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

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

Self-Regulation of Solar Coronal Heating Process via Collisionless Reconnection Condition

I propose a new paradigm for solar coronal heating viewed as a self-regulating process keeping the plasma marginally collisionless. The mechanism is based on the coupling between two effects. First, coronal density controls the plasma collisionality and hence the transition between the slow collisional Sweet-Parker and the fast collisionless reconnection regimes. In turn, coronal energy release leads to chromospheric evaporation, increasing the density and thus inhibiting subsequent reconnection of the newly-reconnected loops. As a result, statistically, the density fluctuates around some critical level, comparable to that observed in the corona. In the long run, coronal heating can be represented by repeating cycles of fast reconnection events (nano-flares), evaporation episodes, and long periods of slow magnetic stress build-up and radiative cooling of the coronal plasma.Comment: 4 pages; Phys. Rev. Lett., in pres

Particle Acceleration in Turbulence and Weakly Stochastic Reconnection

Fast particles are accelerated in astrophysical environments by a variety of processes. Acceleration in reconnection sites has attracted the attention of researchers recently. In this letter we analyze the energy distribution evolution of test particles injected in three dimensional (3D) magnetohydrodynamic (MHD) simulations of different magnetic reconnection configurations. When considering a single Sweet-Parker topology, the particles accelerate predominantly through a first-order Fermi process, as predicted in previous work (de Gouveia Dal Pino & Lazarian, 2005) and demonstrated numerically in Kowal, de Gouveia Dal Pino & Lazarian (2011). When turbulence is included within the current sheet, the acceleration rate, which depends on the reconnection rate, is highly enhanced. This is because reconnection in the presence of turbulence becomes fast and independent of resistivity (Lazarian & Vishniac, 1999; Kowal et al., 2009) and allows the formation of a thick volume filled with multiple simultaneously reconnecting magnetic fluxes. Charged particles trapped within this volume suffer several head-on scatterings with the contracting magnetic fluctuations, which significantly increase the acceleration rate and results in a first-order Fermi process. For comparison, we also tested acceleration in MHD turbulence, where particles suffer collisions with approaching and receding magnetic irregularities, resulting in a reduced acceleration rate. We argue that the dominant acceleration mechanism approaches a second order Fermi process in this case.Comment: 6 pages, 1 figur

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

Public Policies for Corporate Social Responsibility in Four Nordic Countries: Harmony of Goals and Conflict of Means

Corporate social responsibility (CSR) was historically a business-oriented idea that companies should voluntarily improve their social and environmental practices. More recently, CSR has increasingly attracted governments’ attention, and is now promoted in public policy, especially in the European Union (EU). Conflicts can arise, however, when advanced welfare states introduce CSR into public policy. The reason for such conflict is that CSR leaves key public welfare issues to the discretion of private business. This voluntary issue assignment contrasts starkly with advanced welfare states’ traditions favoring negotiated agreements and strong regulation to control corporate conduct. This article analyzes the conflicts and compatibilities arising when advanced welfare states introduce CSR, focusing on how the two traditions diverge and on how conflicts are reconciled. Empirically the study focuses on four Nordic countries—Denmark, Finland, Norway, and Sweden—widely recognized as the most advanced welfare states, and increasingly as leaders in CSR public policy. From interviews of 55 officials of government ministries, nongovernmental organizations (NGOs), labor unions, and employer associations, the authors conclude that tension indeed exists between CSR public policies and advanced welfare state traditions in all four countries. Whereas CSR’s aims are compatible with Nordic institutional traditions, the means promoted in CSR is in conflict with such Nordic traditions as corporatist agreements and rights-based welfare state regulation of social and environmental issues. There is harmony of goals, but conflict in means between the four Nordic countries studied

Media(ted) fabrications: How the science-media symbiosis helped ‘sell’ cord banking

This paper considers the problematic role of the science–media symbiosis in the dissemination of misleading and emotionally manipulative information regarding services offered by CordBank, New Zealand's only umbilical cord blood banking facility. As this case study illustrates, the growing reliance of health and science reporters on the knowledge capital of medical specialists, biogenetic researchers, and scientists potentially enhances the ability of ‘expert’ sources to set the agenda for media representations of emerging medical and scientific developments, and may undermine the editorial independence of journalists and editors, many of whom in this case failed to critically evaluate deeply problematic claims regarding the current and future benefits of cord banking. Heavy reliance on established media frames of anecdotal personalization and technoboosterism also reinforced a proscience journalistic culture in which claims by key sources were uncritically reiterated and amplified, with journalistic assessments of the value of cord banking emphasizing potential benefits for individual consumers. It is argued that use of these media frames potentially detracts from due consideration of the broader social, ethical, legal, and health implications of emerging biomedical developments, along with the professional, personal, and increasingly also financial interests at stake in their public promotion, given the growing commercialization of biogenetic technologies

Design and fabrication of a long-life Stirling cycle cooler for space application. Phase 3: Prototype model

A second-generation, Stirling-cycle cryocooler (cryogenic refrigerator) for space applications, with a cooling capacity of 5 watts at 65 K, was recently completed. The refrigerator, called the Prototype Model, was designed with a goal of 5 year life with no degradation in cooling performance. The free displacer and free piston of the refrigerator are driven directly by moving-magnet linear motors with the moving elements supported by active magnetic bearings. The use of clearance seals and the absence of outgassing material in the working volume of the refrigerator enable long-life operation with no deterioration in performance. Fiber-optic sensors detect the radial position of the shafts and provide a control signal for the magnetic bearings. The frequency, phase, stroke, and offset of the compressor and expander are controlled by signals from precision linear position sensors (LVDTs). The vibration generated by the compressor and expander is cancelled by an active counter balance which also uses a moving-magnet linear motor and magnetic bearings. The driving signal for the counter balance is derived from the compressor and expander position sensors which have wide bandwidth for suppression of harmonic vibrations. The efficiency of the three active members, which operate in a resonant mode, is enhanced by a magnetic spring in the expander and by gas springs in the compressor and counterbalance. The cooling was achieved with a total motor input power of 139 watts. The magnetic-bearing stiffness was significantly increased from the first-generation cooler to accommodate shuttle launch vibrations

Fast and slow two-fluid magnetic reconnection

We present a two-fluid magnetohydrodynamics (MHD) model of quasi-stationary, two-dimensional magnetic reconnection in an incompressible plasma composed of electrons and ions. We find two distinct regimes of slow and fast reconnection. The presence of these two regimes can provide a possible explanation for the initial slow build up and subsequent rapid release of magnetic energy frequently observed in cosmic and laboratory plasmas.Comment: 16 pages, 2 figures, 1 tabl