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.     

Synthesis of an Al-ZrO2 composite by infiltration of Zr-chelates into an Al matrix

Aluminium-based matrix composites were prepared by infiltration with an ammoniacal zirconium chelate within an Al matrix synthesized via Aluminium powder compactation. After infiltration, this chelate can be transformed in situ by sol-gel method that leads to tetragonal phases in zirconia, which in turn, transforms to monoclinic structure on heating. Based on Differential Thermal Analysis (DTA), Fourier Transformed Infrared (FTIR), X-Ray Diffraction (XRD), and Scanning Electron Microscopy (SEM), we confirm the reaction sequence to obtain the tetramer, the phase transformation sequence within the Al matrix, and the development of phases that leads to the synthesis of the Al-ZrO₂ composite.     

Magnetometry of Individual Polycrystalline Ferromagnetic Nanowires

Ferromagnetic nanowires are finding use as untethered sensors and actuators for probing micro‐ and nanoscale biophysical phenomena, such as for localized sensing and application of forces and torques on biological samples, for tissue heating through magnetic hyperthermia, and for microrheology. Quantifying the magnetic properties of individual isolated nanowires is crucial for such applications. Dynamic cantilever magnetometry is used to measure the magnetic properties of individual sub‐500 nm diameter polycrystalline nanowires of Ni and Ni₈₀Co₂₀ fabricated by template‐assisted electrochemical deposition. The values are compared with bulk, ensemble measurements when the nanowires are still embedded within their growth matrix. It is found that single‐particle and ensemble measurements of nanowires yield significantly different results that reflect inter‐nanowire interactions and chemical modifications of the sample during the release process from the growth matrix. The results highlight the importance of performing single‐particle characterization for objects that will be used as individual magnetic nanoactuators or nanosensors in biomedical applications.     

In situ developed laminates with large microstructural differences between layers of similar composition

Fabrication of alumina-aluminium titanate laminates that combine high strength external layers with flaw tolerant internal layers is limited by the difficulty of the co-sintering of layers with large differences in the green state. This work describes a new method to obtain alumina-aluminium titanate layered materials constituted by layers with large differences in terms of grain size starting from green bodies with similar microstructures. The approach is based on the effect of small amounts of titania (TiO₂) as agents for alumina grain growth enhancement. Starting from a fine grained green body that combined alumina layers with composite layers made of mixtures of alumina and titania, a two step sintering schedule led to a layered structure with external layers of small grain sized alumina combined with internal alumina layers with large grain size due to the diffusion of titanium. The large grain sized alumina layers conferred flaw tolerant behaviour to the laminate due to crack branching and bridging.     

Effect-Size Indices for Dichotomized Outcomes in Meta-Analysis.

It is very common to find meta-analyses in which some of the studies compare 2 groups on continuous dependent variables and others compare groups on dichotomized variables. Integrating all of them in a meta-analysis requires an effect-size index in the same metric that can be applied to both types of outcomes. In this article, the performance in terms of bias and sampling variance of 7 different effect-size indices for estimating the population standardized mean difference from a 2 × 2 table is examined by Monte Carlo simulation, assuming normal and nonnormal distributions. The results show good performance for 2 indices, one based on the probit transformation and the other based on the logistic distribution. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Metal-Coated <100>-Cut GaAs Coupled to Tapered Parallel-Plate Waveguide for Cherenkov-Phase-Matched Terahertz Detection: Influence of Crystal Thickness

The influence of crystal thickness of metal-coated <100>-cut GaAs (M-G-M) on Cherenkov-phase-matched terahertz (THz) pulse detection was studied. The M-G-M detectors were utilized in conjunction with a metallic tapered parallel-plate waveguide (TPPWG). Polarization-sensitive measurements were carried out to exemplify the efficacy of GaAs in detecting transverse magnetic (TM)- and transverse electric (TE)-polarized THz waves. The reduction of GaAs’ thickness increased the THz amplitude spectra of the detected TM-polarized THz electro-optic (EO) signal due to enhanced electric field associated with a more tightly-focused and well-concentrated THz radiation on the thinner M-G-M. The higher-fluence THz beam coupled to the thinner M-G-M improved the integrated intensity of the detected THz amplitude spectrum. This trend was not observed for TE-polarized THz waves, wherein the integrated intensities were almost comparable. Nevertheless, good agreement of spectral line shapes of the superposed TM- and TE-polarized THz-EO signals with that of elliptically polarized THz-EO signal demonstrates excellent polarization-resolved detection capabilities of M-G-M via Cherenkov-phase-matched EO sampling technique.     

An open-source library for the numerical modeling of mass-transfer in solid oxide fuel cells

The generation of direct current electricity using solid oxide fuel cells (SOFCs) involves several interplaying transport phenomena. Their simulation is crucial for the design and optimization of reliable and competitive equipment, and for the eventual market deployment of this technology. An open-source library for the computational modeling of mass-transport phenomena in SOFCs is presented in this article. It includes several multicomponent mass-transport models (i.e. Fickian, Stefan–Maxwell and Dusty Gas Model), which can be applied both within porous media and in porosity-free domains, and several diffusivity models for gases. The library has been developed for its use with OpenFOAM^®, a widespread open-source code for fluid and continuum mechanics. The library can be used to model any fluid flow configuration involving multicomponent transport phenomena and it is validated in this paper against the analytical solution of one-dimensional test cases. In addition, it is applied for the simulation of a real SOFC and further validated using experimental data.Program summaryProgram title: multiSpeciesTransportModelsCatalogue identifier: AEKB_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEKB_v1_0.htmlProgram obtainable from: CPC Program Library, Queen?s University, Belfast, N. IrelandLicensing provisions: GNU General Public LicenseNo. of lines in distributed program, including test data, etc.: 18 140No. of bytes in distributed program, including test data, etc.: 64 285Distribution format: tar.gzProgramming language:: C++Computer: Any x86 (the instructions reported in the paper consider only the 64 bit case for the sake of simplicity)Operating system: Generic Linux (the instructions reported in the paper consider only the open-source Ubuntu distribution for the sake of simplicity)Classification: 12External routines: OpenFOAM® (version 1.6-ext) (http://www.extend-project.de)Nature of problem: This software provides a library of models for the simulation of the steady state mass and momentum transport in a multi-species gas mixture, possibly in a porous medium. The software is particularly designed to be used as the mass-transport library for the modeling of solid oxide fuel cells (SOFC). When supplemented with other sub-models, such as thermal and charge-transport ones, it allows the prediction of the cell polarization curve and hence the cell performance.Solution method: Standard finite volume method (FVM) is used for solving all the conservation equations. The pressure-velocity coupling is solved using the SIMPLE algorithm (possibly adding a porous drag term if required). The mass transport can be calculated using different alternative models, namely Fick, Maxwell–Stefan or dusty gas model. The code adopts a segregated method to solve the resulting linear system of equations. The different regions of the SOFC, namely gas channels, electrodes and electrolyte, are solved independently, and coupled through boundary conditions.Restrictions: When extremely large species fluxes are considered, current implementation of the Neumann and Robin boundary conditions do not avoid negative values of molar and/or mass fractions, which finally end up with numerical instability. However this never happened in the documented runs. Eventually these boundary conditions could be reformulated to become more robust.Running time: From seconds to hours depending on the mesh size and number of species. For example, on a 64 bit machine with Intel Core Duo T8300 and 3 GBytes of RAM, the provided test run requires less than 1 second.     

Chemical Characterization of Virgin Almond and Hazelnut Oils and Their By‐Products

Various cultivars of almonds (“Ferragnes,” “Guara,” “Largueta,” and “Marcona”) and hazelnuts (“Negret,” “Pauetet,” and “Tonda”), particularly their virgin oils and by‐products, are evaluated in this study. The almond and hazelnut virgin oils present high contents of oleic acid (59–73% and 76–80%, respectively) and α‐tocopherol (420–542 and 310–378 mg kg^–1, respectively), as compared with other virgin vegetable oils. Aldehydes are the major contributors to their aromatic profile (54–74% almond oil and 30–40% hazelnut oil of total content), especially, benzaldehyde in almond oils (1.35–7.52 mg kg^–1), and hexanal in hazelnut oils (0.99–1.27 mg kg^–1). Statistical differences exist between the virgin almond and hazelnut oils and their varieties, for most of the chemical compounds studied. While all the nut varieties are high in polar phenolic compounds, “Ferragnes” almonds (1262 mg kg^–1) and “Negret” hazelnuts (1720 mg kg^–1) stand out. Accordingly, high antioxidant activity is also observed. Finally, the residual cakes may be considered a good source of polar phenolic compounds (823–2064 mg kg^–1 almond cakes, 2261–4179 mg kg^–1 hazelnut cakes), possessing high antioxidant capacity with potential applications of these by‐products as functional ingredients in food and non‐food formulations. Practical Applications: Virgin nut oils are gaining consumers’ preference due to their unique organoleptic attributes and potential health effects. It is therefore very relevant to establish their specific chemical composition, directly related to their properties, and that are greatly affected by the cultivar.