Functional site prediction selects correct protein models

<p>Abstract</p> <p>Background</p> <p>The prediction of protein structure can be facilitated by the use of constraints based on a knowledge of functional sites. Without this information it is still possible to predict which residues are likely to be part of a functional site and this information can be used to select model structures from a variety of alternatives that would correspond to a functional protein.</p> <p>Results</p> <p>Using a large collection of protein-like decoy models, a score was devised that selected those with predicted functional site residues that formed a cluster. When tested on a variety of small <it>α</it>/<it>β</it>/<it>α </it>type proteins, including enzymes and non-enzymes, those that corresponded to the native fold were ranked highly. This performance held also for a selection of larger <it>α</it>/<it>β</it>/<it>α </it>proteins that played no part in the development of the method.</p> <p>Conclusion</p> <p>The use of predicted site positions provides a useful filter to discriminate native-like protein models from non-native models. The method can be applied to any collection of models and should provide a useful aid to all modelling methods from <it>ab initio </it>to homology based approaches.</p

Mathematical models for the cure and viscosity characteristics of an epoxy resin and their applications in computer simulations of composite material manufacturing processes

Aspects that affect the manufacture ofaeroengine components in carbon fibre reinforced epoxyresin composite material are described and in particular.factors influencing the process of consolidation ofpreimpregnated material laminates to final componentform are critically assessed. Attention is drawn to theneed both to acquire a full understanding of the physicsof the consolidation process and to obtain quantitativeprocess control data for efficient development andsubsequent production of new components.All the variables associated with the processof laminate consolidation are dependent on basic matrixresin characteristics especially its cure advancement andthe consequent effect on the resin viscosity at allstages of a moulding cycle. To quantify the matrix resinchernorheological behaviour, methods for the generation ofmathematical models for the cure and viscosity changesundergone by a dicyandiamide (DICY) cured epoxy resinsystem are described. By the use of these mathematicalmodels a program for use on a personal computer has beenwritten by means of which the cure,exotherTnic heatgeneration and viscosity of the resin may be simulatedunder both isothermal and linear temperature rampconditions.Examples are included of the application of themodels in the solution of problems encountered in theautoclave process for composoite material components

Stochastic programming approach for optimal day-ahead market bidding curves of a microgrid

The deregulation of electricity markets has driven the need to optimise market bidding strategies, e.g. when and how much electricity to buy or sell, in order to gain an economic advantage in a competitive market environment. The present work aims to determine optimal day-ahead market bidding curves for a microgrid comprised of a battery, power generator, photovoltaic (PV) system and an electricity load from a commercial building. Existing day-ahead market bidding models heuristically fix price values for each allowed bidding curve point prior to the optimisation problem or relax limitations set by market rules on the number of price–quantity points per curve. In contrast, this work integrates the optimal selection of prices for the construction of day-ahead market bidding curves into the optimisation of the energy system schedule; aiming to further enhance the bidding curve accuracy while remaining feasible under present market rules. The examined optimisation problem is formulated as a mixed integer linear programming (MILP) model, embedded in a two-stage stochastic programming approach. Uncertainty is considered in the electricity price and the PV power. First stage decisions are day-ahead market bidding curves, while the overall objective is to minimise the expected operational cost of the microgrid. The bidding strategy derived is then examined through Monte Carlo simulations by comparing it against a deterministic approach and two alternative stochastic bidding approaches from literature

Surface Chemistry of Perfluoropolyethers and Hydrogenated Analogs: Are Studies of Model Compounds Useful?

We have studied adsorption, desorption, and decomposition of ethers on Ru(001), an atomically-smooth metal surface. We have compared diethers with monoethers, and fluorinated ethers with hydrogenated ethers. The number of ether linkages does not strongly influence adsorption bond strength, nor the extent of decomposition. Fluorination does weaken the adsorption bond strength and prevents decomposition. These studies suggest that the surface properties of monomeric ethers can be used to predict properties of oligomeric, and perhaps even polymeric, ethers

A revised edition of the readiness to change questionnaire (treatment version)

The UK Alcohol Treatment Trial provided an opportunity to examine the factor structure of the Readiness to Change Questionnaire-Treatment Version (RCQ[TV]) in a large sample (N = 742) of individuals in treatment for alcohol problems who were given the RCQ[TV] at baseline, 3-months and 12-months follow-up. Confirmatory factor analysis of the previously reported factor structure (5 items for each of Precontemplation, Contemplation and Action scales) resulted in a relatively poor fit to the data. Removal of one item from each of the scales resulted in a 12-item instrument for which goodness-of-fit indices were improved, without loss of internal consistency of the three scales, on all three measurement occasions. Inspection of relationships between stage allocation by the new instrument and negative alcohol outcome expectancies provided evidence of improved construct validity for the revised edition of the RCQ[TV]. There was also a strong relationship between stage allocation at 3-months follow-up and outcome of treatment at 12 months. The revised edition of the RCQ[TV] offers researchers and clinicians a shorter and improved measurement of stage of change in the alcohol treatment population

Simulating Reionization: Character and Observability

In recent years there has been considerable progress in our understanding of the nature and properties of the reionization process. In particular, the numerical simulations of this epoch have made a qualitative leap forward, reaching sufficiently large scales to derive the characteristic scales of the reionization process and thus allowing for realistic observational predictions. Our group has recently performed the first such large-scale radiative transfer simulations of reionization, run on top of state-of-the-art simulations of early structure formation. This allowed us to make the first realistic observational predictions about the Epoch of Reionization based on detailed radiative transfer and structure formation simulations. We discuss the basic features of reionization derived from our simulations and some recent results on the observational implications for the high-redshift Ly-alpha sources.Comment: 3 pages, to appear in the Proceedings of First Stars III, Santa Fe, July 2007, AIP Conference Serie

Negative and positive selection of antigen-specific cytotoxic T lymphocytes affected by the α3 domain of MHC I molecules

THE α1 and α2 domains of major histocompatibility complex (MHC) class I molecules function in the binding and presentation of foreign peptides to the T-cell antigen receptor and control both negative and positive selection of the T-cell repertoire. Although the α3 domain of class I is not involved in peptide binding, it does interact with the T-cell accessory molecule, CDS. CDS is important in the selection of T cells as anti-CDS antibody injected into perinatal mice interfers with this process. We previously used a hybrid class I molecule with the α1/α2 domains from L^d and the α3 domain from Q7^b and showed that this molecule binds an L^d-restricted peptide but does not interact with CD8-dependent cytotoxic T lymphocytes. Expression of this molecule in transgenic mice fails to negatively select a subpopulation of anti-L^d cytotoxic T lymphocytes. In addition, positive selection of virus-specific L^d-restricted cytotoxic T lymphocytes does not occur. We conclude that besides the α1/α2 domains of class I, the α3 domain plays an important part in both positive and negative selection of antigen-specific cells

The Risk of Unexploded Ordnance on Construction Sites in London

Greater London, among many large cities, was subject to bombing by the German military in both the World Wars and was the target of many air raids during the Second World War (WW2). This was particularly the case during the Blitz, September 1940 – May 1941, when over 28,000 high explosive bombs and parachute mines were dropped on London. Post war research conducted in 1949 estimated that approximately 12,750 t of bombs, including V1 and V2 rockets, were dropped on London. The night of 16th – 17th April 1941 was one of the worst bombing raids, when 446 t of bombs were dropped on London and over 58 t did not detonate. Unexploded bombs remain buried underground today, as they were unidentified at the time or abandoned owing to difficulties in recovering them. Uncharted bombs continue to pose a potentially significant hazard for developments around London. This paper considers the probability of discovering unexploded ordnance (UXO), particularly WW2 ordnance, during intrusive groundworks in London. The prevalence of unexploded ordnance has been assessed using data obtained from governmental organisations to estimate the likelihood of discovery in London

Elementary Forms of the Metaphorical Life : Tropes at Work in Durkheim’s Theory of the Religious

Peer reviewedPostprin