Trapped electron mode turbulence driven intrinsic rotation in Tokamak plasmas

Progress from global gyrokinetic simulations in understanding the origin of intrinsic rotation in toroidal plasmas is reported. The turbulence-driven intrinsic torque associated with nonlinear residual stress generation due to zonal flow shear induced asymmetry in the parallel wave number spectrum is shown to scale close to linearly with plasma gradients and the inverse of the plasma current, qualitatively reproducing experimental empirical scalings of intrinsic rotation. The origin of current scaling is found to be enhanced k(∥) symmetry breaking induced by the increased radial variation of the safety factor as the current decreases. The intrinsic torque is proportional to the pressure gradient because both turbulence intensity and zonal flow shear, which are two key ingredients for driving residual stress, increase with turbulence drive, which is R/L(T(e)) and R/L(n(e)) for the trapped electron mode.     

Application of reversed phase high performance liquid chromatography to the analysis of sulphidopeptide leukotrienes in pig bile

Reversed phase HPLC methodology has been developed for separation of peptide leukotrienes and indomethacin in porcine bile. Reproducible recoveries were obtained using radioactive leukotrienes ([3H]LTC4, 57.1 +/- 2.5%; [3H]LTE4, 62.7 +/- 1.9%; [3H]LTD4, 54.3 +/- 2.7%). Radioimmunoassay of column eluant demonstrated that as little as 300 pg of exogenous leukotrienes could be measured in bile fluids, with similar recoveries. Analysis of bile sampled 60-90 min after initiation of experimental endotoxic shock in indomethacin treated pigs revealed a leukotriene concentration of 5.24 +/- 1.16 ng/mL(LTD4). This was significantly greater (p less than 0.05, n = 3) than that observed in samples collected prior to endotoxin (0.42 +/- 0.23 ng/mL), or from untreated animals (0.85 +/- 0.51 ng/mL). This method is thus applicable to investigation of the role of 5-lipoxygenase products in porcine models of human disease, including shock conditions such as endotoxaemia, during cyclooxygenase inhibition by indomethacin.     

Drag Force Calculations in Polydisperse DEM Simulations with the Coarse-Grid Method: Influence of the Weighting Method and Improved Predictions Through Artificial Neural Networks

Transport in Porous Media - Several methods are employed for drag force calculations with the discrete element method depending on the desired accuracy and the number of particles involved. For...     

BIO-Fully Automated Sample Treatment high-performance liquid chromatography and radioimmunoassay for leukotriene E4 in human urine from asthmatics

BIO-Fully Automated Sample Treatment (BIO-FAST) high-performance liquid chromatography (HPLC) is a sophisticated column-switching technique in which a fresh pre-column is used for each sample prior to reversed-phase HPLC. The pre-columns, Varian Advanced Automated Sample Processor (AASP) cartridges, are held and automatically advanced by the Varian AASP. A rapid and efficient extraction and separation for leukotrienes C4 and E4 from human urine has been developed using a C8 cartridge and subsequent C18 analytical HPLC column. Quantitation of leukotriene E4, accomplished by post-column radioimmunoassay, shows significantly increased leukotriene E4 concentrations in urine samples from asthmatics after antigen challenge. This further confirms an active role for leukotrienes in the pathogenesis of bronchial asthma.     

Sets of orthogonal hypercubes of class r

A (d,n,r,t)-hypercube is an n×n×?×n (d-times) array on nr symbols such that when fixing t coordinates of the hypercube (and running across the remaining d−t coordinates) each symbol is repeated nd−r−t times. We introduce a new parameter, r, representing the class of the hypercube. When r=1, this provides the usual definition of a hypercube and when d=2 and r=t=1 these hypercubes are Latin squares. If d?2r, then the notion of orthogonality is also inherited from the usual definition of hypercubes. This work deals with constructions of class r hypercubes and presents bounds on the number of mutually orthogonal class r hypercubes. We also give constructions of sets of mutually orthogonal hypercubes when n is a prime power.     

Global and site-specific detection of human integrin alpha 5 beta 1 glycosylation using tandem mass spectrometry and the StrOligo algorithm

Glycans are oligosaccharides associated with proteins, and are known to confer specific functions and conformations on glycoproteins. As protein tridimensional structures are related to function, the study of glycans and their impact on protein folding can provide important information to the field of proteomics. The subdiscipline of glycomics (or glycoproteomics) is rapidly growing in importance as glycans in proteins have shown to be involved in protein-protein or protein-(drug, virus, antibody) interactions. Glycomics studies most often aim at identifying glycosylation sites, and thus are performed on deglycosylated proteins resulting in loss of site-specific details concerning the glycosylation. In order to obtain such details by mass spectrometry (MS), either whole glycoproteins must be digested and analyzed as mixtures of peptides and glycopeptides, or glycans must be isolated from glycopeptide fractions and analyzed as pools. This article describes parallel experiments involving both approaches, designed to take advantage of the StrOligo algorithm functionalities with the aim of characterizing glycosylation microheterogeneity on a specific site. A hybrid quadrupole-quadrupole-time-of-flight (QqTOF) instrument equipped with a matrix-assisted laser desorption/ionization (MALDI) source was used. Glycosylation of alpha 5 beta 1 subunits of human integrin was studied to test the methodology. The sample was divided in two aliquots, and glycans from the first aliquot were released enzymatically, labelled with 2-aminobenzamide, and identified using tandem mass spectrometry (MS/MS) and the StrOligo program. The other aliquot was digested with trypsin and the resulting peptides separated by reversed-phase high-performance liquid chromatography (HPLC). A specific collected fraction was then analyzed by MS before and after glycan release. These spectra allowed, by comparison, detection of a glycopeptide (several glycoforms) and elucidation of peptide sequence. Compositions of glycans present were proposed, and identification of possible glycan structures was conducted using MS/MS and StrOligo.     

Analysis of protein interaction networks using mass spectrometry compatible techniques

The ability to map protein-protein interactions has grown tremendously over the last few years, making it possible to envision the mapping of whole or targeted protein interaction networks and to elucidate their temporal dynamics. The use of mass spectrometry for the study of protein complexes has proven to be an invaluable tool due to its ability to unambiguously identify proteins from a variety of biological samples. Furthermore, when affinity purification is combined with mass spectrometry analysis, the identification of multimeric protein complexes is greatly facilitated. Here, we review recent developments for the analysis of protein interaction networks by mass spectrometry and discuss the integration of different bioinformatic tools for predicting, validating, and managing interaction datasets.