A study to examine the operation and function of a virtual UK environmental specimen bank (UK-ESB). Final report

Executive Summary: 1. Environmental specimen banking is recognised internationally as an integral part of long-term environmental research and monitoring. Analysis of preserved environmental samples is often needed to detect and quantify patterns and rate of environmental change, and the emergence and progression of environmental hazards and risks. 2. National Environmental Specimen Banks have been established in several countries; they vary in scope and breadth. There are a few specialised environmental specimen holdings in the UK but no national-scale catalogue of holdings, despite an estimated annual spend of £16 million to store specimens. This lack of information results in under-exploitation of archived specimens and is a lost opportunity to facilitate world-class science and identify emerging pressures and threats on the environment. 3. An earlier project had identified key stakeholder organisations either engaged in archiving nationally important environmental specimens or who wished to utilise such specimens. These stakeholders had agreed there was a need for a national metadata catalogue of environmental specimens (subsequently termed a virtual UK-ESB). The objective of the current project was to further develop a virtual UK-ESB. Specifically, the aim was to work with stakeholders to establish the correct metadata entry fields, the search capabilities, the functionality and the nature of the hosting website of a virtual UK-ESB. 4. More than 80 stakeholder organisations that had previously expressed an interest in a UK-ESB were approached to provide feedback either electronically or by attending a stakeholder workshop. Thirty eight organisations responded. All remained interested in the UK-ESB concept and seventeen answered the survey questions. 5. Mock-ups of data entry screens, search screens and ideas around the functionality of a UK-ESB were developed by the CEH project team. These were mailed to stakeholders for feedback. Initial feedback was incorporated into the mock-ups which were then presented for discussion at a workshop comprising 15 attendees from across the specimen archiving community, CEH and the UK-EOF. 6. Workshop participants reviewed and agreed the format of 23 mandatory or optional data-entry fields for a virtual UK-ESB that, in the absence of standard for material samples and archives, were aligned with ISO19115 (geospatial metadata standard) and DublinCore (metadata standard). These fields were sub-divided into the following headings: Sample description, Categorisation, keywords and links, Storage Information and Contact information. Workshop participants also made a number of recommendations as to the format of the data entry screens and inclusion of extra fields. 7. Workshop participants reviewed options for search capabilities and made recommendations as to simple and advanced searching methods and their formats. It was also recommended that search facilities of the ESBs of other countries be examined to determine what is used, ease of use, and how they match the recommendations from the workshop. 8. Workshop participants reviewed options for functionality and agreed a detailed list of prioritised requirements. 9. Workshop participants agreed that a virtual UK-ESB should be hosted through a dedicated website that would also provide wider information, such as recently updated or added specimen holdings, most downloaded information, links to other groups, standard operating procedures, etc. 10. The next step for the development of a virtual UK-ESB is to implement the design and development ideas captured in the current report and build a test version of a virtual UK-ESB. This would be tested and refined, and could then be launched on a specifically designed website. This would need to be accompanied by a communication strategy. There is potential to link and co-brand a virtual UK-ESB with the UK-Environmental Observation Framework (UK-EOF)

Hurst spit stabilisation: a partnering case study

The stabilization of a 2 km shingle spit in southern England was initially planned as a traditional civil engineering contract. However, an unforseen delay at the start meant there was a real danger of not completing the work before winter storms, so a partnering approach was introduced - with successful results. This paper starts off by investigating the potential of partnering to achieve the UK's construction improvement targets. Using Hurst Spit as a case study it demonstrates that partnering can provide significant benefits for a one-off project without the need for formal agreements. It analyses in particular the culture changes which are required to achieve the full benefits of a partnering way of working

Vanishing Gamow-Teller Transition Rate for A=14 and the Nucleon-Nucleon Interaction in the Medium

The problem of the near vanishing of the Gamow-Teller transition ($GT$) in the A=14 system between the lowest $J=0^+~ T=1$ and $J=1^+~ T=0$ states is revisited. The model space is extended from the valence space $(p^{-2})$ to the valence space plus all 2$\hbar \omega$ excitations. The question is addressed as to what features of the effective nucleon-nucleon interaction in the medium are required to obtain the vanishing $GT$ strength in this extended space. It turns out that a combination of a realistic strength of the tensor force combined with a spin-orbit interaction which is enhanced as compared to the free interaction yields a vanishing $GT$ strength. Such an interaction can be derived from a microscopic meson exchange potential if the enhancement of the small component of the Dirac spinors for the nucleons is taken into account.Comment: RevTex file, 7 pages, four postscript figures. submitted to Phys. Rev. C as a brief repor

Structural and functional properties of glutamate dehydrogenases

Glutamate dehydrogenases are homooligomeric enzymes that catalyse the reversible oxidative deamination of glutamate to 2-oxoglutarate, thereby linking nitrogen metabolism and the tricarboxylic acid cycle. Four different classes of the enzyme are known in microbes that differ in size and cofactor specificity. Despite some common features, the kinetic properties of the enzymes from different species vary considerably. We consider the relationship between the sequences, those structures that are available and the enzyme kinetics in the context of the metabolic role of the enzyme

The implications of alternative developer decision-making strategies on land-use and land-cover in an agent-based land market model

Land developers play a key role in land-use and land cover change, as\ud they directly make land development decisions and bridge the land and housing\ud markets. Developers choose and purchase land from rural land owners, develop\ud and subdivide land into parcel lots, build structures on lots, and sell houses to residential households. Developers determine the initial landscaping states of developed parcels, affecting the state and future trajectories of residential land cover, as well as land market activity. Despite their importance, developers are underrepresented in land use change models due to paucity of data and knowledge regarding their decision-making. Drawing on economic theories and empirical literature, we have developed a generalized model of land development decision-making within a broader agent-based model of land-use change via land markets. Developer’s strategies combine their specialty in developing of particular subdivision types, their perception of and attitude towards market uncertainty, and their learning and adaptation strategies based on the dynamics of the simulated land and housing markets. We present a new agent-based land market model that includes these elements. The model will be used to experiment with these different development decision-making methods and compare their impacts on model outputs, particularly on the quantity and spatial pattern of resultant land use changes. Coupling between the land market and a carbon sequestration model, developed for the larger SLUCE2 project, will allow us, in future work, to examine how different developer’s strategies will affect the carbon balance in residential\ud landscape

In silico design of context-responsive mammalian promoters with user-defined functionality

Comprehensive de novo-design of complex mammalian promoters is restricted by unpredictable combinatorial interactions between constituent transcription factor regulatory elements (TFREs). In this study, we show that modular binding sites that do not function cooperatively can be identified by analyzing host cell transcription factor expression profiles, and subsequently testing cognate TFRE activities in varying homotypic and heterotypic promoter architectures. TFREs that displayed position-insensitive, additive function within a specific expression context could be rationally combined together in silico to create promoters with highly predictable activities. As TFRE order and spacing did not affect the performance of these TFRE-combinations, compositions could be specifically arranged to preclude the formation of undesirable sequence features. This facilitated simple in silico-design of promoters with context-required, user-defined functionalities. To demonstrate this, we de novo-created promoters for biopharmaceutical production in CHO cells that exhibited precisely designed activity dynamics and long-term expression-stability, without causing observable retroactive effects on cellular performance. The design process described can be utilized for applications requiring context-responsive, customizable promoter function, particularly where co-expression of synthetic TFs is not suitable. Although the synthetic promoter structure utilized does not closely resemble native mammalian architectures, our findings also provide additional support for a flexible billboard model of promoter regulation

Correlation between the quenching of total GT+ strength and the increase of E2 strength

Relations between the total beta+ Gamow-Teller (GT+) strength and the E2 strength are further examined. It is found that in shell-model calculations for N=Z nuclei, in which changes in deformation are induced by varying the single-particle energies, the total GT+ or GT- strength decreases monotonically with increasing values of the B(E2) from the ground state to the first excited J=2+ state. Similar trends are also seen for the double GT transition amplitude (with some exceptions) and for the spin part of the total M1 strength as a function of B(E2).Comment: 11 pages and 3 figures (Figures will be sent on request

The response to high magnetic fields of the vacuum phototriodes for the compact muon solenoid endcap electromagnetic calorimeter

The endcap electromagnetic calorimeter of the Compact Muon Solenoid (CMS) detects particles with the dense fast scintillator lead tungstate (PbWO4). Due to the low light yield of this scintillator photodetectors with internal gain are required. Silicon avalanche photodiodes cannot be used in the endcap region due to the intense neutron flux. Following an extensive R&D programme 26 mm diameter single-stage photomultipliers (vacuum phototriodes) have been chosen as the photodetector in the endcap region. The first 1400 production devices are currently being evaluated following recent tests of a pre-production batch of 500 tubes. Tubes passing our acceptance tests have responses, averaged over the angular acceptance of the endcap calorimeter, corresponding to the range 20 to 55 electrons per MeV deposited in PbWO4. These phototriodes operate, with a typical gain of 10, in magnetic fields up to 4T.PPARC, EC(INTAS-CERN scheme 99-424

Camera distortion self-calibration using the plumb-line constraint and minimal Hough entropy

In this paper we present a simple and robust method for self-correction of camera distortion using single images of scenes which contain straight lines. Since the most common distortion can be modelled as radial distortion, we illustrate the method using the Harris radial distortion model, but the method is applicable to any distortion model. The method is based on transforming the edgels of the distorted image to a 1-D angular Hough space, and optimizing the distortion correction parameters which minimize the entropy of the corresponding normalized histogram. Properly corrected imagery will have fewer curved lines, and therefore less spread in Hough space. Since the method does not rely on any image structure beyond the existence of edgels sharing some common orientations and does not use edge fitting, it is applicable to a wide variety of image types. For instance, it can be applied equally well to images of texture with weak but dominant orientations, or images with strong vanishing points. Finally, the method is performed on both synthetic and real data revealing that it is particularly robust to noise.Comment: 9 pages, 5 figures Corrected errors in equation 1

Orbital evolution of P\v{r}\'{i}bram and Neuschwanstein

The orbital evolution of the two meteorites P\v{r}\'{i}bram and Neuschwanstein on almost identical orbits and also several thousand clones were studied in the framework of the N-body problem for 5000 years into the past. The meteorites moved on very similar orbits during the whole investigated interval. We have also searched for photographic meteors and asteroids moving on similar orbits. There were 5 meteors found in the IAU MDC database and 6 NEAs with currently similar orbits to P\v{r}\'{i}bram and Neuschwanstein. However, only one meteor 161E1 and one asteroid 2002 QG46 had a similar orbital evolution over the last 2000 years.Comment: 7 pages, 2 figures, 3 table