NKT and NKT-like Cells in Autoimmune Neuroinflammatory Diseases—Multiple Sclerosis,Myasthenia Gravis and Guillain-Barre Syndrome

NKT cells comprise three subsets—type I (invariant, iNKT), type II, and NKT-like cells, of which iNKT cells are the most studied subset. They are capable of rapid cytokine production after the initial stimulus, thus they may be important for polarisation of Th cells. Due to this, they may be an important cell subset in autoimmune diseases. In the current review, we are summarising results of NKT-oriented studies in major neurological autoimmune diseases—multiple sclerosis, myasthenia gravis, and Guillain-Barre syndrome and their corresponding animal models.     

Global kinase screening. Applications of frontal affinity chromatography coupled to mass spectrometry in drug discovery

Utilizing frontal affinity chromatography with mass spectrometry detection (FAC-MS), we have identified novel applications in the discovery of small-molecule hits to protein targets that are difficult if not impossible to accomplish using traditional assays. We demonstrate for the first time an ability to distinguish between competitive ligands for the ATP and substrate sites of protein kinase C independently in the same experiment and show that ATP competitive ligands using a functionally inactive receptor tyrosine kinase can be identified. This ability of FAC-MS to simultaneously monitor binding at the ATP and substrate binding sites, as well as measure ligand binding to both active and inactive kinases, suggests that FAC-MS can be used as a "global kinase binding assay".     

Experimental and theoretical investigations of birefringent holey fibers with a triple defect

We have manufactured and characterized a birefringent holey fiber of a new construction. The birefringence in this fiber is induced by the highly elliptical shape of the core, which consists of a triple defect in a hexagonal structure. Using a hybrid edge-nodal finite-element method, we calculated the spectral dependence of phase and group modal birefringence for spatial modes E11 and E21 in idealized and in real fiber, whose geometry we determined by using a scanning-electron microscope. Results of our calculations show that technological imperfections significantly affect the fiber's birefringence. Normalized cutoff wavelengths for higher-order modes relative to the filling factor were also determined for the idealized structure. We observed a significant disagreement between theoretical and experimental values of cutoff wavelengths, which was attributed to high confinement losses near the cutoff condition. We also measured the spectral dependence of the phase and the group modal birefringence for spatial modes E11 and E21. The measured parameters showed good agreement with the results of modeling.     

Quantitative determination of titin and nebulin in poultry meat by SDS-PAGE with an internal standard

The method of quantitative determination of titin and nebulin in chicken meat by SDS-PAGE electrophoresis technique was developed by application of β-galactosidase as the internal standard. The method was tested first on marker protein samples of known concentrations (myosin, transferrin, glutamic dehydrogenase) and then the method was used in the determination of titin and nebulin content in chicken meat. The method demonstrated high accuracy, confirmed by correlation coefficient 0.91÷0.99. Two gel analysis techniques, i.e. scanning and densitometry were also compared. By the use of marker proteins as well as titin and nebulin, higher accuracy and precision were achieved in scanning than in the densitometric technique. Recoveries of three marker proteins were between 93 and 102% for the technique of the scanning of the gel and between 99 and 116% for the densitometry.     

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.     

Piezoelectric micromachined ultrasonic transducers based on PZT thin films

This paper describes fabrication and characterization results of piezoelectric micromachined ultrasonic transducers (pMUTs) based on 2-microm-thick Pb(Zr0.53Ti0.47O3) (PZT) thin films. The applied structures are circular plates held at four bridges, thus partially unclamped. A simple analytical model for the fully clamped structure is used as a reference to optimize design parameters such as thickness relations and electrodes, and to provide approximate predictions for coupling coefficients related to previously determined thin film properties. The best coupling coefficient was achieved with a 270-microm plate and amounted to kappa2 = 5.3%. This value compares well with the calculated value based on measured small signal dielectric (epsilon = 1050) and piezoelectric (e3l,f = 15 Cm(-2)) properties of the PZT thin film at 100 kV/cm dc bias. The resonances show relatively large Q-factors, which can be partially explained by the small diameters as compared to the sound wavelength in air and in the test liquid (Fluorinert 77). A transmit-receive experiment with two quasi-identical pMUTs was performed showing significant signal transmission up to a distance of 20 cm in air and 2 cm in the test liquid.     

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.     

Influence of forward and multiple light scatter on the measurement of beam attenuation in highly scattering marine environments

Using three-dimensional Monte Carlo radiative transfer simulations, we examine the effect of beam transmissometer geometry on the relative error in the measurement of the beam-attenuation coefficient in an aquatic environment characterized by intense light scattering, especially within submerged bubble clouds entrained by surface-wave breaking. We discuss the forward-scattering error associated with the detection of photons scattered at small angles (< 1 degrees) and the multiple-scattering error associated with the detection of photons scattered more than once along the path length of the instrument. Several scattering phase functions describing bubble clouds at different bubble void fractions in the water are considered. Owing to forward-scattering error, a beam-attenuation meter (beam transmissometer) with a half-angle of receiver acceptance of 1.0 degrees and a path length of 0.1 m can underestimate the true beam attenuation within the bubble cloud by more than 50%. For bubble clouds with a beam attenuation of as much as 100 m(-1), the multiple-scattering error is no more than a few percent. These results are compared with simulations for some example phase functions that are representative of other scattering regimes found in natural waters. The forward-scattering error for the Petzold phase function of turbid waters is 16% for a typical instrument geometry, whereas for the Henyey-Greenstein phase function with the asymmetry parameter of 0.7 and 0.9 the error range is 8-28%.     

Rose bengal-sensitized photooxidation of 2-chlorophenol in water using solar simulated light

The decomposition of 2-chlorophenol (2CP) in an aqueous solution by means of photosensitized oxidation using rose bengal has been studied. The influence of initial 2CP concentration, pH of reaction mixture and oxygen content on reaction rate has been observed. The reaction of 2CP with singlet oxygen (type II of photooxidation) appeared the most important pathway of degradation. The rate constants of singlet oxygen quenching and reaction with 2CP were determined and the rate constant of excited rose bengal quenching by 2CP was also estimated. An attempt was made to identify the main photooxidation products.     

A discrete model of a two-particle contact applied to cohesive granular materials

In this paper, we consider the complex problem of how to simulate particle contacts, taking into account the cohesion effect. In accordance with the molecular dynamics models, we propose a novel expression for the repulsive force which controls dynamically the transfer and dissipation of energy in granular media. This expression is formulated under fractional calculus, where a fractional derivative accumulates the whole history of the virtual overlap over time in weighted form. We then discuss and illustrate the basic properties of the repulsive force in a normal direction to the contacting surfaces. This approach allows us to perform simulations of arbitrary multiparticle contacts as well as granular cohesion dynamics.