Software modelling languages: A wish list

© 2015 IEEE. Contemporary software engineering modelling tends to rely on general-purpose languages, such as the Unified Modeling Language. However, such languages are practice-based and seldom underpinned with a solid theory-be it mathematical, ontological or concomitant with language use. The future of software modelling deserves research to evaluate whether a language base that is compatible with these various elements as well as being philosophically coherent offers practical advantages to software developers

Preparation of 32P labelled phosphorous acid.

Phosphorous acid labelled with 32P has been prepared on a small scale starting from neutron-irradiated phosphorus. The compound is intended for tracer studies in the development of novel fungicides

Retaining young people in a longitudinal sexual health survey: a trial of strategies to maintain participation

<p>BACKGROUND:There is an increasing trend towards lower participation in questionnaire surveys. This reduces representativeness, increases costs and introduces particular challenges to longitudinal surveys, as researchers have to use complex statistical techniques which attempt to address attrition. This paper describes a trial of incentives to retain longitudinal survey cohorts from ages 16 to 20, to question them on the sensitive topic of sexual health.</p> <p>METHODS: A longitudinal survey was conducted with 8,430 eligible pupils from two sequential year groups from 25 Scottish schools. Wave 1 (14 years) and Wave 2 (16 years) were conducted largely within schools. For Wave 3 (18 years), when everyone had left school, the sample was split into 4 groups that were balanced across predictors of survey participation: 1) no incentive; 2) chance of winning one of twenty-five vouchers worth 20 pounds; 3) chance of winning one 500 pounds voucher; 4) a definite reward of a 10 pounds voucher sent on receipt of their completed questionnaire. Outcomes were participation at Wave 3 and two years later at Wave 4. Analysis used logistic regression and adjusted for clustering at school level.</p> <p>RESULTS: The only condition that had a significant and beneficial impact for pupils was to offer a definite reward for participation (Group 4). Forty-one percent of Group 4 participated in Wave 3 versus 27% or less for Groups 1 to 3. At Wave 4, 35% of Group 4 took part versus 25% or less for the other groups. Similarly, 22% of Group 4 participated in all four Waves of the longitudinal study, whereas for the other three groups it was 16% or less that participated in full.</p> <p>CONCLUSIONS: The best strategy for retaining all groups of pupils and one that improved retention at both age 18 and age 20 was to offer a definite reward for participation. This is expensive, however, given the many benefits of retaining a longitudinal sample, we recommend inclusion of this as a research cost for cohort and other repeat-contact studies.</p&gt

Measuring every particle's size from three-dimensional imaging experiments

Often experimentalists study colloidal suspensions that are nominally monodisperse. In reality these samples have a polydispersity of 4-10%. At the level of an individual particle, the consequences of this polydispersity are unknown as it is difficult to measure an individual particle size from microscopy. We propose a general method to estimate individual particle radii within a moderately concentrated colloidal suspension observed with confocal microscopy. We confirm the validity of our method by numerical simulations of four major systems: random close packing, colloidal gels, nominally monodisperse dense samples, and nominally binary dense samples. We then apply our method to experimental data, and demonstrate the utility of this method with results from four case studies. In the first, we demonstrate that we can recover the full particle size distribution {\it in situ}. In the second, we show that accounting for particle size leads to more accurate structural information in a random close packed sample. In the third, we show that crystal nucleation occurs in locally monodisperse regions. In the fourth, we show that particle mobility in a dense sample is correlated to the local volume fraction.Comment: 7 pages, 5 figure

Monitoring the health of the greater Mekong’s rivers

The methods used for biomonitoring can be sophisticated, producing highly accurate results, but can also be simplified for communities to use. In countries where budgets for biomonitoring are low, using community-based biomonitoring systems can effectively and cheaply tell us about a river’s health

Mathematical and Statistical Techniques for Systems Medicine: The Wnt Signaling Pathway as a Case Study

The last decade has seen an explosion in models that describe phenomena in systems medicine. Such models are especially useful for studying signaling pathways, such as the Wnt pathway. In this chapter we use the Wnt pathway to showcase current mathematical and statistical techniques that enable modelers to gain insight into (models of) gene regulation, and generate testable predictions. We introduce a range of modeling frameworks, but focus on ordinary differential equation (ODE) models since they remain the most widely used approach in systems biology and medicine and continue to offer great potential. We present methods for the analysis of a single model, comprising applications of standard dynamical systems approaches such as nondimensionalization, steady state, asymptotic and sensitivity analysis, and more recent statistical and algebraic approaches to compare models with data. We present parameter estimation and model comparison techniques, focusing on Bayesian analysis and coplanarity via algebraic geometry. Our intention is that this (non exhaustive) review may serve as a useful starting point for the analysis of models in systems medicine.Comment: Submitted to 'Systems Medicine' as a book chapte

Frequent burning promotes invasions of alien plants into a mesic African savanna

Fire is both inevitable and necessary for maintaining the structure and functioning of mesic savannas. Without disturbances such as fire and herbivory, tree cover can increase at the expense of grass cover and over time dominate mesic savannas. Consequently, repeated burning is widely used to suppress tree recruitment and control bush encroachment. However, the effect of regular burning on invasion by alien plant species is little understood. Here, vegetation data from a long-term fire experiment, which began in 1953 in a mesic Zimbabwean savanna, were used to test whether the frequency of burning promoted alien plant invasion. The fire treatments consisted of late season fires, lit at 1-, 2-, 3-, and 4-year intervals, and these regularly burnt plots were compared with unburnt plots. Results show that over half a century of frequent burning promoted the invasion by alien plants relative to areas where fire was excluded. More alien plant species became established in plots that had a higher frequency of burning. The proportion of alien species in the species assemblage was highest in the annually burnt plots followed by plots burnt biennially. Alien plant invasion was lowest in plots protected from fire but did not differ significantly between plots burnt triennially and quadrennially. Further, the abundance of five alien forbs increased significantly as the interval (in years) between fires became shorter. On average, the density of these alien forbs in annually burnt plots was at least ten times as high as the density of unburnt plots. Plant diversity was also altered by long-term burning. Total plant species richness was significantly lower in the unburnt plots compared to regularly burnt plots. These findings suggest that frequent burning of mesic savannas enhances invasion by alien plants, with short intervals between fires favouring alien forbs. Therefore, reducing the frequency of burning may be a key to minimising the risk of alien plant spread into mesic savannas, which is important because invasive plants pose a threat to native biodiversity and may alter savanna functioning