SANS/WANS time-resolving neutron scattering studies of polymer phase transitions using NIMROD

We use new neutron scattering instrumentation to follow in a single quantitative time-resolving experiment, the three key scales of structural development which accompany the crystallisation of synthetic polymers. These length scales span 3 orders of magnitude of the scattering vector. The study of polymer crystallisation dates back to the pioneering experiments of Keller and others who discovered the chain-folded nature of the thin lamellae crystals which are normally found in synthetic polymers. The inherent connectivity of polymers makes their crystallisation a multiscale transformation. Much understanding has developed over the intervening fifty years but the process has remained something of a mystery. There are three key length scales. The chain folded lamellar thickness is ~ 10nm, the crystal unit cell is ~ 1nm and the detail of the chain conformation is ~ 0.1nm. In previous work these length scales have been addressed using different instrumention or were coupled using compromised geometries. More recently researchers have attempted to exploit coupled time-resolved small-angle and wide-angle x-ray experiments. These turned out to be challenging experiments much related to the challenge of placing the scattering intensity on an absolute scale. However, they did stimulate the possibility of new phenomena in the very early stages of crystallisation. Although there is now considerable doubt on such experiments, they drew attention to the basic question as to the process of crystallisation in long chain molecules. We have used NIMROD on the second target station at ISIS to follow all three length scales in a time-resolving manner for poly(e-caprolactone). The technique can provide a single set of data from 0.01 to 100Å-1 on the same vertical scale. We present the results using a multiple scale model of the crystallisation process in polymers to analyse the results.

Using synoptic type analysis to understand New Zealand climate during the Mid-Holocene

Diagnosing the climate of New Zealand from low-resolution General Circulation Models (GCMs) is notoriously difficult due to the interaction of the complex topography and the Southern Hemisphere (SH) mid-latitude westerly winds. Therefore, methods of downscaling synoptic scale model data for New Zealand are useful to help understand past climate. New Zealand also has a wealth of palaeoclimate-proxy data to which the downscaled model output can be compared, and to provide a qualitative method of assessing the capability of GCMs to represent, in this case, the climate 6000 yr ago in the Mid-Holocene. In this paper, a synoptic weather and climate regime classification system using Empirical Orthogonal Function (EOF) analysis of GCM and reanalysis data was used. The climate regimes are associated with surface air temperature and precipitation anomalies over New Zealand. From the analysis in this study, we find at 6000 BP that increased trough activity in summer and autumn led to increased precipitation, with an increased north-south pressure gradient ("zonal events") in winter and spring leading to drier conditions. Opposing effects of increased (decreased) temperature are also seen in spring (autumn) in the South Island, which are associated with the increased zonal (trough) events; however, the circulation induced changes in temperature are likely to have been of secondary importance to the insolation induced changes. Evidence from the palaeoclimate-proxy data suggests that the Mid-Holocene was characterized by increased westerly wind events in New Zealand, which agrees with the preference for trough and zonal regimes in the models.

Nature of vegetation and building morphology characteristics across a city: influence on shadow patterns and mean radiant temperatures in London

Vegetation and building morphology characteristics are investigated at 19 sites on a north-south LiDAR transect across the megacity of London. Local maxima of mean building height and building plan area density at the city centre are evident. Surprisingly, the mean vegetation height (zv3) is also found to be highest in the city centre. From the LiDAR data various morphological parameters are derived as well as shadow patterns. Continuous images of the effects of buildings and of buildings plus vegetationon sky view factor (Ψ) are derived. A general reduction of Ψ is found, indicating the importance of including vegetation when deriving Ψ in urban areas. The contribution of vegetation to the shadowing at ground level is higher during summer than in autumn. Using these 3D data the influence on urban climate and mean radiant temperature (T mrt ) is calculated with SOLWEIG. The results from these simulations highlight that vegetation can be most effective at reducing heat stress within dense urban environments in summer. The daytime average T mrt is found to be lowest in the densest urban environments due to shadowing; foremost from buildings but also from trees. It is clearly shown that this method could be used to quantify the influence of vegetation on T mrt within the urban environment. The results presented in this paper highlight a number of possible climate sensitive planning practices for urban areas at the local scale (i.e. 102- 5 × 103 m).

Modelling of urban sensible heat flux at multiple spatial scales : a demonstration using airborne hyperspectral imagery of Shanghai and a temperature–emissivity separation approach

Urbanization related alterations to the surface energy balance impact urban warming (‘heat islands’), the growth of the boundary layer, and many other biophysical processes. Traditionally, in situ heat flux measures have been used to quantify such processes, but these typically represent only a small local-scale area within the heterogeneous urban environment. For this reason, remote sensing approaches are very attractive for elucidating more spatially representative information. Here we use hyperspectral imagery from a new airborne sensor, the Operative Modular Imaging Spectrometer (OMIS), along with a survey map and meteorological data, to derive the land cover information and surface parameters required to map spatial variations in turbulent sensible heat flux (QH). The results from two spatially-explicit flux retrieval methods which use contrasting approaches and, to a large degree, different input data are compared for a central urban area of Shanghai, China: (1) the Local-scale Urban Meteorological Parameterization Scheme (LUMPS) and (2) an Aerodynamic Resistance Method (ARM). Sensible heat fluxes are determined at the full 6 m spatial resolution of the OMIS sensor, and at lower resolutions via pixel aggregation and spatial averaging. At the 6 m spatial resolution, the sensible heat flux of rooftop dominated pixels exceeds that of roads, water and vegetated areas, with values peaking at ∼ 350 W m− 2, whilst the storage heat flux is greatest for road dominated pixels (peaking at around 420 W m− 2). We investigate the use of both OMIS-derived land surface temperatures made using a Temperature–Emissivity Separation (TES) approach, and land surface temperatures estimated from air temperature measures. Sensible heat flux differences from the two approaches over the entire 2 × 2 km study area are less than 30 W m− 2, suggesting that methods employing either strategy maybe practica1 when operated using low spatial resolution (e.g. 1 km) data. Due to the differing methodologies, direct comparisons between results obtained with the LUMPS and ARM methods are most sensibly made at reduced spatial scales. At 30 m spatial resolution, both approaches produce similar results, with the smallest difference being less than 15 W m− 2 in mean QH averaged over the entire study area. This is encouraging given the differing architecture and data requirements of the LUMPS and ARM methods. Furthermore, in terms of mean study QH, the results obtained by averaging the original 6 m spatial resolution LUMPS-derived QH values to 30 and 90 m spatial resolution are within ∼ 5 W m− 2 of those derived from averaging the original surface parameter maps prior to input into LUMPS, suggesting that that use of much lower spatial resolution spaceborne imagery data, for example from Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) is likely to be a practical solution for heat flux determination in urban areas.

Linking urban water balance and energy balance models to analyse urban design options

Using a water balance modelling framework, this paper analyses the effects of urban design on the water balance, with a focus on evapotranspiration and storm water. First, two quite different urban water balance models are compared: Aquacycle which has been calibrated for a suburban catchment in Canberra, Australia, and the single-source urban evapotranspiration-interception scheme (SUES), an energy-based approach with a biophysically advanced representation of interception and evapotranspiration. A fair agreement between the two modelled estimates of evapotranspiration was significantly improved by allowing the vegetation cover (leaf area index, LAI) to vary seasonally, demonstrating the potential of SUES to quantify the links between water sensitive urban design and microclimates and the advantage of comparing the two modelling approaches. The comparison also revealed where improvements to SUES are needed, chiefly through improved estimates of vegetation cover dynamics as input to SUES, and more rigorous parameterization of the surface resistance equations using local-scale suburban flux measurements. Second, Aquacycle is used to identify the impact of an array of water sensitive urban design features on the water balance terms. This analysis confirms the potential to passively control urban microclimate by suburban design features that maximize evapotranspiration, such as vegetated roofs. The subsequent effects on daily maximum air temperatures are estimated using an atmospheric boundary layer budget. Potential energy savings of about 2% in summer cooling are estimated from this analysis. This is a clear ‘return on investment’ of using water to maintain urban greenspace, whether as parks distributed throughout an urban area or individual gardens or vegetated roofs.

Recent climatic trends and linkages to river discharge in Central Vietnam

In this study, change in rainfall, temperature and river discharge are analysed over the last three decades in Central Vietnam. Trends and rainfall indices are evaluated using non-parametric tests at different temporal levels. To overcome the sparse locally available network, the high resolution APHRODITE gridded dataset is used in addition to the existing rain gauges. Finally, existing linkages between discharge changes and trends in rainfall and temperature are explored. Results are indicative of an intensification of rainfall (+15%/decade), with more extreme and longer events. A significant increase in winter rainfall and a decrease in consecutive dry days provides strong evidence for a lengthening wet season in Central Vietnam. In addition, trends based on APHRODITE suggest a strong orographic signal in winter and annual trends. These results underline the local variability in the impacts of climatic change at the global scale. Consequently, it is important that change detection investigations are conducted at the local scale. A very weak signal is detected in the trend of minimum temperature (+0.2°C/decade). River discharge trends show an increase in mean discharge (31 to 35%/decade) over the last decades. Between 54 and 74% of this increase is explained by the increase in precipitation. The maximum discharge also responds significantly to precipitation changes leading to a lengthened wet season and an increase in extreme rainfall events. Such trends can be linked with a likely increase in floods in Central Vietnam, which is important for future adaptation planning and management and flood preparedness in the region. Copyright © 2012 John Wiley & Sons, Ltd.

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.

Drivers of change in mountain farming in Slovakia: from socialist collectivisation to the Common Agricultural Policy

The transformations in Slovak agriculture from the 1950s to the present day, considering both the generic (National and EU) and site-specific (local) drivers of landscape change, were analysed in five mountain study areas in the country. An interdisciplinary approach included analysis of population trends, evaluation of land use and landscape change combined with exploration of the perceptions of local stakeholders and results of previous biodiversity studies. The generic processes active from the 1950s to 1970s were critical for all study areas with impacts lasting right up until the present day. Agricultural collectivisation, agricultural intensification and land abandonment had negative effects in all study areas. However, the precise impacts on the landscape were different in the different study areas due to site-specific attributes (e.g. population trends, geographic localisation and local attitudes and opportunities), and these played a decisive role in determining the trajectory of change. Regional contrasts in rural development between these territories have increased in the last two decades, also due to the imperfect preconditions of governmental support. The recent Common Agricultural Policy developments are focused on maintenance of intensive large-scale farming rather than direct enhancement of agro-biodiversity and rural development at the local scale. In this context, local, site-specific attributes can and must form an essential part of rural development plans, to meet the demands for management of the diversity of agricultural mountain landscapes and facilitate the multifunctional role of agriculture.

IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences

IntFOLD is an independent web server that integrates our leading methods for structure and function prediction. The server provides a simple unified interface that aims to make complex protein modelling data more accessible to life scientists. The server web interface is designed to be intuitive and integrates a complex set of quantitative data, so that 3D modelling results can be viewed on a single page and interpreted by non-expert modellers at a glance. The only required input to the server is an amino acid sequence for the target protein. Here we describe major performance and user interface updates to the server, which comprises an integrated pipeline of methods for: tertiary structure prediction, global and local 3D model quality assessment, disorder prediction, structural domain prediction, function prediction and modelling of protein-ligand interactions. The server has been independently validated during numerous CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiments, as well as being continuously evaluated by the CAMEO (Continuous Automated Model Evaluation) project. The IntFOLD server is available at: http://www.reading.ac.uk/bioinf/IntFOLD/

Climate responses to anthropogenic emissions of short-lived climate pollutants

Policies to control air quality focus on mitigating emissions of aerosols and their precursors, and other short-lived climate pollutants (SLCPs). On a local scale, these policies will have beneficial impacts on health and crop yields, by reducing particulate matter (PM) and surface ozone concentrations; however, the climate impacts of reducing emissions of SLCPs are less straightforward to predict. In this paper we consider a set of idealised, extreme mitigation strategies, in which the total anthropogenic emissions of individual SLCP emissions species are removed. This provides an upper bound on the potential climate impacts of such air quality strategies. We focus on evaluating the climate responses to changes in anthropogenic emissions of aerosol precursor species: black carbon (BC), organic carbon (OC) and sulphur dioxide (SO2). We perform climate integrations with four fully coupled atmosphere-ocean global climate models (AOGCMs), and examine the effects on global and regional climate of removing the total land-based anthropogenic emissions of each of the three aerosol precursor species. We find that the SO2 emissions reductions lead to the strongest response, with all three models showing an increase in surface temperature focussed in the northern hemisphere high latitudes, and a corresponding increase in global mean precipitation and run-off. Changes in precipitation and run-off patterns are driven mostly by a northward shift in the ITCZ, consistent with the hemispherically asymmetric warming pattern driven by the emissions changes. The BC and OC emissions reductions give a much weaker forcing signal, and there is some disagreement between models in the sign of the climate responses to these perturbations. These differences between models are due largely to natural variability in sea-ice extent, circulation patterns and cloud changes. This large natural variability component to the signal when the ocean circulation and sea-ice are free-running means that the BC and OC mitigation measures do not necessarily lead to a discernible climate response.

Walking in a winter wonderland? Strategies for Early and Middle Pleistocene survival in mid-latitude Europe

Any occupation of northern Europe by Lower Palaeolithic hominins, even those occurring during full interglacials, must have addressed the challenges of marked seasonality and cold winters. These would have included the problems of: wind-chill and frostbite; duration, distribution and depth of snow-cover; reduced daylight hours; and distribution and availability of animal and plant foods. Solutions can essentially be characterised as a ‘stick or twist’ choice: i.e. year-round presence on a local scale vs. extensive annual mobility. However these options, and the ‘interim’ strategies that lie between them, present various problems, including maintaining core body temperature, meeting the energetic demands of mobility, coping with reduced resource availability and increasing patchiness, and meeting nutritional requirements. The feasibility of different winter survival strategies are explored with reference to Lower Palaeolithic palaeoenvironmental reconstructions and on-site behavioural evidence. Emphasis is placed upon possible strategies for (i) avoiding the excessive lean meat protein problem of ‘rabbit starvation’ (e.g. through exploitation of ‘residential’ species with significant winter body fat and/or by targeting specific body parts, following modern ethnographic examples, supplemented by the exploitation of winter plants); and (ii) maintaining body temperatures (e.g. through managed pyrotechnology, and/or other forms of cultural insulation). The paper concludes with a suggested winter strategy.

Cross-sector surveys assessing perceptions of key stakeholders towards barriers, concerns and facilitators to the appropriate use of adaptive designs in confirmatory trials

Background Appropriately conducted adaptive designs (ADs) offer many potential advantages over conventional trials. They make better use of accruing data, potentially saving time, trial participants, and limited resources compared to conventional, fixed sample size designs. However, one can argue that ADs are not implemented as often as they should be, particularly in publicly funded confirmatory trials. This study explored barriers, concerns, and potential facilitators to the appropriate use of ADs in confirmatory trials among key stakeholders. Methods We conducted three cross-sectional, online parallel surveys between November 2014 and January 2015. The surveys were based upon findings drawn from in-depth interviews of key research stakeholders, predominantly in the UK, and targeted Clinical Trials Units (CTUs), public funders, and private sector organisations. Response rates were as follows: 30(55 %) UK CTUs, 17(68 %) private sector, and 86(41 %) public funders. A Rating Scale Model was used to rank barriers and concerns in order of perceived importance for prioritisation. Results Top-ranked barriers included the lack of bridge funding accessible to UK CTUs to support the design of ADs, limited practical implementation knowledge, preference for traditional mainstream designs, difficulties in marketing ADs to key stakeholders, time constraints to support ADs relative to competing priorities, lack of applied training, and insufficient access to case studies of undertaken ADs to facilitate practical learning and successful implementation. Associated practical complexities and inadequate data management infrastructure to support ADs were reported as more pronounced in the private sector. For funders of public research, the inadequate description of the rationale, scope, and decision-making criteria to guide the planned AD in grant proposals by researchers were all viewed as major obstacles. Conclusions There are still persistent and important perceptions of individual and organisational obstacles hampering the use of ADs in confirmatory trials research. Stakeholder perceptions about barriers are largely consistent across sectors, with a few exceptions that reflect differences in organisations’ funding structures, experiences and characterisation of study interventions. Most barriers appear connected to a lack of practical implementation knowledge and applied training, and limited access to case studies to facilitate practical learning. Keywords: Adaptive designs; flexible designs; barriers; surveys; confirmatory trials; Phase 3; clinical trials; early stopping; interim analyses

Assessing species’ habitat associations from occurrence records, standardised monitoring data and expert opinion: a test with British butterflies

Accurate knowledge of species’ habitat associations is important for conservation planning and policy. Assessing habitat associations is a vital precursor to selecting appropriate indicator species for prioritising sites for conservation or assessing trends in habitat quality. However, much existing knowledge is based on qualitative expert opinion or local scale studies, and may not remain accurate across different spatial scales or geographic locations. Data from biological recording schemes have the potential to provide objective measures of habitat association, with the ability to account for spatial variation. We used data on 50 British butterfly species as a test case to investigate the correspondence of data-derived measures of habitat association with expert opinion, from two different butterfly recording schemes. One scheme collected large quantities of occurrence data (c. 3 million records) and the other, lower quantities of standardised monitoring data (c. 1400 sites). We used general linear mixed effects models to derive scores of association with broad-leaf woodland for both datasets and compared them with scores canvassed from experts. Scores derived from occurrence and abundance data both showed strongly positive correlations with expert opinion. However, only for occurrence data did these fell within the range of correlations between experts. Data-derived scores showed regional spatial variation in the strength of butterfly associations with broad-leaf woodland, with a significant latitudinal trend in 26% of species. Sub-sampling of the data suggested a mean sample size of 5000 occurrence records per species to gain an accurate estimation of habitat association, although habitat specialists are likely to be readily detected using several hundred records. Occurrence data from recording schemes can thus provide easily obtained, objective, quantitative measures of habitat association.

Fighting in fig wasps: do males avoid killing brothers or do they never meet them?

1. In many fig wasp species, armoured wingless males regularly engage in lethal fights for access to females inside figs, which act as discrete mating patches. 2. Kin selection generally opposes killing brothers, because their reproductive success provides indirect genetic benefits (inclusive fitness). However, siblicide may be avoided if (i) brothers do not occur in the same figs, or (ii) males avoid fighting brothers in the same fig. Alternatively, (iii) siblicide may occur because intense mate competition between brothers at the local scale overcomes kin selection effects, or (iv) males do not recognise kin. 3. A fig may also contain wasps from other closely related species and it is not known if males also fight with these individuals. 4. Nine microsatellite loci were used in the first genetic analysis of fighting in fig wasps. We assigned species and sibling identities to males and tested alternative fighting scenarios for three Sycoscapter wasp species in figs of Ficus rubiginosa. 5. Approximately 60% of figs contained males frommore than one Sycoscapter species and approximately 80% of fights were between conspecifics, but a surprising 20% were between heterospecific males. 6.Within species, fewfigs contained brothers, suggesting that females typically lay one son per fig. Overall, most males do not compete with brothers and all fights observed were between unrelated males. Key words:Competition, fighting, genetics, kin selection, microsatellites, relatedness.

New perspectives on the synoptic and mesoscale structure of Hurricane Catarina

This work explores in detail synoptic and mesoscale features of Hurricane Catarina during its life cycle from a decaying baroclinic wave to a tropical depression that underwent tropical transition (TT) and finally to a Category 2 hurricane at landfall over Santa Catarina State coast, southern Brazil. This unique system caused 11 deaths mostly off the Brazilian coast and an estimated half billion dollars in damage in a matter of a few hours on 28 March 2004. Although the closest meteorological station available was tens of kilometres away from the eye, in situ meteorological measurements provided by a work-team sent to the area where the eye made landfall unequivocally reproduces the tropical signature with category 2 strength, adding to previous analysis where this data was not available. Further analyses are based mostly on remote sensing data available at the time of the event. A classic dipole blocking set synoptic conditions for Hurricane Catarina to develop, dynamically contributing to the low wind shear observed. On the other hand, on its westward transit, large scale subsidence limited its strength and vertical development. Catarina had relatively cool SST conditions, but this was mitigated by favourable air-sea fluxes leading to latent heat release-driven processes during the mature phase. The ocean`s dynamic topography also suggested the presence of nearby warm core rings which may have facilitated the transition and post-transition intensification. Since there were no records of such a system at least in the past 30 years and given that SSTs were generally below 26 degrees C and vertical shear was usually strong, despite all satellite data available, the system was initially classified as an extratropical cyclone. Here we hypothesise that this categorization was based oil inadequate regional scale model outputs which did not account for the importance of the latent heat fluxes over the ocean. Hurricane Catarina represents a dramatic event on weather systems in South America. It has attracted attention worldwide and poses questions as whether or not it is a symptom of global warming. (C) 2009 Elsevier B.V. All rights reserved.