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Systematic Determination (systematic + determination)

Distribution by Scientific Domains

Medical Sciences	28%
Chemistry	28%

Selected Abstracts

Systematic determination of ion score cutoffs based on calculated false positive rates: application for identifying ubiquitinated proteins by tandem mass spectrometry

JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 3 2008
Julian Vasilescu
Abstract We report a simple approach for determining ion score cutoffs that permit the confident identification of ubiquitinated proteins by tandem mass spectrometry (MS/MS). Initial experiments involving the analysis of gel bands containing multi-Ubiquitin chains with quadrupole time-of-flight and quadrupole ion trap mass spectrometers revealed that standard ion score cutoffs used for database searching were not sufficiently stringent. We also found that false positive and false negative rates (FPR and FNR) varied significantly depending on the cutoff scores used and that appropriate cutoffs could only be determined following a systematic evaluation of false positive rates. When standard cutoff scores were used for the analysis of complex mixtures of ubiquitinated proteins, unacceptably high FPR were observed. Finally, we found that FPR for ubiquitinated proteins are affected by the size of the protein database that is searched. These observations may be applicable for the study of other post-translational modifications. Copyright © 2007 John Wiley & Sons, Ltd. [source]

Regulation of In Situ Skeletal Muscle Arteriolar Tone: Interactions Between Two Parameters

MICROCIRCULATION, Issue 6 2002
JEFFERSON C. FRISBEEArticle first published online: 26 JAN 2010
ABSTRACT Objective: The growing understanding of the complexity of mechanisms regulating arteriolar tone demands that a systematic determination of how these processes interact to alter diameter be undertaken. This study examined how five mediators of skeletal muscle distal arteriolar tone [adenosine concentration, oxygen content, ,-adrenergic activation (norepinephrine), intravascular pressure and wall shear rate], taken two parameters at a time, interact to regulate vessel diameter. Methods: The reactivity of distal arterioles of in situ rat cremaster muscle after alterations in each of the above mediators was assessed. In addition, arteriolar responses to all two-parameter combinations were evaluated to determine the effect of altered environment on vascular reactivity to stimuli. Results: Arteriolar dilation to adenosine was unaltered by changes in other parameters. In contrast, wall shear rate-induced arteriolar dilation was impaired by 60,88% after increases in the other parameters. Myogenic reactivity was reduced by 28% with elevated O2 and by 65% with norepinephrine (because of vessel closure) and was impaired by 89% with elevated adenosine. O2 -induced arteriolar reactivity was impaired by 56% with increased adenosine and by 44% with increased norepinephrine concentration but was largely unaffected by elevated intravascular pressure. Adrenergic reactivity was attenuated with elevated intravascular pressure (by 69%) and O2 (by 54%) because of vessel closure but was unaltered with elevated adenosine. Conclusions: These data suggest that (1) individual mediators contributing to the regulation of arteriolar tone exist within a hierarchy of importance and (2) mechanisms regulating arteriolar tone can be impacted by unidentified alterations in other processes. Ongoing investigation into interactions between multiple processes regulating arteriolar tone will allow for a more integrated understanding of how microvessels regulate their diameter. [source]

Molecular Fluorescence Excitation,Emission Matrices Relevant to Tissue Spectroscopy,

PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2003
Ralph S. DaCosta
ABSTRACT In vivo and ex vivo studies of fluorescence from endogenous and exogenous molecules in tissues and cells are common for applications such as detection or characterization of early disease. A systematic determination of the excitation,emission matrices (EEM) of known and putative endogenous fluorophores and a number of exogenous fluorescent photodynamic therapy drugs has been performed in solution. The excitation wavelength range was 250,520 nm, with fluorescence emission spectra collected in the range 260,750 nm. In addition, EEM of intact normal and adenomatous human colon tissues are presented as an example of the relationship to the EEM of constituent fluorophores and illustrating the effects of tissue chromophore absorption. As a means to make this large quantity of spectral data generally available, an interactive database has been developed. This currently includes EEM and also absorption spectra of 35 different endogenous and exogenous fluorophores and chromophores and six photosensitizing agents. It is intended to maintain and extend this database in the public domain, accessible through the Photochemistry and Photobiology website (http://www.aspjournal.com). [source]

Optical micro-characterization of group-III-nitrides: correlation of structural, electronic and optical properties

PHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 6 2003
J. Christen
Abstract For a detailed understanding of complex semiconductor heterostructures and the physics of devices based on them, a systematic determination and correlation of the structural, chemical, electronic, and optical properties on a micro- or nano-scale is essential. Luminescence techniques belong to the most sensitive, non-destructive methods of semiconductor research. The combination of luminescence spectroscopy with the high spatial resolution of a scanning electron microscope, as realized by the technique of cathodoluminescence microscopy, provides a powerful tool for the optical nano-characterization of semiconductors, their heterostructures as well as their interfaces. Additional access to the local electronic and structural properties is provided by micro-Raman spectroscopy, e.g. giving insight into the local free carrier concentration and local stress. In this paper, the properties of group-III-nitrides are investigated by highly spatially and spectrally resolved cathodoluminescence microscopy in conjunction with micro-Raman spectroscopy. Complex phenomena of self-organization and their strong impact on the microscopic and nanoscopic properties of both binary and ternary nitrides are presented. As the ultimate measure of device performance, the microscopic properties of light emitting diodes are assessed under operation. Using micro-electroluminescence mapping in the optical microscope as well as in the near field detection mode of a scanning near field optical microscope, the microscopic origin of the macroscopic spectral red shift in light emitting diodes is identified. (© 2003 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

Analysis of critical motions of floating structures

PROCEEDINGS IN APPLIED MATHEMATICS & MECHANICS, Issue 1 2006
Marc-André Pick
Validation of numerical methods for describing the motion of a ship in sea conditions by adequate experiments is a major research field in ocean engineering. For the development of a method for the systematic determination of critical and safe operational conditions and for the classification of capsize scenarios bifurcation analyses are performed. The computational effort for these analyses is enormous using a full model describing the nonlinear dynamics of a floating body. Therefore, a method for model reduction is currently being developed at the Institute of Mechanics and Ocean Engineering at TUHH. Bases for the validation of this new method are experiments conducted in the institute's wave tank. The determination of position and attitude of the body is performed with an integrated measurement system: An inertial measurement unit and a video system are combined using an extended Kalman Filter. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

Nanoparticles of [Fe(NH2 -trz)3]Br2,3,H2O (NH2 -trz=2-Amino-1,2,4-triazole) Prepared by the Reverse Micelle Technique: Influence of Particle and Coherent Domain Sizes on Spin-Crossover Properties

CHEMISTRY - A EUROPEAN JOURNAL, Issue 25 2009
Thibaut Forestier Dr.
Abstract By changing the surfactant/water ratio, nanoparticles of the iron(II) spin crossover material, [Fe(NH2 -trz)3]Br2,3,H2O (with NH2 -trz=4-amino-1,2,4-triazole), have been synthesised from 1,,m down to 30,nm (see figure). Magnetic and reflectivity experiments indicate that the critical size for observing a thermal hysteresis in this 1D polymer family is around 50,nm, and powder X-ray diffraction shows that particles of about 30,nm are constituted by about one coherent domain. This paper describes the synthesis of iron(II) spin-crossover nanoparticles prepared by the reverse micelle technique by using the non-ionic surfactant Lauropal (Ifralan D0205) from the polyoxyethylenic family. By changing the surfactant/water ratio, the size of the particles of [Fe(NH2 -trz)3]Br2,3H2O (with NH2trz=4-amino-1,2,4-triazole) can be controlled. On the macroscopic scale this complex exhibits cooperative thermal spin crossovers at 305 and 320,K. We find that when the size is reduced down to 50,nm, the spin transition becomes gradual and no hysteresis can be detected. For our data it seems that the critical size, for which the existence of a thermal hysteresis can be detected, is around 50,nm. Interestingly, the change of the particle size induces almost no change in the temperature of the thermal spin transition. A systematic determination of coherent domain size carried out on the nanoparticles by powder X-ray diffraction indicates that at approximately 30,nm individual particles consist of one coherent domain. [source]

Linking Pneumocystis jiroveci sulfamethoxazole resistance to the alleles of the DHPS gene using functional complementation in Saccharomyces cerevisiae

CLINICAL MICROBIOLOGY AND INFECTION, Issue 5 2010
R. Moukhlis
Clin Microbiol Infect 2010; 16: 501,507 Abstract Curative and prophylactic therapy for Pneumocystis jiroveci pneumonia relies mainly on cotrimoxazole, an association of trimethoprim and sulfamethoxazole (SMX). SMX inhibits the folic acid pathway through competition with para-aminobenzoic acid (pABA), one of the two substrates of the dihydropteroate synthase (DHPS), a key enzyme in de novo folic acid synthesis. The most frequent non-synonymous single nucleotide polymorphisms (SNPs) in P. jiroveci DHPS are seen at positions 165 and 171, the combination leading to four possible different genetic alleles. A number of reports correlate prophylaxis failure and mutation in the P. jiroveci DHPS but, because of the impossibility of reliably cultivating P. jiroveci, the link between DHPS mutation(s) and SMX susceptibility is not definitively proven. To circumvent this limitation, the yeast Saccharomyces cerevisiae was used as a model. The introduction of the P. jiroveci DHPS gene, with or without point mutations, directly amplified from a clinical specimen and cloned in a centromeric plasmid into a DHPS-deleted yeast strain, allowed a fully effective complementation. However, in the presence of SMX at concentrations >250 mg/L, yeasts complemented with the double mutated allele showed a lower susceptibility compared with strains complemented with either a single mutated allele or wild-type alleles. These results confirm the need for prospective study of pneumocystosis, including systematic determination of the DHPS genotype, to clarify further the impact of mutations on clinical outcome. Additionally, the S. cerevisiae model proves to be useful for the study of still uninvestigated biological properties of P. jiroveci. [source]