Cloud optical and microphysical properties derived from ground-based and satellite sensors over a site in the Yangtze Delta region

Comprehensive surface-based retrievals of cloud optical and microphysical properties were made at Taihu, a highly polluted site in the central Yangtze Delta region, during a research campaign from May 2008 to December 2009. Cloud optical depth (COD), effective radius (Re), and liquid water path (LWP) were retrieved from measurements made with a suite of ground-based and spaceborne instruments, including an Analytical Spectral Devices spectroradiometer, a multi␣lter rotating shadowband radiometer, a multichannel microwave radiometer profiler, and the Moderate Resolution Imaging Spectroradiometer (MODIS) on Terra and Aqua satellites. Retrievals from zenith radiance measurements capture better the temporal variation of cloud properties than do retrievals from hemispherical fluxes. Annual mean LWP, COD, and Re are 115.8 ± 90.8 g/m2, 28.5 ± 19.2, and 6.9 ± 4.2 microns. Over 90% of LWP values are less than 250 g/m2. Most of the COD values (>90%) fall between 5 and 60, and ~80% of Re values are less than 10 microns. Maximum (minimum) values of LWP and Re occur in summer (winter); COD is highest in winter and spring. Raining and nonraining clouds have signi␣cant differences in LWP, COD, and Re. Rainfall frequency is best correlated with LWP, followed by COD and Re. Cloud properties retrieved from multiple ground-based instruments are also compared with those from satellite retrievals. On average, relative to surface retrievals, mean differences of satellite retrievals in cloud LWP, COD, and Re were -33.6 g/m2 (-26.4%), -5.8 (-31.4%), and 2.9 ␣m (29.3%) for 11 MODIS-Terra overpasses and -43.3 g/m2 (-22.3%), -3.0 (-10.0%), and -1.3 ␣m (-12.0%) for 8 MODIS-Aqua overpasses, respectively. These discrepancies indicate that MODIS cloud products still suffer from large uncertainties in this region.

Settlement patterns in the late Mesolithic of western Scotland: the implications of Bayesian analysis of radiocarbon dates and inter-site technological comparisons

The character of settlement patterns within the late Mesolithic communities of north-west Europe is a topic of substantial debate. An important case study concerns the five shell middens on the island of Oronsay, Inner Hebrides, western Scotland. Two conflicting interpretations have been proposed: the evidence from seasonality indicators and stable isotope analysis of human bones has been used to support a model of year-round settlement on this small island; alternatively, the middens have been interpreted as resulting from short-term intermittent visits to Oronsay within a regionally mobile settlement pattern. We contribute to this debate by describing Storakaig, a newly discovered site on the nearby island of Islay, undertaking a Bayesian chronological analysis and providing evidence for technological continuity between Oronsay and sites elsewhere in the region. While this new evidence remains open to alternative interpretation, we suggest that it makes regional mobility rather than year-round settlement on Oronsay a more viable interpretation for the Oronsay middens. Our analysis also confirms the likely overlap of the late Mesolithic with the earliest Neolithic within western Scotland.

Multi-site evaluation of an urban land-surface model: intra-urban heterogeneity, seasonality and parameter complexity requirements

An extensive off-line evaluation of the Noah/Single Layer Urban Canopy Model (Noah/SLUCM) urban land-surface model is presented using data from 15 sites to assess (1) the ability of the scheme to reproduce the surface energy balance observed in a range of urban environments, including seasonal changes, and (2) the impact of increasing complexity of input parameter information. Model performance is found to be most dependent on representation of vegetated surface area cover; refinement of other parameter values leads to smaller improvements. Model biases in net all-wave radiation and trade-offs between turbulent heat fluxes are highlighted using an optimization algorithm. Here we use the Urban Zones to characterize Energy partitioning (UZE) as the basis to assign default SLUCM parameter values. A methodology (FRAISE) to assign sites (or areas) to one of these categories based on surface characteristics is evaluated. Using three urban sites from the Basel Urban Boundary Layer Experiment (BUBBLE) dataset, an independent evaluation of the model performance with the parameter values representative of each class is performed. The scheme copes well with both seasonal changes in the surface characteristics and intra-urban heterogeneities in energy flux partitioning, with RMSE performance comparable to similar state-of-the-art models for all fluxes, sites and seasons. The potential of the methodology for high-resolution atmospheric modelling application using the Weather Research and Forecasting (WRF) model is highlighted. This analysis supports the recommendations that (1) three classes are appropriate to characterize the urban environment, and (2) that the parameter values identified should be adopted as default values in WRF.

Site-specific and geographical segmental social, environmental and ethical disclosures by the Ghanaian mining sector

Purpose: This paper explores the extent of site-specific and geographic segmental social, environmental and ethical reporting by mining companies operating in Ghana. We aim to: (i) establish a picture of corporate transparency relating to geographic segmentation of social, environmental and ethical reporting which is specific to operating sites and country of operation, and; (ii) gauge the impact of the introduction of integrated reporting on site-specific social, environmental and ethical reporting. Methodology/Approach: We conducted an interpretive content analysis of the annual/integrated reports of mining companies for the years 2009, 2010 and 2011 in order to extract site-specific social, environmental and ethical information relating to the companies’ mining operations in Ghana. Findings and Implications: We found that site-specific social, environmental and ethical reporting is extremely patchy and inconsistent between the companies’ reports studied. We also found that there was no information relating to certain sites, which were in operation, according to the Ghana Minerals Commission. This could simply be because operations were not in progress. Alternatively it could be that decisions are made concerning which site-specific information is reported according to a certain benchmark. One policy implication arising from this research is that IFRS should require geographic segmental reporting of material social, environmental and ethical information in order to bring IFRS into line with global developments in integrated reporting. Originality: Although there is a wealth of sustainability reporting research and an emergent literature on integrated reporting, there is currently no academic research exploring site-specific social, environmental and ethical reporting

Pit clusters and the temporality of occupation: an earlier Neolithic site at Kilverstone, Thetford, Norfolk

This paper discusses 226 earlier Neolithic pits found at Kilverstone in Norfolk. In particular, it focuses on the dynamics involved in the site's creation, investigating what had happened to the material found in the pits prior to deposition, and exploring the material connections (refitting sherds and flints) across the site. As a result of these material insights, it proved possible to shed important light on the character of that place in particular, and on the temporality of Neolithic deposition and occupation in general.

Ion acceleration at both the interior and exterior Alfvén waves associated with the magnetopause reconnection site: Signatures in cusp precipitation

We present evidence for the acceleration of magnetospheric ions by reflection off two Alfvén waves, launched by the reconnection site into the inflow regions on both sides of the reconnecting magnetopause. The “exterior” wave stands in the inflow from the magnetosheath and is the magnetopause, in the sense that the majority of the field rotation occurs there. The other, “interior” wave stands in the inflow region on the magnetospheric side of the boundary. The population reflected by the interior wave is the more highly energized of the two and appears at low altitudes on open field lines, immediately equatorward of the cusp precipitation. In addition, we identify the population of magnetosheath ions transmitted across the exterior Alfvén wave, as well as a population of magnetospheric ions which are accelerated, after transmission through the interior wave, by reflection off the exterior wave. The ion populations near the X line are modeled and, with allowance for time-of-flight effects, are also derived from observations in the dayside auroral ionosphere. Agreement between observed and theoretical spectra is very good and the theory also explains the observed total fluxes and average energies of the precipitations poleward of the open/closed field line boundary. The results offer a physical interpretation of all the various classifications of precipitation into the dayside ionosphere (central plasma sheet, dayside boundary plasma sheet, void, low-latitude boundary layer, cusp, and mantle) and allow the conditions in both the magnetosphere and the magnetosheath adjacent to the X line to be studied.

Vertical structure and physical processes of the Madden-Julian oscillation: Linking hindcast fidelity to simulated diabatic heating and moistening

Many theories for the Madden-Julian oscillation (MJO) focus on diabatic processes, particularly the evolution of vertical heating and moistening. Poor MJO performance in weather and climate models is often blamed on biases in these processes and their interactions with the large-scale circulation. We introduce one of three components of a model-evaluation project, which aims to connect MJO fidelity in models to their representations of several physical processes, focusing on diabatic heating and moistening. This component consists of 20-day hindcasts, initialised daily during two MJO events in winter 2009-10. The 13 models exhibit a range of skill: several have accurate forecasts to 20 days' lead, while others perform similarly to statistical models (8-11 days). Models that maintain the observed MJO amplitude accurately predict propagation, but not vice versa. We find no link between hindcast fidelity and the precipitation-moisture relationship, in contrast to other recent studies. There is also no relationship between models' performance and the evolution of their diabatic-heating profiles with rain rate. A more robust association emerges between models' fidelity and net moistening: the highest-skill models show a clear transition from low-level moistening for light rainfall to mid-level moistening at moderate rainfall and upper-level moistening for heavy rainfall. The mid-level moistening, arising from both dynamics and physics, may be most important. Accurately representing many processes may be necessary, but not sufficient for capturing the MJO, which suggests that models fail to predict the MJO for a broad range of reasons and limits the possibility of finding a panacea.

Nicked-site substrates for a serine recombinase reveal enzyme–DNA communications and an essential tethering role of covalent enzyme–DNA linkages

To analyse the mechanism and kinetics of DNA strand cleavages catalysed by the serine recombinase Tn3 resolvase, we made modified recombination sites with a single-strand nick in one of the two DNA strands. Resolvase acting on these sites cleaves the intact strand very rapidly, giving an abnormal half-site product which accumulates. We propose that these reactions mimic second-strand cleavage of an unmodified site. Cleavage occurs in a synapse of two sites, held together by a resolvase tetramer; cleavage at one site stimulates cleavage at the partner site. After cleavage of a nicked-site substrate, the half-site that is not covalently linked to a resolvase subunit dissociates rapidly from the synapse, destabilizing the entire complex. The covalent resolvase–DNA linkages in the natural reaction intermediate thus perform an essential DNA-tethering function. Chemical modifications of a nicked-site substrate at the positions of the scissile phosphodiesters result in abolition or inhibition of resolvase-mediated cleavage and effects on resolvase binding and synapsis, providing insight into the serine recombinase catalytic mechanism and how resolvase interacts with the substrate DNA.

A Lateglacial archaeological site in the far north-west of Europe at Rubha Port an t-Seilich, Isle of Islay, western Scotland: Ahrensburgian-style artefacts, absolute dating and geoarchaeology

The exact pattern, process and timing of the human re-colonization of northern Europe after the end of the last Ice Age remain controversial. Recent research has provided increasingly early dates for at least pioneer explorations of latitudes above 54°N in many regions, yet the far north-west of the European landmass, Scotland, has remained an unexplained exception to this pattern. Although the recently described Hamburgian artefacts from Howburn and an assemblage belonging to the arch-backed point complex from Kilmelfort Cave have established at least a sporadic human presence during earlier stages of the Lateglacial Interstadial, we currently lack evidence for Younger Dryas/Greenland Stadial 1 (GS-1) activity other than rare stray finds that have been claimed to be of Ahrensburgian affiliation but are difficult to interpret in isolation. We here report the discovery of chipped stone artefacts with technological and typological characteristics similar to those of the continental Ahrensburgian at a locality in western Scotland. A preliminary analysis of associated tephra, pollen and phytoliths, along with microstratigraphic analysis, suggest the artefacts represent one or more episodes of human activity that fall within the second half of GS-1 and the Preboreal period

The curious case of the camelthorn: competition, coexistence and nest-site limitation in a multispecies mutualism

Myrmecophyte plants house ants in domatia in exchange for protection from herbivores. Ant-myrmecophyte mutualisms exhibit two general patterns due to competition between ants for plant occupancy: i) domatia nest-sites are a limiting resource and ii) each individual plant hosts one ant species at a time. However, individual camelthorn trees (Vachellia erioloba) typically host two to four ant species simultaneously, often coexisting in adjacent domatia on the same branch. Such fine-grain spatial coexistence brings into question the conventional wisdom on ant-myrmecophyte mutualisms. Camelthorn ants appear not to be nest-site limited, despite low abundance of suitable domatia, and have random distributions of nest-sites within and across trees. These patterns suggest a lack of competition between ants for domatia and contrast strongly with other ant-myrmecophyte systems. Comparison of this unusual case with others suggests that spatial scale is crucial to coexistence or competitive exclusion involving multiple ant species. Furthermore, coexistence may be facilitated when co-occurring ant species diverge strongly on at least one niche axis. Our conclusions provide recommendations for future ant-myrmecophyte research, particularly in utilising multispecies systems to further our understanding of mutualism biology.

Proteins and their interacting partners: an introduction to protein–ligand binding site prediction methods

Elucidating the biological and biochemical roles of proteins, and subsequently determining their interacting partners, can be difficult and time consuming using in vitro and/or in vivo methods, and consequently the majority of newly sequenced proteins will have unknown structures and functions. However, in silico methods for predicting protein–ligand binding sites and protein biochemical functions offer an alternative practical solution. The characterisation of protein–ligand binding sites is essential for investigating new functional roles, which can impact the major biological research spheres of health, food, and energy security. In this review we discuss the role in silico methods play in 3D modelling of protein–ligand binding sites, along with their role in predicting biochemical functionality. In addition, we describe in detail some of the key alternative in silico prediction approaches that are available, as well as discussing the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and the Continuous Automated Model EvaluatiOn (CAMEO) projects, and their impact on developments in the field. Furthermore, we discuss the importance of protein function prediction methods for tackling 21st century problems.

Can site and landscape-scale environmental attributes buffer bird populations against weather events?

Projected impacts of climate change on the populations and distributions of species pose a challenge for conservationists. In response, a number of adaptation strategies to enable species to persist in a changing climate have been proposed. Management to maximise the quality of habitat at existing sites may reduce the magnitude or frequency of climate-driven population declines. In addition large-scale management of landscapes could potentially improve the resilience of populations by facilitating inter-population movements. A reduction in the obstacles to species’ range expansion, may also allow species to track changing conditions better through shifts to new locations, either regionally or locally. However, despite a strong theoretical base, there is limited empirical evidence to support these management interventions. This makes it difficult for conservationists to decide on the most appropriate strategy for different circumstances. Here extensive data from long-term monitoring of woodland birds at individual sites are used to examine the two-way interactions between habitat and both weather and population count in the previous year. This tests the extent to which site-scale and landscape-scale habitat attributes may buffer populations against variation in winter weather (a key driver of woodland bird population size) and facilitate subsequent population growth. Our results provide some support for the prediction that landscape-scale attributes (patch isolation and area of woodland habitat) may influence the ability of some woodland bird species to withstand weather-mediated population declines. These effects were most apparent among generalist woodland species. There was also evidence that several, primarily specialist, woodland species are more likely to increase following population decline where there is more woodland at both site and landscape scales. These results provide empirical support for the concept that landscape-scale conservation efforts may make the populations of some woodland bird species more resilient to climate change. However in isolation, management is unlikely to provide a universal benefit to all species.