AS2TS system for protein structure modeling and analysis

We present a set of programs and a website designed to facilitate protein structure comparison and protein structure modeling efforts. Our protein structure analysis and comparison services use the LGA (local-global alignment) program to search for regions of local similarity and to evaluate the level of structural similarity between compared protein structures. To facilitate the homology-based protein structure modeling process, our AL2TS service translates given sequence–structure alignment data into the standard Protein Data Bank (PDB) atom records (coordinates). For a given sequence of amino acids, the AS2TS (amino acid sequence to tertiary structure) system calculates (e.g. using PSI-BLAST PDB analysis) a list of the closest proteins from the PDB, and then a set of draft 3D models is automatically created. Web services are available at

MannDB – A microbial database of automated protein sequence analyses and evidence integration for protein characterization

BACKGROUND: MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. DESCRIPTION: MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins) are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. CONCLUSION: MannDB comprises a large number of genomes and comprehensive protein sequence analyses representing organisms listed as high-priority agents on the websites of several governmental organizations concerned with bio-terrorism. MannDB provides the user with a BLAST interface for comparison of native and non-native sequences and a query tool for conveniently selecting proteins of interest. In addition, the user has access to a web-based browser that compiles comprehensive and extensive reports. Access to MannDB is freely available at

Percentile reference values for anthropometric body composition indices in European children from the IDEFICS study

INTRODUCTION: To characterise the nutritional status in children with obesity or wasting conditions, European anthropometric reference values for body composition measures beyond the body mass index (BMI) are needed. Differentiated assessment of body composition in children has long been hampered by the lack of appropriate references. OBJECTIVES: The aim of our study is to provide percentiles for body composition indices in normal weight European children, based on the IDEFICS cohort (Identification and prevention of Dietary-and lifestyle-induced health Effects in Children and infantS). METHODS: Overall 18 745 2.0-10.9-year-old children from eight countries participated in the study. Children classified as overweight/obese or underweight according to IOTF (N = 5915) were excluded from the analysis. Anthropometric measurements (BMI (N = 12 830); triceps, subscapular, fat mass and fat mass index (N = 11 845-11 901); biceps, suprailiac skinfolds, sum of skinfolds calculated from skinfold thicknesses (N = 8129-8205), neck circumference (N = 12 241); waist circumference and waist-to-height ratio (N = 12 381)) were analysed stratified by sex and smoothed 1st, 3rd, 10th, 25th, 50th, 75th, 90th, 97th and 99th percentile curves were calculated using GAMLSS. RESULTS: Percentile values of the most important anthropometric measures related to the degree of adiposity are depicted for European girls and boys. Age-and sex-specific differences were investigated for all measures. As an example, the 50th and 99th percentile values of waist circumference ranged from 50.7-59.2 cm and from 51.3-58.7 cm in 4.5-to < 5.0-year-old girls and boys, respectively, to 60.6-74.5 cm in girls and to 59.9-76.7 cm in boys at the age of 10.5-10.9 years. CONCLUSION: The presented percentile curves may aid a differentiated assessment of total and abdominal adiposity in European children

The Role of Creativity in Entrepreneurship

This paper evaluates the contribution of creativity to entrepreneurship theory and practice in terms of building an holistic and transdisciplinary understanding of its impact. Acknowledgement is made of the subjectivist theory of entrepreneurship which embraces randomness, uncertainty and ambiguity but these factors should then be embedded in wider business and social contexts. The analysis is synthesised into a number of themes, from consideration of its definition, its link with personality and cognitive style, creativity as a process and the use of biography in uncovering data on creative entrepreneurial behaviour. Other relevant areas of discussion include creativity&rsquo;s link with motivation, actualisation and innovation, as well as the interrogation of entrepreneurial artists as owner/managers. These factors are embedded in a critical evaluation of how creativity contributes to successful entrepreneurship practice. Modelling, measuring and testing entrepreneurial creativity are also considered and the paper includes detailed consideration of several models of creativity in entrepreneurship. Recommendations for future theory and practice are also made

An investigation of psychological, social and environmental correlates of obesity and weight gain in young women

Objectives: This study explored the biological, psychological, social and environmental correlates of young women\u27s current weight and retrospective 2-year weight change. Methods: A total of 790 young women (mean age 26.8 years), sampled from the Australian Longitudinal Study on Women\u27s Health, provided self-reported data on their height and weight, sociodemographics and a range of biological, psychological, social and environmental variables. Results: Several variables from all domains (biological, psychological, social support and environmental) were correlated with higher body mass index, and less strongly greater 2-year weight change. Key correlates included the tendency to never put on weight, no matter what; self-efficacy for avoiding weight gain, and for healthy eating; attention paid to weight; family support and friends\u27 support/sabotage of physical activity/healthy eating; and perceived difficulty of taking the stairs rather than the elevator as part of the daily routine. Conclusions: Intervention strategies aimed at reducing weight gain and obesity may need to focus on social and environmental, as well as psychological factors; however, further research is necessary to confirm these findings given that a number of hypothesized associations were not observed.<br /

Recruitment into diabetes prevention programs : what is the impact of errors in self-reported measures of obesity?

BackgroundError in self-reported measures of obesity has been frequently described, but the effect of self-reported error on recruitment into diabetes prevention programs is not well established. The aim of this study was to examine the effect of using self-reported obesity data from the Finnish diabetes risk score (FINDRISC) on recruitment into the Greater Green Triangle Diabetes Prevention Project (GGT DPP).MethodsThe GGT DPP was a structured group-based lifestyle modification program delivered in primary health care settings in South-Eastern Australia. Between 2004&ndash;05, 850 FINDRISC forms were collected during recruitment for the GGT DPP. Eligible individuals, at moderate to high risk of developing diabetes, were invited to undertake baseline tests, including anthropometric measurements performed by specially trained nurses. In addition to errors in calculating total risk scores, accuracy of self-reported data (height, weight, waist circumference (WC) and Body Mass Index (BMI)) from FINDRISCs was compared with baseline data, with impact on participation eligibility presented.ResultsOverall, calculation errors impacted on eligibility in 18 cases (2.1%). Of n&thinsp;=&thinsp;279 GGT DPP participants with measured data, errors (total score calculation, BMI or WC) in self-report were found in n&thinsp;=&thinsp;90 (32.3%). These errors were equally likely to result in under- or over-reported risk. Under-reporting was more common in those reporting lower risk scores (Spearman-rho&thinsp;=&thinsp;&minus;0.226, p-value&thinsp;&lt;&thinsp;0.001). However, underestimation resulted in only 6% of individuals at high risk of diabetes being incorrectly categorised as moderate or low risk of diabetes.ConclusionsOverall FINDRISC was found to be an effective tool to screen and recruit participants at moderate to high risk of diabetes, accurately categorising levels of overweight and obesity using self-report data. The results could be generalisable to other diabetes prevention programs using screening tools which include self-reported levels of obesity.<br /

Epidemiology of cardiovascular risk factors in Greece: aims, design and baseline characteristics of the ATTICA study

BACKGROUND: In an attempt to evaluate the levels of several cardiovascular risk factors in Greece we conducted a population-based health and nutrition survey, the "ATTICA study". In this work we present the design and the methodology of the study, as well as the status of various baseline characteristics of the participants. METHODS: From May 2001 to December 2002 we randomly enrolled 1514 adult men and 1528 adult women, stratified by age – gender (census 2000), from the greater area of Athens. More than 300 demographic, lifestyle, behavioral, dietary, clinical and biochemical variables have been recorded. RESULTS: Regarding the frequency of the classical cardiovascular risk factors we observed that 51% of men and 39% of women reported smokers (p < 0.05), 37% of men and 25% of women were defined as hypertensives (p < 0.05), 46% of men and 40% of women had total serum cholesterol levels above 200 mg/dl (p < 0.05) and 8% of men and 6% of women had history of diabetes mellitus. Moreover, 20% of men and 15% of women were obese (p < 0.05), while men were more physically active as compared to women (42% vs. 39%, p < 0.05). 19% of men and 38% of women had mild to severe depressive symptoms (p < 0.01). Finally, 72 men (5%) and 45 (3%) women reported history of coronary heart disease at entry evaluation. CONCLUSIONS: The prevalence of the common cardiovascular risk factors in our population seems high. As a consequence a considerable proportion of Greek adults are at "high-risk" for future cardiovascular events

The effect of body mass index on global brain volume in middle-aged adults: a cross sectional study

BACKGROUND: Obesity causes or exacerbates a host of medical conditions, including cardiovascular, pulmonary, and endocrine diseases. Recently obesity in elderly women was associated with greater risk of dementia, white matter ischemic changes, and greater brain atrophy. The purpose of this study was to determine whether body type affects global brain volume, a marker of atrophy, in middle-aged men and women. METHODS: T1-weighted 3D volumetric magnetic resonance imaging was used to assess global brain volume for 114 individuals 40 to 66 years of age (average = 54.2 years; standard deviation = 6.6 years; 43 men and 71 women). Total cerebrospinal fluid and brain volumes were obtained with an automated tissue segmentation algorithm. A regression model was used to determine the effect of age, body mass index (BMI), and other cardiovascular risk factors on brain volume and cognition. RESULTS: Age and BMI were each associated with decreased brain volume. BMI did not predict cognition in this sample; however elevated diastolic blood pressure was associated with poorer episodic learning performance. CONCLUSION: These findings suggest that middle-aged obese adults may already be experiencing differentially greater brain atrophy, and may potentially be at greater risk for future cognitive decline

Health related quality of life of obese adolescents in Kuwait

Obesity impairs health related quality of life (HRQL) in adolescents, but most evidence in this area has mostly come from western societies. We wanted to test the hypothesis that obesity impairs HRQL in Kuwaiti adolescents, and to test for differences in HRQL assessed by self-report and parent-proxy report. In 500 Kuwaiti 10-14 year olds HRQL was assessed using the Peds QL (TM) with both adolescent self-reports (n = 500) and parent-proxy reports (n = 374). Obesity was not significantly associated with HRQL in regression analysis. In a paired comparison of 98 pairs of obese adolescents vs. 98 healthy weight peers, impairment of HRQL reached significance only for physical score (95% CI = -1.5, -9.4), not for psychosocial score or total score. In a paired comparison of parent-proxy vs. self-reports for the obese adolescents, total score (95% CI = -4.9, -10.9), physical score (95% CI = -3.2, -11.0), and psychosocial score (95% CI = -4.2, -10.8) were all significantly lower in the parent reports. Obesity is not associated with marked impairment of HRQL in adolescents in Kuwait, in contrast to studies in western societies. This may reflect cultural differences in attitudes towards obesity