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

Evaluation of advanced lift concepts and potential fuel conservation for short-haul aircraft

The effect of different field lengths, cruise requirements, noise level, and engine cycle characteristics on minimizing fuel consumption and minimizing operating cost at high fuel prices were evaluated for some advanced short-haul aircraft. The conceptual aircraft were designed for 148 passengers using the upper surface-internally blown jet flap, the augmentor wing, and the mechanical flap lift systems. Advanced conceptual STOL engines were evaluated as well as a near-term turbofan and turboprop engine. Emphasis was given to designs meeting noise levels equivalent to 95-100 EPNdB at 152 m (500 ft) sideline

A snap-back free Shorted Anode Super-Junction TCIGBT

A novel structure called the Shorted-Anod e Super-Junction Trench Clustered IGBT (SA-SJ-TCIGB T) is proposed and demonstrated through numerical simulations in 1.2-k V, Field-Stop technology. This device is based on the Super-Junction Trench Clustered IGBT (SJ-TCIGBT) concept. In the S A-SJ-TCIGBT structure, due to the introduction of a segmented n + -anode, the device can operate in both forward conducting m ode and freewheeling diode mode without any snap-ba ck in the current voltage characteristics. In comparison to t he SJ-TCIGBT structure, the proposed device shows s ignificant improvement in trade-off relationship between forwa rd voltage drop and switch off energy losses. Simu lation results show that 25% decrease in switching energy losses can be achieved. Moreover, the tail current is effective ly reduced without any increase in the overshoot voltage. Detailed two dim ensional modelling of the structure shows that sign ificant amount of excess electrons are extracted through the shorted- anode structure during turn-off process

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

The SAMI Galaxy Survey: Satellite galaxies undergo little structural change during their quenching phase

At fixed stellar mass, satellite galaxies show higher passive fractions than centrals, suggesting that environment is directly quenching their star formation. Here, we investigate whether satellite quenching is accompanied by changes in stellar spin (quantified by the ratio of the rotational to dispersion velocity V/$\sigma$) for a sample of massive ($M_{*}>$10$^{10}$ M$_{\odot}$) satellite galaxies extracted from the SAMI Galaxy Survey. These systems are carefully matched to a control sample of main sequence, high $V/\sigma$ central galaxies. As expected, at fixed stellar mass and ellipticity, satellites have lower star formation rate (SFR) and spin than the control centrals. However, most of the difference is in SFR, whereas the spin decreases significantly only for satellites that have already reached the red sequence. We perform a similar analysis for galaxies in the EAGLE hydro-dynamical simulation and recover differences in both SFR and spin similar to those observed in SAMI. However, when EAGLE satellites are matched to their `true' central progenitors, the change in spin is further reduced and galaxies mainly show a decrease in SFR during their satellite phase. The difference in spin observed between satellites and centrals at $z\sim$0 is primarily due to the fact that satellites do not grow their angular momentum as fast as centrals after accreting into bigger halos, not to a reduction of $V/\sigma$ due to environmental effects. Our findings highlight the effect of progenitor bias in our understanding of galaxy transformation and they suggest that satellites undergo little structural change before and during their quenching phase.Comment: 11 pages, 7 figures. Accepted for publication in MNRA

A Model for Patchy Reconnection in Three Dimensions

We show, theoretically and via MHD simulations, how a short burst of reconnection localized in three dimensions on a one-dimensional current sheet creates a pair of reconnected flux tubes. We focus on the post-reconnection evolution of these flux tubes, studying their velocities and shapes. We find that slow-mode shocks propagate along these reconnected flux tubes, releasing magnetic energy as in steady-state Petschek reconnection. The geometry of these three-dimensional shocks, however, differs dramatically from the classical two-dimensional geometry. They propagate along the flux tube legs in four isolated fronts, whereas in the two-dimensional Petschek model, they form a continuous, stationary pair of V-shaped fronts. We find that the cross sections of these reconnected flux tubes appear as teardrop shaped bundles of flux propagating away from the reconnection site. Based on this, we argue that the descending coronal voids seen by Yohkoh SXT, LASCO, and TRACE are reconnected flux tubes descending from a flare site in the high corona, for example after a coronal mass ejection. In this model, these flux tubes would then settle into equilibrium in the low corona, forming an arcade of post-flare coronal loops.Comment: 27 pages plus 16 figure

BK channels mediate a novel ionic mechanism that regulates glucose-dependent electrical activity and insulin secretion in mouse pancreatic β-cells

BK channels are large unitary conductance K + channels cooperatively activated by intracellular calcium and membrane depolarisation. We show that BK channels regulate electrical activity in β-cells of mouse pancreatic islets exposed to elevated glucose. In 11.1 m m glucose, the non-peptidyl BK channel blocker paxilline increased the height of β-cell action potentials (APs) by 21 mV without affecting burst- or silent-period durations. In isolated β-cells, paxilline increased AP height by 16 mV without affecting resting membrane potential. In voltage clamp, paxilline blocked a transient component of outward current activated by a short depolarisation, which accounted for at least 90% of the initial outward K + current. This BK current ( I BK ) was blocked by the Ca 2+ channel blockers Cd 2+ (200 μ m ) or nimodipine (1 μ m ), and potentiated by FPL-64176 (1 μ m ). I BK was also 56% blocked by the BK channel blocker iberiotoxin (100 n m ). I BK activated more than 10-fold faster than the delayed rectifier I Kv over the physiological voltage range, and partially inactivated. An AP-like command revealed that I BK activated and deactivated faster than I Kv and accounted for 86% of peak I K , explaining why I BK block increased AP height. A higher amplitude AP-like command, patterned on an AP recorded in 11.1 m m glucose plus paxilline, activated 4-fold more I Kv and significantly increased Ca 2+ entry. Paxilline increased insulin secretion in islets exposed to 11.1 m m glucose by 67%, but did not affect basal secretion in 2.8 m m glucose. These data suggest a modified model of β-cell AP generation where I BK and I Kv coordinate the AP repolarisation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/79246/1/jphysiol.2009.184341.pd

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

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