Automatic design of decision-tree induction algorithms tailored to flexible-receptor docking data

Background: This paper addresses the prediction of the free energy of binding of a drug candidate with enzyme InhA associated with Mycobacterium tuberculosis. This problem is found within rational drug design, where interactions between drug candidates and target proteins are verified through molecular docking simulations. In this application, it is important not only to correctly predict the free energy of binding, but also to provide a comprehensible model that could be validated by a domain specialist. Decision-tree induction algorithms have been successfully used in drug-design related applications, specially considering that decision trees are simple to understand, interpret, and validate. There are several decision-tree induction algorithms available for general-use, but each one has a bias that makes it more suitable for a particular data distribution. In this article, we propose and investigate the automatic design of decision-tree induction algorithms tailored to particular drug-enzyme binding data sets. We investigate the performance of our new method for evaluating binding conformations of different drug candidates to InhA, and we analyze our findings with respect to decision tree accuracy, comprehensibility, and biological relevance. Results: The empirical analysis indicates that our method is capable of automatically generating decision-tree induction algorithms that significantly outperform the traditional C4.5 algorithm with respect to both accuracy and comprehensibility. In addition, we provide the biological interpretation of the rules generated by our approach, reinforcing the importance of comprehensible predictive models in this particular bioinformatics application. Conclusions: We conclude that automatically designing a decision-tree algorithm tailored to molecular docking data is a promising alternative for the prediction of the free energy from the binding of a drug candidate with a flexible-receptor.

Automatic aspect discrimination in data clustering

The attributes describing a data set may often be arranged in meaningful subsets, each of which corresponds to a different aspect of the data. An unsupervised algorithm (SCAD) that simultaneously performs fuzzy clustering and aspects weighting was proposed in the literature. However, SCAD may fail and halt given certain conditions. To fix this problem, its steps are modified and then reordered to reduce the number of parameters required to be set by the user. In this paper we prove that each step of the resulting algorithm, named ASCAD, globally minimizes its cost-function with respect to the argument being optimized. The asymptotic analysis of ASCAD leads to a time complexity which is the same as that of fuzzy c-means. A hard version of the algorithm and a novel validity criterion that considers aspect weights in order to estimate the number of clusters are also described. The proposed method is assessed over several artificial and real data sets.

A structural model of emotions of cognitive dissonances

Cognitive dissonance is the stress that comes from holding two conflicting thoughts simultaneously in the mind, usually arising when people are asked to choose between two detrimental or two beneficial options. In view of the well-established role of emotions in decision making, here we investigate whether the conventional structural models used to represent the relationships among basic emotions, such as the Circumplex model of affect, can describe the emotions of cognitive dissonance as well. We presented a questionnaire to 34 anonymous participants, where each question described a decision to be made among two conflicting motivations and asked the participants to rate analogically the pleasantness and the intensity of the experienced emotion. We found that the results were compatible with the predictions of the Circumplex model for basic emotions. (C) 2012 Elsevier Ltd. All rights reserved.

Evidence-based guidelines for interpreting change scores for the European Organisation for the Research and Treatment of Cancer Quality of Life Questionnaire Core 30

Aim: To use published literature and experts' opinion to investigate the clinical meaning and magnitude of changes in the Quality of Life (QOL) of groups of patients measured with the European Organisation for the Research and Treatment of Cancer Quality of Life Questionnaire Core 30 (EORTC QLQ-C30). Methods: An innovative method combining systematic review of published studies, expert opinions and meta-analysis was used to estimate large, medium, and small mean changes over time for QLQ-C30 scores. Results: Nine hundred and eleven papers were identified, leading to 118 relevant papers. One thousand two hundred and thirty two mean changes in QOL over time were combined in the meta-analysis, with timescales ranging from four days to five years. Guidelines were produced for trivial, small, and medium size classes, for each subscale and for improving and declining scores separately. Estimates for improvements were smaller than respective estimates for declines. Conclusions: These guidelines can be used to aid sample size calculations and interpretation of mean changes over time from groups of patients. Observed mean changes in the QLQ-C30 scores are generally small in most clinical situations, possibly due to response shift. Careful consideration is needed when planning studies where QOL changes over time are of primary interest; the timing of follow up, sample attrition, direction of QOL changes, and subscales of primary interest are key considerations. (C) 2012 Elsevier Ltd. All rights reserved.

Validation of the Short-Version of Rose Angina Questionnaire in Brazil

Background: Stable angina pectoris is a serious condition with few epidemiological studies in Brazil. Objective: To validate the short-version of the Rose angina questionnaire in Brazilian Portuguese for its implementation in surveys and longitudinal studies. Methods: A total of 116 consecutive patients from an outpatient clinic without prior myocardial infarction and/or coronary revascularization were enrolled for application of three questions of the Rose angina questionnaire addressing chest pain after exertion. We used the treadmill test as the gold standard with the Ellestad protocol. Results: The short-version of the Rose angina questionnaire of the 116 subjects submitted to the exercise treadmill test disclosed 89.7% of accuracy, 25% of sensitivity, 92.0% of specificity, 10.0% of positive predictive value, 97.2% of negative predictive value, and 3.1 of positive likelihood ratio and 0.82 of negative likelihood ratio. Conclusion: The Portuguese version with three items of the Rose angina questionnaire is suitable for epidemiological purposes. (Arq Bras Cardiol 2012; 99(5): 1056-1059)

Validity of the Brazilian version of the freezing of gait questionnaire

Objective: To validate the freezing of gait questionnaire (FOG-Q) for a Brazilian population of Parkinson's disease (PD) patients. Methods: One hundred and seven patients with a diagnosis of PD were evaluated by shortened UPDRS motor scale (sUPDRm), Hoehn and Yahr (HY), Schwab and England scale (SE), Berg balance scale (BBS), falls efficacy scale international (FES-I), gait and balance scale (GABS), and the FOG-Q Brazilian version. Results: 47.7% of PD patients had FOG episodes; this group had worse scores on sUPDRSm, FOGQ, FES-I, BBS, GABS and FOG item of UPDRS when compared to the PD group without FOG. The internal consistency was 0.86, intra-rater 0.82 and inter-rater 0.78. The FOG-Q Brazilian version was significantly correlated with items related to gait and balance. The ROC curve was 0.94, the sensitivity was 0.90 and specificity was 0.92. Conclusion: Our study suggests that the FOG-Q Brazilian version is a reliable and valid instrument for assessing FOG in PD patients.

Reliability and validity of spirituality questionnaire by Parsian and Dunning in the Spanish version

The aim of this methodological study was to translate, culturally adapt and assess the internal consistency and validity of the Spanish version of the "Spirituality Questionnaire". The sample comprised 204 young people between 18 and 25 years of age from two universities in Bogota. Cronbach's Alpha was used for reliability, while groups of experts and young people were used for construct validity. The reliability score of the total instrument was 0.88. The overall index of content validity corresponded to 0.90. Exploratory factor analysis showed that four factors explain 52.60% of the variance. The originally proposed theoretical model was confirmed and, in two dimensions, a different structure was proposed. In conclusion, the instrument "Spirituality Questionnaire" by Parsian and Dunning is reliable and valid in the Spanish version.

Estimate of corrected values and the effect of correction for measurement error in dietary data obtained by the Food Frequency Questionnaire for Adolescents (AFFQ)

The scope of this study was to estimate calibrated values for dietary data obtained by the Food Frequency Questionnaire for Adolescents (FFQA) and illustrate the effect of this approach on food consumption data. The adolescents were assessed on two occasions, with an average interval of twelve months. In 2004, 393 adolescents participated, and 289 were then reassessed in 2005. Dietary data obtained by the FFQA were calibrated using the regression coefficients estimated from the average of two 24-hour recalls (24HR) of the subsample. The calibrated values were similar to the the 24HR reference measurement in the subsample. In 2004 and 2005 a significant difference was observed between the average consumption levels of the FFQA before and after calibration for all nutrients. With the use of calibrated data the proportion of schoolchildren who had fiber intake below the recommended level increased. Therefore, it is seen that calibrated data can be used to obtain adjusted associations due to reclassification of subjects within the predetermined categories.

Thoughts on the diversity of convergent evolution of bioluminescence on earth

The widespread independent evolution of analogous bioluminescent systems is one of the most impressive and diverse examples of convergent evolution on earth. There are roughly 30 extant bioluminescent systems that have evolved independently on Earth, with each system likely having unique enzymes responsible for catalysing the bioluminescent reaction. Bioluminescence is a chemical reaction involving a luciferin molecule and a luciferase or photoprotein that results in the emission of light. Some independent systems utilize the same luciferin, such as the use of tetrapyrrolic compounds by krill and dinoflagellates, and the wide use of coelenterazine by marine organisms, while the enzymes involved are unique. One common thread among all the different bioluminescent systems is the requirement of molecular oxygen. Bioluminescence is found in most forms of life, especially marine organisms. Bioluminescence in known to benefit the organism by: attraction, repulsion, communication, camouflage, and illumination. The marine ecosystem is significantly affected by bioluminescence, the only light found in the pelagic zone and below is from bioluminescent organisms. Transgenic bioluminescent organisms have revolutionized molecular research, medicine and the biotechnology industry. The use of bioluminescence in studying molecular pathways and disease allows for non-invasive and real-time analysis. Bioluminescence-based assays have been developed for several analytes by coupling luminescence to many enzyme-catalysed reactions. Received 17 February 2012, accepted 27 March 2012, first published online 2 May 2012