Immersive Projection for biochemical pattern matching

In all biological processes, protein molecules and other small molecules interact to function and form transient macromolecular complexes. This interaction of two or more molecules can be described by a docking event. Docking is an important phase for structure-based drug design strategies, as it can be used as a method to simulate protein-ligand interactions. Various docking programs exist that allow automated docking, but most of them have limited visualization and user interaction. It would be advantageous if scientists could visualize the molecules participating in the docking process, manipulate their structures and manually dock them before submitting the new conformations to an automated docking process in an immersive environment, which can help stimulate the design/docking process. This also could greatly reduce docking time and resources. To achieve this, we propose a new virtual modelling/docking program, whereby the advantages of virtual modelling programs and the efficiency of the algorithms in existing docking programs will be merged.

Estimating surface CO2 fluxes from space-borne dry air mole fraction observations using an Ensemble Kalman filter

We have developed an ensemble Kalman Filter (EnKF) to estimate 8-day regional surface fluxes of CO2 from space-borne CO2 dry-air mole fraction observations (XCO2) and evaluate the approach using a series of synthetic experiments, in preparation for data from the NASA Orbiting Carbon Observatory (OCO). The 32-day duty cycle of OCO alternates every 16 days between nadir and glint measurements of backscattered solar radiation at short-wave infrared wavelengths. The EnKF uses an ensemble of states to represent the error covariances to estimate 8-day CO2 surface fluxes over 144 geographical regions. We use a 12×8-day lag window, recognising that XCO2 measurements include surface flux information from prior time windows. The observation operator that relates surface CO2 fluxes to atmospheric distributions of XCO2 includes: a) the GEOS-Chem transport model that relates surface fluxes to global 3-D distributions of CO2 concentrations, which are sampled at the time and location of OCO measurements that are cloud-free and have aerosol optical depths <0.3; and b) scene-dependent averaging kernels that relate the CO2 profiles to XCO2, accounting for differences between nadir and glint measurements, and the associated scene-dependent observation errors. We show that OCO XCO2 measurements significantly reduce the uncertainties of surface CO2 flux estimates. Glint measurements are generally better at constraining ocean CO2 flux estimates. Nadir XCO2 measurements over the terrestrial tropics are sparse throughout the year because of either clouds or smoke. Glint measurements provide the most effective constraint for estimating tropical terrestrial CO2 fluxes by accurately sampling fresh continental outflow over neighbouring oceans. We also present results from sensitivity experiments that investigate how flux estimates change with 1) bias and unbiased errors, 2) alternative duty cycles, 3) measurement density and correlations, 4) the spatial resolution of estimated flux estimates, and 5) reducing the length of the lag window and the size of the ensemble. At the revision stage of this manuscript, the OCO instrument failed to reach its orbit after it was launched on 24 February 2009. The EnKF formulation presented here is also applicable to GOSAT measurements of CO2 and CH4.

Diversity and difference in the everyday lives of Ugandan street children: The significance of age and gender for understanding the use of space

Childhood is characterised by diversity and difference across and within societies. Street children have a unique relationship to the urban environment evident through their use of the city. The everyday geographies that street children produce are diversified through the spaces they frequent and the activities they engage in. Drawing on a range of children-centred qualitative methods, this article focuses on street children's use of urban space in Kampala, Uganda. The article demonstrates the importance of considering variables such as gender and age in the analysis of street children's socio-spatial experiences, which, to date, have rarely been considered in other accounts of street children's lives. In addition the article highlights the need for also including street children's individuality and agency into understanding their use of space. The article concludes by arguing for policies to be sensitive to the diversity that characterises street children's lives and calls for a more nuanced approach where policies are designed to accommodate street children's age and gender differences, and their individual needs, interests and abilities.

Microbial perchlorate reduction: A precise laboratory determination of the chlorine isotope fractionation and its possible biochemical basis

Perchlorate-reducing bacteria fractionate chlorine stable isotopes giving a powerful approach to monitor the extent of microbial consumption of perchlorate in contaminated sites undergoing remediation or natural perchlorate containing sites. This study reports the full experimental data and methodology used to re-evaluate the chlorine isotope fractionation of perchlorate reduction in duplicate culture experiments of Azospira suillum strain PS at 37 degrees C (Delta Cl-37(Cr)--ClO4-) previously reported, without a supporting data set by Coleman et al. [Coleman, M.L., Ader, M., Chaudhuri, S., Coates,J.D., 2003. Microbial Isotopic Fractionation of Perchlorate Chlorine. Appl. Environ. Microbiol. 69, 4997-5000] in a reconnaissance study, with the goal of increasing the accuracy and precision of the isotopic fractionation determination. The method fully described here for the first time, allows the determination of a higher precision Delta Cl-37(Cl)--ClO4- value, either from accumulated chloride content and isotopic composition or from the residual perchlorate content and isotopic composition. The result sets agree perfectly, within error, giving average Delta Cl-37(Cl)--ClO4- = -14.94 +/- 0.15%omicron. Complementary use of chloride and perchlorate data allowed the identification and rejection of poor quality data by applying mass and isotopic balance checks. This precise Delta Cl-37(Cl)--ClO4-, value can serve as a reference point for comparison with future in situ or microcosm studies but we also note its similarity to the theoretical equilibrium isotopic fractionation between a hypothetical chlorine species of redox state +6 and perchlorate at 37 degrees C and suggest that the first electron transfer during perchlorate reduction may occur at isotopic equilibrium between art enzyme-bound chlorine and perchlorate. (C) 2008 Elsevier B.V. All rights reserved.

Microbial and biochemical soil quality indicators and their potential for differentiating areas under contrasting agricultural management regimes

The aim of this study was to examine interrelationships between functional biochemical and microbial indicators of soil quality, and their suitability to differentiate areas under contrasting agricultural management regimes. The study included five 0.8 ha areas on a sandy-loam soil which had received contrasting fertility and cropping regimes over a 5 year period. These were organically managed vegetable, vegetable -cereal and arable rotations, an organically managed grass clover ley, and a conventional cereal rotation. The organic areas had been converted from conventional cereal production 5 years prior to the start of the study. All of the biochemical analyses, including light fraction organic matter (LFOM) C and N, labile organic N (LON), dissolved organic N and water-soluble carbohydrates showed significant differences between the areas, although the nature of the relationships between the areas varied between the different parameters, and were not related to differences in total soil organic matter content. The clearest differences were seen in LFOM C and N and LON, which were higher in the organic arable area relative to the other areas. In the case of the biological parameters, there were differences between the areas for biomass-N, ATP, chitin content, and the ratios of ATP: biomass and basal respiration: biomass. For these parameters, the precise relationships between the areas varied. However, relative to the conventionally managed area, areas under organic management generally had lower biomass-N and higher ATP contents. Arbuscular mycorrhizal fungus colonization potential was extremely low in the conventional area relative to the organic areas. Further, metabolic diversity and microbial community level physiological profiles, determined by analysis of microbial community metabolism using Biolog GN plates and the activities of eight key nutrient cycling enzymes, grouped the organic areas together, but separated them from the conventional area. We conclude that microbial parameters are more effective and consistent indicators of management induced changes to soil quality than biochemical parameters, and that a variety of biochemical and microbial analyses should be used when considering the impact of management on soil quality. (C) 2004 Elsevier Ltd. All rights reserved.

Remaking place and securitising space: Urban regeneration and the strategies, tactics and practices of policing in the UK

Urban regeneration programmes in the UK over the past 20 years have increasingly focused on attracting investors, middle-class shoppers and visitors by transforming places and creating new consumption spaces. Ensuring that places are safe and are seen to be safe has taken on greater salience as these flows of income are easily disrupted by changing perceptions of fear and the threat of crime. At the same time, new technologies and policing strategies and tactics have been adopted in a number of regeneration areas which seek to establish control over these new urban spaces. Policing space is increasingly about controlling human actions through design, surveillance technologies and codes of conduct and enforcement. Regeneration agencies and the police now work in partnerships to develop their strategies. At its most extreme, this can lead to the creation of zero-tolerance, or what Smith terms 'revanchist', measures aimed at particular social groups in an effort to sanitise space in the interests of capital accumulation. This paper, drawing on an examination of regeneration practices and processes in one of the UK's fastest-growing urban areas, Reading in Berkshire, assesses policing strategies and tactics in the wake of a major regeneration programme. It documents and discusses the discourses of regeneration that have developed in the town and the ways in which new urban spaces have been secured. It argues that, whilst security concerns have become embedded in institutional discourses and practices, the implementation of security measures has been mediated, in part, by the local socio-political relations in and through which they have been developed.

Changing times, changing places: urban development and the politics of space - time

Much of the writing on urban regeneration in the UK has been focused on the types of urban spaces that have been created in city centres. Less has been written about the issue of when the benefits of regeneration could and should be delivered to a range of different interests, and the different time frames that exist in any development area. Different perceptions of time have been reflected in dominant development philosophies in the UK and elsewhere. The trickle-down agendas of the 1980s, for example, were criticised for their focus on the short-term time frames and needs of developers, often at the expense of those of local communities. The recent emergence of sustainability discourses, however, ostensibly changes the time focus of development and promotes a broader concern with new imagined futures. This paper draws on the example of development in Salford Quays, in the North West of England, to argue that more attention needs to be given to the politics of space-time in urban development processes. It begins by discussing the importance and relevance of this approach before turning to the case study and the ways in which the local politics of space-time has influenced development agendas and outcomes. The paper argues that such an approach harbours the potential for more progressive, far-reaching, and sustainable development agendas to be developed and implemented.

Diversity and difference in the everyday lives of Ugandan street children: The significance of age and gender for understanding the use of space

Childhood is characterised by diversity and difference across and within societies. Street children have a unique relationship to the urban environment evident through their use of the city. The everyday geographies that street children produce are diversified through the spaces they frequent and the activities they engage in. Drawing on a range of children-centred qualitative methods, this article focuses on street children's use of urban space in Kampala, Uganda. The article demonstrates the importance of considering variables such as gender and age in the analysis of street children's socio-spatial experiences, which, to date, have rarely been considered in other accounts of street children's lives. In addition the article highlights the need for also including street children's individuality and agency into understanding their use of space. The article concludes by arguing for policies to be sensitive to the diversity that characterises street children's lives and calls for a more nuanced approach where policies are designed to accommodate street children's age and gender differences, and their individual needs, interests and abilities.

Space-efficient Indexing of Chess Endgame Tables

Chess endgame tables should provide efficiently the value and depth of any required position during play. The indexing of an endgame’s positions is crucial to meeting this objective. This paper updates Heinz’ previous review of approaches to indexing and describes the latest approach by the first and third authors. Heinz’ and Nalimov’s endgame tables (EGTs) encompass the en passant rule and have the most compact index schemes to date. Nalimov’s EGTs, to the Distance-to-Mate (DTM) metric, require only 30.6 × 10^9 elements in total for all the 3-to-5-man endgames and are individually more compact than previous tables. His new index scheme has proved itself while generating the tables and in the 1999 World Computer Chess Championship where many of the top programs used the new suite of EGTs.

Space-efficient indexing of endgame tables for chess

Chess endgame tables should provide efficiently the value and depth of any required position during play. The indexing of an endgame’s positions is crucial to meeting this objective. This paper updates Heinz’ previous review of approaches to indexing and describes the latest approach by the first and third authors. Heinz’ and Nalimov’s endgame tables (EGTs) encompass the en passant rule and have the most compact index schemes to date. Nalimov’s EGTs, to the Distance-to-Mate (DTM) metric, require only 30.6 × 109 elements in total for all the 3-to-5-man endgames and are individually more compact than previous tables. His new index scheme has proved itself while generating the tables and in the 1999 World Computer Chess Championship where many of the top programs used the new suite of EGTs.

Influences of space, soil, nematodes and plants on microbial community composition of chalk grassland soils

Microbial communities respond to a variety of environmental factors related to resources (e.g. plant and soil organic matter), habitat (e.g. soil characteristics) and predation (e.g. nematodes, protozoa and viruses). However, the relative contribution of these factors on microbial community composition is poorly understood. Here, we sampled soils from 30 chalk grassland fields located in three different chalk hill ridges of Southern England, using a spatially explicit sampling scheme. We assessed microbial communities via phospholipid fatty acid (PLFA) analyses and PCR-denaturing gradient gel electrophoresis (DGGE) and measured soil characteristics, as well as nematode and plant community composition. The relative influences of space, soil, vegetation and nematodes on soil microorganisms were contrasted using variation partitioning and path analysis. Results indicate that soil characteristics and plant community composition, representing habitat and resources, shape soil microbial community composition, whereas the influence of nematodes, a potential predation factor, appears to be relatively small. Spatial variation in microbial community structure was detected at broad (between fields) and fine (within fields) scales, suggesting that microbial communities exhibit biogeographic patterns at different scales. Although our analysis included several relevant explanatory data sets, a large part of the variation in microbial communities remained unexplained (up to 92% in some analyses). However, in several analyses, significant parts of the variation in microbial community structure could be explained. The results of this study contribute to our understanding of the relative importance of different environmental and spatial factors in driving the composition of soil-borne microbial communities.