Visibility graphs and landscape visibility analysis

Visibility analysis based on viewsheds is one of the most frequently used GIS analysis tools. In this paper we present an approach to visibility analysis based on the visibility graph. A visibility graph records the pattern of mutual visibility relations in a landscape, and provides a convenient way of storing and further analysing the results of multiple viewshed analyses for a particular landscape region. We describe how a visibility graph may be calculated for a landscape. We then give examples, which include the interactive exploration ofa landscape, and the calculation of new measures of a landscape?s visual properties based on graph metrics ? in particular, neighbourhood clustering coefficient and path length analysis. These analyses suggest that measures derived from the visibility graph may be of particular relevance to the growing interest in quantifying the perceptual characteristics of landscapes

Agent-based models and individualism: is the world agent-based?

Agent-based models (ABMs) are an increasingly popular tool in the social sciences. This trend seems likely to continue, so that they will become widely used in geography and in urban and regional planning. We present an overview of examples of these models in the life sciences, economics, planning, sociology, and archaeology. We conclude that ABMs strongly tend towards an individualist view of the social world. This point is reinforced by closer consideration of particular examples. This discussion pays attention to the inadequacy of an individualist model of society with reference to debates in social theory. We argue that because models are closed representations of an open world it is important that institutions and other social structures be explicitly included, or that their omission be explained. A tentative explanation for the bias of ABMs is offered, based on an examination of early research in artificial intelligence and distributed artificial intelligence from which disciplines the approach is derived. Some implications of these findings are discussed. We indicate some useful research directions which are beginning to tackle the individualism issue directly. We further note that the underlying assumptions of ABMs are often hidden in the implementation details. We conclude that such models must be subject to critical examination of their assumptions, and that model builders should engage with social theory if the approach is to realise its full potential

STREETS: an agent-based pedestrian model.

8-11 Septembe

High-throughput DNA sequencing to survey bacterial histidine and tyrosine decarboxylases in raw milk cheeses

peer-reviewedBackground The aim of this study was to employ high-throughput DNA sequencing to assess the incidence of bacteria with biogenic amine (BA; histamine and tyramine) producing potential from among 10 different cheeses varieties. To facilitate this, a diagnostic approach using degenerate PCR primer pairs that were previously designed to amplify segments of the histidine (hdc) and tyrosine (tdc) decarboxylase gene clusters were employed. In contrast to previous studies in which the decarboxylase genes of specific isolates were studied, in this instance amplifications were performed using total metagenomic DNA extracts. Results Amplicons were initially cloned to facilitate Sanger sequencing of individual gene fragments to ensure that a variety of hdc and tdc genes were present. Once this was established, high throughput DNA sequencing of these amplicons was performed to provide a more in-depth analysis of the histamine- and tyramine-producing bacteria present in the cheeses. High-throughput sequencing resulted in generation of a total of 1,563,764 sequencing reads and revealed that Lactobacillus curvatus, Enterococcus faecium and E. faecalis were the dominant species with tyramine producing potential, while Lb. buchneri was found to be the dominant species harbouring histaminogenic potential. Commonly used cheese starter bacteria, including Streptococcus thermophilus and Lb. delbreueckii, were also identified as having biogenic amine producing potential in the cheese studied. Molecular analysis of bacterial communities was then further complemented with HPLC quantification of histamine and tyramine in the sampled cheeses. Conclusions In this study, high-throughput DNA sequencing successfully identified populations capable of amine production in a variety of cheeses. This approach also gave an insight into the broader hdc and tdc complement within the various cheeses. This approach can be used to detect amine producing communities not only in food matrices but also in the production environment itself.This work was funded by the Department of Agriculture, Food and the Marine under the Food Institutional Research Measure through the ‘Cheeseboard 2015’ project. Daniel J. O’Sullivan is in receipt of a Teagasc Walsh Fellowship, Grant Number: 2012205

Combining ontologies and open standards to derive a middle layer information model for interoperability of personal and electronic health records

Objectives: To enable better interoperability between Personal Health Record (PHR) and Electronic Health Record (EHR) systems to allow exchange of data from patients to providers and vice versa in order to encourage PHR use and patient self-management. Methods: A non-binding middleware based on open technologies and standards that resides between a PHR and EHR system has been developed. Specifically, the middleware consists of an ontology-driven information model based on the HL7 Reference Information Model (RIM) and a set of transformation rules that work in conjunction with the information model to process data exported from a PHR or EHR system and prepare it according to constraints imposed by the receiving system. Results: The information model was evaluated by executing a set of use case scenarios containing data exported from a PHR system, transformed according to the transformation rules, transferred to an EHR system and vice versa (EHR to PHR). This allowed various challenges to emerge as well as revealed gaps in current standards in use. Conclusions: The proposed middleware information model offers a number of advantages. When modifications are made to either a PHR or EHR system, they can be incorporated by altering only the instantiation of the information model. The model uses classes and attributes based on HL7 RIM to define how data is captured which allows greater flexibility in how data can be manipulated by receiving systems. The solution is applicable to existing PHR systems, or could be used as a blueprint to develop new PHR applications

Sequencing-Based Analysis of the Bacterial and Fungal Composition of Kefir Grains and Milks from Multiple Sources

peer-reviewedKefir is a fermented milk-based beverage to which a number of health-promoting properties have been attributed. The microbes responsible for the fermentation of milk to produce kefir consist of a complex association of bacteria and yeasts, bound within a polysaccharide matrix, known as the kefir grain. The consistency of this microbial population, and that present in the resultant beverage, has been the subject of a number of previous, almost exclusively culture-based, studies which have indicated differences depending on geographical location and culture conditions. However, culture-based identification studies are limited by virtue of only detecting species with the ability to grow on the specific medium used and thus culture-independent, molecular-based techniques offer the potential for a more comprehensive analysis of such communities. Here we describe a detailed investigation of the microbial population, both bacterial and fungal, of kefir, using high-throughput sequencing to analyse 25 kefir milks and associated grains sourced from 8 geographically distinct regions. This is the first occasion that this technology has been employed to investigate the fungal component of these populations or to reveal the microbial composition of such an extensive number of kefir grains or milks. As a result several genera and species not previously identified in kefir were revealed. Our analysis shows that the bacterial populations in kefir are dominated by 2 phyla, the Firmicutes and the Proteobacteria. It was also established that the fungal populations of kefir were dominated by the genera Kazachstania, Kluyveromyces and Naumovozyma, but that a variable sub-dominant population also exists.The Alimentary Pharmabiotic Centre is a research centre funded by Science Foundation Ireland (SFI), through the Irish Government’s National Development Plan. The authors and their work were supported by SFI CSET grant APC CSET 2 grant 07/CE/B1368

From isovists to visibility graphs: a methodology for the analysis of architectural space

An isovist, or viewshed, is the area in a spatial environment directly visible from a location within the space. Here we show how a set of isovists can be used to generate a graph of mutual visibility between locations. We demonstrate that this graph can also be constructed without reference to isovists and that we are in fact invoking the more general concept of a visibility graph. Using the visibility graph, we can extend both isovist and current graph-based analyses of architectural space to form a new methodology for the investigation of configurational relationships. The measurement of local and global characteristics of the graph, for each vertex or for the system as a whole, is of interest from an architectural perspective, allowing us to describe a configuration with reference to accessibility and visibility, to compare from location to location within a system, and to compare systems with different geometries. Finally we show that visibility graph properties may be closely related to manifestations of spatial perception, such as way-finding, movement, and space use

Temporal and spatial differences in microbial composition during the manufacture of a Continental-type cheese

peer-reviewedWe sought to determine if the time, within a production day, that a cheese is manufactured has an influence on the microbial community present within that cheese. To facilitate this, 16S rRNA amplicon sequencing was used to elucidate the microbial community dynamics of brine salted Continental-type cheese in cheeses produced early and late in the production day. Differences in microbial composition of the core and rind of the cheese were also investigated. Throughout ripening, it was apparent that late production day cheeses had a more diverse microbial population than their early day equivalents. Spatial variation between the cheese core and rind was also noted in that cheese rinds were found to initially have a more diverse microbial population but thereafter the opposite was the case. Interestingly, the genera Thermus, Pseudoalteromonas and Bifidobacterium, not routinely associated with a Continental-type cheese produced from pasteurised milk were detected. The significance, if any, of the presence of these genera will require further attention. Ultimately, the use of high throughput sequencing has facilitated a novel and detailed analysis of the temporal and spatial distribution of microbes in this complex cheese system and established that the period during a production cycle at which a cheese is manufactured can influence its microbial composition.This work was funded by the Department of Agriculture, Food and the Marine under the Food Institutional Research Measure through the ‘Cheeseboard 2015’ project. Daniel J. O’Sullivan is in receipt of a Teagasc Walsh Fellowship, Grant Number: 201220

Canine dystocia in 50 UK first-opinion emergency-care veterinary practices: prevalence and risk factors

Dystocia can represent a major welfare issue for dogs of certain breeds and morphologies. First-opinion emergency-care veterinary caseloads represent a useful data resource for epidemiological research because dystocia can often result in emergency veterinary care. The study analysed a merged database of clinical records from 50 first-opinion emergency-care veterinary practices participating in the VetCompass Programme. Multivariable logistic regression modelling was used for risk factors analysis. There were 701 dystocia cases recorded among 18,758 entire female dogs, resulting in a dystocia prevalence of 3.7 per cent (95 per cent CI 3.5–4.0 per cent). Breeds with the highest odds of dystocia compared with crossbred bitches were French Bulldog (OR: 15.9, 95 per cent CI 9.3 to 27.2, P<0.001), Boston Terrier (OR: 12.9, 95 per cent CI 5.6 to 29.3, P<0.001), Chihuahua (OR: 10.4, 95 per cent CI 7.0 to 15.7, P<0.001) and Pug (OR: 11.3, 95 per cent CI 7.1 to 17.9, P<0.001). Bitches aged between 3.0 and 5.9 years had 3.1 (95 per cent CI 2.6 to 3.7, P<0.001) times the odds of dystocia compared with bitches aged under 3.0years. Certain breeds, including some brachycephalic and toy breeds, appeared at high risk of dystocia. Opportunities to improve this situation are discussed