their output signals, in situations where the fluctuation-dissipation relation is not of great help.

Conductance of amyloid β based peptide filaments: structure–function relations.

Controlling the morphology of self-assembled peptide nanostructures, particularly those based on amyloid peptides, has been the focus of intense research. In order to exploit these structures in electronic applications, further understanding of their electronic behavior is required. In this work, the role of peptide morphology in determining electronic conduction along self-assembled peptide nanofilament networks is demonstrated. The peptides used in this work were based on the sequence AAKLVFF, which is an extension of a core sequence from the amyloid b peptide. We show that the incorporation of a non-natural amino acid, 2-thienylalanine, instead of phenylalanine improves the obtained conductance with respect to that obtained for a similar structure based on the native sequence, which was not the case for the incorporation of 3-thienylalanine. Furthermore, we demonstrate that the morphology of the self-assembled structures, which can be controlled by the solvent used in the assembly process, strongly affects the conductance, with larger conduction obtained for a morphology of long, straight filaments. Our results demonstrate that, similar to natural systems, the assembly and folding of peptides could be of great importance for optimizing their function as components of electronic devices. Hence, sequence design and assembly conditions can be used to control the performance of peptide based structures in such electronic applications.