Anatomical ontologies: names and places in biology

Ontology has long been the preserve of philosophers and logicians. Recently, ideas from this field have been picked up by computer scientists as a basis for encoding knowledge and with the hope of achieving interoperability and intelligent system behavior. In bioinformatics, ontologies might allow hitherto impossible query and data-mining activities. We review the use of anatomy ontologies to represent space in biological organisms, specifically mouse and human

Resilience and recovery: SME experiences of extreme weather events and other external threats

Objectives: To examine how small and medium-sized firms deal with external shocks of various kinds, with particular reference to extreme weather events. The research asks how business owners and managers prepare themselves for these inherently uncertain events and how they deal with immediate impact on the business when it faced with an external crisis. It also explores the longer term effects of exposure to adverse conditions, to see whether these experiences tend to undermine businesses, or help to make them more resilient over time. Prior Work: The research is informed by contributions to the resilience literature, which spans individual, organisational, inter-organisational and regional levels of analysis. It identifies a variety of factors as potential sources of resilience for smaller firms and potential vulnerabilities. Some empirical work has been conducted in this area but there is scope for a more in-depth examination of the ways that SME owners and managers perceive and prepare for external threats, their experiences in responding to crises, and implications of the promotion of environmentally sustainable practices. Approach: Evidence was collected from a large quarterly survey of SMEs in Britain. Statistical findings are based on 1,353 useable questionnaire responses comprising a sub-sample drawn from a larger telephone omnibus survey, supplemented by a sub-sample of respondents to a slightly longer online version. The statistical data were augmented by qualitative evidence from online respondents and a series of six semi-structured interviews which explored issues emerging from the survey in greater detail. Results: Organisational resilience is an important issue for SMEs. Nearly three quarters (73%) of respondents identified at least one external event that posed a ‘real threat’ to their business over the last five years and many identified multiple threats. Extreme weather conditions were identified as a real threat by 27% of respondents, a finding underlined by graphic qualitative accounts of damage caused to businesses by events such as flooding and heavy snowfall (n.b. the survey was conducted prior to the extended period of storms and flooding that disrupted many businesses in late 2013). Value: This working paper makes an empirical contribution to the organisational resilience literature by providing evidence from a relatively large and broadly representative sample of British SMEs, coupled with tentative policy implications and suggestions for further research. Recent years have seen a policy focus on promoting high growth firms. Given continuing economic uncertainties and the prospect of increasing threats from extreme weather events, it may also be advisable to consider initiatives that foster the longer-term resilience of SMEs, and to pay particular attention to the needs of smaller and more vulnerable firms

Quarterly Survey of Small Business in Britain - 30th anniversary issue

This special issue marks a particular milestone: it is now three decades since the Quarterly Survey of Small Business in Britain began the task of monitoring emerging trends and examining the experiences and opinions of business owners and managers. In this report, we have assembled contributions from a variety of sources with the following aims: to shed some new light on this important period in the history of small firms’ research in the UK; to explore the main changes and continuities in the small firms landscape over this extended period; and lastly, to draw some lessons for future work in this important research field. The remainder of the report comprises three parts: Section 2 sets out the historical background to the launch of the Quarterly Survey in 1984. This includes an account of the highly influential Bolton Committee Report of 1971, drafted by John Bolton’s biographer, and personal accounts from two small business specialists who were directly involved in establishing the Quarterly Survey. Section 3 opens with a small selection of the survey’s research topics and findings over the last 30 years. This is followed by a review of the technical challenges of conducting survey-based research, particularly when the work extends over such a long period, and an assessment of the Quarterly Survey’s contribution to the SME research and policy communities. We also hear from the editor in chief of the International Small Business Journal, which was also established in the early 1980s, on the challenges of establishing an academic publication that addresses the issues faced by smaller firms. In Section 4, some of our longest-serving panel respondents discuss the trends and changes that their businesses have faced over this period and comment on the prospects for 2015. They also reflect on the experience of completing all of those survey questionnaires. Section 5 offers some brief concluding remarks and comments on possible future directions for research of this kind

Web tools for large-scale 3D biological images and atlases

<p>Abstract</p> <p>Background</p> <p>Large-scale volumetric biomedical image data of three or more dimensions are a significant challenge for distributed browsing and visualisation. Many images now exceed 10GB which for most users is too large to handle in terms of computer RAM and network bandwidth. This is aggravated when users need to access tens or hundreds of such images from an archive. Here we solve the problem for 2D section views through archive data delivering compressed tiled images enabling users to browse through very-large volume data in the context of a standard web-browser. The system provides an interactive visualisation for grey-level and colour 3D images including multiple image layers and spatial-data overlay.</p> <p>Results</p> <p>The standard Internet Imaging Protocol (IIP) has been extended to enable arbitrary 2D sectioning of 3D data as well a multi-layered images and indexed overlays. The extended protocol is termed IIP3D and we have implemented a matching server to deliver the protocol and a series of Ajax/Javascript client codes that will run in an Internet browser. We have tested the server software on a low-cost linux-based server for image volumes up to 135GB and 64 simultaneous users. The section views are delivered with response times independent of scale and orientation. The exemplar client provided multi-layer image views with user-controlled colour-filtering and overlays.</p> <p>Conclusions</p> <p>Interactive browsing of arbitrary sections through large biomedical-image volumes is made possible by use of an extended internet protocol and efficient server-based image tiling. The tools open the possibility of enabling fast access to large image archives without the requirement of whole image download and client computers with very large memory configurations. The system was demonstrated using a range of medical and biomedical image data extending up to 135GB for a single image volume.</p

Integrated analysis of Wnt signalling system component gene expression

Wnt signalling controls patterning and differentiation across many tissues and organs of the developing embryo through temporally and spatially restricted expression of multi-gene families encoding ligands, receptors, pathway modulators and intracellular components. Here, we report an integrated analysis of key genes in the 3D space of the mouse embryo across multiple stages of development. We applied a method for 3D/3D image transformation to map all gene expression patterns to a single reference embryo for each stage, providing both visual analysis and volumetric mapping allowing computational methods to interrogate the combined expression patterns. We identify territories where multiple Wnt and Fzd genes are co-expressed and cross-compare all patterns, including all seven Wnt paralogous gene pairs. The comprehensive analysis revealed regions in the embryo where no Wnt or Fzd gene expression is detected, and where single Wnt genes are uniquely expressed. This work provides insight into a previously unappreciated level of organisation of expression patterns, as well as presenting a resource that can be utilised further by the research community for whole-system analysis

Spatial organization of active and inactive genes and noncoding DNA within chromosome territories

The position of genes within the nucleus has been correlated with their transcriptional activity. The interchromosome domain model of nuclear organization suggests that genes preferentially locate at the surface of chromosome territories. Conversely, high resolution analysis of chromatin fibers suggests that chromosome territories do not present accessibility barriers to transcription machinery

Integrating partonomic hierarchies in anatomy ontologies

<p>Abstract</p> <p>Background</p> <p>Anatomy ontologies play an increasingly important role in developing integrated bioinformatics applications. One of the primary relationships between anatomical tissues represented in such ontologies is <it>part-of</it>. As there are a number of ways to divide up the anatomical structure of an organism, each may be represented by more than one valid partonomic (part-of) hierarchy. This raises the issue of how to represent and integrate multiple such hierarchies.</p> <p>Results</p> <p>In this paper we describe a solution that is based on our work on an anatomy ontology for mouse embryo development, which is part of the Edinburgh Mouse Atlas Project (EMAP). The paper describes the basic conceptual aspects of our approach and discusses strengths and limitations of the proposed solution. A prototype was implemented in Prolog for evaluation purposes.</p> <p>Conclusion</p> <p>With the proposed name set approach, rather than having to standardise hierarchies, it is sufficient to agree on a suitable set of basic tissue terms and their meaning in order to facilitate the integration of multiple partonomic hierarchies.</p