SAS macros for point and interval estimation of area under the receiver operating characteristic curve for non-proportional and proportional hazards Weibull models

Aims and objectives  For prediction of risk of cardiovascular end points using survival models the proportional hazards assumption is often not met. Thus, non-proportional hazards models are more appropriate for developing risk prediction equations in such situations. However, computer program for evaluating the prediction performance of such models has been rarely addressed. We therefore developed SAS macro programs for evaluating the discriminative ability of a non-proportional hazards Weibull model developed by Anderson (1991) and that of a proportional hazards Weibull model using the area under receiver operating characteristic (ROC) curve.

Method  Two SAS macro programs for non-proportional hazards Weibull model using Proc NLIN and Proc NLP respectively and model validation using area under ROC curve (with its confidence limits) were written with SAS IML language. A similar SAS macro for proportional hazards Weibull model was also written.

Results  The computer program was applied to data on coronary heart disease incidence for a Framingham population cohort. The five risk factors considered were current smoking, age, blood pressure, cholesterol and obesity. The predictive ability of the non-proportional hazard Weibull model was slightly higher than that of its proportional hazard counterpart. An advantage of SAS Proc NLP in terms of the example provided here is that it provides significance level for the parameter estimates whereas Proc NLIN does not.

Conclusion  The program is very useful for evaluating the predictive performance of non-proportional and proportional hazards Weibull models.

Molecular dynamics study of response of liquid N,N-dimethylformamide to externally applied electric field using a polarizable force field

The behavior of Liquid N,N-dimethylformamide subjected to a wide range of externally applied electric fields (from 0.001 V/nm to 1 V/nm) has been investigated through molecular dynamics simulation. To approach the objective the AMOEBA polarizable force field was extended to include the interaction of the external electric field with atomic partial charges and the contribution to the atomic polarization. The simulation results were evaluated with quantum mechanical calculations. The results from the present force field for the liquid at normal conditions were compared with the experimental and molecular dynamics results with non-polarizable and other polarizable force fields. The uniform external electric fields of higher than 0.01 V/nm have a significant effect on the structure of the liquid, which exhibits a variation in numerous properties, including molecular polarization, local cluster structure, rotation, alignment, energetics, and bulk thermodynamic and structural properties.

Water repellency, near-saturated infiltration and preferential solute transport in a macroporous clay soil

Little attention has been paid to the possibility that soil water repellency could enhance non-equilibrium water flow and solute transport through macropores present in structured clay soils. In this study, we measured infiltration and solute transport in a clay soil under near-saturated conditions in both the field using tension infiltrometers and in the laboratory on undisturbed soil columns. Measurements were made on adjacent plots under grass and continuous arable cultivation. Steady-state field infiltration rates measured using water and ethanol as the infiltrating fluids demonstrated that the soil macroporosity under grass was better developed, but that much of the structural pore system was inactive due to water repellency. No water repellency was detected on the arable plot disturbed by tillage. Dye tracing showed that the conducting macroporosity was largely comprised of earthworm channels in the grassed plot and inter-aggregate voids resulting from ploughing in the arable plot. Tracer breakthrough curves measured on field-dry soil indicated rapid macropore transport in columns taken from both plots, although the degree of non-equilibrium transport appeared somewhat stronger under grass. This result, which was attributed to water repellency, was also consistent with the larger flow-weighted mean pore size found in the field infiltration experiments. It is concluded that water repellency in undisturbed structured clay soils can have significant effects on the occurrence of non-equilibrium water and solute transport in macropores.

Urban growth in arid environments : developing water sustainability indicators for Abu Dhabi (UAE)

The United Arab Emirates (UAE) face a serious water problem. It has a very dry climate, high evaporation rate, combined with large water consumption from fast growing population, economic activities and uncontrolled uses of water for irrigation. Currently, UAE has one of the largest water footprints in the world. Groundwater is overexploited. Waste water is increasingly being treated to supply non-drinking water, but it still cover a small proportion of the demand. Desalination of sea water is the main source of potable water in UAE, but the high economic cost of desalination, its intensive energy demand and the adverse effects of its effluents on the marine life are a major concern. Other factors contributing to the problem are the focus of water management policies on keep supplying the growing demand for water, the increase of the per capita water consumption, and the free water charge for most of population. This research goal is to develop a water sustainability set of indicators for the challenging context of UAE. This paper presents the first stage of the research. Based on a review of the literature, the proposed framework involves 19 indicators, divided into four categories: water availability; water quality; water use efficiency; and policy and governance. Using an integrated cause-effect approach (DSR - Driving force, State, Response), the indicators were related in terms of their interdependencies, with a holistic view of the city water cycle. A preliminary test of the indicators to Abu Dhabi as a case study allowed an evaluation of the main 'Driving force' on the system, such as the scarcity of water due to natural constraints of the region, and increasing water consumption patterns of modern society; an assessment of the current 'state', which is under serious water stress. Also it indicated some potential 'responses', such as implementing policies for increasing efficient use.

Community-based study on knowledge, attitude and practice on the mode of transmission, prevention and treatment of the Buruli ulcer in Ga West District, Ghana

Buruli ulcer disease (BUD), a devastating tropical disease caused by Mycobacterium ulcerans, occurs in more than 80% of the administrative districts of Ghana. To elucidate community perceptions and
understanding of the aetiology of BUD, attitudes towards Buruli patients and treatment-seeking behaviours, we conducted a survey with 504 heads of households and seven focus group discussions in Ga West District, Ghana. Although 67% of participants regarded BUD as a health problem, 53% did not know its cause. Sixteen per cent attributed the cause to drinking non-potable water, 8.1% mentioned poor personal hygiene or dirty surroundings, and 5.5% identified swimming or wading in ponds as a risk factor. About 5.2% thought that witchcraft and curses cause BUD, and 71.8% indicated that BU sufferers first seek treatment from herbalists and only refer to the hospital as a last resort. The main
reasons were prospects of prolonged hospital stay, cost of transport, loss of earnings and opportunity associated with parents attending their children’s hospitalization over extended period, delays in being
attended by medical staff, and not knowing the cause of the disease or required treatment. The level of acceptance of BUD sufferers was high in adults but less so in children. The challenge facing health workers is to break the vicious cycle of poor medical outcomes leading to poor attitudes to hospital treatment in the community. Because herbalists are often the first people consulted by those who contract the disease, they need to be trained in early recognition of the pre-ulcerative stage of Buruli lesions.

Heavy metal accumulation in soils at three field sites subject to effluent irrigation

Three field sites were chosen to study the environmental assimilative capacity of heavy metals in soil. These sites were the Werribee Farm and the Myome Farm in Australia and Shenyang Zhangshi Irrigation Area in China. The Werribee Farm and the Shenyang Zhangshi Irrigation Area received sewage treatment and application on land for a long time. The Myome farm is an experimental site in which investigations on land application of municipal wastewater on water repellent soils is currently being trailed. Heavy metal contamination, in particular Cr, Cu and Zn, in the Land Filtration soil of Werribee Farm was widespread. More than a century of sewage irrigation has occurred in the Werribee Farm. The temporal distribution pattern of heavy metals (Cd, Cr, Cu, Ni, Pb and Zn) in the soil at this site follow an exponential trend with time and the spatial distribution pattern of accumulation of heavy metals in different paddocks correlates with the number of years of sewage irrigation at that site in the Farm. Extensive sewage irrigation at Shenyang Zhangshi Irrigation Area resulted in significant Cd pollution in soil-plant (rice) system and poses a significant threat to the health of local people. Even after eight years since cessation of sewage irrigation, the bioavailable fractions of Cd in the soil as analyzed by sequential extraction techniques were very high thus illustrating long-term persistence. The simultaneous competitive adsorption of metals in water repellent soils (at Myome Farm in South Australia) was studied. In the competitive situation, Cr, Pb and Cu are the heavy metal cations more strongly adsorbed by the soil, whereas Cd, Ni and Zn are the least adsorbed. The increase in Freundlich adsorption capacity by clay amendment suggested that clayed soils are capable sorption of higher heavy metal loadings compared to the non-clayed water repellent soil, which is more vulnerable to heavy metal inputs. A simple model of environmental assimilative capacity is proposed. The results of comparison of the three field sites shows that the Werribee Farm has a higher environmental assimilative capacity of heavy metals in soil than the soils at Shenyang Zhangshi Irrigation Area and Myome Farm, however heavy metal contamination at Werribee Farm is still a concern. The model of environmental assimilative capacity of heavy metals in soil is an effective tool to assist management of effluent applied land irrigation systems and can be used to better design environmental engineering systems.

Application of sequential nonparametric confidence bands in finance

In a nonparametric setting, the functional form of the relationship between the response variable and the associated predictor variables is assumed to be unknown when data is fitted to the model. Non-parametric regression models can be used for the same types of applications such as estimation, prediction, calibration, and optimization that traditional regression models are used for. The main aim of nonparametric regression is to highlight an important structure in the data without any assumptions about the shape of an underlying regression function. Hence the nonparametric approach allows the data to speak for itself. Applications of sequential procedures to a nonparametric regression model at a given point are considered.

The primary goal of sequential analysis is to achieve a given accuracy by using the smallest possible sample sizes. These sequential procedures allow an experimenter to make decisions based on the smallest number of observations without compromising accuracy. In the nonparametric regression model with a random design based on independent and identically distributed pairs of observations (X ,Y ), where the regression function m(x) is given bym(x) = E(Y X = x), estimation of the Nadaraya-Watson kernel estimator (m (x)) NW and local linear kernel estimator (m (x)) LL for the curve m(x) is considered. In order to obtain asymptotic confidence intervals form(x), two stage sequential procedure is used under which some asymptotic properties of Nadaraya-Watson and local linear estimators have been obtained.

The proposed methodology is first tested with the help of simulated data from linear and nonlinear functions. Encouraged by the preliminary findings from simulation results, the proposed method is applied to estimate the nonparametric regression curve of CAPM.

Large-scale statistical modeling of motion patterns : a Bayesian nonparametric approach

We propose a novel framework for large-scale scene understanding in static camera surveillance. Our techniques combine fast rank-1 constrained robust PCA to compute the foreground, with non-parametric Bayesian models for inference. Clusters are extracted in foreground patterns using a joint multinomial+Gaussian Dirichlet process model (DPM). Since the multinomial distribution is normalized, the Gaussian mixture distinguishes between similar spatial patterns but different activity levels (eg. car vs bike). We propose a modification of the decayed MCMC technique for incremental inference, providing the ability to discover theoretically unlimited patterns in unbounded video streams. A promising by-product of our framework is online, abnormal activity detection. A benchmark video and two surveillance videos, with the longest being 140 hours long are used in our experiments. The patterns discovered are as informative as existing scene understanding algorithms. However, unlike existing work, we achieve near real-time execution and encouraging performance in abnormal activity detection.

The impact of smoking in adolescence on early adult anxiety symptoms and the relationship between infant vulnerability factors for anxiety and early adult anxiety symptoms : The TOPP Study

Cigarette smoking is increased in people with trait anxiety and anxiety disorders, however no longitudinal data exist illuminating whether smoking in adolescence can influence the developmental trajectory of anxiety symptoms from early vulnerability in infancy to adult anxiety expression. Using The Tracing Opportunities and Problems in Childhood and Adolescence (TOPP) Study, a community-based cohort of children and adolescents from Norway who were observed from the age of 18months to age 18–19years, we explored the relationship between adolescent smoking, early vulnerability for anxiety in infancy (e.g. shyness, internalizing behaviors, emotional temperaments) and reported early adult anxiety.

Structural equation modeling demonstrated that adolescent active smoking was positively associated with increased early adulthood anxiety (β = 0.17, p<0.05), after controlling for maternal education (proxy for socioeconomic status). Adolescent anxiety did not predict early adult smoking. Adolescent active smoking was a significant effect modifier in the relationship between some infant vulnerability factors and later anxiety; smoking during adolescence moderated the relationship between infant internalizing behaviors (total sample: active smokers: β = 0.85,p<0.01, non-active smokers: ns) and highly emotional temperament (total sample: active smokers: β = 0.55,p<0.01,non-active smokers: ns), but not shyness, and anxiety in early adulthood. The results support a model where smoking acts as an exogenous risk factor in the development of anxiety, and smoking may alter the developmental trajectory of anxiety from infant vulnerability to early adult anxiety symptom expression. Although alternative non-mutually exclusive models may explain these findings, the results suggest that adolescent smoking may be a risk factor for adult anxiety, potentially by influencing anxiety developmental trajectories. Given the known adverse health effects of cigarette smoking and significant health burden imposed by anxiety disorders, this study supports the importance of smoking prevention and cessation programs targeting children and adolescence.

Habitat classification of temperate marine macroalgal communities using bathymetric LiDAR

Here, we evaluated the potential of using bathymetric Light Detection and Ranging (LiDAR) to characterise shallow water (<30 m) benthic habitats of high energy subtidal coastal environments. Habitat classification, quantifying benthic substrata and macroalgal communities, was achieved in this study with the application of LiDAR and underwater video groundtruth data using automated classification techniques. Bathymetry and reflectance datasets were used to produce secondary terrain derivative surfaces (e.g., rugosity, aspect) that were assumed to influence benthic patterns observed. An automated decision tree classification approach using the Quick Unbiased Efficient Statistical Tree (QUEST) was applied to produce substrata, biological and canopy structure habitat maps of the study area. Error assessment indicated that habitat maps produced were primarily accurate (>70%), with varying results for the classification of individual habitat classes; for instance, producer accuracy for mixed brown algae and sediment substrata, was 74% and 93%, respectively. LiDAR was also successful for differentiating canopy structure of macroalgae communities (i.e., canopy structure classification), such as canopy forming kelp versus erect fine branching algae. In conclusion, habitat characterisation using bathymetric LiDAR provides a unique potential to collect baseline information about biological assemblages and, hence, potential reef connectivity over large areas beyond the range of direct observation. This research contributes a new perspective for assessing the structure of subtidal coastal ecosystems, providing a novel tool for the research and management of such highly dynamic marine environments. © 2014 by the authors; licensee MDPI, Basel, Switzerland.

Simultaneous pattern and size optimisation of rock bolts for underground excavations

Designing a rock bolt reinforcement system for underground excavation involves determining bolt pattern, spacing, and size. In this paper, a topology optimisation technique is presented and employed to simultaneously optimise these design variables. To improve rock bolt design, the proposed technique minimises a displacement based function around the opening after bolt installation. This optimisation technique is independent of the material model and can be easily applied to any material model for rock and bolts. It is also extremely flexible in that it can be applied to any mechanical analysis method. To illustrate the capabilities of this method, numerical examples with non-linear material models and discontinuities in the host rock are presented. It is shown that the complexity of systems optimised using this approach is only restricted by limitations of the method used to analyse mechanical system responses.

Lizard responses to forest fire and timber harvesting: complementary insights from species and community approaches

Understanding the relationship between community composition and ecosystem function is essential for managing forests with complex disturbance regimes. Studies of animal responses to fire and timber harvesting in forest ecosystems typically focus on a single level of community diversity. Measures of species abundance and diversity at the community level, along with measures of functional diversity that incorporate information on species traits, provide opportunities for complementary insights into biodiversity responses to disturbances. We quantified community and functional responses of a temperate forest lizard community to fire and rotational logging using metrics including species-specific abundance, community abundance, species richness and evenness, as well as trait-based measures of functional diversity. We used non-linear regression models to examine the relationships between reptile data and time since fire and timber harvesting, using sites arrayed along a 30-years post-disturbance chronosequence. We modelled responses separately in two major vegetation types: coastal Banksia woodland and lowland eucalypt forests. Species and community measures offered different insights into the role of fire and logging. Species responses to disturbance differed between disturbance type and vegetation type. Four species exhibited significant population responses to either fire or timber harvesting, while the rest were unaffected by either disturbance. At the community level, species richness and community abundance increased significantly with time since fire in woodland vegetation. In forest vegetation, community abundance decreased with time since fire. Surprisingly, community evenness and functional diversity did not show marked responses to fire or timber harvesting. This is likely a result of trait homogeneity and the asynchrony in species responses to disturbance. We advocate using multiple measures of community composition - incorporating species-specific information, community metrics and functional traits - to ensure a more holistic understanding of disturbance ecology in forest landscapes.

Quantitative microbial risk assessment models for consumption of raw vegetables irrigated with reclaimed water

Quantitative microbial risk assessment models for estimating the annual risk of enteric virus infection associated with consuming raw vegetables that have been overhead irrigated with nondisinfected secondary treated reclaimed water were constructed. We ran models for several different scenarios of crop type, viral concentration in effluent, and time since last irrigation event. The mean annual risk of infection was always less for cucumber than for broccoli, cabbage, or lettuce. Across the various crops, effluent qualities, and viral decay rates considered, the annual risk of infection ranged from 10–3 to 10–1 when reclaimed-water irrigation ceased 1 day before harvest and from 10–9 to 10–3 when it ceased 2 weeks before harvest. Two previously published decay coefficients were used to describe the die-off of viruses in the environment. For all combinations of crop type and effluent quality, application of the more aggressive decay coefficient led to annual risks of infection that satisfied the commonly propounded benchmark of ≤10–4, i.e., one infection or less per 10,000 people per year, providing that 14 days had elapsed since irrigation with reclaimed water. Conversely, this benchmark was not attained for any combination of crop and water quality when this withholding period was 1 day. The lower decay rate conferred markedly less protection, with broccoli and cucumber being the only crops satisfying the 10–4 standard for all water qualities after a 14-day withholding period. Sensitivity analyses on the models revealed that in nearly all cases, variation in the amount of produce consumed had the most significant effect on the total uncertainty surrounding the estimate of annual infection risk. The models presented cover what would generally be considered to be worst-case scenarios: overhead irrigation and consumption of vegetables raw. Practices such as subsurface, furrow, or drip irrigation and postharvest washing/disinfection and food preparation could substantially lower risks and need to be considered in future models, particularly for developed nations where these extra risk reduction measures are more common.

Regional-scale models for relating land cover to basin surface-water quality using remotely sensed data in a GIS

Plant-based management systems implementing deep-rooted, perennial vegetation have been identified as important in mitigating the spread of secondary dryland salinity due to its capacity to influence water table depth. The Glenelg Hopkins catchment is a highly modified watershed in the southwest region of Victoria, where dryland salinity management has been identified as a priority. Empirical relationships between the proportion of native vegetation and in-stream salinity were examined in the Glenelg Hopkins catchment using a linear regression approach. Whilst investigations of these relationships are not unique, this is the first comprehensive attempt to establish a link between land use and in-stream salinity in the study area. The results indicate that higher percentage land cover with native vegetation was negatively correlated with elevated in-stream salinity. This inverse correlation was consistent across the 3 years examined (1980, 1995, and 2002). Recognising the potential for erroneously inferring causal relationships, the methodology outlined here was both a time and cost-effective tool to inform management strategies at a regional scale, particularly in areas where processes may be operating at scales not easily addressed with on-site studies.