Protein fold recognition score functions: Unusual construction strategies

We describe two ways of optimizing score functions for protein sequence to structure threading. The first method adjusts parameters to improve sequence to structure alignment. The second adjusts parameters so as to improve a score function's ability to rank alignments calculated in the first score function. Unlike those functions known as knowledge-based force fields, the resulting parameter sets do not rely on Boltzmann statistics, have no claim to representing free energies and are purely constructions for recognizing protein folds. The methods give a small improvement, but suggest that functions can be profitably optimized for very specific aspects of protein fold recognition, Proteins 1999;36:454-461. (C) 1999 Wiley-Liss, Inc.

Prediction of mortality in patients without angina: Use of an exercise score and exercise echocardiography

Background Exercise testing has limited efficacy for identifying coronary artery disease (CAD) in the absence of anginal. symptoms. Exercise echocardiography is more accurate than standard exercise testing, but its efficacy in this situation has not been defined. We sought to identify whether the Duke treadmill. score or exercise echocardiography (ExE) could be used to identify risk in patients without anginal symptoms. Methods We studied 1859 patients without typical or atypical angina, heart failure, or a history or ECG evidence of infarction or CAD, who were referred for ExE, of whom 1832 (age 51 15 years, 944 men) were followed for up to 10 years. The presence and extent of ischaemia and scar were interpreted by expert reviewers at the time of the original study. Results Exercise provoked significant (>0.1 mV) ST segment depression in 215 patients (12%), and wall motion abnormalities in 137 (8%). Seventy-eight patients (4%) died before revascularization, only 17 from known cardiac causes. The independent predictors of death were age (RR 1.1, p

A clinical and echocardiographic score for assigning risk of major events after dobutamine echocardiograms

OBJECTIVES We sought to develop and validate a risk score combining both clinical and dobutamine echocardiographic (DbE) features in 4,890 patients who underwent DbE at three expert laboratories and were followed for death or myocardial infarction for up to five years. BACKGROUND In contrast to exercise scores, no score exists to combine clinical, stress, and echocardiographic findings with DbE. METHODS Dobutamine echocardiography was performed for evaluation of known or suspected coronary artery disease in 3,156 patients at two sites in the U.S. After exclusion of patients with incomplete follow-up, 1,456 DbEs were randomly selected to develop a multivariate model for prediction of events. After simplification of each model for clinical use, the models were internally validated in the remaining DbE patients in the same series and externally validated in 1,733 patients in an independent series. RESULTS The following score was derived from regression models in the modeling group (160 events): DbE risk = (age (.) 0.02) + (heart failure + rate-pressure product <15,000) (.) 0.4 + (ischemia + scar) (.) 0.6. The presence of each variable was scored as 1 and its absence scored as 0, except for age (continuous variable). Using cutoff values of 1.2 and 2.6, patients were classified into groups with five-year event-free survivals >95%, 75% to 95%, and <75%. Application of the score in the internal validation group (265 events) gave equivalent results, as did its application in the external validation group (494 events, C index = 0.72). CONCLUSIONS A risk score based on clinical and echocardiographic data may be used to quantify the risk of events in patients undergoing DbE. (C) 2004 by the American College of Cardiology Foundation.

A simple lifestyle score predicts survival in healthy elderly men

Background. Although improvements in life expectancy have been attributed in part to the adoption or a more prudent lifestyle, few studies have examined the association of lifestyle with survival, using several lifestyle factors simultaneously, in a healthy elderly population. Methods. We investigated the association of health related behaviors with mortality in 7989 men aged 65 to 83 years participating in a population-based trial in Perth, Western Australia, by calculating a lifestyle score as a simple tally of flow many or eight prudent behaviors each individual followed. Results. Invitations to screening produced a corrected response of 70.5%. Out of a possible score of 8.46% of men had a score of less than 5. Within 5 years, a total of 703 men (9%) had died from any cause. The hazard ratio in men with a low lifestyle score was 1.3 [95% confidence interval (CI): 1.1-1.5] compared with men with a score of 5 or more. Conclusions. Lifestyle remains an important predictor of mortality even in old age. Survival in older men without a history of cardiovascular disease can potentially be enhanced by promoting a healthy lifestyle. © 2004 Elsevier Inc, All rights reserved.

Genes for the majority of group A streptococcal virulence factors and extracellular surface proteins do not confer an increased propensity to cause invasive disease

Background. The factors behind the reemergence of severe, invasive group A streptococcal (GAS) diseases are unclear, but it could be caused by altered genetic endowment in these organisms. However, data from previous studies assessing the association between single genetic factors and invasive disease are often conflicting, suggesting that other, as-yet unidentified factors are necessary for the development of this class of disease. Methods. In this study, we used a targeted GAS virulence microarray containing 226 GAS genes to determine the virulence gene repertoires of 68 GAS isolates (42 associated with invasive disease and 28 associated with noninvasive disease) collected in a defined geographic location during a contiguous time period. We then employed 3 advanced machine learning methods (genetic algorithm neural network, support vector machines, and classification trees) to identify genes with an increased association with invasive disease. Results. Virulence gene profiles of individual GAS isolates varied extensively among these geographically and temporally related strains. Using genetic algorithm neural network analysis, we identified 3 genes with a marginal overrepresentation in invasive disease isolates. Significantly, 2 of these genes, ssa and mf4, encoded superantigens but were only present in a restricted set of GAS M-types. The third gene, spa, was found in variable distributions in all M-types in the study. Conclusions. Our comprehensive analysis of GAS virulence profiles provides strong evidence for the incongruent relationships among any of the 226 genes represented on the array and the overall propensity of GAS to cause invasive disease, underscoring the pathogenic complexity of these diseases, as well as the importance of multiple bacteria and/ or host factors.

Development of a clinical and echocardiographic score for assigning risk of major events after exercise and dobutamine echocardiograms

The prognostic value of exercise (EXE) and dobutamine echocardiograms (DbE) has been well defined in large studies. However, while risk is determined by both clinical and echo features, no simple means of combining these data has been defined. We sought to combine these data into risk scores. Methods. At 3 expert centers, 7650 pts underwent standard EXE (n=5211) and DbE (w2439) for evaluation of known or suspected CAD and were followed for up to 10 years (mean 5-2) for major events (death or myocardial infarction). A subgroup of 2953 EXE and 1025 DbE pts was randomly selected to develop separate multivariate models for prediction of events. After simplication of each model for clinical use, models were validated in the remaining EXE and DbE pts. ResuI1s. The total number of events was 200 in the EXE and 225 in the DbE pts, of which 58 and 99 events occurred in the respective testing groups. The following regression equations gave equivalent results I” the testing and validation groups for both EXE and DbE; DbE = (Age’O.02) + (DM’l .O) + (Low RPP’0.6) + ([CHF+lschemia+Scar]‘O.7) EXE = ([DM+CHF]‘O.S) + O.S(lschemla #) + l.B(Scar#) - (METS0.19) (where each categorical variable scored 1 when present and 0 when absent, Ischemia# = 1 for l-2 VD. 6 for 3 VD; Scar# = 1 for 1-2 VD, 1.7 for 3 VD). The table summarizes the scores and equivalent outcomes for EXE and DbE. Conclusions. Risk scores based on clinical and EXE or DbE results may be used to quantify the risk of events during follow-up.

Assessing the competitiveness of loss allocation methods in a deregulated electricity market

This paper critically assesses several loss allocation methods based on the type of competition each method promotes. This understanding assists in determining which method will promote more efficient network operations when implemented in deregulated electricity industries. The methods addressed in this paper include the pro rata [1], proportional sharing [2], loss formula [3], incremental [4], and a new method proposed by the authors of this paper, which is loop-based [5]. These methods are tested on a modified Nordic 32-bus network, where different case studies of different operating points are investigated. The varying results obtained for each allocation method at different operating points make it possible to distinguish methods that promote unhealthy competition from those that encourage better system operation.

Calculation of line integrals in boundary integral methods

We propose quadrature rules for the approximation of line integrals possessing logarithmic singularities and show their convergence. In some instances a superconvergence rate is demonstrated.

A framework for electricity price spike analysis with advanced data mining methods

There are many techniques for electricity market price forecasting. However, most of them are designed for expected price analysis rather than price spike forecasting. An effective method of predicting the occurrence of spikes has not yet been observed in the literature so far. In this paper, a data mining based approach is presented to give a reliable forecast of the occurrence of price spikes. Combined with the spike value prediction techniques developed by the same authors, the proposed approach aims at providing a comprehensive tool for price spike forecasting. In this paper, feature selection techniques are firstly described to identify the attributes relevant to the occurrence of spikes. A simple introduction to the classification techniques is given for completeness. Two algorithms: support vector machine and probability classifier are chosen to be the spike occurrence predictors and are discussed in details. Realistic market data are used to test the proposed model with promising results.

A demonstration of artificial dissipation effects in some finite volume solution methods for the Navier-Stokes equations

The artificial dissipation effects in some solutions obtained with a Navier-Stokes flow solver are demonstrated. The solvers were used to calculate the flow of an artificially dissipative fluid, which is a fluid having dissipative properties which arise entirely from the solution method itself. This was done by setting the viscosity and heat conduction coefficients in the Navier-Stokes solvers to zero everywhere inside the flow, while at the same time applying the usual no-slip and thermal conducting boundary conditions at solid boundaries. An artificially dissipative flow solution is found where the dissipation depends entirely on the solver itself. If the difference between the solutions obtained with the viscosity and thermal conductivity set to zero and their correct values is small, it is clear that the artificial dissipation is dominating and the solutions are unreliable.

A shift from passive teaching at medical conferences to more interactive methods improves physician learning

Conferences that deliver interactive sessions designed to enhance physician participation, such as role play, small discussion groups, workshops, hands-on training, problem- or case-based learning and individualised training sessions, are effective for physician education.

Appropriate surveying methods in the Philippines: Can modern GPS units help?

An investigation was undertaken to test the effectiveness of two procedures for recording boundaries and plot positions for scientific studies on farms on Leyte Island, the Philippines. The accuracy of a Garmin 76 Global Positioning System (GPS) unit and a compass and chain was checked under the same conditions. Tree canopies interfered with the ability of the satellite signal to reach the GPS and therefore the GPS survey was less accurate than the compass and chain survey. Where a high degree of accuracy is required, a compass and chain survey remains the most effective method of surveying land underneath tree canopies, providing operator error is minimised. For a large number of surveys and thus large amounts of data, a GPS is more appropriate than a compass and chain survey because data are easily up-loaded into a Geographic Information System (GIS). However, under dense canopies where satellite signals cannot reach the GPS, it may be necessary to revert to a compass survey or a combination of both methods.