Chaste: a test-driven approach to software development for biological modelling

Chaste (‘Cancer, heart and soft-tissue environment’) is a software library and a set of test suites for computational simulations in the domain of biology. Current functionality has arisen from modelling in the fields of cancer, cardiac physiology and soft-tissue mechanics. It is released under the LGPL 2.1 licence.\ud \ud Chaste has been developed using agile programming methods. The project began in 2005 when it was reasoned that the modelling of a variety of physiological phenomena required both a generic mathematical modelling framework, and a generic computational/simulation framework. The Chaste project evolved from the Integrative Biology (IB) e-Science Project, an inter-institutional project aimed at developing a suitable IT infrastructure to support physiome-level computational modelling, with a primary focus on cardiac and cancer modelling

Rapid Optical Fluctuations in the Black Hole Binary, V4641 Sgr

We report on unprecedented short-term variations detected in the optical flux from the black hole binary system, V4641 Sgr. Amplitudes of the optical fluctuations were larger at longer time scales, and surprisingly reached ~60% around a period of ~10 min. The power spectra of fluctuations are characterized by a power law. It is the first case in black hole binaries that the optical emission was revealed to show short-term and large-amplitude variations given by such a power spectrum. The optical emission from black hole binaries is generally dominated by the emission from the outer portion of an accretion disc. The rapid optical fluctuations however indicate that the emission from an inner accretion region significantly contributes to the optical flux. In this case, cyclo-synchrotron emission associated with various scales of magnetic flares is the most promising mechanism for the violently variable optical emission.Comment: 5 pages, 2 figures, accepted for publication in PAS

Constellations of identity: place-ma(r)king beyond heritage

This paper will critically consider the different ways in which history and belonging have been treated in artworks situated in the Citadel development in Ayr on the West coast of Scotland. It will focus upon one artwork, Constellation by Stephen Hurrel, as an alternative to the more conventional landscapes of heritage which are adjacent, to examine the relationship between personal history and place history and argue the primacy of participatory process in the creation of place and any artwork therein. Through his artwork, Hurrel has attempted to adopt a material process through which place can be created performatively but, in part due to its non-representational form, proves problematic, aesthetically and longitudinally, in wholly engaging the community. The paper will suggest that through variants of ‘new genre public art’ such as this, personal and place histories can be actively re-created through the redevelopment of contemporary urban landscapes but also highlight the complexities and indeterminacies involved in the relationship between artwork, people and place

Movement 4. Breath sigh tempest: On the temporal dimensions of re‐arrangements

The fourth movement explores the temporal relationship between arrangements and re-arrangements, addressing the question of how an obdurate and ‘sticky’ temporal order may give way to palpable re-arrangement of the ways in which subjects experience time. Eschewing a concern with linear homogenous time, it addresses the processes of re-arrangement by understanding the dynamics of grave events, hauntings of the past, subtly changing rhythms of everyday life, and the force of potential futures in synchrony

Movement 5. Sensing the affective lives of arrangements

This final movement explores whether thinking with re-arrangements can help us account for that which is hidden, unseen or nested in the recesses and folds of urban practices. And if so, how we might then talk about and account for elusive parts of an arrangement that both exert an influence and are influenced. This essay uses sensibilities as an entry point into the intangible interactions between subjects and (re)arrangements

On urban re‐arrangements: a suite in five movements

This movement introduces the ethos of the collective project: its conceptual and practical preoccupations. It focuses on our concern with urban processes on the cusp of change, in the midst of being re-arranged, and thus homes in on the various polyrhythms of intersections, how things come together and diverge, how possibilities open and close in urban contexts of continuously shifting horizons

Experiences of Receiving a Diagnosis of Autism Spectrum Disorder: A Survey of Adults in the United Kingdom

A total of 128 adults with high-functioning autism spectrum disorders were surveyed concerning the process they went through to obtain their diagnosis and the subsequent support they received. Results suggested that routes to diagnosis were quite heterogeneous and overall levels of satisfaction with the diagnostic process were mixed; 40 % of respondents were ‘very/quite’ dissatisfied, whilst 47 % were ‘very/quite’ satisfied. The extent of delays, number of professionals seen, quality of information given at diagnosis and levels of post-diagnostic support predicted overall satisfaction with the diagnostic process. Important areas and suggestions for improvement were noted for all stages of the diagnostic pathway. Respondents also displayed above average levels of depressed mood and anxiety, with greater support being requested in this area

COVID-19: Rapid antigen detection for SARS-CoV-2 by lateral flow assay: A national systematic evaluation of sensitivity and specificity for mass-testing

Background Lateral flow device (LFD) viral antigen immunoassays have been developed around the world as diagnostic tests for SARS-CoV-2 infection. They have been proposed to deliver an infrastructure-light, cost-economical solution giving results within half an hour. Methods LFDs were initially reviewed by a Department of Health and Social Care team, part of the UK government, from which 64 were selected for further evaluation from 1st August to 15th December 2020. Standardised laboratory evaluations, and for those that met the published criteria, field testing in the Falcon-C19 research study and UK pilots were performed (UK COVID-19 testing centres, hospital, schools, armed forces). Findings 4/64 LFDs so far have desirable performance characteristics (orient Gene, Deepblue, Abbott and Innova SARS-CoV-2 Antigen Rapid Qualitative Test). All these LFDs have a viral antigen detection of >90% at 100,000 RNA copies/ml. 8951 Innova LFD tests were performed with a kit failure rate of 5.6% (502/8951, 95% CI: 5.1–6.1), false positive rate of 0.32% (22/6954, 95% CI: 0.20–0.48). Viral antigen detection/sensitivity across the sampling cohort when performed by laboratory scientists was 78.8% (156/198, 95% CI 72.4–84.3). Interpretation Our results suggest LFDs have promising performance characteristics for mass population testing and can be used to identify infectious positive individuals. The Innova LFD shows good viral antigen detection/sensitivity with excellent specificity, although kit failure rates and the impact of training are potential issues. These results support the expanded evaluation of LFDs, and assessment of greater access to testing on COVID-19 transmission. Funding Department of Health and Social Care. University of Oxford. Public Health England Porton Down, Manchester University NHS Foundation Trust, National Institute of Health Research