Controls on inorganic nitrogen leaching from Finnish catchments assessed using a sensitivity and uncertainty analysis of the INCA-N model

The semi-distributed, dynamic INCA-N model was used to simulate the behaviour of dissolved inorganic nitrogen (DIN) in two Finnish research catchments. Parameter sensitivity and model structural uncertainty were analysed using generalized sensitivity analysis. The Mustajoki catchment is a forested upstream catchment, while the Savijoki catchment represents intensively cultivated lowlands. In general, there were more influential parameters in Savijoki than Mustajoki. Model results were sensitive to N-transformation rates, vegetation dynamics, and soil and river hydrology. Values of the sensitive parameters were based on long-term measurements covering both warm and cold years. The highest measured DIN concentrations fell between minimum and maximum values estimated during the uncertainty analysis. The lowest measured concentrations fell outside these bounds, suggesting that some retention processes may be missing from the current model structure. The lowest concentrations occurred mainly during low flow periods; so effects on total loads were small.

Identification of potential drug targets in Salmonella Typhimurium using metabolic modelling and experimental validation

almonella enterica serovar Typhimurium is an established model organism for Gram-negative, intracellular pathogens. Owing to the rapid spread of resistance to antibiotics among this group of pathogens, new approaches to identify suitable target proteins are required. Based on the genome sequence of Salmonella Typhimurium and associated databases, a genome-scale metabolic model was constructed. Output was based on an experimental determination of the biomass of Salmonella when growing in glucose minimal medium. Linear programming was used to simulate variations in energy demand, while growing in glucose minimal medium. By grouping reactions with similar flux responses, a sub-network of 34 reactions responding to this variation was identified (the catabolic core). This network was used to identify sets of one and two reactions, that when removed from the genome-scale model interfered with energy and biomass generation. 11 such sets were found to be essential for the production of biomass precursors. Experimental investigation of 7 of these showed that knock-outs of the associated genes resulted in attenuated growth for 4 pairs of reactions, while 3 single reactions were shown to be essential for growth.

Study of picosecond processes of an intercalated dipyridophenazine Cr(iii) complex bound to defined sequence DNAs using transient absorption and time-resolved infrared methods

Picosecond transient absorption (TA) and time-resolved infrared (TRIR) measurements of rac-[Cr(phen)2(dppz)]3+ (1) intercalated into double-stranded guanine-containing DNA reveal that the excited state is very rapidly quenched. As no evidence was found for the transient electron transfer products, it is proposed that the back electron transfer reaction must be even faster (<3 ps).

The MELODIES project: integrating diverse data using Linked Data and cloud computing

We present an overview of the MELODIES project, which is developing new data-intensive environmental services based on data from Earth Observation satellites, government databases, national and European agencies and more. We focus here on the capabilities and benefits of the project’s “technical platform”, which applies cloud computing and Linked Data technologies to enable the development of these services, providing flexibility and scalability.

Opportunities for magnetospheric research using EISCAT/ESR and CLUSTER

The four Cluster spacecraft offer a unique opportunity to study structure and dynamics in the magnetosphere and we discuss four general ways in which ground-based remote-sensing observations of the ionosphere can be used to support the in-situ measurements. The ionosphere over the Svalbard islands will be studied in particular detail, not only by the ESR and EISCAT incoherent scatter radars, but also by optical instruments, magnetometers, imaging riometers and the CUTLASS bistatic HF radar. We present an on-line procedure to plan coordinated measurements by the Cluster spacecraft with these combined ground-based systems. We illustrate the philosophy of the method, using two important examples of the many possible configurations between the Cluster satellites and the ground-based instruments.

The dependence of high-latitude dayside ionospheric flows on the North-South component of the IMF: A high time resolution correlation analysis using EISCAT “Polar” and AMPTE UKS and IRM data

In 1984 and 1985 a series of experiments was undertaken in which dayside ionospheric flows were measured by the EISCAT “Polar” experiment, while observations of the solar wind and interplanetary magnetic field (IMF) were made by the AMPTE UKS and IRM spacecraft upstream from the Earth's bow shock. As a result, 40 h of simultaneous data were acquired, which are analysed in this paper to investigate the relationship between the ionospheric flow and the North-South (Bz) component of the IMF. The ionospheric flow data have 2.5 min resolution, and cover the dayside local time sector from ∼ 09:30 to ∼ 18:30 M.L.T. and the latitude range from 70.8° to 74.3°. Using cross-correlation analysis it is shown that clear relationships do exist between the ionospheric flow and IMF Bz, but that the form of the relations depends strongly on latitude and local time. These dependencies are readily interpreted in terms of a twinvortex flow pattern in which the magnitude and latitudinal extent of the flows become successively larger as Bz becomes successively more negative. Detailed maps of the flow are derived for a range of Bz values (between ± 4 nT) which clearly demonstrate the presence of these effects in the data. The data also suggest that the morning reversal in the East-West component of flow moves to earlier local times as Bz, declines in value and becomes negative. The correlation analysis also provides information on the ionospheric response time to changes in IMF Bz, it being found that the response is very rapid indeed. The most rapid response occurs in the noon to mid-afternoon sector, where the westward flows of the dusk cell respond with a delay of 3.9 ± 2.2 min to changes in the North-South field at the subsolar magnetopause. The flows appear to evolve in form over the subsequent ~ 5 min interval, however, as indicated by the longer response times found for the northward component of flow in this sector (6.7 ±2.2 min), and in data from earlier and later local times. No evidence is found for a latitudinal gradient in response time; changes in flow take place coherently in time across the entire radar field-of-view.

Using experimental archaeology and micromorphology to reconstruct timber-framed buildings from Roman Silchester: a new approach

Determining the internal layout of archaeological structures and their uses has always been challenging, particularly in timber-framed or earthen walled buildings where doorways and divisions are difficult to trace. In temperate conditions however, soil formation processes may hold the key to understanding how buildings were used. The abandoned Roman town of Silchester, UK, provides a perfect case study for testing a new approach combining experimental archaeology and micromorphology. The results show that this technique can resolve previously uncertain features of urban architecture such as the presence of a roof and the changes in internal organisation and use over time.

Re-creation of heathland on improved pasture using topsoil removal and sulphur amendments: edaphic drivers and impacts on ericoid mycorrhizas

Understanding the factors that drive successful re-creation and restoration of lowland heaths is crucially important for achieving the long-term conservation of this threatened habitat type. In this study we investigated the changes in soil chemistry, plant community and interactions between Calluna vulgaris and symbiotic ericoid mycorrhizas (ERM) that occurred when improved pasture was subjected to one of three treatments (i) acidification with elemental sulphur (ii) acidification with ferrous sulphur (iii) removal of the topsoil. We found that the soil stripping treatment produced the greatest reduction in available phosphate but did not decrease soil pH. Conversely, acidification with elemental sulphur decreased pH but increased availability of phosphate and potentially toxic cations. The elemental sulphur treatment produced plant communities that most closely resembled those on surrounding heaths and acid grasslands. The most important driver was low pH and concomitant increased availability of potentially toxic cations. Plant community development was found to be little related to levels of available soil phosphate, particularly at low pH. The elemental sulphur treatment also produced the best germination and growth of C. vulgaris over 4–5 years. However, this treatment was found to inhibit the development of symbiotic relationships between C. vulgaris and ERM. This may affect the long-term persistence of re-created vegetation and its interactions with other components of heathland communities.

Characterization of para-Nitrophenol-degrading bacterial communities in river water by using functional markers and stable isotope probing

Microbial degradation is a major determinant of the fate of pollutants in the environment. para-Nitrophenol (PNP) is an EPA listed priority pollutant with a wide environmental distribution, but little is known about the microorganisms that degrade it in the environment. We studied the diversity of active PNP-degrading bacterial populations in river water using a novel functional marker approach coupled with [13C6]PNP stable isotope probing (SIP). Culturing together with culture-independent terminal restriction fragment length polymorphism analysis of 16S rRNA gene amplicons identified Pseudomonas syringae to be the major driver of PNP degradation in river water microcosms. This was confirmed by SIP-pyrosequencing of amplified 16S rRNA. Similarly, functional gene analysis showed that degradation followed the Gram-negative bacterial pathway and involved pnpA from Pseudomonas spp. However, analysis of maleylacetate reductase (encoded by mar), an enzyme common to late stages of both Gram-negative and Gram-positive bacterial PNP degradation pathways, identified a diverse assemblage of bacteria associated with PNP degradation, suggesting that mar has limited use as a specific marker of PNP biodegradation. Both the pnpA and mar genes were detected in a PNP-degrading isolate, P. syringae AKHD2, which was isolated from river water. Our results suggest that PNP-degrading cultures of Pseudomonas spp. are representative of environmental PNP-degrading populations.

Limitations to recording larger mammalian predators in savannah using camera traps and spoor

Traditionally, spoor (tracks, pug marks) have been used as a cost effective tool to assess the presence of larger mammals. Automated camera traps are now increasingly utilized to monitor wildlife, primarily as the cost has greatly declined and statistical approaches to data analysis have improved. While camera traps have become ubiquitous, we have little understanding of their effectiveness when compared to traditional approaches using spoor in the field. Here, we a) test the success of camera traps in recording a range of carnivore species against spoor; b) ask if simple measures of spoor size taken by amateur volunteers is likely to allow individual identification of leopards and c) for a trained tracker, ask if this approach may allow individual leopards to be followed with confidence in savannah habitat. We found that camera traps significantly under-recorded mammalian top and meso-carnivores, with camera traps more likely under-record the presence of smaller carnivores (civet 64%; genet 46%, Meller’s mongoose 45%) than larger (jackal sp. 30%, brown hyena 22%), while leopard was more likely to be recorded by camera trap (all recorded by camera trap only). We found that amateur trackers could be beneficial in regards to collecting presence data; however the large variance in measurements of spoor taken in the field by volunteers suggests that this approach is unlikely to add further data. Nevertheless, the use of simple spoor measurements in the field by a trained field researcher increases their ability to reliably follow a leopard trail in difficult terrain. This allows researchers to glean further data on leopard behaviour and habitat utilisation without the need for complex analysis.

Managing the complexity of information flow for construction small and medium-sized enterprises (CSMEs) using system dynamics and collaborative technologies

With the increase in e-commerce and the digitisation of design data and information,the construction sector has become reliant upon IT infrastructure and systems. The design and production process is more complex, more interconnected, and reliant upon greater information mobility, with seamless exchange of data and information in real time. Construction small and medium-sized enterprises (CSMEs), in particular,the speciality contractors, can effectively utilise cost-effective collaboration-enabling technologies, such as cloud computing, to help in the effective transfer of information and data to improve productivity. The system dynamics (SD) approach offers a perspective and tools to enable a better understanding of the dynamics of complex systems. This research focuses upon system dynamics methodology as a modelling and analysis tool in order to understand and identify the key drivers in the absorption of cloud computing for CSMEs. The aim of this paper is to determine how the use of system dynamics (SD) can improve the management of information flow through collaborative technologies leading to improved productivity. The data supporting the use of system dynamics was obtained through a pilot study consisting of questionnaires and interviews from five CSMEs in the UK house-building sector.

Be careful how you ask! Using focus groups and nominal group technique to explore the barriers to learning

Schools have a legal duty to make reasonable adjustments for disabled pupils who experience barriers to learning. Inclusive approaches to data collection ensure that the needs of all children who are struggling are not overlooked. However, it is important that the methods promote sustained reflection on the part of all children, do not inadvertently accentuate differences between pupils, and do not allow individual needs to go unrecognized. This paper examines more closely the processes involved in using Nominal Group Technique to collect the views of children with and without a disability on the difficulties experienced in school. Data were collected on the process as well as the outcomes of using this technique to examine how pupil views are transformed from the individual to the collective, a process that involves making the private, public. Contrasts are drawn with questionnaire data, another method of data collection favoured by teachers. Although more time-efficient this can produce unclear and cursory responses. The views that surface from pupils need also to be seen within the context of the ways in which schools customize the data collection process and the ways in which the format and organization of the activity impact on the responses and responsiveness of the pupils.

Mesh adaptation on the sphere using optimal transport and the numerical solution of a Monge-Ampère type equation

An equation of Monge-Ampère type has, for the first time, been solved numerically on the surface of the sphere in order to generate optimally transported (OT) meshes, equidistributed with respect to a monitor function. Optimal transport generates meshes that keep the same connectivity as the original mesh, making them suitable for r-adaptive simulations, in which the equations of motion can be solved in a moving frame of reference in order to avoid mapping the solution between old and new meshes and to avoid load balancing problems on parallel computers. The semi-implicit solution of the Monge-Ampère type equation involves a new linearisation of the Hessian term, and exponential maps are used to map from old to new meshes on the sphere. The determinant of the Hessian is evaluated as the change in volume between old and new mesh cells, rather than using numerical approximations to the gradients. OT meshes are generated to compare with centroidal Voronoi tesselations on the sphere and are found to have advantages and disadvantages; OT equidistribution is more accurate, the number of iterations to convergence is independent of the mesh size, face skewness is reduced and the connectivity does not change. However anisotropy is higher and the OT meshes are non-orthogonal. It is shown that optimal transport on the sphere leads to meshes that do not tangle. However, tangling can be introduced by numerical errors in calculating the gradient of the mesh potential. Methods for alleviating this problem are explored. Finally, OT meshes are generated using observed precipitation as a monitor function, in order to demonstrate the potential power of the technique.

Evaluation of simulated sea-ice concentrations from sea-ice/ocean models using satellite data and polynya classification methods

Sea-ice concentrations in the Laptev Sea simulated by the coupled North Atlantic-Arctic Ocean-Sea-Ice Model and Finite Element Sea-Ice Ocean Model are evaluated using sea-ice concentrations from Advanced Microwave Scanning Radiometer-Earth Observing System satellite data and a polynya classification method for winter 2007/08. While developed to simulate largescale sea-ice conditions, both models are analysed here in terms of polynya simulation. The main modification of both models in this study is the implementation of a landfast-ice mask. Simulated sea-ice fields from different model runs are compared with emphasis placed on the impact of this prescribed landfast-ice mask. We demonstrate that sea-ice models are not able to simulate flaw polynyas realistically when used without fast-ice description. Our investigations indicate that without landfast ice and with coarse horizontal resolution the models overestimate the fraction of open water in the polynya. This is not because a realistic polynya appears but due to a larger-scale reduction of ice concentrations and smoothed ice-concentration fields. After implementation of a landfast-ice mask, the polynya location is realistically simulated but the total open-water area is still overestimated in most cases. The study shows that the fast-ice parameterization is essential for model improvements. However, further improvements are necessary in order to progress from the simulation of large-scale features in the Arctic towards a more detailed simulation of smaller-scaled features (here polynyas) in an Arctic shelf sea.