Statistical model for large-scale peptide identification in databases from tandem mass spectra using SEQUEST

Recent technological advances have made multidimensional peptide separation techniques coupled with tandem mass spectrometry the method of choice for high-throughput identification of proteins. Due to these advances, the development of software tools for large-scale, fully automated, unambiguous peptide identification is highly necessary. In this work, we have used as a model the nuclear proteome from Jurkat cells and present a processing algorithm that allows accurate predictions of random matching distributions, based on the two SEQUEST scores Xcorr and DeltaCn. Our method permits a very simple and precise calculation of the probabilities associated with individual peptide assignments, as well as of the false discovery rate among the peptides identified in any experiment. A further mathematical analysis demonstrates that the score distributions are highly dependent on database size and precursor mass window and suggests that the probability associated with SEQUEST scores depends on the number of candidate peptide sequences available for the search. Our results highlight the importance of adjusting the filtering criteria to discriminate between correct and incorrect peptide sequences according to the circumstances of each particular experiment.     

Second-order advantage achieved with four-way fluorescence excitation-emission-kinetic data processed by parallel factor analysis and trilinear least-squares. Determination of methotrexate and leucovorin in human urine

Four-way fluorescence data recorded by following the kinetic evolution of excitation-emission fluorescence matrices (EEMs) have been analyzed by parallel factor analysis and trilinear least-squares algorithms. These methodologies exploit the second-order advantage of the studied data, allowing analyte concentrations to be estimated even in the presence of an uncalibrated fluorescent background. They were applied to the simultaneous determination of the components of the anticancer combination of methotrexate and leucovorin in human urine samples. Both analytes were converted into highly fluorescent compounds by oxidation with potassium permanganate, and the kinetics of the reaction was continuously monitored by recording full EEM of the samples at different reaction times. A commercial fast scanning spectrofluorometer has been used for the first time to measure the four-way EEM kinetic data. The rapid scanning instrument allows the acquisition of a complete EEM in 12 s at a wavelength scanning speed of 24 000 nm/min. The emission spectra were recorded from 335 to 490 nm at 5-nm intervals, exciting from 255 to 315 nm at 6-nm intervals. Ten successive EEMs were measured at 72-s intervals, to follow the fluorescence kinetic evolution of the mixture components. Good recoveries were obtained in synthetic binary samples and also in spiked urine samples. The excitation, emission, and kinetic time profiles recovered by both chemometric techniques are in good agreement with experimental observations.     

Dual holographic interferometry for measuring the three velocity components in a fluid plane

A technique that allows one to measure simultaneously the three velocity components in a fluid plane is presented. One obtains the quantitative information from only one holographic recording by combining two different reconstruction processes. As both processes use an interferometric comparison of two waves, we refer to this technique as dual holographic interferometry. The far-field fringe pattern that is obtained when reconstruction is made with an expanded laser beam allows one to determine the in-plane velocity components. The image-field fringe pattern that is obtained when a pointwise laser beam is used for reconstruction contains information about an out-of-plane velocity component. As the two reconstruction processes have different sensitivities, two different ways to combine them are proposed. The system has been demonstrated in a fluidlike solid object and in a convective flow.     

A computational tool based on voxel geometry for dose reconstruction of a radiological accident due to external exposure

In the case of overexposure to ionising radiation, estimation of the absorbed dose in the organism is an important indicator for evaluating the biological consequences of this exposure. The physical dosimetry approach is based either on real reconstruction of the accident, using physical phantoms, or on calculation techniques. Tools using Monte Carlo simulations associated with geometric models are very powerful since they offer the possibility to simulate faithfully the victim and the environment for dose calculations in various accidental situations. Their work presents a new computational tool, called SESAME, dedicated to dose reconstruction of radiological accidents based on anthropomorphic voxel phantoms built from real medical images of the victim in association with the MCNP Monte Carlo code. The utility was, as a first step, validated for neutrons by experimental means using a physical tissue-equivalent phantom.     

Statistical thermodynamic analysis and designof DNA-based computers

A principal research area in biomolecular computing is the development of analytical methods for evaluating computational fidelity and efficiency. In this work, the equilibrium theory of the DNA helix-coil transition is reviewed and expanded, as applied to the analysis and design of oligonucleotide-based computers. After a review of the equilibrium apparatus for modeling the helix-coil transition for single dsDNA species, application to complex hybridizing systems is discussed, via decomposition into component equilibria, which are presumed to proceed independently. The alternative approach, which involves estimation of a mean error probability per hybridized structure, or computational incoherence, is then presented, along with a discussion of a special-case exact solution (directed dimer formation), and an approximate general solution, applicable to conditions of uniform fractional-saturation. In order to clarify the opposing nature of the predictions of these two models, simulations are presented for the uniform saturation solution for , as applied to a small Tag–Antitag (TAT) system, along with the behavior expected via isolated melting curves. By a comparison with the predictions of a recent, TAT-specific solution for , the views provided by these generalized approximate models are shown to define the opposing limits of a more general error-response.     

Halasz syndrome revealed in the newborn infant by pulmonary arterial hypertension. Study of 4 cases

In the 4 studied patients presenting with an Halasz's syndrome, the disease was complicated since the neonatal period by pulmonary arterial hypertension and heart failure. Three out of the 4 infants rapidly died, one after pneumonectomy. The fourth is surviving and benefitted solely from medical cardiotonic treatment. The pathogenesis of early pulmonary arterial hypertension in Halasz's syndrome is complex. The possibly associated cardiac malformations, the persistance of fetal obstructive hypertension due to the increase of the flow in the left pulmonary artery, the left to right shunt induced by the abnormal venous return and predominantly by the systemic blood supply to the right lung, are responsible, at various degrees, for pulmonary hypertension. Among surgical procedures to be proposed, the simple ligation of abnormal arteries which take their origin from the aorta seems to be preferable to pneumonectomy.     

Investigation of a metal-ionic conductor interface in thin film samples using X-ray photoelectron spectroscopy and electrical measurements

The surface of an evaporated thin film of the ionic conductor β-PbF₂ was analysed using X-ray photoelectron spectroscopy (XPS). The results were compared with those obtained from nuclear and secondary ion mass spectrometry measurements. An analysis of the Au-β-PbF₂ interface shows the presence of a thin layer of partly oxidized metallic lead. Part of this interfacial lead diffused across the gold film towards the external surface where it became bound to oxygen. An electrical analysis of the interface was performed by studying the capacitance as a function of the surface potential. The differences between experimental and calculated values are discussed in the light of the XPS measurements.     

Interactions between a bitumen,its components and model fillers

The interactions between bitumen, or its components, and (especially) silicas have been studied using solution adsorption techniques. Bitumen dissolved in carbon disulphide or carbon tetrachloride forms multilayers on the solid surfaces. It is shown that the reactive part of the bitumen is the asphaltene which forms, by chemisorption on the silanol groups of the silica, a monolayer having a thickness which compares fairly well with the published dimensions of the asphaltene molecules. Adsorption of the asphaltenes onto other pigments demonstrates the specificity of the interaction.