Webscience, 'social machines' and principles for redesigning theories of agency: a prolegomenon

This paper argues that the advent of the WWW and the principles now developing for the move ‘social machines’ has posed serious challenges to traditional social theory. In particular, it is argued that the concept of social machines and the forms of distributed agency they imply amplify ‘deep flaws’ in the underlying principles of current agency theories that make empirical work using such frameworks ‘undecidable’. The occasioning of social machines and the WWW here are examined for the ways in which the traditional models of agency, involving reflexivity/skill dynamics, can be dismantled and new principles for re-designed agency theory posed. One key problem and three re-design principles are identified

Discovering bipartite substructure in directed networks

Bipartivity is an important network concept that can be applied to nodes, edges and communities. Here we focus on directed networks and look for subnetworks made up of two distinct groups of nodes, connected by “one-way” links. We show that a spectral approach can be used to find hidden substructure of this form. Theoretical support is given for the idealised case where there is limited overlap between subnetworks. Numerical experiments show that the approach is robust to spurious and missing edges. A key application of this work is in the analysis of high-throughput gene expression data, and we give an example where a biologically meaningful directed bipartite subnetwork is found from a cancer microarray dataset

DNA meets the SVD

This paper introduces an important area of computational cell biology where complex, publicly available genomic data is being examined by linear algebra methods, with the aim of revealing biological and medical insights

Flux sampling is a powerful tool to study metabolism under changing environmental conditions

The development of high-throughput ‘omic techniques has sparked a rising interest in genome-scale metabolic models, with applications ranging from disease diagnostics to crop adaptation. Efficient and accurate methods are required to analyze large metabolic networks. Flux sampling can be used to explore the feasible flux solutions in metabolic networks by generating probability distributions of steady-state reaction fluxes. Unlike other methods, flux sampling can be used without assuming a particular cellular objective. We have undertaken a rigorous comparison of several sampling algorithms and concluded that the coordinate hit-and-run with rounding (CHRR) algorithm is the most efficient based on both run-time and multiple convergence diagnostics. We demonstrate the power of CHRR by using it to study the metabolic changes that underlie photosynthetic acclimation to cold of Arabidopsis thaliana plant leaves. In combination with experimental measurements, we show how the regulated interplay between diurnal starch and organic acid accumulation defines the plant acclimation process. We confirm fumarate accumulation as a requirement for cold acclimation and further predict γ–aminobutyric acid to have a key role in metabolic signaling under cold conditions. These results demonstrate how flux sampling can be used to analyze the feasible flux solutions across changing environmental conditions, whereas eliminating the need to make assumptions which introduce observer bias

Stability of β-lactam antibiotics in bacterial growth media

Laboratory assays such as MIC tests assume that antibiotic molecules are stable in the chosen growth medium-but rapid degradation has been observed for antibiotics including β-lactams under some conditions in aqueous solution. Degradation rates in bacterial growth medium are less well known. Here, we develop a 'delay time bioassay' that provides a simple way to estimate antibiotic stability in bacterial growth media, using only a plate reader and without the need to measure the antibiotic concentration directly. We use the bioassay to measure degradation half-lives of the β-lactam antibiotics mecillinam, aztreonam and cefotaxime in widely-used bacterial growth media based on MOPS and Luria-Bertani (LB) broth. We find that mecillinam degradation can occur rapidly, with a half-life as short as 2 hours in MOPS medium at 37°C and pH 7.4, and 4-5 hours in LB, but that adjusting the pH and temperature can increase its stability to a half-life around 6 hours without excessively perturbing growth. Aztreonam and cefotaxime were found to have half-lives longer than 6 hours in MOPS medium at 37°C and pH 7.4, but still shorter than the timescale of a typical minimum inhibitory concentration (MIC) assay. Taken together, our results suggest that care is needed in interpreting MIC tests and other laboratory growth assays for β-lactam antibiotics, since there may be significant degradation of the antibiotic during the assay

dc readout experiment at the Caltech 40m prototype interferometer

The Laser Interferometer Gravitational Wave Observatory (LIGO) operates a 40m prototype interferometer on the Caltech campus. The primary mission of the prototype is to serve as an experimental testbed for upgrades to the LIGO interferometers and for gaining experience with advanced interferometric techniques, including detuned resonant sideband extraction (i.e. signal recycling) and dc readout (optical homodyne detection). The former technique will be employed in Advanced LIGO, and the latter in both Enhanced and Advanced LIGO. Using dc readout for gravitational wave signal extraction has several technical advantages, including reduced laser and oscillator noise couplings as well as reduced shot noise, when compared to the traditional rf readout technique (optical heterodyne detection) currently in use in large-scale ground-based interferometric gravitational wave detectors. The Caltech 40m laboratory is currently prototyping a dc readout system for a fully suspended interferometric gravitational wave detector. The system includes an optical filter cavity at the interferometer's output port, and the associated controls and optics to ensure that the filter cavity is optimally coupled to the interferometer. We present the results of measurements to characterize noise couplings in rf and dc readout using this system

How stigma impacts on people with psychosis: The mediating effect of self-esteem and hopelessness on subjective recovery and psychotic experiences

This study aimed to examine how stigma impacts on symptomatic and subjective recovery from psychosis, both concurrently and longitudinally. We also aimed to investigate whether self-esteem and hopelessness mediated the observed associations between stigma and outcomes. 80 service-users with psychosis completed symptom (Positive and Negative Syndrome Scale) and subjective recovery measures (Process of Recovery Questionnaire) at baseline and 6-months later, and also completed the King Stigma Scale, the Self-Esteem Rating Scale and the Beck Hopelessness Scale at baseline. In cross sectional regression and multiple mediation analyses of the baseline data, we found that stigma predicted both symptomatic and subjective recovery, and the effects of stigma on these outcomes were mediated by hopelessness and self-esteem. When the follow-up data were examined, stigma at baseline continued to predict recovery judgements and symptoms. However, self-esteem only mediated the effect of stigma on PANSS passive social withdrawal. Self-esteem and hopelessness should be considered in interventions to reduce the effects of stigma. Interventions that address the current and long-term effects of stigma may positively affect outcome for people being treated for psychosis