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.

Does increased hydrochemical model complexity decrease robustness?

The aim of this study was, within a sensitivity analysis framework, to determine if additional model complexity gives a better capability to model the hydrology and nitrogen dynamics of a small Mediterranean forested catchment or if the additional parameters cause over-fitting. Three nitrogen-models of varying hydrological complexity were considered. For each model, general sensitivity analysis (GSA) and Generalized Likelihood Uncertainty Estimation (GLUE) were applied, each based on 100,000 Monte Carlo simulations. The results highlighted the most complex structure as the most appropriate, providing the best representation of the non-linear patterns observed in the flow and streamwater nitrate concentrations between 1999 and 2002. Its 5% and 95% GLUE bounds, obtained considering a multi-objective approach, provide the narrowest band for streamwater nitrogen, which suggests increased model robustness, though all models exhibit periods of inconsistent good and poor fits between simulated outcomes and observed data. The results confirm the importance of the riparian zone in controlling the short-term (daily) streamwater nitrogen dynamics in this catchment but not the overall flux of nitrogen from the catchment. It was also shown that as the complexity of a hydrological model increases over-parameterisation occurs, but the converse is true for a water quality model where additional process representation leads to additional acceptable model simulations. Water quality data help constrain the hydrological representation in process-based models. Increased complexity was justifiable for modelling river-system hydrochemistry. Increased complexity was justifiable for modelling river-system hydrochemistry.

Climate variability-observations, reconstructions, and model simulations for the Atlantic-European and Alpine region from 1500-2100 AD

A detailed analysis is undertaken of the Atlantic-European climate using data from 500-year-long proxy-based climate reconstructions, a long climate simulation with perpetual 1990 forcing, as well as two global and one regional climate change scenarios. The observed and simulated interannual variability and teleconnectivity are compared and interpreted in order to improve the understanding of natural climate variability on interannual to decadal time scales for the late Holocene. The focus is set on the Atlantic-European and Alpine regions during the winter and summer seasons, using temperature, precipitation, and 500 hPa geopotential height fields. The climate reconstruction shows pronounced interdecadal variations that appear to “lock” the atmospheric circulation in quasi-steady long-term patterns over multi-decadal periods controlling at least part of the temperature and precipitation variability. Different circulation patterns are persistent over several decades for the period 1500 to 1900. The 500-year-long simulation with perpetual 1990 forcing shows some substantial differences, with a more unsteady teleconnectivity behaviour. Two global scenario simulations indicate a transition towards more stable teleconnectivity for the next 100 years. Time series of reconstructed and simulated temperature and precipitation over the Alpine region show comparatively small changes in interannual variability within the time frame considered, with the exception of the summer season, where a substantial increase in interannual variability is simulated by regional climate models.

Sources of multi-decadal variability in Arctic sea ice extent

The observed dramatic decrease in September sea ice extent (SIE) has been widely discussed in the scientific literature. Though there is qualitative agreement between observations and ensemble members of the Third Coupled Model Intercomparison Project (CMIP3), it is concerning that the observed trend (1979–2010) is not captured by any ensemble member. The potential sources of this discrepancy include: observational uncertainty, physical model limitations and vigorous natural climate variability. The latter has received less attention and is difficult to assess using the relatively short observational sea ice records. In this study multi-centennial pre-industrial control simulations with five CMIP3 climate models are used to investigate the role that the Arctic oscillation (AO), the Atlantic multi-decadal oscillation (AMO) and the Atlantic meridional overturning circulation (AMOC) play in decadal sea ice variability. Further, we use the models to determine the impact that these sources of variability have had on SIE over both the era of satellite observation (1979–2010) and an extended observational record (1953–2010). There is little evidence of a relationship between the AO and SIE in the models. However, we find that both the AMO and AMOC indices are significantly correlated with SIE in all the models considered. Using sensitivity statistics derived from the models, assuming a linear relationship, we attribute 0.5–3.1%/decade of the 10.1%/decade decline in September SIE (1979–2010) to AMO driven variability.

A kinetic model for the formation of acrylamide during the finish-frying of commercial French fries

Acrylamide is formed from reducing sugars and asparagine during the preparation of French fries. The commercial preparation of French fries is a multi-stage process involving the preparation of frozen, par-fried potato strips for distribution to catering outlets where they are finish fried. The initial blanching, treatment in glucose solution and par-frying steps are crucial since they determine the levels of precursors present at the beginning of the finish frying process. In order to minimize the quantities of acrylamide in cooked fries, it is important to understand the impact of each stage on the formation of acrylamide. Acrylamide, amino acids, sugars, moisture, fat and color were monitored at time intervals during the frying of potato strips which had been dipped in varying concentrations of glucose and fructose during a typical pretreatment. A mathematical model of the finish-frying was developed based on the fundamental chemical reaction pathways, incorporating moisture and temperature gradients in the fries. This showed the contribution of both glucose and fructose to the generation of acrylamide, and accurately predicted the acrylamide content of the final fries.

Comparative study of the performance of the M-cycle counter-flow and cross-flow heat exchangers for indirect evaporative cooling - paving the path towards sustainable cooling of buildings

This paper provides a comparative study of the performance of cross-flow and counter-flow M-cycle heat exchangers for dew point cooling. It is recognised that evaporative cooling systems offer a low energy alternative to conventional air conditioning units. Recently emerged dew point cooling, as the renovated evaporative cooling configuration, is claimed to have much higher cooling output over the conventional evaporative modes owing to use of the M-cycle heat exchangers. Cross-flow and counter-flow heat exchangers, as the available structures for M-cycle dew point cooling processing, were theoretically and experimentally investigated to identify the difference in cooling effectiveness of both under the parallel structural/operational conditions, optimise the geometrical sizes of the exchangers and suggest their favourite operational conditions. Through development of a dedicated computer model and case-by-case experimental testing and validation, a parametric study of the cooling performance of the counter-flow and cross-flow heat exchangers was carried out. The results showed the counter-flow exchanger offered greater (around 20% higher) cooling capacity, as well as greater (15%–23% higher) dew-point and wet-bulb effectiveness when equal in physical size and under the same operating conditions. The cross-flow system, however, had a greater (10% higher) Energy Efficiency (COP). As the increased cooling effectiveness will lead to reduced air volume flow rate, smaller system size and lower cost, whilst the size and cost are the inherent barriers for use of dew point cooling as the alternation of the conventional cooling systems, the counter-flow system is considered to offer practical advantages over the cross-flow system that would aid the uptake of this low energy cooling alternative. In line with increased global demand for energy in cooling of building, largely by economic booming of emerging developing nations and recognised global warming, the research results will be of significant importance in terms of promoting deployment of the low energy dew point cooling system, helping reduction of energy use in cooling of buildings and cut of the associated carbon emission.

Correction of atmospheric delay effects in radar interferometry using a nested mesoscale atmospheric model

The temporal variability of the atmosphere through which radio waves pass in the technique of differential radar interferometry can seriously limit the accuracy with which the method can measure surface motion. A forward, nested mesoscale model of the atmosphere can be used to simulate the variable water content along the radar path and the resultant phase delays. Using this approach we demonstrate how to correct an interferogram of Mount Etna in Sicily associated with an eruption in 2004-5. The regional mesoscale model (Unified Model) used to simulate the atmosphere at higher resolutions consists of four nested domains increasing in resolution (12, 4, 1, 0.3 km), sitting within the analysis version of a global numerical model that is used to initiate the simulation. Using the high resolution 3D model output we compute the surface pressure, temperature and the water vapour, liquid and solid water contents, enabling the dominant hydrostatic and wet delays to be calculated at specific times corresponding to the acquisition of the radar data. We can also simulate the second-order delay effects due to liquid water and ice.

The role of northern Arabian Sea surface temperature biases in CMIP5 model simulations and future projections of Indian summer monsoon rainfall

Many climate models have problems simulating Indian summer monsoon rainfall and its variability, resulting in considerable uncertainty in future projections. Problems may relate to many factors, such as local effects of the formulation of physical parametrisation schemes, while common model biases that develop elsewhere within the climate system may also be important. Here we examine the extent and impact of cold sea surface temperature (SST) biases developing in the northern Arabian Sea in the CMIP5 multi-model ensemble, where such SST biases are shown to be common. Such biases have previously been shown to reduce monsoon rainfall in the Met Office Unified Model (MetUM) by weakening moisture fluxes incident upon India. The Arabian Sea SST biases in CMIP5 models consistently develop in winter, via strengthening of the winter monsoon circulation, and persist into spring and summer. A clear relationship exists between Arabian Sea cold SST bias and weak monsoon rainfall in CMIP5 models, similar to effects in the MetUM. Part of this effect may also relate to other factors, such as forcing of the early monsoon by spring-time excessive equatorial precipitation. Atmosphere-only future time-slice experiments show that Arabian Sea cold SST biases have potential to weaken future monsoon rainfall increases by limiting moisture flux acceleration through non-linearity of the Clausius-Clapeyron relationship. Analysis of CMIP5 model future scenario simulations suggests that, while such effects are likely small compared to other sources of uncertainty, models with large Arabian Sea cold SST biases suppress the range of potential outcomes for changes to future early monsoon rainfall.

Janus PEG-based dendrimers for use in combination therapy: controlled multi-drug loading and sequential release

The increasing use of drug combinations to treat disease states, such as cancer, calls for improved delivery systems that are able to deliver multiple agents. Herein, we report a series of novel Janus dendrimers with potential for use in combination therapy. Different generations (first and second) of PEG-based dendrons containing two different “model drugs”, benzyl alcohol (BA) and 3-phenylpropionic acid (PPA), were synthesized. BA and PPA were attached via two different linkers (carbonate and ester, respectively) to promote differential drug release. The four dendrons were coupled together via (3 + 2) cycloaddition chemistries to afford four Janus dendrimers, which contained varying amounts and different ratios of BA and PPA, namely, (BA)2-G1-G1-(PPA)2, (BA)4-G2-G1-(PPA)2, (BA)2-G1-G2-(PPA)4, and (BA)4-G2-G2-(PPA)4. Release studies in plasma showed that the dendrimers provided sequential release of the two model drugs, with BA being released faster than PPA from all of the dendrons. The different dendrimers allowed delivery of increasing amounts (0.15–0.30 mM) and in exact molecular ratios (1:2; 2:1; 1:2; 2:2) of the two model drug compounds. The dendrimers were noncytotoxic (100% viability at 1 mg/mL) toward human umbilical vein endothelial cells (HUVEC) and nontoxic toward red blood cells, as confirmed by hemolysis studies. These studies demonstrate that these Janus PEG-based dendrimers offer great potential for the delivery of drugs via combination therapy.

Hurricane-type vortices in a general circulation model

A very high resolution atmospheric general circulation model, T106-L19, has been used for the simulation of hurricanes in a multi-year numerical experiment. Individual storms as well as their geographical and seasonal distribution agree remarkably well with observations. In spite of the fact that only the thermal and dynamical structure of the storms have been used as criteria of their identification, practically all of them occur in areas where the sea surface temperature is higher or equal to 26 °C. There are considerable variations from year to year in the number of storms in spite of the fact that there are no interannual variations in the SST pattern. It is found that the number of storms in particular areas appear to depend on the intensity of the Hadley-Walker cell. The result is clearly resolution-dependant. At lower horizonal resolution, T42, for example, the intensity of the storms is significantly reduced and their overall structure is less realistic, including their vertical form and extent.

Reliability of regional climate model trends

A necessary condition for a good probabilistic forecast is that the forecast system is shown to be reliable: forecast probabilities should equal observed probabilities verified over a large number of cases. As climate change trends are now emerging from the natural variability, we can apply this concept to climate predictions and compute the reliability of simulated local and regional temperature and precipitation trends (1950–2011) in a recent multi-model ensemble of climate model simulations prepared for the Intergovernmental Panel on Climate Change (IPCC) fifth assessment report (AR5). With only a single verification time, the verification is over the spatial dimension. The local temperature trends appear to be reliable. However, when the global mean climate response is factored out, the ensemble is overconfident: the observed trend is outside the range of modelled trends in many more regions than would be expected by the model estimate of natural variability and model spread. Precipitation trends are overconfident for all trend definitions. This implies that for near-term local climate forecasts the CMIP5 ensemble cannot simply be used as a reliable probabilistic forecast.

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 influence of anthropogenic aerosol on multi-decadal variations of historical global climate

Analysis of single forcing runs from CMIP5 (the fifth Coupled Model Intercomparison Project) simulations shows that the mid-twentieth century temperature hiatus, and the coincident decrease in precipitation, is likely to have been influenced strongly by anthropogenic aerosol forcing. Models that include a representation of the indirect effect of aerosol better reproduce inter-decadal variability in historical global-mean near-surface temperatures, particularly the cooling in the 1950s and 1960s, compared to models with representation of the aerosol direct effect only. Models with the indirect effect also show a more pronounced decrease in precipitation during this period, which is in better agreement with observations, and greater inter-decadal variability in the inter-hemispheric temperature difference. This study demonstrates the importance of representing aerosols, and their indirect effects, in general circulation models, and suggests that inter-model diversity in aerosol burden and representation of aerosol–cloud interaction can produce substantial variation in simulations of climate variability on multi decadal timescales.

Multi-agent based modeling and simulation of complex system in hospital

This study puts forward a method to model and simulate the complex system of hospital on the basis of multi-agent technology. The formation of the agents of hospitals with intelligent and coordinative characteristics was designed, the message object was defined, and the model operating mechanism of autonomous activities and coordination mechanism was also designed. In addition, the Ontology library and Norm library etc. were introduced using semiotic method and theory, to enlarge the method of system modelling. Swarm was used to develop the multi-agent based simulation system, which is favorable for making guidelines for hospital's improving it's organization and management, optimizing the working procedure, improving the quality of medical care as well as reducing medical charge costs.

A semiotic approach of multi-agent simulation for policy evaluation

Nowadays the changing environment becomes the main challenge for most of organizations, since they have to evaluate proper policies to adapt to the environment. In this paper, we propose a multi-agent simulation method to evaluate policies based on complex adaptive system theory. Furthermore, we propose a semiotic EDA (Epistemic, Deontic, Axiological) agent model to simulate agent's behavior in the system by incorporating the social norms reflecting the policy. A case study is also provided to validate our approach. Our research present better adaptability and validity than the qualitative analysis and experiment approach and the semiotic agent model provides high creditability to simulate agents' behavior.