Essential guidelines for computational method benchmarking

In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different methods using well-characterized benchmark datasets, to determine the strengths of each method or to provide recommendations regarding suitable choices of methods for an analysis. However, benchmarking studies must be carefully designed and implemented to provide accurate, unbiased, and informative results. Here, we summarize key practical guidelines and recommendations for performing high-quality benchmarking analyses, based on our experiences in computational biology.Comment: Minor update

Essential guidelines for computational method benchmarking

In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different methods using well-characterized benchmark datasets, to determine the strengths of each method or to provide recommendations regarding suitable choices of methods for an analysis. However, benchmarking studies must be carefully designed and implemented to provide accurate, unbiased, and informative results. Here, we summarize key practical guidelines and recommendations for performing high-quality benchmarking analyses, based on our experiences in computational biology

Is Your Neighborhood Designed to Support Physical Activity? A Brief Streetscape Audit Tool.

INTRODUCTION:Macro level built environment factors (eg, street connectivity, walkability) are correlated with physical activity. Less studied but more modifiable microscale elements of the environment (eg, crosswalks) may also affect physical activity, but short audit measures of microscale elements are needed to promote wider use. This study evaluated the relation of a 15-item neighborhood environment audit tool with a full version of the tool to assess neighborhood design on physical activity in 4 age groups. METHODS:From the 120-item Microscale Audit of Pedestrian Streetscapes (MAPS) measure of street design, sidewalks, and street crossings, we developed the 15-item version (MAPS-Mini) on the basis of associations with physical activity and attribute modifiability. As a sample of a likely walking route, MAPS-Mini was conducted on a 0.25-mile route from participant residences toward the nearest nonresidential destination for children (n = 758), adolescents (n = 897), younger adults (n = 1,655), and older adults (n = 367). Active transportation and leisure physical activity were measured with age-appropriate surveys, and accelerometers provided objective physical activity measures. Mixed-model regressions were conducted for each MAPS item and a total environment score, adjusted for demographics, participant clustering, and macrolevel walkability. RESULTS:Total scores of MAPS-Mini and the 120-item MAPS correlated at r = .85. Total microscale environment scores were significantly related to active transportation in all age groups. Items related to active transport in 3 age groups were presence of sidewalks, curb cuts, street lights, benches, and buffer between street and sidewalk. The total score was related to leisure physical activity and accelerometer measures only in children. CONCLUSION:The MAPS-Mini environment measure is short enough to be practical for use by community groups and planning agencies and is a valid substitute for the full version that is 8 times longer

Perceived environmental factors related to adults’ leisure-time physical activity : findings from Europe, Australia and the USA

This journal suppl. entitled: Be Avtive 2012Session 204B - Environments and physical activity: Adults: paper no. 524INTRODUCTION: A growing body of evidence shows that objective and perceived built environment factors are positively associated with physical activity in adults. However, built environment correlates are behavior-specific and the factors associated with leisure-time physical activity are less understood than those associated with active transportation. Furthermore, most previous studies of associations of built environment attributes with physical activity have been conducted in single countries. Limited within-country variability in environmental attributes and physical activity levels can potentially contribute to an underestimation of the strength of the associations. Therefore, the purpose of this study was to examine the strength, direction and shape of the associations of neighborhood environmental perceptions with recreational walking and leisure-time moderate-to-vigorous physical activity, using pooled data from four study sites (Baltimore [USA], Seattle [USA], Adelaide [Australia] and Ghent [Belgium]) in culturally- and environmentally-diverse countries. Moreover, site- and gender-specificity of the associations were examined. METHODS: Data from the four study sites were pooled. In total, 6,014 adults (20–65 years, 55.7% women) were randomly recruited in high-/low-walkable and high-/low-income neighborhoods in the four sites. All participants completed the Neighborhood Environmental Walkability Scale (environmental perceptions) and the International Physical Activity Questionnaire. General additive mixed models were used to estimate the strength and shape of the associations between environmental perceptions and leisure-time activity (walking and moderate-to-vigorous physical activity). RESULTS: Perceived residential density, aesthetics and reporting few barriers to physical activity in the neighborhood were included in a ‘recreational walking-friendliness’ index. This index was linearly positively related to recreational walking in all study sites except Ghent. No gender-differences were observed. The ‘leisure-time activity friendliness’ index consisted of perceived residential density, proximity to recreation facilities, aesthetics and perceiving few barriers in the neighborhood. This index had a positive linear association with leisure-time moderate-to-vigorous physical activity that was significant in all sites but Ghent. Again, no gender-differences in the associations were found. DISCUSSION: Similar environmental attributes were related to both outcome measures in men and women, but the present findings were clearly site-specific, imposing possible challenges for built environment recommendations. In Europe, interventions to promote leisure-time activity may need to target promotion of existing opportunities rather than built environment improvements. In the USA and Australia, a focus on the factors identified in this study, may be of most relevance for promoting leisure-time physical activity

The Escherichia coli transcriptome mostly consists of independently regulated modules

Underlying cellular responses is a transcriptional regulatory network (TRN) that modulates gene expression. A useful description of the TRN would decompose the transcriptome into targeted effects of individual transcriptional regulators. Here, we apply unsupervised machine learning to a diverse compendium of over 250 high-quality Escherichia coli RNA-seq datasets to identify 92 statistically independent signals that modulate the expression of specific gene sets. We show that 61 of these transcriptomic signals represent the effects of currently characterized transcriptional regulators. Condition-specific activation of signals is validated by exposure of E. coli to new environmental conditions. The resulting decomposition of the transcriptome provides: a mechanistic, systems-level, network-based explanation of responses to environmental and genetic perturbations; a guide to gene and regulator function discovery; and a basis for characterizing transcriptomic differences in multiple strains. Taken together, our results show that signal summation describes the composition of a model prokaryotic transcriptome

Reliability and validity of three questionnaires measuring context-specific sedentary behaviour and associated correlates in adolescents, adults and older adults

BACKGROUND: Reliable and valid measures of total sedentary time, context-specific sedentary behaviour (SB) and its potential correlates are useful for the development of future interventions. The purpose was to examine test-retest reliability and criterion validity of three newly developed questionnaires on total sedentary time, context-specific SB and its potential correlates in adolescents, adults and older adults. METHODS: Reliability and validity was tested in six different samples of Flemish (Belgium) residents. For the reliability study, 20 adolescents, 22 adults and 20 older adults filled out the age-specific SB questionnaire twice. Test-retest reliability was analysed using Kappa coefficients, Intraclass Correlation Coefficients and/or percentage agreement, separately for the three age groups. For the validity study, data were retrieved from 62 adolescents, 33 adults and 33 older adults, with activPAL as criterion measure. Spearman correlations and Bland-Altman plots (or non-parametric approach) were used to analyse criterion validity, separately for the three age groups and for weekday, weekend day and average day. RESULTS: The test-retest reliability for self-reported total sedentary time indicated following values: ICC = 0.37-0.67 in adolescents; ICC = 0.73-0.77 in adults; ICC = 0.68-0.80 in older adults. Item-specific reliability results (e.g. context-specific SB and its potential correlates) showed good-to-excellent reliability in 67.94%, 68.90% and 66.38% of the items in adolescents, adults and older adults respectively. All items belonging to sedentary-related equipment and simultaneous SB showed good reliability. The sections of the questionnaire with lowest reliability were: context-specific SB (adolescents), potential correlates of computer use (adults) and potential correlates of motorized transport (older adults). Spearman correlations between self-reported total sedentary time and the activPAL were different for each age group: rho = 0.02-0.42 (adolescents), rho = 0.06-0.52 (adults), rho = 0.38-0.50 (older adults). Participants over-reported total sedentary time (except for weekend day in older adults) compared to the activPAL, for weekday, weekend day and average day respectively by +57.05%, +46.29%, +53.34% in adolescents; +40.40%, +19.15%, +32.89% in adults; +10.10%, -6.24%, +4.11% in older adults. CONCLUSIONS: The questionnaires showed acceptable test-retest reliability and criterion validity. However, over-reporting of total SB was noticeable in adolescents and adults. Nevertheless, these questionnaires will be useful in getting context-specific information on SB

A respiratory syncytial virus vaccine based on the small hydrophobic protein ectodomain presented with a novel lipid-based formulation is highly immunogenic and safe in adults : a first-in-humans study

Background: Respiratory syncytial virus infection can cause lower respiratory tract infection in older adults comparable to influenza, but no vaccines are available. Methods: This was a randomized, observer-blinded, first-in-humans study of a novel synthetic RSV antigen based on the ectodomain of the small hydrophobic glycoprotein (SHe) of RSV subgroup A, formulated with either the lipid and oil-based vaccine platform DepoVax (DPX-RSV[A]) or alum (RSV[A]-Alum), in healthy, 50-64-year-old individuals. Two dose levels (10 or 25 mu g) of SHe with each formulation were compared to placebo. A booster dose was administered on day 56. Results: There was no indication that the vaccine was unsafe. Mild pain, drowsiness, and muscles aches were the most common solicited adverse events (AEs), and the frequencies of the AEs did not increase after dose 2. Robust anti-SHe-specific immune responses were demonstrated in the DPX-RSV(A) 10-mu g and 25-mu g groups (geometric mean titer, approximately 10-fold and 100-fold greater than that of placebo at days 56 and 236, respectively), and responses were sustained in the DPX-RSV(A) 25-mu g group at day 421. Responses to the RSV(A)-Alum vaccines were very low. Conclusions: A novel antigen from the SH protein of RSV, formulated in a lipid and oil-based vaccine platform, was highly immunogenic, with sustained antigen-specific antibody responses, and had an acceptable safety profile

Perceived and objective neighborhood support for outside of school physical activity in South African children.

The neighborhood environment has the potential to influence children's participation in physical activity. However, children's outdoor play is controlled by parents to a great extent. This study aimed to investigate whether parents' perceptions of the neighborhood environment and the objectively measured neighborhood environment were associated with children's moderate-to-vigorous intensity physical activity (MVPA) outside of school hours; and to determine if these perceptions and objective measures of the neighborhood environment differ between high and low socio-economic status (SES) groups.In total, 258 parents of 9-11 year-old children, recruited from the South African sample of the International Study of Childhood Obesity, Lifestyle and the Environment (ISCOLE), completed a questionnaire concerning the family and neighborhood environment. Objective measures of the environment were also obtained using Geographic Information Systems (GIS). Children wore an Actigraph (GT3X+) accelerometer for 7 days to measure levels of MVPA. Multilevel regression models were used to determine the association between the neighborhood environment and MVPA out of school hours.Parents' perceptions of the neighborhood physical activity facilities were positively associated with children's MVPA before school (β = 1.50 ± 0.51, p = 0.003). Objective measures of neighborhood safety and traffic risk were associated with children's after-school MVPA (β = -2.72 ± 1.35, p = 0.044 and β = -2.63 ± 1.26, p = 0.038, respectively). These associations were significant in the low SES group (β = -3.38 ± 1.65, p = 0.040 and β = -3.76 ± 1.61, p = 0.020, respectively), but unrelated to MVPA in the high SES group.This study found that several of the objective measures of the neighborhood environment were significantly associated with children's outside-of-school MVPA, while most of the parents' perceptions of the neighborhood environment were unrelated

Association between perceived built environmental attributes and physical activity among adults in South Africa

Background: To investigate the association between perceived environmental attributes and leisure-time and transport-related physical activity. Methods: This was a cross-sectional survey involving 671 South Africans aged ?35 years from urban and rural settings. International Physical Activity Questionnaire and Neighbourhood Walkability Scale were used to collect data. Multivariable logistic regressions were used to investigate the associations. Results: Significant urban vs. rural differences were apparent in the distribution of most attributes of neighborhood environment. After adjusting for gender, age, setting and relevant interaction terms, proximity to local stores was significantly associated with leisure-time physical activity (OR: 4.26; 95% CI, 1.00-18.08); while proximity to transit stops (2.44; 1.48-4.02), pleasant scenery (1.93; 1.07-3.46), sidewalks (2.36; 1.25-4.44), shade from trees (2.14; 1.19-3.85), traffic (2.17; 91.21-3.91) and well-lit streets (2.01; 1.04-3.89) were significantly associated with walking for leisure. Four-way intersections (4.54; 1.54-13.43), pleasant scenery (3.84; 1.35-10.99), traffic (0.28; 0.09-0.89), sidewalks (3.75; 1.06-13.27) and crosswalks were associated with transport related physical activity. Proximity to transit stops (2.12; 1.17-3.84) and well maintained sidewalks (2.69; 2.20-10.02) were significantly associated with total physical activity. Significant interactions by setting were apparent in some of the associations. Conclusion: Some, but not all attributes of a neighborhood environment were significantly associated in expected directions with the three physical activity domains in this mixed urban and rural population. This study highlights the need for policy strategies aimed at improving or maintaining these perceived environmental attributes to promote physical activity.IS