PPD v1.0—an integrated, web-accessible database of experimentally determined protein pK(a) values

The Protein pK(a) Database (PPD) v1.0 provides a compendium of protein residue-specific ionization equilibria (pK(a) values), as collated from the primary literature, in the form of a web-accessible postgreSQL relational database. Ionizable residues play key roles in the molecular mechanisms that underlie many biological phenomena, including protein folding and enzyme catalysis. The PPD serves as a general protein pK(a) archive and as a source of data that allows for the development and improvement of pK(a) prediction systems. The database is accessed through an HTML interface, which offers two fast, efficient search methods: an amino acid-based query and a Basic Local Alignment Search Tool search. Entries also give details of experimental techniques and links to other key databases, such as National Center for Biotechnology Information and the Protein Data Bank, providing the user with considerable background information. The database can be found at the following URL:

From catchment to national scale rainfall-runoff modelling: demonstration of a hydrological modelling framework

The increasing availability of digital databases (e.g. of climatology, topography, soils and land use) has enabled research into the generalisation of hydrological model parameter values from physical properties and the development of grid-based models. A hydrological modelling framework (HMF) is being developed to exploit this generalisation and provide a flexible gridded infrastructure, operational over regional, national or larger scales at a range of spatial and temporal resolutions. The capability of the framework is demonstrated through adaptation of an existing semi-distributed catchment-based rainfall-runoff model, CLASSIC, for which a generalised methodology exists to determine parameter values. The main change required was to ensure consistency of parameter values between the runoff procedure in CLASSIC and flow routing in the HMF. Assessment is by comparison of modelled and observed flow at grid points in Britain corresponding to gauging stations, both for catchments previously modelled and for new locations, for a range of catchment areas and physical properties and for four spatial resolutions (10, 5, 2.5 and 1 km). Good model performance is achieved for 90% of catchments tested, with a 5 km resolution proving adequate for catchments larger than 500 km2. Applications are outlined for which the framework could be used to test alternative modelling approaches or undertake consistent studies across the range of resolutions

The Impact of the Menai Bay Marine Protected Area on the Livelihoods of Small Scale Fishing Communities on Zanzibar, Tanzania

This paper presents the findings of a field survey carried out within small scale fishing communities on the island of Zanzibar in 2004. The study was designed to assess the impact of the Menai Bay marine protected area on the livelihoods of fishing households located within its boundaries using the sustainable livelihoods approach (SLA) as its basis. The survey finds that although the MPA helped to reduce conflict between fishermen and provided the impetus for establishing a local management framework, pressures on natural resources caused by factors largely outside the control of the MPA management system, may have suppressed some of the biological or economic benefits that the designation could have conveyed

A national-scale seasonal hydrological forecast system: development and evaluation over Britain

Skilful winter seasonal predictions for the North Atlantic circulation and northern Europe have now been demonstrated and the potential for seasonal hydrological forecasting in the UK is now being explored. One of the techniques being used combines seasonal rainfall forecasts provided by operational weather forecast systems with hydrological modelling tools to provide estimates of seasonal mean river flows up to a few months ahead. The work presented here shows how spatial information contained in a distributed hydrological model typically requiring high-resolution (daily or better) rainfall data can be used to provide an initial condition for a much simpler forecast model tailored to use low-resolution monthly rainfall forecasts. Rainfall forecasts (“hindcasts”) from the GloSea5 model (1996 to 2009) are used to provide the first assessment of skill in these national-scale flow forecasts. The skill in the combined modelling system is assessed for different seasons and regions of Britain, and compared to what might be achieved using other approaches such as use of an ensemble of historical rainfall in a hydrological model, or a simple flow persistence forecast. The analysis indicates that only limited forecast skill is achievable for Spring and Summer seasonal hydrological forecasts; however, Autumn and Winter flows can be reasonably well forecast using (ensemble mean) rainfall forecasts based on either GloSea5 forecasts or historical rainfall (the preferred type of forecast depends on the region). Flow forecasts using ensemble mean GloSea5 rainfall perform most consistently well across Britain, and provide the most skilful forecasts overall at the 3-month lead time. Much of the skill (64 %) in the 1-month ahead seasonal flow forecasts can be attributed to the hydrological initial condition (particularly in regions with a significant groundwater contribution to flows), whereas for the 3-month ahead lead time, GloSea5 forecasts account for  ∼ 70 % of the forecast skill (mostly in areas of high rainfall to the north and west) and only 30 % of the skill arises from hydrological memory (typically groundwater-dominated areas). Given the high spatial heterogeneity in typical patterns of UK rainfall and evaporation, future development of skilful spatially distributed seasonal forecasts could lead to substantial improvements in seasonal flow forecast capability, potentially benefitting practitioners interested in predicting hydrological extremes, not only in the UK but also across Europe

Spatially consistent physical characteristics of UK rivers: 1‐km data

The physical river characteristics datasets described here provide spatially consistent information to support hydrological and inundation modelling at a 1 km × 1 km resolution across the United Kingdom, on the British National Grid. The datasets of physical river characteristics provide gridded datasets (outflow drainage directions, catchment areas, widths of bankfull rivers and depths of bankfull rivers) and a comma-separated table of NRFA (National River Flow Archive) gauging station locations. These datasets are derived from a range of sources: outflow drainage directions, catchment area and bankfull river widths are derived from existing higher resolution datasets, whereas bankfull river depths were harder to source and instead are derived from sparse historical measurements. The new gridded datasets provide a derived value for each UK land cell on the British National Grid (BNG). The comma-separated NRFA gauging station locations table provides the most appropriate locations of 1,499 river flow gauging stations on the 1 km resolution grids, together with the approximate error in the 1 km × 1 km gridded delineation of the upstream catchment area. This article explains how UK-wide 1-km grids of these variables were estimated, their format and how to use them. The data are available from the Environmental Information Data Centre (EIDC)

Identities in the Superintegrable Chiral Potts Model

We present proofs for a number of identities that are needed to study the superintegrable chiral Potts model in the $Q\ne0$ sector.Comment: LaTeX 2E document, using iopart.cls with iopams packages. 11 pages, uses eufb10 and eurm10 fonts. Typeset twice! vs2: Two equations added. vs3: Introduction adde

How might climate change affect river flows across West Africa?

West Africa and its semi-arid Sahelian region are one of the world’s most vulnerable regions to climate change with a history of extreme climate variability. There is still considerable uncertainty as to how projected climate change will affect precipitation at local and regional scales and the consequent impact on river flows and water resources across West Africa. Here, we aim to address this uncertainty by configuring a regional-scale hydrological model to West Africa. The model (hydrological modelling framework for West Africa—HMF-WA) simulates spatially consistent river flows on a 0.1° × 0.1° grid (approximately 10 km × 10 km) continuously across the whole domain and includes estimates of anthropogenic water use, wetland inundation, and local hydrological features such as endorheic regions. Regional-scale hydrological simulations driven by observed weather data are assessed against observed flows before undertaking an analysis of the impact of projected future climate scenarios from the CMIP5 on river flows up to the end of the twenty-first century. The results indicate that projected future changes in river flows are highly spatially variable across West Africa, particularly across the Sahelian region where the predicted changes are more pronounced. The study shows that median peak flows are projected to decrease by 23% in the west (e.g. Senegal) and increase by 80% in the eastern region (e.g. Chad) by the 2050s. The projected reductions in river flows in western Sahel lead to future droughts and water shortages more likely, while in the eastern Sahel, projected increases lead to future frequent floods

Eigenvectors in the Superintegrable Model I: sl_2 Generators

In order to calculate correlation functions of the chiral Potts model, one only needs to study the eigenvectors of the superintegrable model. Here we start this study by looking for eigenvectors of the transfer matrix of the periodic tau_2(t)model which commutes with the chiral Potts transfer matrix. We show that the degeneracy of the eigenspace of tau_2(t) in the Q=0 sector is 2^r, with r=(N-1)L/N when the size of the transfer matrix L is a multiple of N. We introduce chiral Potts model operators, different from the more commonly used generators of quantum group U-tilde_q(sl-hat(2)). From these we can form the generators of a loop algebra L(sl(2)). For this algebra, we then use the roots of the Drinfeld polynomial to give new explicit expressions for the generators representing the loop algebra as the direct sum of r copies of the simple algebra sl(2).Comment: LaTeX 2E document, 11 pages, 1 eps figure, using iopart.cls with graphicx and iopams packages. v2: Appended text to title, added acknowledgments and made several minor corrections v3: Added reference, eliminated ambiguity, corrected a few misprint

Engaging Opportunities: Connecting young people with contemporary research and researchers

This is the final report for ‘Engaging Opportunities’, an RCUK-funded School-University Partnership between the Open University and the Denbigh Teaching School Alliance. Informed by action research, this four-year project was designed to create structured, strategic, sustainable and equitable mechanisms for effective school-university engagement with research. The report describes an evidence-based strategy designed to embed school-university engagement with research within the University’s strategic planning for research and the operational practices of researchers. Through the early stages of our partnership we noted a lack of suitable planning tools that work for researchers, teachers and students. We therefore introduced a flexible and adaptable framework of four types of activity—open lectures, open dialogues, open inquiry and open creativity—combined with an upstream approach to planning based on a set of six principles. A sub-set of these activities were evaluated through a combination of surveys, interviews and interventions. In conclusion, we argue that institutional and professional cultures can be resistant to the prospect of fully embedding school-university engagement with research in a structured, strategic and sustainable manner, and offer suggestions for how this context could and should be changed