Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information

Background The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomerization is known to play a critical role in protein folding, splicing, cell signaling and transmembrane active transport. Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function. Results In this paper, we propose a new approach to predict the proline cis/trans isomerization in proteins using support vector machine (SVM). The preliminary results indicated that using Radial Basis Function (RBF) kernels could lead to better prediction performance than that of polynomial and linear kernel functions. We used single sequence information of different local window sizes, amino acid compositions of different local sequences, multiple sequence alignment obtained from PSI-BLAST and the secondary structure information predicted by PSIPRED. We explored these different sequence encoding schemes in order to investigate their effects on the prediction performance. The training and testing of this approach was performed on a newly enlarged dataset of 2424 non-homologous proteins determined by X-Ray diffraction method using 5-fold cross-validation. Selecting the window size 11 provided the best performance for determining the proline cis/trans isomerization based on the single amino acid sequence. It was found that using multiple sequence alignments in the form of PSI-BLAST profiles could significantly improve the prediction performance, the prediction accuracy increased from 62.8% with single sequence to 69.8% and Matthews Correlation Coefficient (MCC) improved from 0.26 with single local sequence to 0.40. Furthermore, if coupled with the predicted secondary structure information by PSIPRED, our method yielded a prediction accuracy of 71.5% and MCC of 0.43, 9% and 0.17 higher than the accuracy achieved based on the singe sequence information, respectively. Conclusion A new method has been developed to predict the proline cis/trans isomerization in proteins based on support vector machine, which used the single amino acid sequence with different local window sizes, the amino acid compositions of local sequence flanking centered proline residues, the position-specific scoring matrices (PSSMs) extracted by PSI-BLAST and the predicted secondary structures generated by PSIPRED. The successful application of SVM approach in this study reinforced that SVM is a powerful tool in predicting proline cis/trans isomerization in proteins and biological sequence analysis.

Making use of theories about literacy and justice: teachers re-searching practice

This article considers teachers’ work as they grapple with theories in practice in the everyday worlds of their classroom. It argues that Bourdieu’s theory of practice and the concept of habitus may be useful in moving past theory/practice dichotomies. After establishing the historical context for teacher research in South Australia, the work of two school-based literacy educators with an overt social justice standpoint is explored. The complexity of teachers’ intellectual work and identity formation over time is outlined and implications for teacher education are discussed.

Physical activity, sitting and depression during pregnancy

Aims The aim of this cross sectional study is to explore levels of physical activity and sitting behaviour amongst a sample of pregnant Australian women (n = 81), and investigate whether reported levels of physical activity and/or time spent sitting were associated with depressive symptom scores after controlling for potential covariates. Methods Study participants were women who attended the antenatal clinic of a large Brisbane maternity hospital between October and November 2006. Data relating to participants. current levels of physical activity, sitting behaviour, depressive symptoms, demographic characteristics and exposure to known risk factors for depression during pregnancy were collected; via on-site survey, follow-up telephone interview (approximately one week later) and post delivery access to participant hospital records. Results Participants were aged 29.5 (¡¾ 5.6) years and mostly partnered (86.4%) with a gross household income above $26,000 per annum (88.9%). Levels of physical activity were generally low, with only 28.4 % of participants reporting sufficient total activity and 16% of participants reporting sufficient planned (leisure-time) activity. The sample mean for depressive symptom scores measured by the Hospital Anxiety and Depression Scale (HADS-D) was 6.38 (¡¾ 2.55). The mean depressive symptom scores for participants who reported total moderate-to-vigorous activity levels of sufficient, insufficient, and none, were 5.43 (¡¾ 1.56), 5.82 (¡¾ 1.77) and 7.63 (¡¾ 3.25), respectively. Hierarchical multivariable linear regression modelling indicated that after controlling for covariates, a statistically significant difference of 1.09 points was observed between mean depressive symptom scores of participants who reported sufficient total physical activity, compared with participants who reported they were engaging in no moderate-to-vigorous activity in a typical week (p = 0.05) but this did not reach the criteria for a clinically meaningful difference. Total physical activity was contributed 2.2% to the total 30.3% of explained variance within this model. The other main contributors to explained variance in multivariable regression models were anxiety symptom scores and the number of existing children. Further, a trend was observed between higher levels of planned sitting behaviour and higher depressive symptom scores (p = 0.06); this correlation was not clinically meaningful. Planned sitting contributed 3.2% to the total 31.3 % of explained variance. The number of regression covariates and limited sample size led to a less than ideal ratio of covariates to participants, probably attenuating this relationship. Specific information about the sitting-based activities in which participants engaged may have provided greater insight about the relationship between planned sitting and depressive symptoms, but these data were not captured by the present study. Conclusions The finding that higher levels of physical activity were associated with lower levels of depressive symptoms is consistent with the current body of existing literature in pregnant women, and with a larger body of evidence based in general population samples. Although this result was not considered clinically meaningful, the criterion for a clinically meaningful result was an a priori decision based on quality of life literature in non-pregnant populations and may not truly reflect a difference in symptoms that is meaningful to pregnant women. Further investigation to establish clinically meaningful criteria for continuous depressive symptom data in pregnant women is required. This result may have implications relating to prevention and management options for depression during pregnancy. The observed trend between planned sitting and depressive symptom scores is consistent with literature based on leisure-time sitting behaviour in general population samples, and suggests that further research in this area, with larger samples of pregnant women and more specific sitting data is required to explore potential associations between activities such as television viewing and depressive symptoms, as this may be an area of behaviour that is amenable to modification.

Motorcycle protective clothing : protection from injury or just the weather?

Background Apart from helmets, little is known about the effectiveness of motorcycle protective clothing in reducing injuries in crashes. The study aimed to quantify the association between usage of motorcycle clothing and injury in crashes. Methods and findings Cross-sectional analytic study. Crashed motorcyclists (n = 212, 71% of identified eligible cases) were recruited through hospitals and motorcycle repair services. Data was obtained through structured face-to-face interviews. The main outcome was hospitalization and motorcycle crash-related injury. Poisson regression was used to estimate relative risk (RR) and 95% confidence intervals for injury adjusting for potential confounders. Results Motorcyclists were significantly less likely to be admitted to hospital if they crashed wearing motorcycle jackets (RR = 0.79, 95% CI: 0.69–0.91), pants (RR = 0.49, 95% CI: 0.25–0.94), or gloves (RR = 0.41, 95% CI: 0.26–0.66). When garments included fitted body armour there was a significantly reduced risk of injury to the upper body (RR = 0.77, 95% CI: 0.66–0.89), hands and wrists (RR = 0.55, 95% CI: 0.38–0.81), legs (RR = 0.60, 95% CI: 0.40–0.90), feet and ankles (RR = 0.54, 95% CI: 0.35–0.83). Non-motorcycle boots were also associated with a reduced risk of injury compared to shoes or joggers (RR = 0.46, 95% CI: 0.28–0.75). No association between use of body armour and risk of fracture injuries was detected. A substantial proportion of motorcycle designed gloves (25.7%), jackets (29.7%) and pants (28.1%) were assessed to have failed due to material damage in the crash. Conclusions Motorcycle protective clothing is associated with reduced risk and severity of crash related injury and hospitalization, particularly when fitted with body armour. The proportion of clothing items that failed under crash conditions indicates a need for improved quality control. While mandating usage of protective clothing is not recommended, consideration could be given to providing incentives for usage of protective clothing, such as tax exemptions for safety gear, health insurance premium reductions and rebates.

Factors influencing health promotion activities in midlife and older Australian women with a chronic disease

Background: Chronic diseases including type 2 diabetes are a leading cause of morbidity and mortality in midlife and older Australian women. There are a number of modifiable risk factors for type 2 diabetes and other chronic diseases including smoking, nutrition, physical activity and overweight and obesity. Little research has been conducted in the Australian context to explore the perceived barriers to health promotion activities in midlife and older Australian women with a chronic disease. Aims: The primary aim of this study was to explore women’s perceived barriers to health promotion activities to reduce modifiable risk factors, and the relationship of perceived barriers to smoking behaviour, fruit and vegetable intake, physical activity and body mass index. A secondary aim of this study was to investigate nurses’ perceptions of the barriers to action for women with a chronic disease, and to compare those perceptions with those of the women. Methods: The study was divided into two phases where Phase 1 was a cross sectional survey of women, aged over 45 years with type 2 diabetes who were attending Diabetes clinics in the Primary and Community Health Service of the Metro North Health Service District of Queensland Health (N = 22). The women were a subsample of women participating in a multi-model lifestyle intervention, the ‘Reducing Chronic Disease among Adult Australian Women’ project. Phase 2 of the study was a cross sectional online survey of nurses working in Primary and Community Health Service in the Metro North Health Service District of Queensland Health (N = 46). Pender’s health promotion model was used as the theoretical framework for this study. Results: Women in this study had an average total barriers score of 32.18 (SD = 9.52) which was similar to average scores reported in the literature for women with a range of physical disabilities and illnesses. The leading five barriers for this group of women were: concern about safety; too tired; not interested; lack of information about what to do; with lack of time and feeling I can’t do things correctly the equal fifth ranked barriers. In this study there was no statistically significant difference in average total barriers scores between women in the intervention group and those is the usual care group of the parent study. There was also no significant relationship between the women’s socio-demographic variables and lifestyle risk factors and their level of perceived barriers. Nurses in the study had an average total barriers score of 44.48 (SD = 6.24) which was higher than all other average scores reported in the literature. The leading five barriers that nurses perceived were an issue for women with a chronic disease were: lack of time and interferes with other responsibilities the leading barriers; embarrassment about appearance; lack of money; too tired and lack of support from family and friends. There was no significant relationship between the nurses’ sociodemographic and nursing variables and the level of perceived barriers. When comparing the results of women and nurses in the study there was a statistically significant difference in the median total barriers score between the groups (p < 0.001), where the nurses perceived the barriers to be higher (Md = 43) than the women (Md = 33). There was also a significant difference in the responses to the individual barriers items in fifteen of the eighteen items (p < 0.002). Conclusion: Although this study is limited by a small sample size, it contributes to understanding the perception of midlife and older women with a chronic disease and also the perception of nurses, about the barriers to healthy lifestyle activities that women face. The study provides some evidence that the perceptions of women and nurses may differ and argues that these differences may have significant implications for clinical practice. The study recommends a greater emphasis on assessing and managing perceived barriers to health promotion activities in health education and policy development and proposes a conceptual model for understanding perceived barriers to action.