Dynamically predicting protein functions from semantic associations of proteins

Predicting functions of un-annotated proteins is a significant challenge in the post-genomics era. Among existing computational approaches, exploiting interactions between proteins to predict functions of un-annotated proteins is widely used. However, it remains difficult to extract semantic associations between proteins (i.e. protein associations in terms of protein functionality) from protein interactions and incorporate extracted semantic associations to more effectively predict protein functions. Furthermore, existing approaches and algorithms regard the function prediction as a one-off procedure, ignoring dynamic and mutual associations between proteins. Therefore, deriving and exploiting semantic associations between proteins to dynamically predict functions are a promising and challenging approach for achieving better prediction results. In this paper, we propose an innovative algorithm to incorporate semantic associations between proteins into a dynamic procedure of protein function prediction. The semantic association between two proteins is measured by the semantic similarity of two proteins which is defined by the similarities of functions two proteins possess. To achieve better prediction results, function similarities are also incorporated into the prediction procedure. The algorithm dynamically predicts functions by iteratively selecting functions for the un-annotated protein and updating the similarities between the un-annotated protein and its neighbour annotated proteins until such suitable functions are selected that the similarities no longer change. The experimental results on real protein interaction datasets demonstrated that our method outperformed the similar and non-dynamic function prediction methods. Incorporating semantic associations between proteins into a dynamic procedure of function prediction reflects intrinsic relationships among proteins as well as dynamic features of protein interactions, and therefore, can significantly improve prediction results.

Business associations and the food processing industry in Australia : how neoliberalism has reinforced employer collectivism

In this paper I argue that factors such as conflicting pressures for food regulation reform and continuing industry assistance programs have made conditions even more favourable for collective business interest representation in Australia's food processing sector. The push by firms for less onerous and more business-friendly regulation has run up against environmental and social pressures/or more rigorous regulatory controls, as awareness grows ofthe risks ofnew technologies. The case of the Australian Food and Grocery Council (AFGC) illustrates the issues. The extent to which this association participates directly in the design and implementation of public policy is indicative of a decline in the autonomy of politicians and the state bureaucracy vis-a-vis the ideology and interests of business.

Associations of physical activity with body weight and fat in men and women

OBJECTIVE: Increasing physical activity is strongly advocated as a key public health strategy for weight gain prevention. We investigated associations of leisure-time physical activity (LTPA) and occupational/domestic physical activity with body mass index (BMI) and a skinfold-derived index of body fat (sum of six skinfolds), among normal-weight and overweight men and women.

DESIGN: Analyses of cross-sectional self-report and measured anthropometric data.

SUBJECTS: A total of 1302 men and women, aged 18-78 y, who were part of a randomly selected sample and who agreed to participate in a physical health assessment.

MEASUREMENTS: Self-report measures of physical activity, measured height and weight, and a skinfold-derived index of body fatness.

RESULTS: Higher levels of LTPA were positively associated with the likelihood of being in the normal BMI and lower body fat range for women, but few or no associations were found for men. No associations were found between measures of occupational/domestic activity and BMI or body fat for men or women.

CONCLUSION: By using a skinfold sum as a more direct measure of adiposity, this study extends and confirms the previous research that has shown an association between BMI and LTPA. Our results suggest gender differences in the relationship of leisure-time physical activity with body fatness. These findings, in conjunction with a better understanding of the causes of such differences, will have important public health implications for the development and targeting of weight gain prevention strategies.

Exploring the benefits and pitfalls of using mutual wills

The purpose of this article is to consider a peculiar type of will known in equity as a mutual will. The major focus is a consideration of the interplay of the legal effect of mutual wills and the practical use of such wills, It is hoped that this discussion will assist legal practitioners in identifying those clients who may benefit from executing mutual wills, identifying those clients who might intend to execute mutual wills, advising clients as to the pros and cons of mutual wills and the benefits of accompanying such wills with a deed or contract.

Children's television viewing and objectively measured physical activity: associations with family circumstances

Background: The contribution of family circumstance to physical activity and television viewing has not been widely investigated in pre-adolescents, and available information is inconsistent. This study examines whether television viewing and objectively measured physical activity vary by different indicators of family circumstance.
Methods: Data from the 2001 Children's Leisure Activity Study and the 2002/3 Health, Eating and Play Study, involving Australian children in Grades Prep (mean age 6y) and 5–6 (mean age 11y), were combined. Children wore accelerometers for six consecutive 24 hour periods. Average min/day in low-intensity activity (1.0–1.9 METs) and moderate-to-vigorous-intensity activity (≥3 METs) were calculated. Parents reported children's television viewing and family circumstance. Linear regression analyses were conducted separately for young girls, young boys, older girls and older boys. Results: Complete data were available for 2458 children. Parental education and, to a lesser extent, employment level were inversely associated with television viewing. Children in single-parent families, those whose fathers were not in paid employment, and those without siblings tended to spend more time in low-intensity activity than their peers. Children with siblings spent more time in moderate-to-vigorous-intensity activity; associations were stronger for girls. Maternal education was positively associated with moderate-to-vigorous-intensity activity for younger children. Maternal employment was positively associated with moderate-to-vigorous-intensity activity for older children. Multivariable models did not demonstrate a cumulative explanatory effect.
Conclusion:  Individual measures of family circumstance were differentially associated with television, low-intensity activity and moderate-to-vigorous-intensity activity and associations were often not consistent across age-by-gender groups. Interventions may need to be tailored accordingly.

Lay people's views of school food policy options: associations with confidence, personal values and demographics

A random population survey administered by mail to examine lay people's views of children's food policies and their associations with demographics, personal values and confidence in authorities was conducted among adults in Victoria, Australia. Three hundred and seventy-seven people responded (response rate 57.6%). The questionnaire contained 35 items about children's healthy eating policy options plus details like personal values, confidence and demographic items. There was widespread support for healthy school food policies. The strongest support was for life skills education and school-based nutrition and physical education programmes. Many age-related associations indicated that people >48 years were more in favour of healthy eating policies than younger people. There were fewer statistically significant associations with parent status and sex. In contrast, many associations showed that respondents with strong equity–harmony values and those with least confidence in the authorities were most in favour of healthy eating policies for schoolchildren. It is concluded that there is widespread support for school-based health and nutrition education and for active school food policies. However, differences between demographic and values groups suggest the need for caution in the promotion of public health nutrition initiatives among schoolchildren.

Discovering associations with numeric variables

This paper further develops Aumann and Lindell's [3] proposal for a variant of association rules for which the consequent is a numeric variable. It is argued that these rules can discover useful interactions with numeric data that cannot be discovered directly using traditional association rules with discretization. Alternative measures for identifying interesting rules are proposed. Efficient algorithms are presented that enable these rules to be discovered for dense data sets for which application of Auman and Lindell's algorithm is infeasible.

Evolutionary structure learning algorithm for Bayesian network and penalized mutual information metric

This paper formulates the problem of learning Bayesian network structures from data as determining the structure that best approximates the probability distribution indicated by the data. A new metric, Penalized Mutual Information metric, is proposed, and a evolutionary algorithm is designed to search for the best structure among alternatives. The experimental results show that this approach is reliable and promising.

Adaptive blind source separation using constant modulus criterion and signal mutual information

We address the problem of adaptive blind source separation (BSS) from instantaneous multi-input multi-output (MIMO) channels. It is known that the constant modulus (CM) criterion can be used to extract unknown source signals. However, the existing CM based algorithms normally extract the source signals in a serial manner. Consequently, the accuracy in extracting each source signal, except for the first one, depends on the accuracy of previous source extraction. This estimation error propagation (accumulation) causes severe performance degradation. In this paper, we propose a new adaptive separation algorithm that can separate all source signals simultaneously by directly updating the separation matrix. The superior performance of the new algorithm is demonstrated by simulation examples

Associations between student pursuit of novel mathematical ideas and resilience

As part of a broader study of characteristics of situations that promote or inhibit spontaneous student exploration of novel mathematical ideas, student inclination to display these spontaneous behaviours was studied in conjunction with resilience. Resilience was operationalised using the dimensions of optimism (Seligman, 1995). Indicators of optimism were identified in post-lesson video-stimulated reconstructive interviews with year eight students. Students who demonstrated the pursuit of novel mathematical ideas were found to also display indicators of resilience.

Revisiting associations between student performance outcomes and formative assessment opportunities: is there any impact on student learning?

This project developed as a result of some inconclusive data from an investigation of whether a relationship existed between the use of formative assessment opportunities and performance, as measured by final grade. We were expecting to show our colleagues and students that use of formative assessment resources had the potential to improve performance. This first study, done in semester 1 2002, indicated that there was no apparent relationship even though the students reported how useful they found the resources. This led us to ask if there was a transition effect
such that students were not yet working in an independent way and making full use of the resources, and/or whether in order to see an effect we needed to persuade non-users of the resources to become users before investigating if use can be correlated with improvement in performance. With the 2002-3 NextEd ASCILITE Research Grant we set out to repeat our project and to look at use and usefulness of resources in both first and second semester, to encourage non-users to become users and to investigate use with performance. Now our story has a different ending.

Associations between family circumstance and weight status of Australian children

To examine associations between weight status and multiple indicators of family circumstance in Australian elementary school children. Data were combined from the 2001 Children's Leisure Activities Study (CLAS Study) and 2002/3 Health, Eating and Play Study (HEAP Study), involving 2520 children in Grades Prep (mean age 6 years) and 5-6 (mean age 11 years) in Melbourne, Australia. Children's body mass index (BMI) was calculated from measured height and weight. Weight status (non-overweight or overweight) was determined according to International Obesity Taskforce cut-off points and BMI was transformed to z-scores based on the 2000 US growth chart data. Parents reported family circumstance (number of parents in the home, marital status, presence of siblings, parental education, parental employment status, parental work hours [HEAP Study only]) and parental BMI. Regression analyses were conducted for the sample overall and separately for young girls, young boys, older girls and older boys. Children in single-parent homes, those without siblings, and those with less educated mothers and fathers tended to have higher z-BMIs (p=0.002, p=0.003, p<0.001 and p<0.001, respectively) and were more likely to be overweight (p=0.003, p<0.001, p<0.001 and p=0.02, respectively). Associations were stronger for older children. Parental employment and work hours were not consistently associated with child weight status. The multivariable models did not demonstrate a cumulative explanatory effect (R2=0.02), except when maternal BMI was included (R2=0.07). Individual measures of family circumstance were differentially associated with child weight status and appeared to be largely independent of other measures of family circumstance. Childhood overweight interventions may need to be tailored based on the age, gender, maternal BMI and family circumstances of the target group.

Associations of children's perceived neighborhood environments with walking and physical activity

Purpose. To examine associations between children's perceptions of the neighborhood environment and walking and physical activity.
Design. Cross-sectional study of a school-based sample.
Setting. Elementary schools in Melbourne, Australia.
Subjects. 280 children aged 10 years (response rate 78%).
Measures. A self-report survey assessed children's perceptions of the neighborhood physical and social environments and their weekly walking frequency. Physical activity was also objectively measured using accelerometers.
Results. Multiple linear regression analyses showed a positive association between walking frequency and the number of accessible destinations in the neighborhood among boys; having a neighborhood that was easy to walk/cycle around and perceiving lots of graffiti were positively associated with walking frequency among girls. Perceiving lots of litter and rubbish was positively associated with boys' overall physical activity, but no environmental variables were associated with girls' overall physical activity.
Conclusion. Several different environmental factors were associated with walking and physical activity. Perceptions of the neighborhood environment were more strongly associated with girls' walking than with objectively-measured physical activity. Future studies should confirm these findings using objective measures and prospective study designs.

Associations among individual, social, and environmental barriers and children's walking or cycling to school

Purpose. To examine associations among individual, social, and environmental barriers and children's walking or cycling to school.

Design. Exploratory cross-sectional study.

Setting. All eight capital cities in Australia.

Subjects. Parents (N = 720) of school-aged children (4-13 years; 27% response rate 49% parents of boys,).

Measures. Multivariate-adjusted odds ratios (OR) and 95% confidence intervals (CI) for parental reporting of barriers to their children's walking or cycling to school, based on a computer-assisted telephone interview.

Results. Forty-one percent of children walked or cycled to school at least once per week. Multivariable analyses found inverse associations with individual ("child prefers to be driven" [OR = 0.4, 95% CI = 0.3-0.6], "no time in the mornings" [OR 0.5, 95% CI = 0.3-0.8]); social ("worry child will take risk" [OR = 0.6, 95% CI = 0.3-0.9], "no other children to walk with" [OR = 0.7, 95% CI = 0.4-0.99], "no adults to walk with" [OR = 0.6, 95% CI = 0.4-0.9]); and environmental barriers ("too far to walk" [OR = 0.1, 95% CI = 0.0- 0.1], "no direct route" [OR = 0.4, 95% CI = 0.2-0. 7]) and positive associations with "concern child may he injured in a road accident" (OR = 1.9, 95% CI = 1.1-3.1) and active commuting.

Conclusion. Working with parents, schools, and local authorities to improve pedestrian, skills and environments may help to overcome barriers.