Identification of bacteria using tandem mass spectrometry combined with a proteome database and statistical scoring

Detection and identification of pathogenic bacteria and their protein toxins play a crucial role in a proper response to natural or terrorist-caused outbreaks of infectious diseases. The recent availability of whole genome sequences of priority bacterial pathogens opens new diagnostic possibilities for identification of bacteria by retrieving their genomic or proteomic information. We describe a method for identification of bacteria based on tandem mass spectrometric (MS/MS) analysis of peptides derived from bacterial proteins. This method involves bacterial cell protein extraction, trypsin digestion, liquid chromatography MS/MS analysis of the resulting peptides, and a statistical scoring algorithm to rank MS/MS spectral matching results for bacterial identification. To facilitate spectral data searching, a proteome database was constructed by translating genomes of bacteria of interest with fully or partially determined sequences. In this work, a prototype database was constructed by the automated analysis of 87 publicly available, fully sequenced bacterial genomes with the GLIMMER gene finding software. MS/MS peptide spectral matching for peptide sequence assignment against this proteome database was done by SEQUEST. To gauge the relative significance of the SEQUEST-generated matching parameters for correct peptide assignment, discriminant function (DF) analysis of these parameters was applied and DF scores were used to calculate probabilities of correct MS/MS spectra assignment to peptide sequences in the database. The peptides with DF scores exceeding a threshold value determined by the probability of correct peptide assignment were accepted and matched to the bacterial proteomes represented in the database. Sequence filtering or removal of degenerate peptides matched with multiple bacteria was then performed to further improve identification. It is demonstrated that using a preset criterion with known distributions of discriminant function scores and probabilities of correct peptide sequence assignments, a test bacterium within the 87 database microorganisms can be unambiguously identified.     

Robust weighted averaging

Signal averaging is often used to extract a useful signal embedded in noise. This method is especially useful for biomedical signals, where the spectra of the signal and noise significantly overlap. In this case, traditional filtering techniques introduce unacceptable signal distortion. In averaging methods, constancy of the noise power is usually assumed, but in reality noise features a variable power. In this case, it is more appropriate to use a weighted averaging. The main problem in this method is the estimation of the noise power in order to obtain the weight values. Additionally, biomedical signals often contain outliers. This requires robust averaging methods. This paper shows that signal averaging can be formulated as a problem of minimization of a criterion function. Based on this formulation new weighted averaging methods are introduced, including weighted averaging based on criterion function minimization (WACFM) and robust epsilon-insensitive WACFM. Performances of these new methods are experimentally compared with the traditional averaging and other weighted averaging methods using electrocardiographic signal with the muscle noise, impulsive noise, and time-misalignment of cycles. Finally, an application to the late potentials extraction is shown.     

The effect of lamellar separation on the properties of a Ti–46Al–2Nb–2Cr intermetallic alloy

The relationships between the γ and ₂ lamellae apparent separation and hardnesses as well as the peak flow stresses estimated in hot compression tests obtained for specimens made of Ti–46Al–2Nb–2Cr alloy are presented. The lamellae separations were estimated using image analysis on the microstructure of the specimens. The procedure employing a fast Fourier transformation of secondary electron microstructural images for fully automatic lamellae separation measurements is described. It was found that the effect of the apparent lamellae separations of γ and ₂ on the peak flow stress is significant. For the microstructure with thick lamellae of γ and ₂ phases, the peak flow stress decreases. The hardness of the specimens decreases with an increase of the lamellae apparent separation as well.     

The changes in the contents of 137Cs in bottom sediments of some Masurian lakes during 10-15 y observation (Poland)

The measurements of radioactive caesium contents in bottom sedimentswere carried out in four lakes. First samples (47) were takenin 1992–95. The repeat sampling (109) was performed fromthe same places in 2005. We examined eight chosen areas in theselakes. In six of them, we observed statistically significantdifferences in the level of radioactive caesium. It indicatesthe permanent decrease in the level of ¹³⁷Cs. The mean annualdecrease in the level of radioactive caesium, taking into considerationthe radioactive decay, was from 4.2 to 7.8%. In two areas ofthe profundal zone, we did not observe statistically significantdifferences in the level of radioactive caesium (lakes Garbasand Rogale Wielkie). Taking into consideration the radioactivedecay of caesium, it means about the appearance of the processof accumulation of ¹³⁷Cs in these areas.     

Comparative analysis of viscosity of complex liquids and cytoplasm of mammalian cells at the nanoscale

We present a scaling formula for size-dependent viscosity coefficients for proteins, polymers, and fluorescent dyes diffusing in complex liquids. The formula was used to analyze the mobilities of probes of different sizes in HeLa and Swiss 3T3 mammalian cells. This analysis unveils in the cytoplasm two length scales: (i) the correlation length ξ (approximately 5 nm in HeLa and 7 nm in Swiss 3T3 cells) and (ii) the limiting length scale that marks the crossover between nano- and macroscale viscosity (approximately 86 nm in HeLa and 30 nm in Swiss 3T3 cells). During motion, probes smaller than ξ experienced matrix viscosity: η(matrix) ≈ 2.0 mPa·s for HeLa and 0.88 mPa·s for Swiss 3T3 cells. Probes much larger than the limiting length scale experienced macroscopic viscosity, η(macro) ≈ 4.4 × 10(-2) and 2.4 × 10(-2) Pa·s for HeLa and Swiss 3T3 cells, respectively. Our results are persistent for the lengths scales from 0.14 nm to a few hundred nanometers.     

Investigation of microstructure and chemical composition of Ni contacts to n-type 4H–SiC

Structure and chemical compositions of the interface layer obtained after nickel deposition on silicon carbide surface and subsequent annealing have been analyzed using time-of-flight secondary ion mass spectrometry (TOF-SIMS), X-ray diffraction (XRD) and Raman spectroscopy. Nickel silicide (Ni₂Si) were characterized as the main product of reaction between nickel and silicon carbide after annealing at temperatures range 700–1000 °C. Raman spectroscopy and TOF-SIMS profiling results confirmed carbon precipitation within contact layer. Obtained results indicate graphitic form of carbon and its non-uniform distribution in the contact layer. Moreover, TOF-SIMS analysis showed modification of nitrogen distribution in the contact area upon Ni/SiC contact annealing.     

Phase-Compensated Time-Varying Butterworth Filters

One of the important problems of signal processing is to design the filters which possess linear phase characteristics. This paper presents the concept of time-varying Butterworth filters with linear phase. The compensation of the phase characteristics is carried out with the aid of phase shifter which is cascade-connected to the structure of the original Butterworth filter given by the transfer function. The parameters of the phase shifter were calculated in this way that the group delay of the designed filter is possible constant in the filter pass–band. Time varying coefficients were introduced to the phase–compensated filter structure for the purpose of minimization of the filter transient state. This paper contains simulation results of proposed filters and comparison with classic circuits.     

Beyond the variable wavelength interferometry—Monitoring the interaction between the ultrashort high power laser pulses and light propagating medium

This paper presents the Variable Wavelength Interferometry (VAWI) technique, its applications and expected research potential of this system equipped with a femtosecond laser. The system is configured for observation and measurement of local optical parameters modified by a high power laser pulse. The VAWI measurement technique has a unique feature that can visualize and enables investigation of the immediate matter response to a single high power laser pulse just in the pulse area, which can locally modify dielectric and optical parameters of matter along the propagation path. It affects the dielectric tensor, refractive indices and it may induce birefringence. The high power laser pulse is responsible for the nonlinear effects in the optical materials like crystals, photonic crystals, optical fibers etc. The VAWI provides the ability to measure very accurately the above optical parameters along the laser pulse propagation path and neighboring regions in the VIS-NIR spectral ranges.     

Asymptotic Preserving scheme for strongly anisotropic parabolic equations for arbitrary anisotropy direction

This paper deals with the numerical study of a strongly anisotropic heat equation. The use of standard schemes in this situation leads to poor results, due to high anisotropy. Furthermore, the recently proposed Asymptotic-Preserving method (Lozinski et al., 2012) allows one to perform simulations regardless of the anisotropy strength but its application is limited to the case where the anisotropy direction is given by a field whose lines are all open. In this paper we introduce a new Asymptotic-Preserving method, which overcomes those limitations without any loss of precision or increase in computational costs. The convergence of the method is shown to be independent of the anisotropy parameter 0<ε<1$0<\epsilon <1$ for fixed coarse Cartesian grids, and for variable anisotropy directions. The context of this work is magnetically confined fusion plasmas.