Estimating Frequencies of Minority Nevirapine-Resistant Strains in Chronically HIV-1-Infected Individuals Naive to Nevirapine by Using Stochastic Simulations and a Mathematical Model

Nevirapine forms the mainstay of our efforts to curtail the pediatric AIDS epidemic through prevention of mother-to-child transmission of HIV-1. A key limitation, however, is the rapid selection of HIV-1 strains resistant to nevirapine following the administration of a single dose. This rapid selection of resistance suggests that nevirapine-resistant strains preexist in HIV-1 patients and may adversely affect outcomes of treatment. The frequencies of nevirapine-resistant strains in vivo, however, remain poorly estimated, possibly because they exist as a minority below current assay detection limits. Here, we employ stochastic simulations and a mathematical model to estimate the frequencies of strains carrying different combinations of the common nevirapine resistance mutations K103N, V106A, Y181C, Y188C, and G190A in chronically infected HIV-1 patients naive to nevirapine. We estimate the relative fitness of mutant strains from an independent analysis of previous competitive growth assays. We predict that single mutants are likely to preexist in patients at frequencies (similar to 0.01% to 0.001%) near or below current assay detection limits (>0.01%), emphasizing the need for more-sensitive assays. The existence of double mutants is subject to large stochastic variations. Triple and higher mutants are predicted not to exist. Our estimates are robust to variations in the recombination rate, cellular superinfection frequency, and the effective population size. Thus, with 10(7) to 10(8) infected cells in HIV-1 patients, even when undetected, nevirapine-resistant genomes may exist in substantial numbers and compromise efforts to prevent mother-to-child transmission of HIV-1, accelerate the failure of subsequent antiretroviral treatments, and facilitate the transmission of drug resistance.

Performance study of high operating temperature HgCdTe mid wave infrared detector through numerical modeling

The design of present generation uncooled Hg1-xCdxTe infrared photon detectors relies on complex heterostructures with a basic unit cell of type (n) under bar (+)/pi/(p) under bar (+). We present an analysis of double barrier (n) under bar (+)/pi/(p) under bar (+) mid wave infrared (x = 0.3) HgCdTe detector for near room temperature operation using numerical computations. The present work proposes an accurate and generalized methodology in terms of the device design, material properties, and operation temperature to study the effects of position dependence of carrier concentration, electrostatic potential, and generation-recombination (g-r) rates on detector performance. Position dependent profiles of electrostatic potential, carrier concentration, and g-r rates were simulated numerically. Performance of detector was studied as function of doping concentration of absorber and contact layers, width of both layers and minority carrier lifetime. Responsivity similar to 0.38 A W-1, noise current similar to 6 x 10(-14) A/Hz(1/2) and D* similar to 3.1 x 10(10)cm Hz(1/2) W-1 at 0.1 V reverse bias have been calculated using optimized values of doping concentration, absorber width and carrier lifetime. The suitability of the method has been illustrated by demonstrating the feasibility of achieving the optimum device performance by carefully selecting the device design and other parameters. (C) 2010 American Institute of Physics. doi:10.1063/1.3463379]

Thermal Fluctuation Spectroscopy of DNA Thermal Denaturation

We have developed the technique of thermal fluctuation spectroscopy to measure the thermal fluctuations in a system. This technique is particularly useful to study the denaturation dynamics of biomolecules like DNA. Here we present a study of the thermal fluctuations during the thermal denaturation (or melting) of double-stranded DNA. We find that the thermal denaturation of heteropolymeric DNA is accompanied by large, non-Gaussian thermal fluctuations. The thermal fluctuations show a two-peak structure as a function of temperature. Calculations of enthalpy exchanged show that the first peak comes from the denaturation of AT rich regions and the second peak from denaturation of GC rich regions. The large fluctuations are almost absent in homopolymeric DNA. We suggest that bubble formation and cooperative opening and closing dynamics of basepairs causes the additional fluctuation at the first peak and a large cooperative transition from a partially molten DNA to a completely denatured state causes the additional fluctuation at the second peak.

Structural Studies of Analgesics and Their Interactions. V.* The Crystal and Molecular Structure of Metamizol Monohydrate

Metamizol, Na[Ct3H16N3045], C13H16N304S-Na +, a sulphonyl derivative of amidopyrine, is perhaps the most widely used non-narcotic analgetic and antiinflammatory pyrazolone derivative. The monohydrate of the compound crystallizes in the monoclinic space group P2Jc with eight molecules in a unit cell of dimensions a = 9.143 (3), b = 49.50 (2), c = 7.314 (2)/k and fl = 90.9 (1) °. The structure was solved by direct methods and refined to an R value of 0.080 for 4466 observed reflections. The two crystallographically independent molecules in the structure have similar dimensions. The elongated molecules are hydrophobic at one end and hydrophilic at the other with the middle portion partly hydrophobic and partly hydrophilic. The pyrazolone group in the structure has dimensions similar to those found in uncomplexed antipyrine and amidopyrine. The crystal structure can be described as consisting of double layers of metamizol molecules stacked perpendicular to the b axis. The adjacent double layers are separated by a layer of Naions and water molecules.

Antibodies raised against guanosine bind to double-stranded DNA

Antibodies elicited against guanosine have been reported to bind to single-stranded DNA. Using an avidin-biotin microELISA, we report that these antibodies also bind to double-stranded DNA. The binding is specific and is completely inhibited by the homologous hapten. The cross-reactivity of double-stranded DNA binding antibodies to single-stranded DNA is low. The antibodies are shown to bind to the topoisomers of plasmid DNA as assessed by a gel retardation assay.

Thermo and photoluminescence properties of Eu3+ activated hexagonal, monoclinic and cubic gadolinium oxide nanorods

Different phases of Eu3+ activated gadolinium oxide (Gd (OH)(3), GdOOH and Gd2O3) nanorods have been prepared by the hydrothermal method with and without cityl trimethyl ammonium bromide (GAB) surfactant. Cubic Gd2O3:Eu (8 mol%) red phosphor has been prepared by the dehydration of corresponding hydroxide Gd(OH)(3):Eu after calcinations at 350 and 600 degrees C for 3 h, respectively. When Eu3+ ions were introduced into Gd(OH)(3), lattice sites which replace the original Gd3+ ions, a strong red emission centered at 613 nm has been observed upon UV illumination, due to the intrinsic Eu3+ transition between D-5(0) and F-7 configurations. Thermoluminescence glow curves of Gd (OH)(3): Eu and Gd2O3:Eu phosphors have been recorded by irradiating with gamma source ((CO)-C-60) in the dose range 10-60 Gy at a heating rate of 6.7 degrees C sec(-1). Well resolved glow peaks in the range 42-45, 67-76,95-103 and 102-125 degrees C were observed. When gamma-irradiation dose increased to 40 Gy, the glow peaks were reduced and with increase in gamma-dose (50 and 60 Gy) results the shift in first two glow peak temperatures at about 20 degrees C and a new shouldered peak at 86 degrees C was observed. It is observed that there is a shift in glow peak temperatures and variation in intensity, which is mainly attributed to different phases of gadolinium oxide. The trapping parameters namely activation energy (E), order of kinetics (b) and frequency factor were calculated using peak shape and the results are discussed. (C) 2010 Elsevier B.V. All rights reserved.

Optical studies of SN 2009jf: a Type Ib supernova with an extremely slow decline and aspherical signature

Optical UBVRI photometry and medium-resolution spectroscopy of the Type Ib supernova SN 2009jf, during the period from similar to -15 to +250 d, with respect to the B maximum are reported. The light curves are broad, with an extremely slow decline. The early post-maximum decline rate in the V band is similar to SN 2008D; however, the late-phase decline rate is slower than other Type Ib supernovae studied. With an absolute magnitude of M-V = -17.96 +/- 0.19 at peak, SN 2009jf is a normally bright supernova. The peak bolometric luminosity and the energy deposition rate via the 56Ni -> 56Co chain indicate that similar to 0.17+0.03(-0.03) M-circle dot of 56Ni was ejected during the explosion. The He i 5876 A line is clearly identified in the first spectrum of day similar to -15, at a velocity of similar to 16 000 km s-1. The O i] 6300-6364 A line seen in the nebular spectrum has a multipeaked and asymmetric emission profile, with the blue peak being stronger. The estimated flux in this line implies that greater than or similar to 1.34 M-circle dot oxygen was ejected. The slow evolution of the light curves of SN 2009jf indicates the presence of a massive ejecta. The high expansion velocity in the early phase and broader emission lines during the nebular phase suggest it to be an explosion with a large kinetic energy. A simple qualitative estimate leads to the ejecta mass of M-ej = 4-9 M-circle dot and kinetic energy E-K = 3-8 x 1051 erg. The ejected mass estimate is indicative of an initial main-sequence mass of greater than or similar to 20-25 M-circle dot.

Lopsidedness in WHISP galaxies I. Rotation curves and kinematic lopsidedness

The frequently observed lopsidedness of the distribution of stars and gas in disc galaxies is still considered as a major problem in galaxy dynamics. It is even discussed as an imprint of the formation history of discs and the evolution of baryons in dark matter haloes. Here, we analyse a selected sample of 70 galaxies from the Westerbork Hi Survey of Spiral and Irregular Galaxies. The Hi data allow us to follow the morphology and the kinematics out to very large radii. In the present paper, we present the rotation curves and study the kinematic asymmetry. We extract the rotation curves of the receding and approaching sides separately and show that the kinematic behaviour of disc galaxies can be classified into five different types: symmetric velocity fields where the rotation curves of the receding and approaching sides are almost identical; global distortions where the rotation velocities of the receding and approaching sides have an offset that is constant with radius; local distortions leading to large deviations in the inner and negligible deviations in the outer parts (and vice versa); and distortions that divide the galaxies into two kinematic systems that are visible in terms of the different behaviour of the rotation curves of the receding and approaching sides, which leads to a crossing and a change in side. The kinematic lopsidedness is measured from the maximum rotation velocities, averaged over the plateau of the rotation curves. This gives a good estimate of the global lopsidedness in the outer parts of the sample galaxies. We find that the mean value of the perturbation parameter denoting the lopsided potential as obtained from the kinematic data is 0.056. Altogether, 36% of the sample galaxies are globally lopsided, which can be interpreted as the disc responding to a halo that was distorted by a tidal encounter. In Paper II, we study the morphological lopsidedness of the same sample of galaxies.

Nonlinear dynamics and chaotic motions in feedback-controlled two- and three-degree-of-freedom robots

The dynamics of a feedback-controlled rigid robot is most commonly described by a set of nonlinear ordinary differential equations. In this paper we analyze these equations, representing the feedback-controlled motion of two- and three-degrees-of-freedom rigid robots with revolute (R) and prismatic (P) joints in the absence of compliance, friction, and potential energy, for the possibility of chaotic motions. We first study the unforced or inertial motions of the robots, and show that when the Gaussian or Riemannian curvature of the configuration space of a robot is negative, the robot equations can exhibit chaos. If the curvature is zero or positive, then the robot equations cannot exhibit chaos. We show that among the two-degrees-of-freedom robots, the PP and the PR robot have zero Gaussian curvature while the RP and RR robots have negative Gaussian curvatures. For the three-degrees-of-freedom robots, we analyze the two well-known RRP and RRR configurations of the Stanford arm and the PUMA manipulator respectively, and derive the conditions for negative curvature and possible chaotic motions. The criteria of negative curvature cannot be used for the forced or feedback-controlled motions. For the forced motion, we resort to the well-known numerical techniques and compute chaos maps, Poincare maps, and bifurcation diagrams. Numerical results are presented for the two-degrees-of-freedom RP and RR robots, and we show that these robot equations can exhibit chaos for low controller gains and for large underestimated models. From the bifurcation diagrams, the route to chaos appears to be through period doubling.

Tidally compressed gas in centers of early-type and ultraluminous galaxies

In this paper we propose that the compressive tidal held in the centers of flat-core early-type galaxies and ultraluminous galaxies compresses molecular clouds producing dense gas observed in the centers of these galaxies. The effect of galactic tidal fields is usually considered disruptive in the literature. However, for some galaxies, the mass profile flattens toward the center and the resulting galactic tidal field is not disruptive, but instead it is compressive within the flat-core region. We have used the virial theorem to determine the minimum density of a molecular cloud to be stable and gravitationally bound within the tidally compressive region of a galaxy. We have applied the mechanism to determine the mean molecular cloud densities in the centers of a sample of flat-core, early-type galaxies and ultraluminous galaxies. For early-type galaxies with a core-type luminosity profile, the tidal held of the galaxy is compressive within half the core radius. We have calculated the mean gas densities for molecular gas in a sample of early-type galaxies which have already been detected in CO emission, and we obtain mean densities of [n] similar to 10(3)-10(6) cm(-3) within the central 100 pc radius. We also use our model to calculate the molecular cloud densities in the inner few hundred parsecs of a sample of ultraluminous galaxies. From the observed rotation curves of these galaxies we show that they have a compressive core within their nuclear region. Our model predicts minimum molecular gas densities in the range 10(2)-10(4) cm(-3) in the nuclear gas disks; the smaller values are applicable typically for galaxies with larger core radii. The resulting density values agree well with the observed range. Also, for large core radii, even fairly low-density gas (similar to 10(2) cm(-3)) can remain bound and stable close to the galactic center.

A finite element assessment of flexural strength of prestressed concrete beams with fiber reinforcement

This paper presents an assessment of the flexural behavior of 15 fully/partially prestressed high strength concrete beams containing steel fibers investigated using three-dimensional nonlinear finite elemental analysis. The experimental results consisted of eight fully and seven partially prestressed beams, which were designed to be flexure dominant in the absence of fibers. The main parameters varied in the tests were: the levels of prestressing force (i.e, in partially prestressed beams 50% of the prestress was reduced with the introduction of two high strength deformed bars instead), fiber volume fractions (0%, 0.5%, 1.0% and 1.5%), fiber location (full depth and partial depth over full length and half the depth over the shear span only). A three-dimensional nonlinear finite element analysis was conducted using ANSYS 5.5 [Theory Reference Manual. In: Kohnke P, editor. Elements Reference Manual. 8th ed. September 1998] general purpose finite element software to study the flexural behavior of both fully and partially prestressed fiber reinforced concrete beams. Influence of fibers on the concrete failure surface and stress-strain response of high strength concrete and the nonlinear stress-strain curves of prestressing wire and deformed bar were considered in the present analysis. In the finite element model. tension stiffening and bond slip between concrete and reinforcement (fibers., prestressing wire, and conventional reinforcing steel bar) have also been considered explicitly. The fraction of the entire volume of the fiber present along the longitudinal axis of the prestressed beams alone has been modeled explicitly as it is expected that these fibers would contribute to the mobilization of forces required to sustain the applied loads across the crack interfaces through their bridging action. A comparison of results from both tests and analysis on all 15 specimens confirm that, inclusion of fibers over a partial depth in the tensile side of the prestressed flexural structural members was economical and led to considerable cost saving without sacrificing on the desired performance. However. beams having fibers over half the depth in only the shear span, did not show any increase in the ultimate load or deformational characteristics when compared to plain concrete beams. (C) 2002 Published by Elsevier Science Ltd.

Effect of screening of intermicellar interactions on the linear and nonlinear rheology of a viscoelastic gel

We report our studies of the linear and nonlinear rheology of aqueous solutions of the surfactant cetyl trimethylammonium tosylate (CTAT) with varying amounts of sodium chloride (NaCl). The CTAT concentration is fixed at 42 mM, and the salt concentration is varied between 0 and 120 mM. On increasing the salt (NaCl) concentration, we see three distinct regimes in the zero-shear viscosity and the high-frequency plateau modulus data. In regime 1, the zero-shear viscosity shows a weak increase with salt concentration due to enhanced micellar growth. The decrease in the zero-shear viscosities with salt concentration in regimes II and III can be explained in terms of intermicellar branching. The most intriguing feature of our data, however, is the anomalous behavior of the high-frequency plateau modulus in regime II (0.12 less than or equal to [NaCl]/[CTAT] less than or equal to 1.42). In this regime, the plateau modulus increases with an increase in NaCl concentration. This is highly interesting, since the correlation length of concentration fluctuations and hence the plateau modulus G(0) are not expected to change appreciably in the semidilute regime. We propose to explain the changes in regime II in terms of a possible unbinding of the organic counterions (tosylate) from the CTA(+) surfaces on the addition of NaCl. In the nonlinear flow curves of the samples with high salt content, significant deviations from the predictions of the Giesekus model for entangled micelles are observed.

Synthesis and characterization of novel cationic lipid and cholesterol-coated gold nanoparticles and their interactions with dipalmitoylphosphatidylcholine membranes

Novel gold nanoparticles bearing cationic single-chain, double-chain, and cholesterol based amphiphilic units have been synthesized. These nanoparticles represent size-stable entities in which various cationic lipids have been immobilized through their thiol group onto the gold nanoparticle core. The resulting colloids have been characterized by UV-vis, (1)H NMR, FT-IR spectroscopy, and transmission electron microscopy. The average size of the resultant nanoparticles could be controlled by the relative bulkiness of the capping agent. Thus, the average diameters of the nanoparticles formed from the cationic single-chain, double-chain, and cholesterol based thiolate-coated materials were 5.9,2.9, and 2.04 nm, respectively. We also examined the interaction of these cationic gold nanoparticles with vesicular membranes generated from dipalmitoylphosphatidylcholine (DPPC) lipid suspensions. Nanoparticle doped DPPC vesicular suspensions displayed a characteristic surface plasmon band in their UV-vis spectra. Inclusion of nanoparticles in vesicular suspensions led to increases in the aggregate diameters, as evidenced from dynamic light scattering. Differential scanning calorimetric examination indicated that incorporation of single-chain, double-chain, and cholesteryl-linked cationic nanoparticles exert variable effects on the DPPC melting transitions. While increased doping of single-chain nanoparticles in DPPC resulted in the phases that melt at higher temperatures, inclusion of an incremental amount of double-chain nanoparticles caused the lowering of the melting temperature of DPPC. On the other hand, the cationic cholesteryl nanoparticle interacted with DPPC in membranes in a manner somewhat analogous to that of cholesterol itself and caused broadening of the DPPC melting transition.

Tuning the structure of surfactant complexes with DNA and other polyelectrolytes

We have carried out small-angle X-ray diffraction studies on complexes formed by the anionic polyelectrolytes, namely, sodium salts of double and single stranded (ds and ss) DNA, poly( glutamic acid) ( PGA), poly( acrylic acid) (PAA), and poly( styrene sulfonate) (PSS) with a cationic surfactant system consisting of cetyltrimethylammonium bromide ( CTAB) and sodium 3-hydroxy-2-naphthoate (SHN). All complexes have a two-dimensional (2D) hexagonal structure at low SHN concentrations. DNA-CTAB-SHN complexes exhibit a hexagonal to lamellar transition near the SHN concentration at which CTAB-SHN micelles show a cylinder to bilayer transformation. On the other hand, PGA and PAA complexes form a 2D centered rectangular phase at higher SHN concentrations, and PSS complexes show a primitive rectangular structure. These results provide a striking example of polyion specificity in polyelectrolytesurfactant interactions.

Mitigation of Alkali Induced Heave in Rectorite Soil with Fly Ash

Mechanisms that control the volume changes behavior of foundation soils are well understood. The changes that occur in the behavior of soil due to migration of pollutants are not well understood. The extent of changes that occur in the presence of small concentration of contaminants can be predicted based on changes in the thickness of double layer and associated fabric changes. Interactions that occur with strong contaminants depends on the type of soil, type and concentration of contamination and duration of interaction etc It has been shown that different concentrations (1N and 4N) of sodium hydroxide solution causes abnormal changes on volume change behaviour of soil due to mineralogical changes. An attempt is made in this paper to stabilize contaminated soil using fly ash, after establishing its stability in alkali solutions. It was found that the effectiveness of fly ash to control the alkali induced heave increases with fly ash content incorporated into the soil. X-ray diffraction studies reveal that the mineralogical changes that occur in soil due to alkali interaction are inhibited by the presence of fly ash.