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

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

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

"So go downtown": simulating pedestrian movement in town centres

Pedestrian movement models have been developed since the 1970s. A review of the literature shows that such models have been developed to explain and predict macro, meso, and micro movement patterns. However, recent developments in modelling techniques, and especially advances in agent-based simulation, open up the possibility of developing integrative and complex models which use existing models as 'building blocks'. In this paper we describe such integrative, modular approach to simulating pedestrian movement behaviour. The STREETS model, developed by using Swarm and GIS, is an agent-based model that focuses on the simulation of the behavioural aspects of pedestrian movement. The modular structure of the simulation is described in detail. This is followed by a discussion of the lessons learned from the development of STREETS, especially the advantages of adopting a modular approach and other aspects of using the agent-based paradigm for modelling

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

On the Anomalous Temperature Distribution of the Intergalactic Medium in the NGC 3411 Group of Galaxies

We present XMM, Chandra and VLA observations of the USGC S152 group and its central elliptical NGC 3411. Imaging of the group X-ray halo suggests it is relaxed with little apparent structure. We investigate the temperature and metal abundance structure of the group halo, and find that while the abundance distribution is fairly typical, the temperature profile is highly unusual, showing a hot inner core surrounded by a cool shell of gas with a radius of \~20-40 kpc, at the center of the larger group halo. Spectral mapping confirms an irregular ring of gas ~0.15 keV cooler than its surroundings. We estimate the total mass, entropy and cooling time profiles within ~200 kpc, and find that the cool shell contains ~9x10^9 Msun of gas. VLA observations at 1.4, 5 and 8 GHz reveal a relatively weak nuclear radio source, with a core radio luminosity L_R=2.7x10^38 erg/s, and a diffuse component extended on scales of a few arcseconds (or more). A lack of evidence for activity at optical or X-ray wavelengths supports the conclusion that the central black hole is currently in a quiescent state. We discuss possible mechanisms for the formation of temperature features observed in the halo, including a previous period of AGN activity, and settling of material stripped from the halo of one of the other group member galaxies.Comment: 15 pages, 8 postscript figures, accepted for publication in ApJ version with high resolution figures available at http://hea-www.harvard.edu/~ejos/files/N3411_hires.pd