Improvement of 3D protein models using multiple templates guided by single-template model quality assessment

Motivation: Modelling the 3D structures of proteins can often be enhanced if more than one fold template is used during the modelling process. However, in many cases, this may also result in poorer model quality for a given target or alignment method. There is a need for modelling protocols that can both consistently and significantly improve 3D models and provide an indication of when models might not benefit from the use of multiple target-template alignments. Here, we investigate the use of both global and local model quality prediction scores produced by ModFOLDclust2, to improve the selection of target-template alignments for the construction of multiple-template models. Additionally, we evaluate clustering the resulting population of multi- and single-template models for the improvement of our IntFOLD-TS tertiary structure prediction method. Results: We find that using accurate local model quality scores to guide alignment selection is the most consistent way to significantly improve models for each of the sequence to structure alignment methods tested. In addition, using accurate global model quality for re-ranking alignments, prior to selection, further improves the majority of multi-template modelling methods tested. Furthermore, subsequent clustering of the resulting population of multiple-template models significantly improves the quality of selected models compared with the previous version of our tertiary structure prediction method, IntFOLD-TS.

Integration of a 3D Variational data assimilation scheme with a coastal area morphodynamic model of Morecambe Bay

This paper describes the implementation of a 3D variational (3D-Var) data assimilation scheme for a morphodynamic model applied to Morecambe Bay, UK. A simple decoupled hydrodynamic and sediment transport model is combined with a data assimilation scheme to investigate the ability of such methods to improve the accuracy of the predicted bathymetry. The inverse forecast error covariance matrix is modelled using a Laplacian approximation which is calibrated for the length scale parameter required. Calibration is also performed for the Soulsby-van Rijn sediment transport equations. The data used for assimilation purposes comprises waterlines derived from SAR imagery covering the entire period of the model run, and swath bathymetry data collected by a ship-borne survey for one date towards the end of the model run. A LiDAR survey of the entire bay carried out in November 2005 is used for validation purposes. The comparison of the predictive ability of the model alone with the model-forecast-assimilation system demonstrates that using data assimilation significantly improves the forecast skill. An investigation of the assimilation of the swath bathymetry as well as the waterlines demonstrates that the overall improvement is initially large, but decreases over time as the bathymetry evolves away from that observed by the survey. The result of combining the calibration runs into a pseudo-ensemble provides a higher skill score than for a single optimized model run. A brief comparison of the Optimal Interpolation assimilation method with the 3D-Var method shows that the two schemes give similar results.

Considering user attitude and behaviour in persuasive systems design: the 3D-RAB model

As in any technology systems, analysis and design issues are among the fundamental challenges in persuasive technology. Currently, the Persuasive Systems Development (PSD) framework is considered to be the most comprehensive framework for designing and evaluation of persuasive systems. However, the framework is limited in terms of providing detailed information which can lead to selection of appropriate techniques depending on the variable nature of users or use over time. In light of this, we propose a model which is intended for analysing and implementing behavioural change in persuasive technology called the 3D-RAB model. The 3D-RAB model represents the three dimensional relationships between attitude towards behaviour, attitude towards change or maintaining a change, and current behaviour, and distinguishes variable levels in a user’s cognitive state. As such it provides a framework which could be used to select appropriate techniques for persuasive technology.

Analyzing the persuasion context of the persuasive systems design model with the 3D-RAB model

Research into design methodology is one of the most challenging issues in the field of persuasive technology. However, the introduction of the Persuasive Systems Design model, and the consideration of the 3-Dimensional Re-lationship between Attitude and Behavior, offer to make persuasive technolo-gies more practically viable. In this paper we demonstrate how the 3-Dimensional Relationship between Attitude and Behavior guides the analysis of the persuasion context in the Persuasive System Design model. As a result, we propose a modification of the persuasion context and assert that the technology should be analyzed as part of strategy instead of event.

Facile production of ordered 3D platinum nanowire networks with “single diamond” bicontinuous cubic morphology

Direct electrochemical templating is carried out using a thin layer of a self-assembled diamond phase (QIID) of phytantriol to create a platinum film with a novel nanostructure. Small-angle X-ray scattering shows that the nanostructured platinum films are asymmetrically templated and exhibit “single diamond” morphology with Fd3m symmetry.

Estimating root–soil contact from 3D X-ray microtomographs

Adequate contact with the soil is essential for water and nutrient adsorption by plant roots, but the determination of root–soil contact is a challenging task because it is difficult to visualize roots in situ and quantify their interactions with the soil at the scale of micrometres. A method to determine root–soil contact using X-ray microtomography was developed. Contact areas were determined from 3D volumetric images using segmentation and iso-surface determination tools. The accuracy of the method was tested with physical model systems of contact between two objects (phantoms). Volumes, surface areas and contact areas calculated from the measured phantoms were compared with those estimated from image analysis. The volume was accurate to within 0.3%, the surface area to within 2–4%, and the contact area to within 2.5%. Maize and lupin roots were grown in soil (<2 mm) and vermiculite at matric potentials of −0.03 and −1.6 MPa and in aggregate fractions of 4–2, 2–1, 1–0.5 and < 0.5 mm at a matric potential of −0.03 MPa. The contact of the roots with their growth medium was determined from 3D volumetric images. Macroporosity (>70 µm) of the soil sieved to different aggregate fractions was calculated from binarized data. Root-soil contact was greater in soil than in vermiculite and increased with decreasing aggregate or particle size. The differences in root–soil contact could not be explained solely by the decrease in porosity with decreasing aggregate size but may also result from changes in particle and aggregate packing around the root.

3D digital elevation model generation

This chapter presents techniques used for the generation of 3D digital elevation models (DEMs) from remotely sensed data. Three methods are explored and discussed—optical stereoscopic imagery, Interferometric Synthetic Aperture Radar (InSAR), and LIght Detection and Ranging (LIDAR). For each approach, the state-of-the-art presented in the literature is reviewed. Techniques involved in DEM generation are presented with accuracy evaluation. Results of DEMs reconstructed from remotely sensed data are illustrated. While the processes of DEM generation from satellite stereoscopic imagery represents a good example of passive, multi-view imaging technology, discussed in Chap. 2 of this book, InSAR and LIDAR use different principles to acquire 3D information. With regard to InSAR and LIDAR, detailed discussions are conducted in order to convey the fundamentals of both technologies.

The ModFOLD4 server for the quality assessment of 3D protein models

Once you have generated a 3D model of a protein, how do you know whether it bears any resemblance to the actual structure? To determine the usefulness of 3D models of proteins, they must be assessed in terms of their quality by methods that predict their similarity to the native structure. The ModFOLD4 server is the latest version of our leading independent server for the estimation of both the global and local (per-residue) quality of 3D protein models. The server produces both machine readable and graphical output, providing users with intuitive visual reports on the quality of predicted protein tertiary structures. The ModFOLD4 server is freely available to all at: http://www.reading.ac.uk/bioinf/ModFOLD/.

Performance analysis of MIMO MRC in 3D mobile-to-mobile double-correlated channels

In this paper, we consider multiple-input multiple- output (MIMO) maximal ratio combining (MRC) systems and assess the system performance in terms of average symbol error probability (SEP), outage probability and ergodic capacity in double-correlated Rayleigh-and-Lognormal fading channels. In order to derive the receive and transmit correlation functions needed for the performance analysis, a three-dimensional (3D) MIMO mobile-to-mobile (M-to-M) channel model, which takes into account the effects of fast fading and shadowing is used. Numerical results are provided to show the effects of system parameters, such as maximum elevation angle of scatterers, orientation angle of antenna array in the x-y plane, angle between x-y plane and the antenna array orientation, and degree of scattering in the x-y plane, on the system performance.

3D cloud reconstructions: evaluation of scanning radar scan strategy with a view to surface shortwave radiation closure

The ability of six scanning cloud radar scan strategies to reconstruct cumulus cloud fields for radiation study is assessed. Utilizing snapshots of clean and polluted cloud fields from large eddy simulations, an analysis is undertaken of error in both the liquid water path and monochromatic downwelling surface irradiance at 870 nm of the reconstructed cloud fields. Error introduced by radar sensitivity, choice of radar scan strategy, retrieval of liquid water content (LWC), and reconstruction scheme is explored. Given an in␣nitely sensitive radar and perfect LWC retrieval, domain average surface irradiance biases are typically less than 3 W m␣2 ␣m␣1, corresponding to 5–10% of the cloud radiative effect (CRE). However, when using a realistic radar sensitivity of ␣37.5 dBZ at 1 km, optically thin areas and edges of clouds are dif␣cult to detect due to their low radar re-ectivity; in clean conditions, overestimates are of order 10 W m␣2 ␣m␣1 (~20% of the CRE), but in polluted conditions, where the droplets are smaller, this increases to 10–26 W m␣2 ␣m␣1 (~40–100% of the CRE). Drizzle drops are also problematic; if treated as cloud droplets, reconstructions are poor, leading to large underestimates of 20–46 W m␣2 ␣m␣1 in domain average surface irradiance (~40–80% of the CRE). Nevertheless, a synergistic retrieval approach combining the detailed cloud structure obtained from scanning radar with the droplet-size information and location of cloud base gained from other instruments would potentially make accurate solar radiative transfer calculations in broken cloud possible for the first time.

Issues and benefits of using 3D Interfaces: visual and verbal tasks

Spatial memory is important for locating objects in hierarchical data structures, such as desktop folders. There are, however, some contradictions in literature concerning the effectiveness of 3D user interfaces when compared to their 2D counterparts. This paper uses a task-based approach in order to investigate the effectiveness of adding a third dimension to specific user tasks, i.e. the impact of depth on navigation in a 3D file manager. Results highlight issues and benefits of using 3D interfaces for visual and verbal tasks, and introduces the possible existence of a correlation between aptitude scores achieved on the Guilford- Zimmerman Orientation Survey and Electroencephalography- measured brainwave activity as participants search for targets of variable perceptual salience in 2D and 3D environments.

Assessing the quality of modelled 3D protein structures using the ModFOLD server

Model quality assessment programs (MQAPs) aim to assess the quality of modelled 3D protein structures. The provision of quality scores, describing both global and local (per-residue) accuracy are extremely important, as without quality scores we are unable to determine the usefulness of a 3D model for further computational and experimental wet lab studies.Here, we briefly discuss protein tertiary structure prediction, along with the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) competition and their key role in driving the field of protein model quality assessment methods (MQAPs). We also briefly discuss the top MQAPs from the previous CASP competitions. Additionally, we describe our downloadable and webserver-based model quality assessment methods: ModFOLD3, ModFOLDclust, ModFOLDclustQ, ModFOLDclust2, and IntFOLD-QA. We provide a practical step-by-step guide on using our downloadable and webserver-based tools and include examples of their application for improving tertiary structure prediction, ligand binding site residue prediction, and oligomer predictions.

Representing 3D shape and location

The 3D shape of an object and its 3D location have traditionally thought of as very separate entities, although both can be described within a single 3D coordinate frame. Here, 3D shape and location are considered as two aspects of a view-based approach to representing depth, avoiding the use of 3D coordinate frames.

Nuclear Factor-kappaB controls the reaggregation of 3D neurosphere cultures in vitro

The approach of reaggregation involves the regeneration and self-renewal of histotypical 3D spheres from isolated tissue kept in suspension culture. Reaggregated spheres can be used as tumour, genetic, biohybrid and neurosphere models. In addition the functional superiority of 3D aggregates over conventional 2D cultures developed the use of neurospheres for brain engineering of CNS diseases. Thus 3D aggregate cultures created enormous interest in mechanisms that regulate the formation of multicellular aggregates in vitro. Here we analyzed mechanisms guiding the development of 3D neurosphere cultures. Adult neural stem cells can be cultured as self-adherent clusters, called neurospheres. Neurospheres are characterised as heterogeneous clusters containing unequal stem cell sub-types. Tumour necrosis factor-alpha (TNF-alpha is one of the crucial inflammatory cytokines with multiple actions on several cell types. TNF-alpha strongly activates the canonical Nuclear Factor Kappa-B (NF- kappaB) pathway. In order to investigate further functions of TNF in neural stem cells (NSCs) we tested the hypothesis that TNF is able to modulate the motility and/or migratory behaviour of SVZ derived adult neural stem cells. We observed a significantly faster sphere formation in TNF treated cultures than in untreated controls. The very fast aggregation of isolated NSCs (<2h) is a commonly observed phenomenon, though the mechanisms of 3D neurosphere formation remain largely unclear. Here we demonstrate for the first time, increased aggregation and enhanced motility of isolated NSCs in response to the TNF-stimulus. Moreover, this phenomenon is largely dependent on activated transcription factor NF-kappaB. Both, the pharmacological blockade of NF-kappaB pathway by pyrrolidine dithiocarbamate (PDTC) or Bay11-7082 and genetic blockade by expression of a transdominant-negative super-repressor IkappaB-AA1 led to decreased aggregation.