Mariela Sued

International study to evaluate PCR methods for detection of Trypanosoma cruzi DNA in blood samples from Chagas disease patients

Background A century after its discovery, Chagas disease still represents a major neglected tropical threat. Accurate diagnostics tools as well as surrogate markers of parasitological response to treatment are research priorities in the field. The purpose of this study was to evaluate the performance of PCR methods in detection of Trypanosoma cruzi DNA by an external quality evaluation. Methodology/Findings An international collaborative study was launched by expert PCR laboratories from 16 countries. Currently used strategies were challenged against serial dilutions of purified DNA from stocks representing T. cruzi discrete typing units (DTU) I, IV and VI (set A), human blood spiked with parasite cells (set B) and Guanidine Hidrochloride-EDTA blood samples from 32 seropositive and 10 seronegative patients from Southern Cone countries (set C). Forty eight PCR tests were reported for set A and 44 for sets B and C; 28 targeted minicircle DNA (kDNA), 13 satellite DNA (Sat-DNA) and the remainder low copy number sequences. In set A, commercial master mixes and Sat-DNA Real Time PCR showed better specificity, but kDNA-PCR was more sensitive to detect DTU I DNA. In set B, commercial DNA extraction kits presented better specificity than solvent extraction protocols. Sat-DNA PCR tests had higher specificity, with sensitivities of 0.05–0.5 parasites/mL whereas specific kDNA tests detected 5.10−3 par/mL. Sixteen specific and coherent methods had a Good Performance in both sets A and B (10 fg/µl of DNA from all stocks, 5 par/mL spiked blood). The median values of sensitivities, specificities and accuracies obtained in testing the Set C samples with the 16 tests determined to be good performing by analyzing Sets A and B samples varied considerably. Out of them, four methods depicted the best performing parameters in all three sets of samples, detecting at least 10 fg/µl for each DNA stock, 0.5 par/mL and a sensitivity between 83.3–94.4%, specificity of 85–95%, accuracy of 86.8–89.5% and kappa index of 0.7–0.8 compared to consensus PCR reports of the 16 good performing tests and 63–69%, 100%, 71.4–76.2% and 0.4–0.5, respectively compared to serodiagnosis. Method LbD2 used solvent extraction followed by Sybr-Green based Real time PCR targeted to Sat-DNA; method LbD3 used solvent DNA extraction followed by conventional PCR targeted to Sat-DNA. The third method (LbF1) used glass fiber column based DNA extraction followed by TaqMan Real Time PCR targeted to Sat-DNA (cruzi 1/cruzi 2 and cruzi 3 TaqMan probe) and the fourth method (LbQ) used solvent DNA extraction followed by conventional hot-start PCR targeted to kDNA (primer pairs 121/122). These four methods were further evaluated at the coordinating laboratory in a subset of human blood samples, confirming the performance obtained by the participating laboratories. Conclusion/Significance This study represents a first crucial step towards international validation of PCR procedures for detection of T. cruzi in human blood samples.

First-principles molecular dynamics simulations at solid-liquid interfaces with a continuum solvent

Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such a continuum approach in a density functional theory framework using plane-wave basis sets and periodic boundary conditions. Our work stems from a recent model designed for Car-Parrinello simulations of quantum solutes in a dielectric medium [D. A. Scherlis et al., J. Chem. Phys. 124, 074103 (2006)], for which the permittivity of the solvent is defined as a function of the electronic density of the solute. This strategy turns out to be inadequate for systems extended in two dimensions: the dependence of the dielectric function on the electronic density introduces a new term in the Kohn-Sham potential, which becomes unphysically large at the interfacial region, seriously affecting the convergence of the self-consistent calculations. If the dielectric medium is properly redefined as a function of the atomic coordinates, a good convergence is obtained and the constant of motion is conserved during the molecular dynamics simulations. The Poisson problem is solved using a multigrid method, and in this way Car-Parrinello molecular dynamics simulations of solid-liquid interfaces can be performed at a very moderate computational cost. This scheme is employed to investigate the acid-base equilibrium at the TiO(2)-water interface. The aqueous behavior of titania surfaces has stimulated a large amount of experimental research, but many open questions remain concerning the molecular mechanisms determining the chemistry of the interface. Here we make an attempt to answer some of them, putting to the test our continuum model.

Brood parasitism disproportionately increases nest provisioning and helper recruitment in a cooperatively breeding bird

Obligate avian brood parasites lay their eggs in nests of other species (hosts), which raise parasitic young. Parasitic nestlings are likely to influence host’s parental behaviours as they typically beg for food more vigorously than young host for a given hunger level. However, few studies have tested this idea, with conflicting results. These prior studies were largely limited to biparental hosts, but little is known about the effect of brood parasitism on parental behaviours in hosts that breed cooperatively. We followed a multimodel approach to examine the effect of brood parasitism on nest provisioning and helper recruitment in the baywing (Agelaioides badius), a cooperative breeder parasitised by screaming (Molothrus rufoaxillaris) and shiny (Molothrus bonariensis) cowbirds. Multimodel inference results indicated that feeding visits increased with nestling age, cooperative group size and number of cowbird nestlings in the brood. Brood size had little influence on feeding visits, which further suggests that baywings adjusted their provisioning effort in response to cowbird parasitism. In addition, nests parasitised artificially with shiny cowbird eggs or hatchlings recruited more helpers than unmanipulated nests having only host or screaming cowbird young. Our results provide novel evidence that brood parasitism and cooperative breeding interact in determining the levels of nest provisioning.

Testing the Equality of Covariance Operators

In many situations, when dealing with several populations, equality of the covariance operators is assumed. In this work, we will study a hypothesis test to validate this assumption.

Numerical Analysis of Stochastic Differential Equations with Explosions

Abstract Stochastic ordinary differential equations may have solutions that explode in finite or infinite time. In this article we design an adaptive numerical scheme that reproduces the explosive behavior. The time step is adapted according to the size of the computed solution in such a way that, under adequate hypotheses, the explosion of the solutions is reproduced.

Mean estimation with data missing at random for functional covariables

In a missing-data setting, we want to estimate the mean of a scalar outcome, based on a sample in which an explanatory variable is observed for every subject while responses are missing by happenstance for some of them. We consider two kinds of estimates of the mean response when the explanatory variable is functional. One is based on the average of the predicted values and the second one is a functional adaptation of the Horvitz–Thompson estimator. We show that the infinite dimensionality of the problem does not affect the rates of convergence by stating that the estimates are root-n consistent, under missing at random (MAR) assumption. These asymptotic features are completed by simulated experiments illustrating the easiness of implementation and the good behaviour on finite sample sizes of the method. This is the first paper emphasizing that the insensitiveness of averaged estimates, well known in multivariate non-parametric statistics, remains true for an infinite-dimensional covariable. In this sense, this work opens the way for various other results of this kind in functional data analysis.

Inference under functional proportional and common principal component models

In many situations, when dealing with several populations with different covariance operators, equality of the operators is assumed. Usually, if this assumption does not hold, one estimates the covariance operator of each group separately, which leads to a large number of parameters. As in the multivariate setting, this is not satisfactory since the covariance operators may exhibit some common structure. In this paper, we discuss the extension to the functional setting of the common principal component model that has been widely studied when dealing with multivariate observations. Moreover, we also consider a proportional model in which the covariance operators are assumed to be equal up to a multiplicative constant. For both models, we present estimators of the unknown parameters and we obtain their asymptotic distribution. A test for equality against proportionality is also considered.

Continuity and differentiability of regression M functionals

This paper deals with the Fisher{consistency, weak continuity and difierentiability of estimating functionals corresponding to a class of both linear and nonlinear regression high breakdown M estimates, which includes S and MM estimates. A restricted type of difierentiability, called weak difierentiability, is deflned, which su-ces to prove the asymptotic normality of estimates based on the functionals. This approach allows to prove the consistency, asymptotic normality and qualitative robustness of M estimates under more general conditions than those required in standard approaches. In particular we prove that regression MM-estimates are asymptotically normal when the observations are `-mixing.

A quantitative model for oxygen uptake and release in a family of hemeproteins

MOTIVATION Hemeproteins have many diverse functions that largely depend on the rate at which they uptake or release small ligands, like oxygen. These proteins have been extensively studied using either simulations or experiments, albeit only qualitatively and one or two proteins at a time. RESULTS We present a physical-chemical model, which uses data obtained exclusively from computer simulations, to describe the uptake and release of oxygen in a family of hemeproteins, called truncated hemoglobins (trHbs). Through a rigorous statistical analysis we demonstrate that our model successfully recaptures all the reported experimental oxygen association and dissociation kinetic rate constants, thus allowing us to establish the key factors that determine the rates at which these hemeproteins uptake and release oxygen. We found that internal tunnels as well as the distal site water molecules control ligand uptake, whereas oxygen stabilization by distal site residues controls ligand release. Because these rates largely determine the functions of these hemeproteins, these approaches will also be important tools in characterizing the trHbs members with unknown functions. CONTACT lboechi@ic.fcen.uba.ar SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

Asymmetries in kinesin‐2 and cytoplasmic dynein contributions to melanosome transport

The mechanisms involved in bidirectional transport along microtubules remain largely unknown. We explored the collective action of kinesin‐2 and dynein motors during transport of melanosomes inXenopus laevis melanophores. These motors are attached to organelles through accessory proteins establishing a complex molecular linker. We determined both the stiffness of this linker and the organelles speed and observed that these parameters depended on the organelle size and cargo direction. Our results suggest that melanosome transport is driven by two dissimilar teams: whereas dynein motors compete with kinesin‐2 affecting the properties of plus‐end directed organelles, kinesin‐2 does not seem to play a similar role during minus‐end transport.