Effect of population stratification on case-control association studies. II. False-positive rates and their limiting behavior as number of subpopulations increases

There has been considerable debate in the literature concerning bias in case-control association mapping studies due to population stratification. In this paper, we perform a theoretical analysis of the effects of population stratification by measuring the inflation in the test's type I error (or false-positive rate). Using a model of stratified sampling, we derive an exact expression for the type I error as a function of population parameters and sample size. We give necessary and sufficient conditions for the bias to vanish when there is no statistical association between disease and marker genotype in each of the subpopulations making up the total population. We also investigate the variation of bias with increasing subpopulations and show, both theoretically and by using simulations, that the bias can sometimes be quite substantial even with a very large number of subpopulations. In a companion simulation-based paper (Heiman et al., Part I, this issue), we have focused on the CRR (confounding risk ratio) and its relationship to the type I error in the case of two subpopulations, and have also quantified the magnitude of the type I error that can occur with relatively low CRR values.     

The effect of organochlorines and heavy metals on sex steroid-binding proteins in vitro in the plasma of nesting green turtles, Chelonia mydas

In this study on green turtles, Chelonia mydas, from Peninsular Malaysia, the effect of selected environmental toxicants was examined in vitro. Emphasis was placed on purported hormone-mimicking chemicals such as dichlorodiphenyltrichloroethane (DDT), dichlorodiphenyldichloroethylene, dieldrin, lead, zinc and copper. Five concentrations were used: high (1 mg/L), medium (10⁻¹ mg/L), low (10⁻² mg/L), very low (10⁻⁶ mg/L) and control (diluted carrier solvent but no toxicants). The results suggest that environmental pesticides and heavy metals may significantly alter the binding of steroids [i.e. testosterone (T) and oestradiol] to the plasma proteins in vitro. Competition studies showed that only Cu competed for binding sites with testosterone in the plasma collected from nesting C. mydas. Dieldrin and all heavy metals competed with oestradiol for binding sites. Furthermore, testosterone binding affinity was affected at various DDT concentrations and was hypothesised that DDT in vivo may act to inhibit steroid-protein interactions in nesting C. mydas. Although the precise molecular mechanism is yet to be described, DDT could have an effect upon the protein conformation thus affecting T binding (e.g. the T binding site on the steroid hormone binding protein molecule).     

Structural platform for the autolytic activity of an intact NS2B-NS3 protease complex from dengue virus

Dengue virus completes its protein synthesis inside human cells on the endoplasmic reticulum membrane by processing the single-chain polyprotein precursor into 10 functional proteins. This vital process relies on the two-component virus-encoded protease complex; nonstructural protein 3 (NS3) possesses the proteolytic activity in its N-terminus, and NS2B acts as a fundamental activator and membrane-anchoring subunit. The membrane-associated NS2B-NS3 complex has essentially not yet been isolated or studied. We describe here a useful protocol for the preparation of the full-length NS2B-NS3 complex from dengue serotype 2 virus by utilizing a Mistic-fusion expression cassette in Escherichia coli. The protease complex was successfully solubilized and stabilized from the bacterial membrane and purified with the use of fos-choline-14 detergent. The detergent-solubilized protease complex retained autolytic activity and, intriguingly, exists as a robust trimer, implying a molecular assembly in the membrane. We further conducted a random mutagenesis study to efficiently scan for entire residues and motifs contributing to autocleavage and provide evidence of the importance of the two distal β-hairpins in the activity of the viral protease. Our results provide the first comprehensive view of an active dengue protease in the membrane-bound form.     

The evolution of law in biopreparedness

The decade following the terrorist attacks on September 11, 2001, and ensuing anthrax exposures that same fall has seen significant legal reforms designed to improve biopreparedness nationally. Over the past 10 years, a transformative series of legal changes have effectively (1) rebuilt components of federal, state, and local governments to improve response efforts; (2) created an entire new legal classification known as "public health emergencies"; and (3) overhauled existing legal norms defining the roles and responsibilities of public and private actors in emergency response efforts. The back story as to how law plays an essential role in facilitating biopreparedness, however, is pocked with controversies and conflicts between law- and policymakers, public health officials, emergency managers, civil libertarians, scholars, and others. Significant legal challenges for the next decade remain. Issues related to interjurisdictional coordination; duplicative legal declarations of emergency, disaster, and public health emergency; real-time legal decision making; and liability protections for emergency responders and entities remain unresolved. This article explores the evolving tale underlying the rise and prominence of law as a pivotal tool in national biopreparedness and response efforts in the interests of preventing excess morbidity and mortality during public health emergencies.     

Continuum modeling and numerical simulation of cell motility

This work proposes a continuum-mechanical model of cell motility which accounts for the dynamics of motility-relevant protein species. For the special case of fish epidermal keratocytes, the stress and cell-substrate traction responses are postulated to depend on selected protein densities in accordance with the structural features of the cells. A one-dimensional version of the model is implemented using Arbitrary Lagrangian–Eulerian finite elements in conjunction with Lagrange multipliers for the treatment of kinematic constraints related to surface growth. Representative numerical tests demonstrate the capacity of the proposed model to simulate stationary and steady crawling states.     

A Framework for the Economic Analysis of Data Collection Methods for Vital Statistics

Background

Over recent years there has been a strong movement towards the improvement of vital statistics and other types of health data that inform evidence-based policies. Collecting such data is not cost free. To date there is no systematic framework to guide investment decisions on methods of data collection for vital statistics or health information in general. We developed a framework to systematically assess the comparative costs and outcomes/benefits of the various data methods for collecting vital statistics.

Methodology

The proposed framework is four-pronged and utilises two major economic approaches to systematically assess the available data collection methods: cost-effectiveness analysis and efficiency analysis. We built a stylised example of a hypothetical low-income country to perform a simulation exercise in order to illustrate an application of the framework.

Findings

Using simulated data, the results from the stylised example show that the rankings of the data collection methods are not affected by the use of either cost-effectiveness or efficiency analysis. However, the rankings are affected by how quantities are measured.

Conclusion

There have been several calls for global improvements in collecting useable data, including vital statistics, from health information systems to inform public health policies. Ours is the first study that proposes a systematic framework to assist countries undertake an economic evaluation of DCMs. Despite numerous challenges, we demonstrate that a systematic assessment of outputs and costs of DCMs is not only necessary, but also feasible. The proposed framework is general enough to be easily extended to other areas of health information.     

Neuronal Network Models of Phase Separation Between Limb CPGs of Digging Sand Crabs

Ordinary differential equations are used to model a peculiar motor behaviour in the anomuran decapod crustacean Emerita analoga. Little is known about the neural circuitry that permits E. analoga to control the phase relationships between movements of the fourth legs and pair of uropods as it digs into sand, so mathematical models might aid in identifying features of the neural structures involved. The geometric arrangement of segmental ganglia controlling the movements of each limb provides an intuitive framework for modelling. Specifically, due to the rhythmic nature of movement, the network controlling the fourth legs and uropods is viewed as three coupled identical oscillators, one dedicated to the control of each fourth leg and one for the pair of uropods, which always move in bilateral synchrony. Systems of Morris–Lecar equations describe the voltage and ion channel dynamics of neurons. Each central pattern generator for a limb is first modelled as a single neuron and then, more realistically as a multi-neuron oscillator. This process results in high-dimensional systems of equations that are difficult to analyse. In either case, reduction to phase equations by averaging yields a two-dimensional system of equations where variables describe only each oscillator’s phase along its limit cycle. The behaviour observed in the reduced equations approximates that of the original system. Results suggest that the phase response function in the two dimensional system, together with minimal input from asymmetric bilateral coupling parameters, is sufficient to account for the observed behaviour.