VLMA: a tool for creating, annotating and sharing virtual museum collections

The Virtual Lightbox for Museums and Archives (VLMA) is a tool for collecting and reusing, in a structured fashion, the online contents of museums and archive datasets. It is not restricted to datasets with visual components although VLMA includes a lightbox service that enables comparison and manipulation of visual information. With VLMA, one can browse and search collections, construct personal collections, annotate them, export these collections to XML or Impress (Open Office) presentation format, and share collections with other VLMA users. VLMA was piloted as an e-Learning tool as part of JISC’s e-Learning focus in its first phase (2004-2005) and in its second phase (2005-2006) it has incorporated new partner collections while improving and expanding interfaces and services. This paper concerns its development as a research and teaching tool, especially to teachers using museum collections, and discusses the recent development of VLMA.

Assimilation of RAPID array observations into an ocean model

Experiments assimilating the RAPID dataset of deep temperature and salinity profiles at 26.5°N on the western and eastern Atlantic boundaries into a 1° global NEMO ocean model have been performed. The meridional overturning circulation (MOC) is then assessed against the transports calculated directly from observations. The best initialization found for this short period was obtained by assimilating the EN3 upper-ocean hydrography database prior to 2004, after which different methods of assimilating 5-day average RAPID profiles at the western boundary were tested. The model MOC is strengthened by ∼ 2 Sv giving closer agreement with the RAPID array transports, when the western boundary profiles are assimilated only below 900 m (the approximate depth of the Florida Straits, which are not well resolved) and when the T,S observations are spread meridionally from 10 to 35°N along the deep western boundary. The use of boundary-focused covariances has the largest impact on the assimilation results, otherwise using more conventional Gaussian covariances has a very local impact on the MOC at 26°N with strong adverse impacts on the MOC stream function at higher and lower latitudes. Even using boundary-focused covariances only enables the MOC to be strengthened for ∼ 2 years, after which the increased transport of warm waters leads to a negative feedback on water formation in the subpolar gyre which then reduces the MOC. This negative feedback can be mitigated if EN3 hydrography data continue to be assimilated along with the RAPID array boundary data. Copyright © 2012 Royal Meteorological Society and Crown in the right of Canada.

Quantifying volcanic ash dispersal and impact of the Campanian Ignimbrite super-eruption

1] We apply a novel computational approach to assess, for the first time, volcanic ash dispersal during the Campanian Ignimbrite (Italy) super-eruption providing insights into eruption dynamics and the impact of this gigantic event. The method uses a 3D time-dependent computational ash dispersion model, a set of wind fields, and more than 100 thickness measurements of the CI tephra deposit. Results reveal that the CI eruption dispersed 250–300 km3 of ash over ∼3.7 million km2. The injection of such a large quantity of ash (and volatiles) into the atmosphere would have caused a volcanic winter during the Heinrich Event 4, the coldest and driest climatic episode of the Last Glacial period. Fluorine-bearing leachate from the volcanic ash and acid rain would have further affected food sources and severely impacted Late Middle-Early Upper Paleolithic groups in Southern and Eastern Europe

Case study part 1: how to calculate appropriate deterministic long-term toxicity to exposure rates (TERs) for birds and mammals

In the European Union, first-tier assessment of the long-term risk to birds and mammals from pesticides is based on calculation of a deterministic long-term toxicity/exposure ratio(TERlt). The ratio is developed from generic herbivores and insectivores and applied to all species. This paper describes two case studies that implement proposed improvements to the way long-term risk is assessed. These refined methods require calculation of a TER for each of five identified phases of reproduction (phase-specific TERs) and use of adjusted No Observed Effect Levels (NOELs)to incorporate variation in species sensitivity to pesticides. They also involve progressive refinement of the exposure estimate so that it applies to particular species, rather than generic indicators, and relates spraying date to onset of reproduction. The effect of using these new methods on the assessment of risk is described. Each refinement did not necessarily alter the calculated TER value in a way that was either predictable or consistent across both case studies. However, use of adjusted NOELs always reduced TERs, and relating spraying date to onset of reproduction increased most phase-specific TERs. The case studies suggested that the current first-tier TERlt assessment may underestimate risk in some circumstances and that phase-specific assessments can help identify appropriate risk-reduction measures. The way in which deterministic phase-specific assessments can currently be implemented to enhance first-tier assessment is outlined.

Case study part 2: probabilistic modelling of long-term effects of pesticides on individual breeding success in birds and mammals

Abstract: Long-term exposure of skylarks to a fictitious insecticide and of wood mice to a fictitious fungicide were modelled probabilistically in a Monte Carlo simulation. Within the same simulation the consequences of exposure to pesticides on reproductive success were modelled using the toxicity-exposure-linking rules developed by R.S. Bennet et al. (2005) and the interspecies extrapolation factors suggested by R. Luttik et al.(2005). We built models to reflect a range of scenarios and as a result were able to show how exposure to pesticide might alter the number of individuals engaged in any given phase of the breeding cycle at any given time and predict the numbers of new adults at the season’s end.

Risk assessment of UK skylark populations using life-history and individual-based landscape models

Abstract: Following a workshop exercise, two models, an individual-based landscape model (IBLM) and a non-spatial life-history model were used to assess the impact of a fictitious insecticide on populations of skylarks in the UK. The chosen population endpoints were abundance, population growth rate, and the chances of population persistence. Both models used the same life-history descriptors and toxicity profiles as the basis for their parameter inputs. The models differed in that exposure was a pre-determined parameter in the life-history model, but an emergent property of the IBLM, and the IBLM required a landscape structure as an input. The model outputs were qualitatively similar between the two models. Under conditions dominated by winter wheat, both models predicted a population decline that was worsened by the use of the insecticide. Under broader habitat conditions, population declines were only predicted for the scenarios where the insecticide was added. Inputs to the models are very different, with the IBLM requiring a large volume of data in order to achieve the flexibility of being able to integrate a range of environmental and behavioural factors. The life-history model has very few explicit data inputs, but some of these relied on extensive prior modelling needing additional data as described in Roelofs et al.(2005, this volume). Both models have strengths and weaknesses; hence the ideal approach is that of combining the use of both simple and comprehensive modeling tools.

Dopant-vacancy binding effects in Li-doped magnesium hydride

We use a combination of ab initio calculations and statistical mechanics to investigate the substitution of Li+ for Mg2+ in magnesium hydride (MgH2) accompanied by the formation of hydrogen vacancies with positive charge (with respect to the original ion at the site). We show that the binding energy between dopants and vacancy defects leads to a significant fraction of trapped vacancies and therefore a dramatic reduction in the number of free vacancies available for diffusion. The concentration of free vacancies initially increases with dopant concentration but reaches a maximum at around 1 mol % Li doping and slowly decreases with further doping. At the optimal level of doping, the corresponding concentration of free vacancies is much higher than the equilibrium concentrations of charged and neutral vacancies in pure MgH2 at typical hydrogen storage conditions. We also show that Li-doped MgH2 is thermodynamically metastable with respect to phase separation into pure magnesium and lithium hydrides at any significant Li concentration, even after considering the stabilization provided by dopant-vacancy interactions and configurational entropic effects. Our results suggest that lithium doping may enhance hydrogen diffusion hydride but only to a limited extent determined by an optimal dopant concentration and conditioned to the stability of the doped phase.

Variation among Attic fine wares: the case of the Pan Painter's pelikai

This paper is a case study of the continuum between standardization and variation in the production of red-figure Athenian fine wares in the first half of the 5th century BC. An investigation of the Pan Painter's pelikai reveals that they fall into 3 distinct groups, according to size. While the pelikai in each group are also distinguishable from each other by shape, pattern, and iconography, the next clearest distinction between the groups (after size) is in their style of decoration. The pelikai in the largest group, which is comprised of small pelikai, are particularly distinct from the Pan Painter's broader oeuvre of ca. 220 vases insofar as they exemplify a lackadaisical painting style, which I have termed banausic, on account of its frequent use for images of craftsmen, women at work, and other such genre images. While this casual style is antithetical to the Pain Painter's refined style, for which he is better known, and which he employs for his large pelikai, affinities between the 2 styles—as judged by his confident line, anatomical details, and other technical features—permit the conclusion that this group of pelikai were executed by one and the same craftsman as the others. As with all of the vases attributed to this talented painter, however, the pelikai—whether large or small—are decorated with a great bariety of images. While most painted Athenian vases are understood to have been individually created, not mass-produced, the Pan Painter's coherent group of small pelikai seem to have been created en masse, in a uniform size and shape and with a distinct decorative style. This group of standardized vases represents a body of work executed under the influence or at the behest of a specific vase workshop. The form of the small pelikai in fact allows us to associate them with the Geras Painter. With his work on these small pelikai, perhaps in the latter part of his career, the Pan Painter may have intentionally minimized variability in favour of standardization, to meet market demands.

Tagged phosphine reagents to assist reaction work-up by phase-switched scavenging using a modular flow reactor

The use of three orthogonally tagged phosphine reagents to assist chemical work-up via phase-switch scavenging in conjunction with a modular flow reactor is described. These techniques (acidic, basic and Click chemistry) are used to prepare various amides and tri-substituted guanidines from in situ generated iminophosphoranes.

[3 + 2] Cycloaddition of acetylenes with azides to give 1,4-disubstituted 1,2,3-triazoles in a modular flow reactor

The cycloaddition of acetylenes with azides to give the corresponding 1,4-disubstituted 1,2,3-triazoles is reported using immobilised reagents and scavengers in pre-packed glass tubes in a modular flow reactor.

Changes in the distribution of red foxes (Vulpes vulpes) in urban areas in Great Britain: findings and limitations of a media-driven nationwide survey

Urbanization is one of the major forms of habitat alteration occurring at the present time. Although this is typically deleterious to biodiversity, some species flourish within these human-modified landscapes, potentially leading to negative and/or positive interactions between people and wildlife. Hence, up-to-date assessment of urban wildlife populations is important for developing appropriate management strategies. Surveying urban wildlife is limited by land partition and private ownership, rendering many common survey techniques difficult. Garnering public involvement is one solution, but this method is constrained by the inherent biases of non-standardised survey effort associated with voluntary participation. We used a television-led media approach to solicit national participation in an online sightings survey to investigate changes in the distribution of urban foxes in Great Britain and to explore relationships between urban features and fox occurrence and sightings density. Our results show that media-based approaches can generate a large national database on the current distribution of a recognisable species. Fox distribution in England and Wales has changed markedly within the last 25 years, with sightings submitted from 91% of urban areas previously predicted to support few or no foxes. Data were highly skewed with 90% of urban areas having <30 fox sightings per 1000 people km-2. The extent of total urban area was the only variable with a significant impact on both fox occurrence and sightings density in urban areas; longitude and percentage of public green urban space were respectively, significantly positively and negatively associated with sightings density only. Latitude, and distance to nearest neighbouring conurbation had no impact on either occurrence or sightings density. Given the limitations associated with this method, further investigations are needed to determine the association between sightings density and actual fox density, and variability of fox density within and between urban areas in Britain.

Using an individual-based model to select among alternative foraging strategies of woodpigeons: data support a memory-based model with a flocking mechanism

Population modelling is increasingly recognised as a useful tool for pesticide risk assessment. For vertebrates that may ingest pesticides with their food, such as woodpigeon (Columba palumbus), population models that simulate foraging behaviour explicitly can help predicting both exposure and population-level impact. Optimal foraging theory is often assumed to explain the individual-level decisions driving distributions of individuals in the field, but it may not adequately predict spatial and temporal characteristics of woodpigeon foraging because of the woodpigeons’ excellent memory, ability to fly long distances, and distinctive flocking behaviour. Here we present an individual-based model (IBM) of the woodpigeon. We used the model to predict distributions of foraging woodpigeons that use one of six alternative foraging strategies: optimal foraging, memory-based foraging and random foraging, each with or without flocking mechanisms. We used pattern-oriented modelling to determine which of the foraging strategies is best able to reproduce observed data patterns. Data used for model evaluation were gathered during a long-term woodpigeon study conducted between 1961 and 2004 and a radiotracking study conducted in 2003 and 2004, both in the UK, and are summarised here as three complex patterns: the distributions of foraging birds between vegetation types during the year, the number of fields visited daily by individuals, and the proportion of fields revisited by them on subsequent days. The model with a memory-based foraging strategy and a flocking mechanism was the only one to reproduce these three data patterns, and the optimal foraging model produced poor matches to all of them. The random foraging strategy reproduced two of the three patterns but was not able to guarantee population persistence. We conclude that with the memory-based foraging strategy including a flocking mechanism our model is realistic enough to estimate the potential exposure of woodpigeons to pesticides. We discuss how exposure can be linked to our model, and how the model could be used for risk assessment of pesticides, for example predicting exposure and effects in heterogeneous landscapes planted seasonally with a variety of crops, while accounting for differences in land use between landscapes.

The Ocean Reanalysis Intercomparison project (ORA-IP)

Uncertainty in ocean analysis methods and deficiencies in the observing system are major obstacles for the reliable reconstruction of the past ocean climate. The variety of existing ocean reanalyses is exploited in a multi-reanalysis ensemble to improve the ocean state estimation and to gauge uncertainty levels. The ensemble-based analysis of signal-to-noise ratio allows the identification of ocean characteristics for which the estimation is robust (such as tropical mixed-layer-depth, upper ocean heat content), and where large uncertainty exists (deep ocean, Southern Ocean, sea ice thickness, salinity), providing guidance for future enhancement of the observing and data assimilation systems.

Intercomparison of the Arctic sea ice cover in global ocean–sea ice reanalyses from the ORA-IP project

Ocean–sea ice reanalyses are crucial for assessing the variability and recent trends in the Arctic sea ice cover. This is especially true for sea ice volume, as long-term and large scale sea ice thickness observations are inexistent. Results from the Ocean ReAnalyses Intercomparison Project (ORA-IP) are presented, with a focus on Arctic sea ice fields reconstructed by state-of-the-art global ocean reanalyses. Differences between the various reanalyses are explored in terms of the effects of data assimilation, model physics and atmospheric forcing on properties of the sea ice cover, including concentration, thickness, velocity and snow. Amongst the 14 reanalyses studied here, 9 assimilate sea ice concentration, and none assimilate sea ice thickness data. The comparison reveals an overall agreement in the reconstructed concentration fields, mainly because of the constraints in surface temperature imposed by direct assimilation of ocean observations, prescribed or assimilated atmospheric forcing and assimilation of sea ice concentration. However, some spread still exists amongst the reanalyses, due to a variety of factors. In particular, a large spread in sea ice thickness is found within the ensemble of reanalyses, partially caused by the biases inherited from their sea ice model components. Biases are also affected by the assimilation of sea ice concentration and the treatment of sea ice thickness in the data assimilation process. An important outcome of this study is that the spatial distribution of ice volume varies widely between products, with no reanalysis standing out as clearly superior as compared to altimetry estimates. The ice thickness from systems without assimilation of sea ice concentration is not worse than that from systems constrained with sea ice observations. An evaluation of the sea ice velocity fields reveals that ice drifts too fast in most systems. As an ensemble, the ORA-IP reanalyses capture trends in Arctic sea ice area and extent relatively well. However, the ensemble can not be used to get a robust estimate of recent trends in the Arctic sea ice volume. Biases in the reanalyses certainly impact the simulated air–sea fluxes in the polar regions, and questions the suitability of current sea ice reanalyses to initialize seasonal forecasts.