Database Search Strategies for Proteomic Data Sets Generated by Electron Capture Dissociation Mass Spectrometry

Large data sets of electron capture dissociation (ECD) mass spectra from proteomic experiments are rich in information; however, extracting that information in an optimal manner is not straightforward. Protein database search engines currently available are designed for low resolution CID data, from which Fourier transform ion cyclotron resonance (FT-ICR) ECD data differs significantly. ECD mass spectra contain both z-prime and z-dot fragment ions (and c-prime and c-dot); ECD mass spectra contain abundant peaks derived from neutral losses from charge-reduced precursor ions; FT-ICR ECD spectra are acquired with a larger precursor m/z isolation window than their low-resolution CID counterparts. Here, we consider three distinct stages of postacquisition analysis: (1) processing of ECD mass spectra prior to the database search; (2) the database search step itself and (3) postsearch processing of results. We demonstrate that each of these steps has an effect on the number of peptides identified, with the postsearch processing of results having the largest effect. We compare two commonly used search engines: Mascot and OMSSA. Using an ECD data set of modest size (3341 mass spectra) from a complex sample (mouse whole cell lysate), we demonstrate that search results can be improved from 630 identifications (19% identification success rate) to 1643 identifications (49% identification success rate). We focus in particular on improving identification rates for doubly charged precursors, which are typically low for ECD fragmentation. We compare our presearch processing algorithm with a similar algorithm recently developed for electron transfer dissociation (ETD) data

2MASS J06164006-6407194: The First Outer Halo L Subdwarf

We present the serendipitous discovery of an L subdwarf, 2MASS J06164006-6407194, in a search of the Two Micron All Sky Survey for T dwarfs. Its spectrum exhibits features indicative of both a cool and metal poor atmosphere including a heavily pressured-broadened K I resonant doublet, Cs I and Rb I lines, molecular bands of CaH, TiO, CrH, FeH, and H2O, and enhanced collision induced absorption of H2. We assign 2MASS 0616-6407 a spectral type of sdL5 based on a comparison of its red optical spectrum to that of near solar-metallicity L dwarfs. Its high proper motion (mu =1.405+-0.008 arcsec yr-1), large radial velocity (Vrad = 454+-15 km s-1), estimated uvw velocities (94, -573, 125) km s-1 and Galactic orbit with an apogalacticon at ~29 kpc are indicative of membership in the outer halo making 2MASS 0616-6407 the first ultracool member of this population.Comment: Accepted for publication in Ap

Two-scale structure of the electron dissipation region during collisionless magnetic reconnection

Particle in cell (PIC) simulations of collisionless magnetic reconnection are presented that demonstrate that the electron dissipation region develops a distinct two-scale structure along the outflow direction. The length of the electron current layer is found to decrease with decreasing electron mass, approaching the ion inertial length for a proton-electron plasma. A surprise, however, is that the electrons form a high-velocity outflow jet that remains decoupled from the magnetic field and extends large distances downstream from the x-line. The rate of reconnection remains fast in very large systems, independent of boundary conditions and the mass of electrons.Comment: Submitted to Physical Review Letters, 4 pages, 4 figure

On the exceptional damage-tolerance of gradient metallic materials

An experimental study is described on the fracture toughness and micro-mechanisms associated with the initiation and propagation of cracks in metallic nickel containing marked gradients in grain size, ranging from ∼30 nm to ∼4 μm. Specifically, cracks are grown in a gradient structured (GS) nickel with grain-size gradient ranging from the coarse macro-scale to nano-scale (CG → NG) and vice versa (NG → CG), with the measured crack-resistance R-curves compared to the corresponding behavior in uniform nano-grained (NG) and coarse-grained (CG) materials. It is found that the gradient structures display a much-improved combination of high strength and toughness compared to uniform grain-sized materials. However, based on J-integral measurements in the gradient materials, the crack-initiation toughness is far higher for cracks grown in the direction of the coarse-to-nano grained gradient than vice versa, a result which we ascribe primarily to excessive crack-tip blunting in the coarse-grained microstructure. Both gradient structures, however, display marked rising R-curve behavior with exceptional crack-growth toughnesses exceeding 200 MPa.m½

Reuse as heuristic : from transmission to nurture in learning activity design

In recent years a combination of ever more flexible and sophisticated Web technologies and an explosion in the quantity of online content has sparked learning technologists around the world to pursue the promise of the 'reusable learning object' or RLO with the idea that RLOs could be reused in different educational contexts, thereby providing greater overall flexibility and return on investment. In 2002 the ACETS Project undertook a three-year study in the UK to investigate whether RLOs worked in practice and how the pursuit of reuse affected the teacher and their teaching. Teachers working in healthcare-related subjects in Higher and Further Education were asked to create an original learning design or activity from third-party digital resources and to reflect both on the process and its outcomes. The expectation was that teachers would be the ones selecting and reusing third-party materials. This paper describes how one of the ACETS exemplifiers reinterpreted this remit, challenged the anticipated transmissive model of learning, and instead, gave their students an opportunity to create their own original learning designs and learning activities from third-party digital resources. By describing the educational enhancements, the resulting heightened levels of critical thinking, and sensitivity to patient needs, 'reuse' will be shown to be an effective heuristic for student self-direction and professional development

Scanning a photonic crystal slab nanocavity by condensation of xenon

Allowing xenon or nitrogen gas to condense onto a photonic crystal slab nanocavity maintained at 10–20 K results in shifts of the nanocavity mode wavelength by as much as 5 nm (~=4 meV). This occurs in spite of the fact that the mode defect is achieved by omitting three holes to form the spacer. This technique should be useful in changing the detuning between a single quantum dot transition and the nanocavity mode for cavity quantum electrodynamics experiments, such as mapping out a strong coupling anticrossing curve. Compared with temperature scanning, it has a much larger scan range and avoids phonon broadening

Rhetoric in the language of real estate marketing

“Des. Res.”, “rarely available”, “viewing essential” – these are all part of the peculiar parlance of housing advertisements which contain a heady mix of euphemism, hyperbole and superlative. Of interest is whether the selling agent’s penchant for rhetoric is spatially uniform or whether there are variations across the urban system. We are also interested in how the use of superlatives varies over the market cycle and over the selling season. For example, are estate agents more inclined to use hyperbole when the market is buoyant or when it is flat, and does it matter whether a house is marketed in the summer or winter? This paper attempts to answer these questions by applying textual analysis to a unique dataset of 49,926 records of real estate transactions in the Strathclyde conurbation over the period 1999 to 2006. The analysis opens up a new avenue of research into the use of real estate rhetoric and its interaction with agency behaviour and market dynamics