Separating the wheat from the chaff: unbiased filtering of background tandem mass spectra improves protein identification

Only a small fraction of spectra acquired in LC-MS/MS runs matches peptides from target proteins upon database searches. The remaining, operationally termed background, spectra originate from a variety of poorly controlled sources and affect the throughput and confidence of database searches. Here, we report an algorithm and its software implementation that rapidly removes background spectra, regardless of their precise origin. The method estimates the dissimilarity distance between screened MS/MS spectra and unannotated spectra from a partially redundant background library compiled from several control and blank runs. Filtering MS/MS queries enhanced the protein identification capacity when searches lacked spectrum to sequence matching specificity. In sequence-similarity searches it reduced by, on average, 30-fold the number of orphan hits, which were not explicitly related to background protein contaminants and required manual validation. Removing high quality background MS/MS spectra, while preserving in the data set the genuine spectra from target proteins, decreased the false positive rate of stringent database searches and improved the identification of low-abundance proteins.

Quantification of chlordesmethyldiazepam by liquid chromatography-tandem mass spectrometry: application to a cloxazolam bioequivalence study

A rapid, sensitive and specific LC-MS/MS method was developed and validated for quantifying chlordesmethyldiazepam (CDDZ or delorazepam), the active metabolite of cloxazolam, in human plasma. In the analytical assay, bromazepam (internal standard) and CDDZ were extracted using a liquid-liquid extraction (diethyl-ether/hexane, 80/20, v/v) procedure. The LC-MS/MS method on a RP-C18 column had an overall run time of 5.0 min and was linear (1/x weighted) over the range 0.5-50 ng/mL (R > 0.999). The between-run precision was 8.0% (1.5 ng/mL), 7.6% (9 ng/mL), 7.4% (40 ng/mL), and 10.9% at the low limit of quantification-LLOQ (0.500 ng/mL). The between-run accuracies were 0.1, -1.5, -2.7 and 8.7% for the above mentioned concentrations, respectively. All current bioanalytical method validation requirements (FDA and ANVISA) were achieved and it was applied to the bioequivalence study (Cloxazolam-test, Eurofarma Lab. Ltda and Olcadil (R)-reference, Novartis Biociencias S/A). The relative bioavailability between both formulations was assessed by calculating individual test/reference ratios for Cmax, AUClast and AUCO-inf. The pharmacokinetic profiles indicated bioequivalence since all ratios were as proposed by FDA and ANVISA. Copyright (C) 2009 John Wiley & Sons, Ltd.

Ciprofibrate quantification in human plasma by high-performance liquid chromatography coupled with electrospray tandem mass spectrometry for pharmacokinetic studies

A rapid, sensitive and specific method for quantifying ciprofibrate in human plasma using bezafibrate as the internal standard (IS) is described. The sample was acidified prior extraction with formic acid (88%). The analyte and the IS were extracted from plasma by liquid-liquid extraction using an organic solvent (diethyl ether/dichloromethane 70/30 (v/v)). The extracts were analyzed by high performance liquid chromatography coupled with electrospray tandem mass spectrometry (HPLC-MS/MS). Chromatography was performed using Genesis C18 4 mu m analytical column (4.6 x 150 mm i.d.) and a mobile phase consisting of acetonitrile/water (70/30, v/v) and 1 mM acetic acid. The method had a chromatographic run time of 3.4 min and a linear calibration curve over the range 0.1-60 mu g/mL (r > 0.99). The limit of quantification was 0.1 mu g/mL. The intra- and interday accuracy and precision values of the assay were less than 13.5%. The stability tests indicated no significant degradation. The recovery of ciprofibrate was 81.2%, 73.3% and 76.2% for the 0.3, 5.0 and 48.0 ng/mL standard concentrations, respectively. For ciprofibrate, the optimized parameters of the declustering potential, collision energy and collision exit potential were -51 V, -16 eV and -5 V, respectively. The method was also validated without the use of the internal standard. This HPLC-MS/MS procedure was used to assess the bioequivalence of two ciprofibrate 100 mg tablet formulations in healthy volunteers of both sexes. The following pharmacokinetic parameters were obtained from the ciprofibrate plasma concentration vs. time curves: AUC(last), AUC(0-168 h), C(max) and T(max). The geometric mean with corresponding 90% confidence interval (CI) for test/reference percent ratios were 93.80% (90% CI = 88.16-99.79%) for C(max), 98.31% (90% CI = 94.91-101.83%) for AUC(last) and 97.67% (90% CI = 94.45-101.01%) for AUC(0-168 h). Since the 90% Cl for AUC(last), AUC(0-168 h) and C(max) ratios were within the 80-125% interval proposed by the US FDA, it was concluded that ciprofibrate (Lipless (R) 100 mg tablet) formulation manufactured by Biolab Sanus Farmaceutica Ltda. is bioequivalent to the Oroxadin (R) (100 mg tablet) formulation for both the rate and the extent of absorption. (C) 2011 Published by Elsevier B.V.

Expression and purification of a recombinant adenovirus fiber knob in a baculovirus system

Objectives: To construct a recombinant baculovirus expressing the fiber knob domain of human adenovirus type 2 modified by the insertion of a foreign peptide, purify this protein after its production in insect cells, and to test its properties. Methods: Recombinant baculoviruses expressing the fiber knob were produced in Sf9 cells. The recombinant fiber knob was recovered from culture supernatants of infected cells and purified by a combination of Ni-NTA and ion-exchange chromatography. Results: Fiber knob was recovered from the culture media as a soluble protein. In the system used, the fiber knob is expressed fused with the V5 epitope and a histidine tag, which allowed purification by Ni-NTA chromatography. The protein was further purified by ion-exchange chromatography. We show that the recombinant fiber knob produced, with 31 extra amino acids in the C-terminus, can oligomerize and bind to the adenovirus receptor CAR, as it can block the infection of a recombinant type 5 adenovirus. Conclusions: The modified form of the fiber knob, produced in insect cells and purified by Ni-NTA and ion-exchange chromatography, retains the properties of oligomerization and binding to the fiber natural receptor, CAR. This construct has the potential to be a new adjuvant. Copyright (C) 2008 S. Karger AG, Basel.

MuRF1 is a muscle fiber-type II associated factor and together with MuRF2 regulates type-II fiber trophicity and maintenance

MuRF1 is a member of the RBCC (RING, B-box, coiled-coil) superfamily that has been proposed to act as an atrogin during muscle wasting. Here, we show that MuRF1 is preferentially induced in type-II muscle fibers after denervation. Fourteen days after denervation, MuRF1 protein was further elevated but remained preferentially expressed in type-II muscle fibers. Consistent with a fiber-type dependent function of MuRF1, the tibialis anterior muscle (rich in type-II muscle fibers) was considerably more protected in MuRF1-KO mice from muscle wasting when compared to soleus muscle with mixed fiber-types. We also determined fiber-type distributions in MuRF1/MuRF2 double-deficient KO (dKO) mice, because MuRF2 is a close homolog of MuRF1. MuRF1/MuRF2 dKO mice showed a profound loss of type-II fibers in soleus muscle. As a potential mechanism we identified the interaction of MuRF1/MuRF2 with myozenin-1, a calcineurin/NFAT regulator and a factor required for maintenance of type-II muscle fibers. MuRF1/MuRF2 dKO mice had lost myozenin-1 expression in tibialis anterior muscle, implicating MuRF1/MuRF2 as regulators of the calcineurin/NFAT pathway. In summary, our data suggest that expression of MuRF1 is required for remodeling of type-II fibers under pathophysiological stress states, whereas MuRF1 and MuRF2 together are required for maintenance of type-II fibers, possibly via the regulation of myozenin-1. (C) 2010 Elsevier Inc. All rights reserved.

Iterative strong coupling of dimensionally heterogeneous models

In this article we address decomposition strategies especially tailored to perform strong coupling of dimensionally heterogeneous models, under the hypothesis that one wants to solve each submodel separately and implement the interaction between subdomains by boundary conditions alone. The novel methodology takes full advantage of the small number of interface unknowns in this kind of problems. Existing algorithms can be viewed as variants of the `natural` staggered algorithm in which each domain transfers function values to the other, and receives fluxes (or forces), and vice versa. This natural algorithm is known as Dirichlet-to-Neumann in the Domain Decomposition literature. Essentially, we propose a framework in which this algorithm is equivalent to applying Gauss-Seidel iterations to a suitably defined (linear or nonlinear) system of equations. It is then immediate to switch to other iterative solvers such as GMRES or other Krylov-based method. which we assess through numerical experiments showing the significant gain that can be achieved. indeed. the benefit is that an extremely flexible, automatic coupling strategy can be developed, which in addition leads to iterative procedures that are parameter-free and rapidly converging. Further, in linear problems they have the finite termination property. Copyright (C) 2009 John Wiley & Sons, Ltd.

EPR in the Characterization of the Shade Effect on Translucence, Remaining Free Radicals, and Polymerization Depth of Commercially Available Resin Composites

The aim of this study was to assess the relation between the number of free radicals generated and the polymerization depth in two different commercial brands of resin composites with different colors and translucence. Electron paramagnetic resonance quantified the radical populations through relative intensity (I (r)) of free radicals generated, and radical decay was monitored. Sample translucence and the classical polymerization depth were measured. The analysis indicated that resin with more color pigments (MA4, I (r) = 0.73 a.u) or more opacity components (ODA2, I (r) = 0.84 a.u) generated smaller populations of free radicals and have the lower polymerization depth than clearer (M, I (r) = 1.20 a.u and MA2, I (r) = 1.02) or more translucent (OEA2, I (r) = 1.00 a.u) composites for the same light-curing time. It seems that irradiation doses have to be adequate to more colored and less translucent resins.

Influence of different light sources and photo-activation methods on degree of conversion and polymerization shrinkage of a nanocomposite resin

The purpose of this study was to evaluate the influence of different light sources and photo-activation methods on degree of conversion (DC%) and polymerization shrinkage (PS) of a nanocomposite resin (Filtek (TM) Supreme XT, 3M/ESPE). Two light-curing units (LCUs), one halogen-lamp (QTH) and one light-emitting-diode (LED), and two different photo-activation methods (continuous and gradual) were investigated in this study. The specimens were divided in four groups: group 1-power density (PD) of 570 mW/cm(2) for 20 s (QTH); group 2-PD 0 at 570 mW/cm(2) for 10 s + 10 s at 570 mW/cm(2) (QTH); group 3-PD 860 mW/cm(2) for 20 s (LED), and group 4-PD 125 mW/cm(2) for 10 s + 10 s at 860 mW/cm(2) (LED). A testing machine EMIC with rectangular steel bases (6 x 1 x 2 mm) was used to record the polymerization shrinkage forces (MPa) for a period that started with the photo-activation and ended after two minutes of measurement. For each group, ten repetitions (n = 40) were performed. For DC% measurements, five specimens (n = 20) for each group were made in a metallic mold (2 mm thickness and 4 mm diameter, ISO 4049) and them pulverized, pressed with bromide potassium (KBr) and analyzed with FT-IR spectroscopy. The data of PS were analyzed by Analysis of Variance (ANOVA) with Welch`s correction and Tamhane`s test. The PS means (MPa) were: 0.60 (G1); 0.47 (G2); 0.52 (G3) and 0.45 (G4), showing significant differences between two photo-activation methods, regardless of the light source used. The continuous method provided the highest values for PS. The data of DC% were analyzed by Analysis of Variance (ANOVA) and shows significant differences for QTH LCUs, regardless of the photo-activation method used. The QTH provided the lowest values for DC%. The gradual method provides lower polymerization contraction, either with halogen lamp or LED. Degree of conversion (%) for continuous or gradual photo-activation method was influenced by the LCUs. Thus, the presented results suggest that gradual method photo-activation with LED LCU would suffice to ensure adequate degree of conversion and minimum polymerization shrinkage.

Two-Photon Polymerization for Fabricating Structures Containing the Biopolymer Chitosan

Two-photon polymerization is a powerful tool for fabricating three-dimensional micro/nano structures for applications ranging from nanophotonics to biology. To tailor such structure for specific purposes it is often important to dope them. In this paper we report on the fabrication of structures, with nanometric surface features (resolution of approximately 700 nm), using two-photon polymerization of an acrylic resin doped with the biocompatible polymer chitosan using a guest-host scheme. The fluorescence background in the Raman spectrum indicates the presence of chitosan throughout the structure. Mechanical characterization reveals that chitosan does not affect the mechanical properties of the host acrylic resin and, consequently, the structures exhibit excellent integrity. The approach presented in this work can be used in the fabrication of micro- and nanostructures containing biopolymers for biomedical applications.

Effect of different dental composite resins on the polymerization process

Dental composite resins possess good esthetic properties, and are currently among the most popular dental restorative materials. Both organic and inorganic phases might influence the material behavior, the filler particle features and rate are the most important factors related to improvement of the mechanical properties of resin composites. Thus, the objective of this study was to evaluate the effect of three different composite resins on the polymerization process by Vickers hardness test. The samples were prepared using three different composite resins, as follow: group I-P-60 (3M/ESPE); group II-Herculite XRV (Kerr), and group III-Durafill (Heraeus-Kulzer). The samples were made in a polytetrafluoroethylene mould, with a rectangular cavity measuring 7 mm in length, 4 mm in width, and 3 mm in thickness. The samples were photo-activated by one light-curing unit based on blue LEDs (Ultrablue III-DMC/Brazil) for 20 and 40 s of irradiation times. The Vickers hardness test was performed 24 h after the photo-activation until the standardized depth of 3 mm. The Vickers hardness mean values varied from 158.9 (+/- 0.81) to 81.4 (+/- 1.94) for P-60, from 138.7 (+/- 0.37) to 61.7 (+/- 0.24) for Herculite XRV, and from 107. 5 (+/- 0.81) to 44.5 (+/- 1.36) for Durafill composite resins photo-activated during 20 s for the 1st and 2nd mm, respectively. During 40 s of photo-activation, the Vickers hardness mean values were: from 181.0 (+/- 0.70) to 15.6 (+/- 0.29) for P-60, and from 161.8 (+/- 0.41) to 11.2 (+/- 0.17) for Herculite XRV composite resins, for the 1st and 3th mm, respectively. For Durafill composite resin the mean values varied from 120.1 (+/- 0.66) to 61.7 (+/- 0.20), for the 1st and 2nd mm, respectively. The variation coefficient (CV) was in the most of the groups lower than 1%, then the descriptive statistic analysis was used. The Vickers hardness mean values for Durafill were lower than P-60 and Herculite XRV composite resins for 20 and 40 s of irradiation time. The polymerization process was greatly affected by the composition of the composite resins.

Effect of light-curing units on push-out fiber post bond strength in root canal dentin

The purpose of this study was to evaluate the effectiveness of different light-curing units on the bond strength (push-out) of glass fiber posts in the different thirds of the root (cervical, middle and apical) with different adhesive luting resin systems (dual-cure total-etch; dual-cured and self-etch bonding system; and dual-cure self-adhesive cements), Disks of the samples (n = 144) were used, with approximately 1 mm of thickness of 48 bovine roots restored with glass fiber posts, that were luted with resin cements photo-activated by halogen LCU (QTH, Optilux 501) and blue LED (Ultraled), with power densities of 600 and 550 mW/cm(2), respectively. A universal testing machine (MTS 810 Material Test System) was used with a 1 mm diameter steel rod at cross-head speed of 0.5 mm/min until post extrusion, with load cell of 50 kg, for evaluation of the push-out strength in the different thirds of each sample. The push-out strength values in kgf were converted to MPa and analyzed through Analysis of Variance and Tukey`s test, at significance level of 5%. The results showed that there were no statistical differences between the QTH and LED LCUs. The self-adhesive resin cement had lower values of retention. The total-etch and self-adhesive system resin cements seem to be a possible alternative for glass fiber posts cementation into the radicular canal and the LED LCU can be applied as an alternative to halogen light on photo-activation of dual-cured resin cements.

Short-time behaviour of demand and price viewed through an exactly solvable model for heterogeneous interacting market agents

We introduce a stochastic heterogeneous interacting-agent model for the short-time non-equilibrium evolution of excess demand and price in a stylized asset market. We consider a combination of social interaction within peer groups and individually heterogeneous fundamentalist trading decisions which take into account the market price and the perceived fundamental value of the asset. The resulting excess demand is coupled to the market price. Rigorous analysis reveals that this feedback may lead to price oscillations, a single bounce, or monotonic price behaviour. The model is a rare example of an analytically tractable interacting-agent model which allows LIS to deduce in detail the origin of these different collective patterns. For a natural choice of initial distribution, the results are independent of the graph structure that models the peer network of agents whose decisions influence each other. (C) 2009 Elsevier B.V. All rights reserved.

ABELIANIZED OBSTRUCTION FOR FIXED POINTS OF FIBER-PRESERVING MAPS OF SURFACE BUNDLES

Let f: M -> M be a fiber-preserving map where S -> M -> B is a bundle and S is a closed surface. We study the abelianized obstruction, which is a cohomology class in dimension 2, to deform f to a fixed point free map by a fiber-preserving homotopy. The vanishing of this obstruction is only a necessary condition in order to have such deformation, but in some cases it is sufficient. We describe this obstruction and we prove that the vanishing of this class is equivalent to the existence of solution of a system of equations over a certain group ring with coefficients given by Fox derivatives.

Fixed points on Klein bottle fiber bundles over the circle

The main purpose of this work is to study fixed points of fiber-preserving maps over the circle S(1) for spaces which are fiber bundles over S(1) and the fiber is the Klein bottle K. We classify all such maps which can be deformed fiberwise to a fixed point free map. The similar problem for torus fiber bundles over S(1) has been solved recently.

Discontinuous Galerkin approximation of two-phase flows in heterogeneous porous media with discontinuous capillary pressures

We design and investigate a sequential discontinuous Galerkin method to approximate two-phase immiscible incompressible flows in heterogeneous porous media with discontinuous capillary pressures. The nonlinear interface conditions are enforced weakly through an adequate design of the penalties on interelement jumps of the pressure and the saturation. An accurate reconstruction of the total velocity is considered in the Raviart-Thomas(-Nedelec) finite element spaces, together with diffusivity-dependent weighted averages to cope with degeneracies in the saturation equation and with media heterogeneities. The proposed method is assessed on one-dimensional test cases exhibiting rough solutions, degeneracies, and capillary barriers. Stable and accurate solutions are obtained without limiters. (C) 2010 Elsevier B.V. All rights reserved.