Model-Predicted Performance of Second-Trimester Down Syndrome Screening With Sonographic Prenasal Thickness

Objective. The purpose of this study was to estimate the Down syndrome detection and false-positive rates for second-trimester sonographic prenasal thickness (PT) measurement alone and in combination with other markers. Methods. Multivariate log Gaussian modeling was performed using numerical integration. Parameters for the PT distribution, in multiples of the normal gestation-specific median (MoM), were derived from 105 Down syndrome and 1385 unaffected pregnancies scanned at 14 to 27 weeks. The data included a new series of 25 cases and 535 controls combined with 4 previously published series. The means were estimated by the median and the SDs by the 10th to 90th range divided by 2.563. Parameters for other markers were obtained from the literature. Results. A log Gaussian model fitted the distribution of PT values well in Down syndrome and unaffected pregnancies. The distribution parameters were as follows: Down syndrome, mean, 1.334 MoM; log(10) SD, 0.0772; unaffected pregnancies, 0.995 and 0.0752, respectively. The model-predicted detection rates for 1%, 3%, and 5% false-positive rates for PT alone were 35%, 51%, and 60%, respectively. The addition of PT to a 4 serum marker protocol increased detection by 14% to 18% compared with serum alone. The simultaneous sonographic measurement of PT and nasal bone length increased detection by 19% to 26%, and with a third sonographic marker, nuchal skin fold, performance was comparable with first-trimester protocols. Conclusions. Second-trimester screening with sonographic PT and serum markers is predicted to have a high detection rate, and further sonographic markers could perform comparably with first-trimester screening protocols.

Investigating the Nature of Noble Gas-Copper Bonds by the Quantum Theory of Atoms in Molecules

We investigated noble gas copper bonds in linear complexes represented by the NgCuX general formula in which Ng and X stand for a noble gas (neon, argon, krypton, or xenon) and a halogen (fluorine, chlorine or bromine), respectively, by coupled cluster methods and modified cc-pVQZ basis sets. The quantum theory of atoms in molecules (QTAIM) shows a linear relation between the dissociation energy or noble gas-copper bonds and the amount of electronic charge transferred mainly from the noble gas to copper during complexation. Large changes in the QTAIM quadrupole moments of copper and noble gases resulting from this bonding and a comparison between NgCuX and NgNaCl systems indicate that these noble gas-copper bonds should be better interpreted as predominantly covalent. Finally, QTAIM atomic dipoles of noble gases in NgNaCl systems agree satisfactorily with atomic dipoles given by a simple model for these NgNa van der Waals bonds.

Mechanism and model of the oscillatory electro-oxidation of methanol

A mechanism for the kinetic instabilities observed in the galvanostatic electro-oxidation of methanol is suggested and a model developed. The model is investigated using stoichiometric network analysis as well as concepts from algebraic geometry (polynomial rings and ideal theory) revealing the occurrence of a Hopf and a saddle-node bifurcation. These analytical solutions are confirmed by numerical integration of the system of differential equations. (C) 2010 American Institute of Physics

Gravitational quasinormal modes of AdS black branes in d spacetime dimensions

The AdS/CFT duality has established a mapping between quantities in the bulk AdS black-hole physics and observables in a boundary finite-temperature field theory. Such a relationship appears to be valid for an arbitrary number of spacetime dimensions, extrapolating the original formulations of Maldacena`s correspondence. In the same sense properties like the hydrodynamic behavior of AdS black-hole fluctuations have been proved to be universal. We investigate in this work the complete quasinormal spectra of gravitational perturbations of d-dimensional plane-symmetric AdS black holes (black branes). Holographically the frequencies of the quasinormal modes correspond to the poles of two-point correlation functions of the field-theory stress-energy tensor. The important issue of the correct boundary condition to be imposed on the gauge-invariant perturbation fields at the AdS boundary is studied and elucidated in a fully d-dimensional context. We obtain the dispersion relations of the first few modes in the low-, intermediate- and high-wavenumber regimes. The sound-wave (shear-mode) behavior of scalar (vector)-type low- frequency quasinormal mode is analytically and numerically confirmed. These results are found employing both a power series method and a direct numerical integration scheme.

Buckling and post-buckling of extensible rods revisited: A multiple-scale solution

An exact non-linear formulation of the equilibrium of elastic prismatic rods subjected to compression and planar bending is presented, electing as primary displacement variable the cross-section rotations and taking into account the axis extensibility. Such a formulation proves to be sufficiently general to encompass any boundary condition. The evaluation of critical loads for the five classical Euler buckling cases is pursued, allowing for the assessment of the axis extensibility effect. From the quantitative viewpoint, it is seen that such an influence is negligible for very slender bars, but it dramatically increases as the slenderness ratio decreases. From the qualitative viewpoint, its effect is that there are not infinite critical loads, as foreseen by the classical inextensible theory. The method of multiple (spatial) scales is used to survey the post-buckling regime for the five classical Euler buckling cases, with remarkable success, since very small deviations were observed with respect to results obtained via numerical integration of the exact equation of equilibrium, even when loads much higher than the critical ones were considered. Although known beforehand that such classical Euler buckling cases are imperfection insensitive, the effect of load offsets were also looked at, thus showing that the formulation is sufficiently general to accommodate this sort of analysis. (c) 2008 Elsevier Ltd. All rights reserved.

Influence diagnostics in nonlinear mixed-effects elliptical models

In this work we propose and analyze nonlinear elliptical models for longitudinal data, which represent an alternative to gaussian models in the cases of heavy tails, for instance. The elliptical distributions may help to control the influence of the observations in the parameter estimates by naturally attributing different weights for each case. We consider random effects to introduce the within-group correlation and work with the marginal model without requiring numerical integration. An iterative algorithm to obtain maximum likelihood estimates for the parameters is presented, as well as diagnostic results based on residual distances and local influence [Cook, D., 1986. Assessment of local influence. journal of the Royal Statistical Society - Series B 48 (2), 133-169; Cook D., 1987. Influence assessment. journal of Applied Statistics 14 (2),117-131; Escobar, L.A., Meeker, W.Q., 1992, Assessing influence in regression analysis with censored data, Biometrics 48, 507-528]. As numerical illustration, we apply the obtained results to a kinetics longitudinal data set presented in [Vonesh, E.F., Carter, R.L., 1992. Mixed-effects nonlinear regression for unbalanced repeated measures. Biometrics 48, 1-17], which was analyzed under the assumption of normality. (C) 2009 Elsevier B.V. All rights reserved.

Tokamak magnetic field lines described by simple maps

The magnetic field line structure in a tokamak can be obtained by direct numerical integration of the field line equations. However, this is a lengthy procedure and the analysis of the solution may be very time-consuming. Otherwise we can use simple two-dimensional, area-preserving maps, obtained either by approximations of the magnetic field line equations, or from dynamical considerations. These maps can be quickly iterated, furnishing solutions that mirror the ones obtained from direct numerical integration, and which are useful when long-term studies of field line behavior are necessary (e.g. in diffusion calculations). In this work we focus on a set of simple tokamak maps for which these advantages are specially pronounced.

Fermion perturbations in string theory black holes

In this paper we study fermion perturbations in four-dimensional black holes of string theory, obtained either from a non-extreme configuration of three intersecting five-branes with a boost along the common string or from a non-extreme intersecting system of two two-branes and two five-branes. The Dirac equation for the massless neutrino field, after conformal re-scaling of the metric, is written as a wave equation suitable to study the time evolution of the perturbation. We perform a numerical integration of the evolution equation, and with the aid of Prony fitting of the time-domain profile, we calculate the complex frequencies that dominate the quasinormal ringing stage, and also determine these quantities by the semi-analytical sixth-order WKB method. We also find numerically the decay factor of fermion fields at very late times, and show that the falloff is identical to those showing for massless fields in other four-dimensional black hole spacetimes.

Numerical study of the atmospheric flow over a coastal cliff

This work presents a numerical method suitable for the study of the development of internal boundary layers (IBL) and their characteristics for flows over various types of coastal cliffs. The IBL is an important meteorological occurrence for flows with surface roughness and topographical step changes. A two-dimensional flow program was used for this study. The governing equations were written using the vorticity-velocity formulation. The spatial derivatives were discretized by high-order compact finite differences schemes. The time integration was performed with a low storage fourth-order Runge-Kutta scheme. The coastal cliff (step) was specified through an immersed boundary method. The validation of the code was done by comparison of the results with experimental and observational data. The numerical simulations were carried out for different coastal cliff heights and inclinations. The results show that the predominant factors for the height of the IBL and its characteristics are the upstream velocity, and the height and form (inclination) of the coastal cliff. Copyright (C) 2010 John Wiley & Sons, Ltd.

Combining Legendre's Polynomials and Genetic Algorithm in the Solution of Nonlinear Initial-Value Problems

This work develops a method for solving ordinary differential equations, that is, initial-value problems, with solutions approximated by using Legendre's polynomials. An iterative procedure for the adjustment of the polynomial coefficients is developed, based on the genetic algorithm. This procedure is applied to several examples providing comparisons between its results and the best polynomial fitting when numerical solutions by the traditional Runge-Kutta or Adams methods are available. The resulting algorithm provides reliable solutions even if the numerical solutions are not available, that is, when the mass matrix is singular or the equation produces unstable running processes.

Direct Computation of Operational Matrices for Polynomial Bases

Several numerical methods for boundary value problems use integral and differential operational matrices, expressed in polynomial bases in a Hilbert space of functions. This work presents a sequence of matrix operations allowing a direct computation of operational matrices for polynomial bases, orthogonal or not, starting with any previously known reference matrix. Furthermore, it shows how to obtain the reference matrix for a chosen polynomial base. The results presented here can be applied not only for integration and differentiation, but also for any linear operation.

Integration and visualization of systems biology data in context of the genome

Background: High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment. Results: The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of user-generated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data. A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for exploring and combining data, the Gaggle Genome Browser adds the ability to visualize diverse types of data in relation to its coordinates on the genome. Conclusions: Genomic coordinates function as a common key by which disparate biological data types can be related to one another. In the Gaggle Genome Browser, heterogeneous data are joined by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation and, ultimately, a better understanding of the mechanisms that enable the cell to dynamically respond to its environment.

Esophageal Ulcer in Brazilian Patients with HIV: Prevalence and Comparative Analysis Among Diagnostic Methods

Esophageal ulcer (EU) represents an important comorbidity in AIDS. We evaluated the prevalence of EU, the accuracy of the endoscopic and histologic methods used to investigate viral EU in HIV-positive Brazilian patients and the numerical relevance of tissue sampling. A total of 399 HIV-positive patients underwent upper gastrointestinal (UGI) endoscopy. HIV-positive patients with EU determined by UGI endoscopy followed by biopsies were analyzed by the hematoxylin-eosin (HE) and immunohistochemical (IH) methods. EU was detected in 41 patients (mean age, 39.2 years; 23 males), with a prevalence of 10.27%. The median CD4 count was 49 cells/mm(3) (range, 1-361 cells/mm(3)) and the viral load was 58,869 copies per milliliter (range, 50-77,3290 copies per milliliter). UGI endoscopy detected 29 of 41 EU suggestive of cytomegalovirus (CMV) infection and 7 of 41 indicating herpes simplex virus (HSV) infection. HE histology confirmed 4 of 29 ulcers induced by CMV, 2 of 7 induced by HSV, and 1 of 7 induced by HSV plus CMV. IH for CMV and HSV confirmed the HE findings and detected one additional CMV-induced case. UGI endoscopy showed 100% sensitivity and 15% specificity for the diagnosis of EU due to CMV or HSV compared to HE and IH. HE proved to be an adequate method for etiologic evaluation, with 87% sensitivity and 100% specificity compared to IH. The number of samples did not influence the etiologic evaluation. The data support the importance of IH as a complementary method for HE in the diagnosis of EU of viral etiology.

PRECESSING JETS AND X-RAY BUBBLES FROM NGC 1275 (3C 84) IN THE PERSEUS GALAXY CLUSTER: A VIEW FROM THREE-DIMENSIONAL NUMERICAL SIMULATIONS

The Perseus galaxy cluster is known to present multiple and misaligned pairs of cavities seen in X-rays, as well as twisted kiloparsec-scale jets at radio wavelengths; both morphologies suggest that the active galactic nucleus (AGN) jet is subject to precession. In this work, we performed three-dimensional hydrodynamical simulations of the interaction between a precessing AGN jet and the warm intracluster medium plasma, whose dynamics are coupled to a Navarro-Frenk-White dark matter gravitational potential. The AGN jet inflates cavities that become buoyantly unstable and rise up out of the cluster core. We found that under certain circumstances precession can originate multiple pairs of bubbles. For the physical conditions in the Perseus cluster, multiple pairs of bubbles are obtained for a jet precession opening angle >40 degrees acting for at least three precession periods, reproducing both radio and X-ray maps well. Based on such conditions, assuming that the Bardeen-Peterson effect is dominant, we studied the evolution of the precession opening angle of this system. We were able to constrain the ratio between the accretion disk and the black hole angular momenta as 0.7-1.4. We were also able to constrain the present precession angle to 30 degrees-40 degrees, as well as the approximate age of the inflated bubbles to 100-150 Myr.

The merging cluster Abell 1758 revisited: multi-wavelength observations and numerical simulations

Context. Cluster properties can be more distinctly studied in pairs of clusters, where we expect the effects of interactions to be strong. Aims. We here discuss the properties of the double cluster Abell 1758 at a redshift z similar to 0.279. These clusters show strong evidence for merging. Methods. We analyse the optical properties of the North and South cluster of Abell 1758 based on deep imaging obtained with the Canada-France-Hawaii Telescope (CFHT) archive Megaprime/Megacam camera in the g' and r' bands, covering a total region of about 1.05 x 1.16 deg(2), or 16.1 x 17.6 Mpc(2). Our X-ray analysis is based on archive XMM-Newton images. Numerical simulations were performed using an N-body algorithm to treat the dark-matter component, a semi-analytical galaxy-formation model for the evolution of the galaxies and a grid-based hydrodynamic code with a parts per million (PPM) scheme for the dynamics of the intra-cluster medium. We computed galaxy luminosity functions (GLFs) and 2D temperature and metallicity maps of the X-ray gas, which we then compared to the results of our numerical simulations. Results. The GLFs of Abell 1758 North are well fit by Schechter functions in the g' and r' bands, but with a small excess of bright galaxies, particularly in the r' band; their faint-end slopes are similar in both bands. In contrast, the GLFs of Abell 1758 South are not well fit by Schechter functions: excesses of bright galaxies are seen in both bands; the faint-end of the GLF is not very well defined in g'. The GLF computed from our numerical simulations assuming a halo mass-luminosity relation agrees with those derived from the observations. From the X-ray analysis, the most striking features are structures in the metal distribution. We found two elongated regions of high metallicity in Abell 1758 North with two peaks towards the centre. In contrast, Abell 1758 South shows a deficit of metals in its central regions. Comparing observational results to those derived from numerical simulations, we could mimic the most prominent features present in the metallicity map and propose an explanation for the dynamical history of the cluster. We found in particular that in the metal-rich elongated regions of the North cluster, winds had been more efficient than ram-pressure stripping in transporting metal-enriched gas to the outskirts. Conclusions. We confirm the merging structure of the North and South clusters, both at optical and X-ray wavelengths.