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

Parental perceived built environment measures and active play in Washington DC metropolitan children

AbstractObjectivePrevious research identified associations between perceived built environment and adult physical activity; however, fewer studies have explored associations in children. The Built Environment and Active Play (BEAP) Study examined relationships between children's active play and parental perceptions of home neighborhood built environments within the Washington, DC metropolitan area (DMV).MethodsWith this cross-sectional study, a questionnaire was administered in 2014 to parents of children (7–12years old) residing in the DMV. Data were collected on children's active play, home built environment parental perceptions, and demographics. Active play response data were dichotomized by whether the child did or did not meet the 60-min/day Physical Activity Guidelines for Americans (PAGAs) recommendation. Perceived home neighborhood built environment data were also dichotomized. Chi-square tests determined differences in parental perceived built environment measures between active and non-active child groups. Logistic regression assessed the association of parental perceived built environment variables with active play while adjusting for demographic variables.ResultsThe BEAP Study population (n=144) included a uniquely diverse population of children with 23.7% African Americans and 10.4% Asian Americans. A statistically significant greater proportion of active children's parents agreed with the importance of neighborhood esthetics, active play areas, walkability and safety as compared to the parents of non-active children. Fully adjusted logistic regression models demonstrated that some parental perceived built environment measures (e.g. access to play equipment) were predictors of their children meeting the 60-min/day PAGA recommendation.ConclusionOur findings support the important role of home neighborhood built environment perceptions on childhood active play

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

Uncertainty in Building Energy Performance Characterization: Impact of Gas Consumption Decomposition on Estimated Heat Loss Coefficient

Characterization of building energy performance indicators such as the Heat Loss Coefficient (HLC) based on in-situ measurement data calls for thorough building physical insight, a well- designed measurement set-up to collect sufficient, qualitative data and adequate data analysis methods. On-board monitoring may be an alternative for dedicated experiments to perform the data collection task. This paper analyses the sensitivity of the end-result of the characterization, the HLC estimate, to flaws in the monitoring data set. More specifically, the impact of not installing submeters to disentangle the gas consumption for space heating and the production of domestic hot water is evaluated. Hereto, multiple gas decomposition methods are applied on a case study monitoring data set, after which the HLC is assessed. The results show deviations up to 33% for the mean estimate. Nevertheless, the 95% confidence intervals largely overlap

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

Built environment and active play among Washington DC metropolitan children: A protocol for a cross-sectional study

Research has demonstrated that children who participate in active play are more likely to be physically active, thereby improving long-term health outcomes. Many adult studies have also shown that neighborhood built environments can encourage or discourage routine physical activity. Limited evidence has demonstrated that children who reside in neighborhoods with a built environment that is more inviting to active play exhibit lower overweight and obesity rates as well as an overall better state of well-being. This Built Environment and Active Play (BEAP) Study aims to develop a neighborhood playability rating system in the Washington, DC (DMV) area. Similar to walkability scores, these playability scores will estimate how affable a neighborhood is to active play. The BEAP Study will attempt to provide a broad view of factors influencing the level and type of active play among children. Using a cross-sectional design, the BEAP Study will collect data using a mail questionnaire administered to the parents and/or guardians of 2000 children aged 7-12 years residing in select DMV areas in October of 2014. Questionnaire data, including information on active play, home and neighborhood characteristics, parental perceptions, and sociodemographic characteristics will be merged through a geographic information system (GIS) with objective built environment measures in the participants’ neighborhoods. An ordered logit model will be used to regress an ordinal active play outcome on built environment exposure variables while adjusting for potential confounders. Upon the construction of the final model, predictor coefficients will be used as parameters in the scoring system to develop neighborhood playability scores. The BEAP Study intends to generate a neighborhood playability index by characterizing and quantifying children’s active play using parent-reported physical activity data in children, GIS data and built environment measures in participant neighborhoods. The BEAP Study will improve our understanding of the built environment and childhood playability relationship while also contributing to the body of evidence-based built environment and physical activity research.https://doi.org/10.1186/s13690-015-0070-

Associations of home and neighborhood environments with children’s physical activity in the U.S.-based Neighborhood Impact on Kids (NIK) longitudinal cohort study

Introduction Physical activity is important for children’s health and well-being. Supportiveness for physical activity of home and neighborhood environments may affect children’s PA, but most studies are cross-sectional. We examined environmental predictors of change in children’s physical activity over two years. Methods Data were from the longitudinal, observational cohort study, ‘Neighborhood Impact on Kids’. Participants were children (initially aged 6–12 years) and their parent/caregiver (n = 727 dyads) living in neighborhoods throughout San Diego County, California and King County (Seattle area), Washington, USA. Children’s moderate-to-vigorous physical activity (MVPA) was measured using accelerometers at T1 (Time 1 or baseline, 2007–2009) and T2, the two-year follow-up. At T1, parents survey-reported on physical activity (PA) equipment at home and demographics. Neighborhood environment was measured using spatial data in Geographic Information Systems (intersection density; park availability) and in-person audits (informal play space near home; park-based PA facilities; land use; support for walking/cycling). Generalized additive mixed models estimated total effects, then direct effects, of environmental attributes on MVPA at T1. Two-way moderating effects of child’s sex and age were examined at T1. To examine associations of environmental exposures with changes in MVPA, we estimated interaction effects of environmental attributes on the association between time and MVPA. Results On average, children accumulated 146 min/day (standard deviation or SD = 53) of MVPA at T1, and 113 (SD = 58) min/day at T2. There were no significant total or direct effects of environmental attributes on MVPA at T1, and no significant two-way interaction effects of child’s age and sex for T1 MVPA. Having informal play spaces proximal to home with more amenities was associated with less MVPA decline from T1 to T2. Higher residential density, higher land use mix, and higher number of PA facilities in nearby parks were unexpectedly associated with greater MVPA decline. Conclusion Higher quality informal play spaces close to home may help offset declines in MVPA during middle childhood, as they may promote unstructured active play with opportunities for parental or neighbor surveillance. Unexpectedly, environmental factors consistent with higher walkability were associated with greater declines in children’s MVPA. As physical activity differs across the lifespan, so may environmental factors that facilitate it

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