Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution

Here we report the crystal structure of the DNA heptanucleotide sequence d(GCATGCT) determined to a resolution of 1.1 Angstrom. The sequence folds into a complementary loop structure generating several unusual base pairings and is stabilised through cobalt hexammine and highly defined water sites. The single stranded loop is bound together through the G(N2)-C(O2) intra-strand H-bonds for the available G/C residues, which form further Watson-Crick pairings to a complementary sequence, through 2-fold symmetry, generating a pair of non-planar quadruplexes at the heart of the structure. Further, four adenine residues stack in pairs at one end, H-bonding through their N7-N6 positions, and are additionally stabilised through two highly conserved water positions at the structural terminus. This conformation is achieved through the rotation of the central thymine base at the pinnacle of the loop structure, where it stacks with an adjacent thymine residue within the lattice. The crystal packing yields two halved biological units, each related across a 2-fold symmetry axis spanning a cobalt hexammine residue between them, which stabilises the quadruplex structure through H-bonds to the phosphate oxygens and localised hydration.

Mapping fibre orientation in complex-shaped biological systems with micrometre resolution by scanning X-ray microdiffraction

A fully automated procedure to extract and to image local fibre orientation in biological tissues from scanning X-ray diffraction is presented. The preferred chitin fibre orientation in the flow sensing system of crickets is determined with high spatial resolution by applying synchrotron radiation based X-ray microbeam diffraction in conjunction with advanced sample sectioning using a UV micro-laser. The data analysis is based on an automated detection of azimuthal diffraction maxima after 2D convolution filtering (smoothing) of the 2D diffraction patterns. Under the assumption of crystallographic fibre symmetry around the morphological fibre axis, the evaluation method allows mapping the three-dimensional orientation of the fibre axes in space. The resulting two-dimensional maps of the local fibre orientations - together with the complex shape of the flow sensing system - may be useful for a better understanding of the mechanical optimization of such tissues.

Involuntary inhibition of movement initiation alters oculomotor competition resolution

Identifying a stimulus as the target for a goal-directed movement involves inhibiting competing responses. Separable inhibitory interconnections bias local competition to ensure only one stimulus is selected and to alter movement initiation. Behavioural evidence of these inhibitory processes comes from the effects of distracters on oculomotor landing positions and saccade latencies. Here, we investigate the relationship between these two sources of inhibition. Targets were presented with or without close and remote distracters. In separate experiments the possible position and identity of the target and distracters were manipulated. In all cases saccade landing position was found to be less affected by the presence of the close distracter when remote distracters were also present. The involuntary increase in the latency of saccade initiation caused by the presence of the remote distracters alters the state of competitive processes involved in selecting the saccade target thus changing its landing position.

User-intimate requirements hierarchy resolution framework (UI-REF)

Abstract. This paper presents the User-Intimate Requirements Hierarchy Resolution Framework (UI-REF) based on earlier work (Badii 1997-2008) to optimise the requirements engineering process particularly to support userintimate interactive systems co-design. The stages of the UI- EF framework for requirements resolution-and-prioritisation are described. UI-REF has been established to ensure that the most-deeply-valued needs of the majority of stakeholders are elicited and ranked, and the root rationale for requirements evolution is trace-able and contextualised so as to help resolve stakeholder conflicts. UI-REF supports the dynamically evolving requirements of the users in the context of digital economy as under-pinned by online service provisioning. Requirements prioritisation in UI-REF is fully resolved while a promotion path for lower priority requirements is delineated so as to ensure that as the requirements evolve so will their resolution and prioritisation.

Towards semantic resolution of security in ambient environments

Driven by new network and middleware technologies such as mobile broadband, near-field communication, and context awareness the so-called ambient lifestyle will foster innovative use cases in different domains. In the EU project Hydra high-level security, trust and privacy concerns such as loss of control, profiling and surveillance are considered at the outset. At the end of this project the. Hydra middleware development platform will have been designed so as to enable developers to realise secure ambient scenarios. This paper gives a short introduction to the Hydra project and its approach to ensure security by design. Based on the results of a focus group analysis of the user domain "building automation" typical threats are evaluated and their risks are assessed. Then, specific security requirements with respect to security, privacy, and trust are derived in order to incorporate them into the Hydra Security Meta-Model. How concepts such as context, semantic resolution of security, and virtualisation support the overall Hydra approach will be introduced and illustrated on the basis of it technical building automation scenario.

Insights into redox cycling of sulfur and iron in peatlands using high-resolution diffusive equilibrium thin film (DET) gel probe sampling

High spatial resolution vertical profiles of pore-water chemistry have been obtained for a peatland using diffusive equilibrium in thin films (DET) gel probes. Comparison of DET pore-water data with more traditional depth-specific sampling shows good agreement and the DET profiling method is less invasive and less likely to induce mixing of pore-waters. Chloride mass balances as water tables fell in the early summer indicate that evaporative concentration dominates and there is negligible lateral flow in the peat. Lack of lateral flow allows element budgets for the same site at different times to be compared. The high spatial resolution of sampling also enables gradients to be observed that permit calculations of vertical fluxes. Sulfate concentrations fall at two sites with net rates of 1.5 and 5.0nmol cm− 3 day− 1, likely due to a dominance of bacterial sulfate reduction, while a third site showed a net gain in sulfate due to oxidation of sulfur over the study period at an average rate of 3.4nmol cm− 3 day− 1. Behaviour of iron is closely coupled to that of sulfur; there is net removal of iron at the two sites where sulfate reduction dominates and addition of iron where oxidation dominates. The profiles demonstrate that, in addition to strong vertical redox related chemical changes, there is significant spatial heterogeneity. Whilst overall there is evidence for net reduction of sulfate within the peatland pore-waters, this can be reversed, at least temporarily, during periods of drought when sulfide oxidation with resulting acid production predominates.

U.K. HiGEM: Simulations of desert dust and biomass burning aerosols with a high-resolution atmospheric GCM

The atmospheric component of the United Kingdom’s new High-resolution Global Environmental Model (HiGEM) has been run with interactive aerosol schemes that include biomass burning and mineral dust. Dust emission, transport, and deposition are parameterized within the model using six particle size divisions, which are treated independently. The biomass is modeled in three nonindependent modes, and emissions are prescribed from an external dataset. The model is shown to produce realistic horizontal and vertical distributions of these aerosols for each season when compared with available satellite- and ground-based observations and with other models. Combined aerosol optical depths off the coast of North Africa exceed 0.5 both in boreal winter, when biomass is the main contributor, and also in summer, when the dust dominates. The model is capable of resolving smaller-scale features, such as dust storms emanating from the Bode´ le´ and Saharan regions of North Africa and the wintertime Bode´ le´ low-level jet. This is illustrated by February and July case studies, in which the diurnal cycles of model variables in relation to dust emission and transport are examined. The top-of-atmosphere annual mean radiative forcing of the dust is calculated and found to be globally quite small but locally very large, exceeding 20 W m22 over the Sahara, where inclusion of dust aerosol is shown to improve the model radiative balance. This work extends previous aerosol studies by combining complexity with increased global resolution and represents a step toward the next generation of models to investigate aerosol–climate interactions. 1. Introduction Accurate modeling of mineral dust is known to be important because of its radiative impact in both numerical weather prediction models (Milton et al. 2008; Haywood et