Highly Sensitive Detection of Individual HEAT and ARM Repeats with HHpred and COACH

BACKGROUND:HEAT and ARM repeats occur in a large number of eukaryotic proteins. As these repeats are often highly diverged, the prediction of HEAT or ARM domains can be challenging. Except for the most clear-cut cases, identification at the individual repeat level is indispensable, in particular for determining domain boundaries. However, methods using single sequence queries do not have the sensitivity required to deal with more divergent repeats and, when applied to proteins with known structures, in some cases failed to detect a single repeat. METHODOLOGY AND PRINCIPAL FINDINGS:Testing algorithms which use multiple sequence alignments as queries, we found two of them, HHpred and COACH, to detect HEAT and ARM repeats with greatly enhanced sensitivity. Calibration against experimentally determined structures suggests the use of three score classes with increasing confidence in the prediction, and prediction thresholds for each method. When we applied a new protocol using both HHpred and COACH to these structures, it detected 82% of HEAT repeats and 90% of ARM repeats, with the minimum for a given protein of 57% for HEAT repeats and 60% for ARM repeats. Application to bona fide HEAT and ARM proteins or domains indicated that similar numbers can be expected for the full complement of HEAT/ARM proteins. A systematic screen of the Protein Data Bank for false positive hits revealed their number to be low, in particular for ARM repeats. Double false positive hits for a given protein were rare for HEAT and not at all observed for ARM repeats. In combination with fold prediction and consistency checking (multiple sequence alignments, secondary structure prediction, and position analysis), repeat prediction with the new HHpred/COACH protocol dramatically improves prediction in the twilight zone of fold prediction methods, as well as the delineation of HEAT/ARM domain boundaries. SIGNIFICANCE:A protocol is presented for the identification of individual HEAT or ARM repeats which is straightforward to implement. It provides high sensitivity at a low false positive rate and will therefore greatly enhance the accuracy of predictions of HEAT and ARM domains

Associations between general self-efficacy and health-related quality of life among 12-13-year-old school children: a cross-sectional survey

<p>Abstract</p> <p>Background</p> <p>While research on school children's health has mainly focused on risk factors and illness, few studies have examined aspects of health promotion. Thus, this study focuses on health promotional factors including general self-efficacy (GSE) and health-related quality of life (HRQOL). GSE refers to a global confidence in coping ability across a wide range of demanding situations, and is related to health. The purpose of this study was to examine associations between GSE and HRQOL, and associations between HRQOL and socio-demographic characteristics. Knowledge of these associations in healthy school children is currently lacking.</p> <p>Methods</p> <p>During 2006 and 2007, 279 school children in the seventh grade across eastern Norway completed a survey assessing their GSE and HRQOL. The children were from schools that had been randomly selected using cluster sampling. T-tests were computed to compare mean subscale values between HRQOL and socio-demographic variables. Single and multiple regression analyses were performed to explore associations among GSE, HRQOL and socio-demographic variables.</p> <p>Results</p> <p>Regression analyses showed a significant relationship between increasing degrees of GSE and increasing degrees of HRQOL. In analyses adjusted for socio-demographic variables, boys scored higher than girls on self-esteem. School children from single-parent families had lower scores on HRQOL than those from two-parent families, and children who had relocated within the last five years had lower scores on HRQOL than those who had not relocated.</p> <p>Conclusion</p> <p>The strong relationship between GSE and HRQOL indicates that GSE might be a resource for increasing the HRQOL for school children.</p