Multiplex semi-nested RT-PCR with exogenous internal control for simultaneous detection of bovine coronavirus and group A rotavirus

Neonatal calf diarrhea is a multi-etiology syndrome of cattle and direct detection of the two major agents of the syndrome, group A rotavirus and Bovine coronavirus (BCoV) is hampered by their fastidious growth in cell culture. This study aimed at developing a multiplex semi-nested RT-PCR for simultaneous detection of BCoV (N gene) and group A rotavirus (VP1 gene) with the addition of an internal control (mRNA ND5). The assay was tested in 75 bovine feces samples tested previously for rotavirus using PAGE and for BCoV using nested RT-PCR targeted to RdRp gene. Agreement with reference tests was optimal for BCoV (kappa = 0.833) and substantial for rotavirus detection (kappa = 0.648). the internal control, ND5 mRNA, was detected successfully in all reactions. Results demonstrated that this multiplex semi-nested RT-PCR was effective in the detection of BCoV and rotavirus, with high sensitivity and specificity for simultaneous detection of both viruses at a lower cost, providing an important tool for studies on the etiology of diarrhea in cattle. (C) 2010 Elsevier B.V. All rights reserved.

A method for simultaneous detection and identification of Brazilian dog- and vampire bat-related rabies virus by reverse transcription loop-mediated isothermal amplification assay

At present, the sporadic occurrence of human rabies in Brazil can be attributed primarily to dog- and vampire bat-related rabies viruses. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) was employed as a simultaneous detection method for both rabies field variants within 60 min. Vampire bat-related rabies viruses could be distinguished from dog variants by digesting amplicons of the RT-LAMP reaction using the restriction enzyme Alwl. Amplification and digestion could both be completed within 120 min after RNA extraction. In addition, the RI-LAMP assay also detected rabies virus in isolates from Brazilian frugivorous bats and Ugandan dog, bovine and goat samples. In contrast, there were false negative results from several Brazilian insectivorous bats and all of Chinese dog, pig, and bovine samples using the RI-LAMP assay. This study showed that the RT-LAMP assay is effective for the rapid detection of rabies virus isolates from the primary reservoir in Brazil. Further improvements are necessary so that the RT-LAMP assay can be employed for the universal detection of genetic variants of rabies virus in the field. (C) 2010 Elsevier B.V. All rights reserved.

GP5+/6+ SYBR Green methodology for simultaneous screening and quantification of human papillomavirus

Background: Detection and quantification of human papillomavirus (HPV) may help in predicting the evolution of HPV infection and progression of associated lesions. Objectives: We propose a novel protocol using consensus primers GP5+/6+ in a SYBR Green quantitative real-time (Q-RT) polymerase chain reaction (PCR). The strategy permits screening for HPV infection and viral load quantification simultaneously. Study design: DNA from 153 archived cervical samples, previously tested for HPV detection by GP5+/6+ PCR and typed by EIA-RLB (enzyme immunoassay-reverse line blot) or sequence analysis, was analysed using SYBR Green Q-RT PCR. Melting temperature assay (T(m)) and cycle threshold (C(t)) were used to evaluate HPV positivity and viral load. The T(m) in the range of 77-82 degrees C was considered to be positive for HPV-DNA. HPV results generated through GP5+/6+ conventional PCR were considered the gold standard against which sensitivity and specificity of our assay were measured. Results: Out of 104 HPV positive samples, 100 (96.2%) were also determined as positive by SYBR Green Q-RT PCR; of the 49 HPV-negative samples, all were determined as negative. There was an excellent positivity agreement (K = 0.94) between the SYBR Green Q-RT and the previous methods employed. The specificity and sensitivity were 100% and 96.2%, respectively. Comparison of SYBR Green Q-RT and TaqMan oligo-probe technologies gave an excellent concordance (pc = 0.95) which validated the proposed strategy. Conclusions: We propose a sensitive and easy-to-perform technique for HPV screening and viral load quantification simultaneously. (C) 2009 Elsevier B.V. All rights reserved.

The SARS algorithm: detrending CoRoT light curves with Sysrem using simultaneous external parameters

Surveys for exoplanetary transits are usually limited not by photon noise but rather by the amount of red noise in their data. In particular, although the CoRoT space-based survey data are being carefully scrutinized, significant new sources of systematic noises are still being discovered. Recently, a magnitude-dependant systematic effect was discovered in the CoRoT data by Mazeh et al. and a phenomenological correction was proposed. Here we tie the observed effect to a particular type of effect, and in the process generalize the popular Sysrem algorithm to include external parameters in a simultaneous solution with the unknown effects. We show that a post-processing scheme based on this algorithm performs well and indeed allows for the detection of new transit-like signals that were not previously detected.

Tyrosine hydroxylase immunoreactivity as indicator of sympathetic activity: simultaneous evaluation in different tissues of hypertensive rats

Burgi K, Cavalleri MT, Alves AS, Britto LRG, Antunes VR, Michelini LC. Tyrosine hydroxylase immunoreactivity as indicator of sympathetic activity: simultaneous evaluation in different tissues of hypertensive rats. Am J Physiol Regul Integr Comp Physiol 300: R264-R271, 2011. First published December 9, 2010; doi: 10.1152/ajpregu.00687.2009.-Vasomotor control by the sympathetic nervous system presents substantial heterogeneity within different tissues, providing appropriate homeostatic responses to maintain basal/stimulated cardiovascular function both at normal and pathological conditions. The availability of a reproducible technique for simultaneous measurement of sympathetic drive to different tissues is of great interest to uncover regional patterns of sympathetic nerve activity (SNA). We propose the association of tyrosine hydroxylase immunoreactivity (THir) with image analysis to quantify norepinephrine (NE) content within nerve terminals in arteries/arterioles as a good index for regional sympathetic outflow. THir was measured in fixed arterioles of kidney, heart, and skeletal muscle of WistarKyoto rats (WKY) and spontaneously hypertensive rats (SHR) (123 +/- 2 and 181 +/- 4 mmHg, 300 +/- 8 and 352 +/- 8 beats/min, respectively). There was a differential THir distribution in both groups: higher THir was observed in the kidney and skeletal muscle (similar to 3-4-fold vs. heart arterioles) of WKY; in SHR, THir was increased in the kidney and heart (2.4- and 5.3-fold vs. WKY, respectively) with no change in the skeletal muscle arterioles. Observed THir changes were confirmed by either: 1) determination of NE content (high-performance liquid chromatography) in fresh tissues (SHR vs. WKY): +34% and +17% in kidney and heart, respectively, with no change in the skeletal muscle; 2) direct recording of renal (RSNA) and lumbar SNA (LSNA) in anesthetized rats, showing increased RSNA but unchanged LSNA in SHR vs. WKY. THir in skeletal muscle arterioles, NE content in femoral artery, and LSNA were simultaneously reduced by exercise training in the WKY group. Results indicate that THir is a valuable technique to simultaneously evaluate regional patterns of sympathetic activity.

Differential effects of neuromuscular blockers on twitches and tetani in the isolated rat muscle: a multiple comparison study using simultaneous confidence intervals

In the present work a comparative quantitative evaluation of the differential effects of neuromuscular blockers on twitches and tetani was performed, encompassing: atracurium, cisatracurium, mivacurium, pancuronium, rocuronium and vecuronium. The sciatic nerve-extensor digitorum longus muscle of the rat was used, in vitro. Twitches were evoked at 0.1 Hz and tetani at 50 Hz. The differential effects of the studied compounds on twitches and tetani were statistically compared using simultaneous confidence intervals for the ratios between mean IC(50) for the block of twitches and mean IC(50) for the block of tetani. The results of ratios of mean IC(50) together with their corresponding 95% simultaneous confidence intervals were: vecuronium: 2.5 (1.8-3.5); mivacurium: 3.8 (3.0-4.9); pancuronium: 3.9 (2.0-7.6); rocuronium: 6.1 (3.8-9.9); atracurium: 9.0 (6.4-12.6); cisatracurium: 13.1 (6.0-28.4). Using the criteria that neuromuscular blockers displaying disjunct confidence intervals for the ratios of mean IC(50) differ statistically with regard to differential effects on twitches and tetani, significant differences in ratios of IC(50) were detected in the following cases: vecuronium vs. rocuronium, vs. atracurium and vs. cisatracurium and mivacurium vs: cisatracurium and vs. atracurium. The results show that the magnitude of the differential effects of neuromuscular blockers on twitches and tetani, as evaluated in the present work in the form of ratios of mean IC(50), does not depend on the chemical structure (comparing steroidal and isoquinolinic compounds), but seems to depend on differential pre- and post-synaptic effects of the compounds. It is also suggested that the greater the ability of a compound to block twitches and tetani in a differential manner, the safer is the compound from the clinical anesthesiology viewpoint.

An evaluation of three upwinding approximations for numerical modeling the flow in tubular membrane of Newtonian and non-Newtonian fluids

In this paper, the laminar fluid flow of Newtonian and non-Newtonian of aqueous solutions in a tubular membrane is numerically studied. The mathematical formulation, with associated initial and boundary conditions for cylindrical coordinates, comprises the mass conservation, momentum conservation and mass transfer equations. These equations are discretized by using the finite-difference technique on a staggered grid system. Comparisons of the three upwinding schemes for discretization of the non-linear (convective) terms are presented. The effects of several physical parameters on the concentration profile are investigated. The numerical results compare favorably with experimental data and the analytical solutions. (C) 2011 Elsevier Inc. All rights reserved.

Effect on the heavy-ion fusion and elastic scattering cross sections of common approximations assumed in coupled-channel calculations

We study the effects of several approximations commonly used in coupled-channel analyses of fusion and elastic scattering cross sections. Our calculations are performed considering couplings to inelastic states in the context of the frozen approximation, which is equivalent to the coupled-channel formalism when dealing with small excitation energies. Our findings indicate that, in some cases, the effect of the approximations on the theoretical cross sections can be larger than the precision of the experimental data.

Energy of bond defects in quantum spin chains obtained from local approximations and from exact diagonalization

We study the influence of ferromagnetic and antiferromagnetic bond defects on the ground-state energy of antiferromagnetic spin chains. In the absence of translational invariance, the energy spectrum of the full Hamiltonian is obtained numerically, by an iterative modi. cation of the power algorithm. In parallel, approximate analytical energies are obtained from a local-bond approximation, proposed here. This approximation results in significant improvement upon the mean-field approximation, at negligible extra computational effort. (C) 2008 Published by Elsevier B.V.

Approximations of modal logics: K and beyond

Inspired by the recent work on approximations of classical logic, we present a method that approximates several modal logics in a modular way. Our starting point is the limitation of the n-degree of introspection that is allowed, thus generating modal n-logics. The semantics for n-logics is presented, in which formulas are evaluated with respect to paths, and not possible worlds. A tableau-based proof system is presented, n-SST, and soundness and completeness is shown for the approximation of modal logics K, T, D, S4 and S5. (c) 2008 Published by Elsevier B.V.

Accurate velocity reconstruction for Discontinuous Galerkin approximations of two-phase porous media flows

We consider Discontinuous Galerkin approximations of two-phase, immiscible porous media flows in the global pressure/fractional flow formulation with capillary pressure. A sequential approach is used with a backward Euler step for the saturation equation, equal-order interpolation for the pressure and the saturation, and without any limiters. An accurate total velocity field is recovered from the global pressure equation to be used in the saturation equation. Numerical experiments show the advantages of the proposed reconstruction. To cite this article: A. Ern et al., C R. Acad. Sci. Paris, Ser. 1347 (2009). (C) 2009 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved.

Ultrasensitive Simultaneous Quantification of 1,N(2)-Etheno-2 `-deoxyguanosine and 1,N(2-)Propano-2 `-deoxyguanosine in DNA by an Online Liquid Chromatography-Electrospray Tandem Mass Spectrometry Assay

Exocyclic DNA adducts produced by exogenous and endogenous compounds are emerging as potential tools to study a variety of human diseases and air pollution exposure. A highly sensitive method involving online reverse-phase high performance liquid chromatography with electrospray tandem mass spectrometry detection in the multiple reaction monitoring mode and employing stable isotope-labeled internal standards was developed for the simultaneous quantification of 1,N(2)-etheno-2`-deoxyguanosine (1,N(2)-epsilon dGuo) and 1,N(2)-propano-2`-deoxyguanosine (1,N(2)-propanodGuo) in DNA. This methodology permits direct online quantification of 2`-deoxyguanosine and ca. 500 amol of adducts in 100 mu g of hydrolyzed DNA M the same analysis. Using the newly developed technique, accurate determinations of 1,N(2)-etheno-2`-deoxyguanosine and 1,N2-propano-2`-deoxyguanosine levels in DNA extracts of human cultured cells (4.01 +/- 0.32 1,N(2)-epsilon dGuo/10(8) dGuo and 3.43 +/- 0.33 1,N(2)-propanodGuo/10(8) dGuo) and rat tissue (liver, 2.47 +/- 0.61 1,N(2)-epsilon dGuo/10(8) dGuo and 4.61 +/- 0.69 1,N(2)-propanodGuo/108 dGuo; brain, 2.96 +/- 1.43,N(2)-epsilon dGuo/10(8) dGuo and 5.66 +/- 3.70 1,N(2)-propanoclGuo/10(8) dGuo; and lung, 0,87 +/- 0.34 1,N(2)-edGuo/ 10(8) dGuo and 2.25 +/- 1.72 1,N(2)-propanodGuo/10(8) dGuo) were performed. The method described herein can be used to study the biological significance of exocyclic DNA adducts through the quantification of different adducts in humans and experimental an with pathological conditions and after air pollution exposure.

Simultaneous determination of chromium and manganese in alumina by slurry sampling graphite furnace atomic absorption spectrometry using NbC and NaF as modifiers

This paper reports a method for the direct and simultaneous determination of Cr and Mn in alumina by slurry sampling graphite furnace atomic absorption spectrometry (SiS-SIMAAS) using niobium carbide (NbC) as a graphite platform modifier and sodium fluoride (NaF) as a matrix modifier. 350 mu g of Nb were thermally deposited on the platform surface allowing the formation of NbC (mp 3500 degrees C) to minimize the reaction between aluminium and carbon of the pyrolytic platform, improving the graphite tube lifetime up to 150 heating cycles. A solution of 0.2 mol L(-1) NaF was used as matrix modifier for alumina dissolution as cryolite-based melt, allowing volatilization during pyrolysis step. Masses (c.a. 50 mg) of sample were suspended in 30 ml of 2.0% (v/v) of HNO(3). Slurry was manually homogenized before sampling. Aliquots of 20 mu l of analytical solutions and slurry samples were co-injected into the graphite tube with 20 mu l of the matrix modifier. In the best conditions of the heating program, pyrolysis and atomization temperatures were 1300 degrees C and 2400 degrees C, respectively. A step of 1000 degrees C was optimized allowing the alumina dissolution to form cryolite. The accuracy of the proposed method has been evaluated by the analysis of standard reference materials. The found concentrations presented no statistical differences compared to the certified values at 95% of the confidence level. Limits of detection were 66 ng g(-1) for Cr and 102 ng g(-1) for Mn and the characteristic masses were 10 and 13 pg for Cr and Mn, respectively.

Multivariant optimization, validation, and application of capillary electrophoresis for simultaneous determination of polyphenols and phenolic acids in Brazilian wines

A method for the simultaneous determination of the stilbene resveratrol, four phenolic acids (syringic, coumaric, caffeic, and gallic acids), and five flavonoids (catechin, rutin, kaempferol, myricetin, and quercetin) in wine by CE was developed and validated. The CE electrolyte composition and instrumental conditions were optimized using 2(7-3) factorial design and response surface analysis, showing sodium tetraborate, MeOH, and their interaction as the most influential variables. The optimal electrophoretic conditions, minimizing the chromatographic resolution statistic values, consisted of 17 mmol/L sodium tetraborate with 20% methanol as electrolyte, constant voltage of 25 kV, hydrodynamic injection at 50 mbar for 3 s, and temperature of 25 degrees C. The R(2) values for linearity varied from 0.994 to 0.999; LOD and LOQ were 0.1 to 0.3 mg/L and 0.4 to 0.8 mg/L, respectively. The RSDs for migration time and peak area obtained from ten consecutive injections were less than 2% and recoveries varied from 97 to 102%. The method was applied to 23 samples of inexpensive Brazilian wines, showing wide compositional variation.

Simultaneous voltammetric detection of ascorbic acid, dopamine and uric acid using a pyrolytic graphite electrode modified into dopamine solution

Pyrolytic graphite electrodes (PGE) were modified into dopamine solutions using phosphate buffer solutions, pH 10 and 6.5, as supporting electrolyte. The modification process involved a previous anodization of the working electrode at +1. 5 V into 0. 1 mol-L-1 NaOH followed by other anodization step, in the same experimental conditions, into dopamine (DA) solutions. pH of the supporting electrolyte performed an important role in the production of a superficial melanin polymeric film, which permitted the simultaneous detection of ascorbic acid (AA), (DA) and uric acid (UA), Delta EAA-DA = 222 mV-, Delta EAA-UA = 360 mV and Delta EDA-UA=138mV, avoiding the superficial poisoning effects. The calculated detection limits were: 1.4 x 10(-6) mol L-1 for uric acid, 1.3x10-(5) molL(-1) for ascorbic acid and 1.1 X 10(-7) mol L-1 for dopamine, with sensitivities of (7.7 +/- 0.5), (0.061 +/- 0.001) and (9.5 +/- 0.05)A mol(-1) cm(-2), respectively, with no mutual interference. Uric acid was determined in urine, blood and serum human samples after dilution in phosphate buffer and no additional sample pre-treatment was necessary. The concentration of uric acid in urine was higher than the values found in blood and serum and the recovery tests (92-102%) indicated that no matrix effects were observed. (C) 2008 Elsevier B.V. All rights reserved.