A web application to perform linkage disequilibrium and linkage analyses on a computational grid

Motivation: Unravelling the genetic architecture of complex traits requires large amounts of data, sophisticated models and large computational resources. The lack of user-friendly software incorporating all these requisites is delaying progress in the analysis of complex traits. Methods: Linkage disequilibrium and linkage analysis (LDLA) is a high-resolution gene mapping approach based on sophisticated mixed linear models, applicable to any population structure. LDLA can use population history information in addition to pedigree and molecular markers to decompose traits into genetic components. Analyses are distributed in parallel over a large public grid of computers in the UK. Results: We have proven the performance of LDLA with analyses of simulated data. There are real gains in statistical power to detect quantitative trait loci when using historical information compared with traditional linkage analysis. Moreover, the use of a grid of computers significantly increases computational speed, hence allowing analyses that would have been prohibitive on a single computer. © The Author 2009. Published by Oxford University Press. All rights reserved.

Effect of driving conditions and suspension parameters on dynamic load-sharing of longitudinal-connected air suspensions

The objective of this research was to investigate the effects of driving conditions and suspension parameters on dynamic load-sharing of longitudinal-connected air suspensions of a tri-axle semi-trailer. A novel nonlinear model of a multi-axle semi-trailer with longitudinal-connected air suspension was formulated based on fluid mechanics and thermodynamics and was validated through test results. The effects of driving conditions and suspension parameters on dynamic load-sharing and road-friendliness of the semi-trailer were analyzed. Simulation results indicate that the road-friendliness metric-DLC (dynamic load coefficient) is not always in accordance with the load-sharing metric-DLSC (dynamic load-sharing coefficient). The effect of employing larger air lines and connectors on the DLSC optimization ratio gives varying results as road roughness increases and as driving speed increases. When the vehicle load reduces, or the static pressure increases, the DLSC optimization ratio declines monotonically. The results also indicate that if the air line diameter is always assumed to be larger than the connector diameter, the influence of air line diameter on load-sharing is more significant than that of the connector.

‘The health-location connection’: using GIS and social media on smartphones to track engagement with the Local urban environment for work, recreation, and physical activity

A technologically innovative study was undertaken across two suburbs in Brisbane, Australia, to assess socioeconomic differences in women's use of the local environment for work, recreation, and physical activity. Mothers from high and low socioeconomic suburbs were instructed to continue with usual daily routines, and to use mobile phone applications (Facebook Places, Twitter, and Foursquare) on their mobile phones to ‘check-in’ at each location and destination they reached during a one-week period. These smartphone applications are able to track travel logistics via built-in geographical information systems (GIS), which record participants’ points of latitude and longitude at each destination they reach. Location data were downloaded to Google Earth and excel for analysis. Women provided additional qualitative data via text regarding the reasons and social contexts of their travel. We analysed 2183 ‘check-ins’ for 54 women in this pilot study to gain quantitative, qualitative, and spatial data on human-environment interactions. Data was gathered on distances travelled, mode of transport, reason for travel, social context of travel, and categorised in terms of physical activity type – walking, running, sports, gym, cycling, or playing in the park. We found that the women in both suburbs had similar daily routines with the exception of physical activity. We identified 15% of ‘check-ins’ in the lower socioeconomic group as qualifying for the physical activity category, compared with 23% in the higher socioeconomic group. This was explained by more daily walking for transport (1.7kms to 0.2kms) and less car travel each week (28.km to 48.4kms) in the higher socioeconomic suburb. We ascertained insights regarding the socio-cultural influences on these differences via additional qualitative data. We discuss the benefits and limitations of using new technologies and Google Earth with implications for informing future physical and social aspects of urban design, and health promotion in socioeconomically diverse cities.

Spatial variation of particle number concentration in school microscale environments and its impact on exposure assessment

It has not yet been established whether the spatial variation of particle number concentration (PNC) within a microscale environment can have an effect on exposure estimation results. In general, the degree of spatial variation within microscale environments remains unclear, since previous studies have only focused on spatial variation within macroscale environments. The aims of this study were to determine the spatial variation of PNC within microscale school environments, in order to assess the importance of the number of monitoring sites on exposure estimation. Furthermore, this paper aims to identify which parameters have the largest influence on spatial variation, as well as the relationship between those parameters and spatial variation. Air quality measurements were conducted for two consecutive weeks at each of the 25 schools across Brisbane, Australia. PNC was measured at three sites within the grounds of each school, along with the measurement of meteorological and several other air quality parameters. Traffic density was recorded for the busiest road adjacent to the school. Spatial variation at each school was quantified using coefficient of variation (CV). The portion of CV associated with instrument uncertainty was found to be 0.3 and therefore, CV was corrected so that only non-instrument uncertainty was analysed in the data. The median corrected CV (CVc) ranged from 0 to 0.35 across the schools, with 12 schools found to exhibit spatial variation. The study determined the number of required monitoring sites at schools with spatial variability and tested the deviation in exposure estimation arising from using only a single site. Nine schools required two measurement sites and three schools required three sites. Overall, the deviation in exposure estimation from using only one monitoring site was as much as one order of magnitude. The study also tested the association of spatial variation with wind speed/direction and traffic density, using partial correlation coefficients to identify sources of variation and non-parametric function estimation to quantify the level of variability. Traffic density and road to school wind direction were found to have a positive effect on CVc, and therefore, also on spatial variation. Wind speed was found to have a decreasing effect on spatial variation when it exceeded a threshold of 1.5 (m/s), while it had no effect below this threshold. Traffic density had a positive effect on spatial variation and its effect increased until it reached a density of 70 vehicles per five minutes, at which point its effect plateaued and did not increase further as a result of increasing traffic density.

Self-regulated learning and executive function : exploring the relationships in a sample of adolescent males

This study investigated relationships between SRL and EF in a sample of 254 school-aged adolescent males. Two hypotheses were tested: that self-reported measures of SRL and EF are closely related and that as different aspects of EF mature during adolescence, the corresponding components of SRL should also improve, leading to an age-related increase in the correlation between EF and SRL. Two self-report instruments were used: the strategies for self-regulated learning survey (SSRLS) and the behavioural rating instrument of executive function (BRIEF). Strong correlations between the measures of EF and SRL were found, especially in areas associated with metacognitive processes. Correlations between EF and SRL were found, with weaker correlations between behavioural regulation and SRL were found to be weaker for the younger participants in the sample while the relationship between EF and SRL appears to grow stronger during the initial years of high school even though self-reported levels of EF along with motivation for SRL and important components of SRL such as goal setting and planning were found to decrease with age. Decreasing levels of motivation for learning during adolescence are speculated to moderate the deployment of SRL and EF in a school context.

Body temperature and its effect on leukocyte mobilization, cytokines and markers of neutrophil activation during and after exercise

We investigated the influence of rectal temperature on the immune system during and after exercise. Ten well-trained male cyclists completed exercise trials (90 min cycling at 60% VO(2max) + 16.1 - km time trial) on three separate occasions: once in 18 degrees C and twice in 32 degrees C. Twenty minutes after the trials in 32 degrees C, the cyclists sat for approximately 20 min in cold water (14 degrees C) on one occasion, whereas on another occasion they sat at room temperature. Rectal temperature increased significantly during cycling in both conditions, and was significantly higher after cycling in 32 degrees C than in 18 degrees C (P < 0.05). Leukocyte counts increased significantly during cycling but did not differ between the conditions. The concentrations of serum interleukin (IL)-6, IL-8 and IL-10, plasma catecholamines, granulocyte-colony stimulating factor, myeloperoxidase and calprotectin increased significantly following cycling in both conditions. The concentrations of serum IL-8 (25%), IL-10 (120%), IL-1 receptor antagonist (70%), tumour necrosis factor-alpha (17%), plasma myeloperoxidase (26%) and norepinephrine (130%) were significantly higher after cycling in 32 degrees C than in 18 degrees C. During recovery from exercise in 32 degrees C, rectal temperature was significantly lower in response to sitting in cold water than at room temperature. However, immune changes during 90 min of recovery did not differ significantly between sitting in cold water and at room temperature. The greater rise in rectal temperature during exercise in 32 degrees C increased the concentrations of serum IL-8, IL-10, IL-1ra, TNF-alpha and plasma myeloperoxidase, whereas the greater decline in rectal temperature during cold water immersion after exercise did not affect immune responses.

Reply - Malnutrition and its impact on cost of hospitalization, length of stay, readmission and 3-year mortality

Dear Editor We thank Dr Klek for his interest in our article and giving us the opportunity to clarify our study and share our thoughts. Our study looks at the prevalence of malnutrition in an acute tertiary hospital and tracked the outcomes prospectively.1 There are a number of reasons why we chose Subjective Global Assessment (SGA) to determine the nutritional status of patients. Firstly, we took the view that nutrition assessment tools should be used to determine nutrition status and diagnose presence and severity of malnutrition; whereas the purpose of nutrition screening tools are to identify individuals who are at risk of malnutrition. Nutritional assessment rather than screening should be used as the basis for planning and evaluating nutrition interventions for those diagnosed with malnutrition. Secondly, Subjective Global Assessment (SGA) has been well accepted and validated as an assessment tool to diagnose the presence and severity of malnutrition in clinical practice.2, 3 It has been used in many studies as a valid prognostic indicator of a range of nutritional and clinical outcomes.4, 5, 6 On the other hand, Malnutrition Universal Screening Tool (MUST)7 and Nutrition Risk Screening 2002 (NRS 2002)8 have been established as screening rather than assessment tools.

The effects of portal website attitude and e-services on branding of e-stores

Purpose –Increasingly the company websites, along with the intermediary websites such as portal sites have become an integral component of the firms brand strategy. This study emphasises the importance of website service elements within portal sites and the impact on e-retailer brand attitudes and brand identity in an ever more competitive digital market-space. Design/methodology/approach– The research employs structural equation modeling technique to capture the relationship among website attitude, e-service quality, brand attitude and brand identity. Findings–The results from the study indicate consumer attitude perceptions toward portal website and e-service elements combine to increase brand attitude and also brand identity for e-retailers. Originality/value –Although there has been a plethora of studies evaluating corporate websites and branding interactions there is limited comprehension of the impact of intermediary portal sites. Moreover, the literature is limited in validating the link between e-services with brand attitude and brand identity within a portal website context. This study develops a framework that highlights the important influence of e-services within portal websites and the impact on the firm’s brand.

Empirical modelling of the relationship between bus and car speeds on signalised urban networks

Vehicle speed is an important attribute for the utility of a transport mode. The speed relationship between multiple modes of transport is of interest to the traffic planners and operators. This paper quantifies the relationship between bus speed and average car speed by integrating Bluetooth data and Transit Signal Priority data from the urban network in Brisbane, Australia. The method proposed in this paper is the first of its kind to relate bus speed and average car speed by integrating multi-source traffic data in a corridor-based method. Three transferable regression models relating not-in-service bus; in-service bus during peak; and in-service bus during off peak periods with average car are proposed. The models are cross-validated and the interrelationships are significant

The influence of temperature and introduction point on the detection of Rhyzopertha dominica in stored grain

The presence of insect pests in grain storages throughout the supply chain is a significant problem for farmers, grain handlers, and distributors world-wide. Insect monitoring and sampling programmes are used in the stored grains industry for the detection and estimation of pest populations. At the low pest densities dictated by economic and commercial requirements, the accuracy of both detection and abundance estimates can be influenced by variations in the spatial structure of pest populations over short distances. Geostatistical analysis of Rhyzopertha dominica populations in 2 and 3 dimensions showed that insect numbers were positively correlated over short (0.5 cm) distances, and negatively correlated over longer (.10 cm) distances. At 35 C, insects were located significantly further from the grain surface than at 25 and 30 C. Dispersion metrics showed statistically significant aggregation in all cases. The observed heterogeneous spatial distribution of R. dominica may also be influenced by factors such as the site of initial infestation and disturbance during handling. To account for these additional factors, I significantly extended a simulation model that incorporates both pest growth and movement through a typical stored-grain supply chain. By incorporating the effects of abundance, initial infestation site, grain handling, and treatment on pest spatial distribution, I developed a supply chain model incorporating estimates of pest spatial distribution. This was used to examine several scenarios representative of grain movement through a supply chain, and determine the influence of infestation location and grain disturbance on the sampling intensity required to detect pest infestations at various infestation rates. This study has investigated the effects of temperature, infestation point, and grain handling on the spatial distribution and detection of R. dominica. The proportion of grain infested was found to be dependent upon abundance, initial pest location, and grain handling. Simulation modelling indicated that accounting for these factors when developing sampling strategies for stored grain has the potential to significantly reduce sampling costs while simultaneously improving detection rate, resulting in reduced storage and pest management cost while improving grain quality.

A density functional theory study of CO2 and N2 adsorption on aluminium nitride single walled nanotubes

Strong binding of isolated carbon dioxide (CO2) on aluminium nitride (AlN) single walled nanotubes is verified using two different functionals. Two optimized configurations corresponding to physisorption and chemisorption are linked by a low energy barrier, such that the chemisorbed state is accessible and thermodynamically favored at low temperatures. In contrast, N2 is found only to form a physisorbed complex with the AlN nanotube, suggesting the potential application of aluminium nitride based materials for CO2 fixation. The effect of nanotube diameter on gas adsorption properties is also discussed. The diameter is found to have an important effect on the chemisorption of CO2, but has little effect on the physisorption of either CO2 or N2.

CO2 capture and gas separation on boron carbon nanotubes

Concern about the increasing atmospheric CO2 concentration and its impact on the environment has led to increasing attention directed toward finding advanced materials and technologies suited for efficient CO2 capture, storage and purification of clean-burning natural gas. In this letter, we have performed comprehensive theoretical investigation of CO2, N2, CH4 and H2 adsorption on B2CNTs. Our study shows that CO2 molecules can form strong interactions with B2CNTs with different charge states. However, N2, CH4 and H2 can only form very weak interactions with B2CNTs. Therefore, the study demonstrates B2CNTs could sever as promising materials for CO2 capture and gas separation.

The impact of co-locating regulatory and directional signs on driver performance

The use of intelligent transport systems is proliferating across the Australian road network, particularly on major freeways. New technology allows a greater range of signs and messages to be displayed to drivers. While there has been a long history of human factors analyses of signage, no evaluation has been conducted on this novel, sometimes dynamic, signage or potential interactions when co-located. The purpose of this driving simulator study was to investigate drivers’ behavioural changes and comprehension resulting from the co-location of Lane Use Management Systems with static signs and (Enhanced) Variable Message Signs on Queensland motorways. A section of motorway was simulated, and nine scenarios were developed which presented a combination of signage cases across levels of driving task complexity. Two higher-risk road user groups were targeted for this research on an advanced driving simulator: older (65+ years, N=21) and younger (18-22 years, N=20) drivers. Changes in sign co-location and task complexity had small effect on driver comprehension of the signs and vehicle dynamics variables, including difference with the posted speed limit, headway, standard deviation of lane keeping and brake jerks. However, increasing the amount of information provided to drivers at a given location (by co-locating several signs) increased participants’ gaze duration on the signs. With co-location of signs and without added task complexity, a single gaze was over 2s for more than half of the population tested for both groups, and up to 6 seconds for some individuals.

Effect of moisture and temperature distribution on dried food microstructure and porosity

Dehydration of food materials requires water removal from it. This removal of moisture prevents the growth and reproduction of microorganisms that cause decay and minimizes many of the moisture-driven deterioration reactions (Brennan, 1994). However, during food drying, many other changes occur simultaneously resulting in a modified overall quality (Kompany et al., 1993). Among the physical attributes of dried food material porosity and microstructure are the important ones that can dominant other quality of dried foods (Aguilera et al., 2000). In addition, this two concerned quality attributes affected by process conditions, material components and raw structure of food stuff. In this work, temperature moisture distribution within food materials during microwave drying will be taken into consideration to observe its participation on the microstructure and porosity of the finished product. Apple is the selective materials for this work. Generally, most of the food materials are found in non-uniformed moisture contained condition. To develop non uniform temperature distribution, food materials have been dried in a microwave oven with different power levels (Chua et al., 2000). First of all, temperature and moisture model is simulated by COMSOL Multiphysics. Later on, digital imaging camera and Image Pro Premier software have been deployed to observation moisture distribution and thermal imaging camera for temperature distribution. Finally, Microstructure and porosity of the food materials are obtained from scanning electron microscope and porosity measuring devices respectively . Moisture distribution and temperature during drying influence the microstructure and porosity significantly. Specially, High temperature and moisture contained regions show less porosity and more rupture. These findings support other literatures of Halder et al. (2011) and Rahman et al (1990). On the other hand, low temperature and moisture regions depict uniform microstructure and high porosity. This work therefore assists in better understanding of the role of moisture and temperature distribution to a prediction of micro structure and porosity of dried food materials.

Methyl ester preparation from peanut oil and its effect on DI diesel engine combustion

This study investigated the preparation of methyl ester (Biodiesel) from peanut oil by transesterification method and its effect on DI diesel engine. Two parameters were measured during the engine operation: one is engine performance (brake thermal efficiency and brake specific fuel consumption), and the other is the exhaust emissions (NOx and CO). The result showed that, when compared with neat diesel fuel, the brake thermal efficiency of biodiesel blend was almost similar or a slight lower. However, brake specific fuel consumption (bsfc) was a little higher than neat diesel. CO was lower and NOx was little higher with biodiesel blend than that of diesel. The engine performance for B10 and B20 was very similar. At medium and high load conditions the engine emissions for B10 and B20 has no significant variation. Hence, B20 can safely be used in diesel engine without any significant penalty in engine performance and emissions.