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

Fast magnetic reconnection in the plasmoid-dominated regime

A conceptual model of resistive magnetic reconnection via a stochastic plasmoid chain is proposed. The global reconnection rate is shown to be independent of the Lundquist number. The distribution of fluxes in the plasmoids is shown to be an inverse square law. It is argued that there is a finite probability of emergence of abnormally large plasmoids, which can disrupt the chain (and may be responsible for observable large abrupt events in solar flares and sawtooth crashes). A criterion for the transition from magnetohydrodynamic to collisionless regime is provided.Comment: 4 pages, 1 figur

On the penetration of meridional circulation below the solar convection zone

Meridional flows with velocities of a few meters per second are observed in the uppermost regions of the solar convection zone. The amplitude and pattern of the flows deeper in the solar interior, in particular near the top of the radiative region, are of crucial importance to a wide range of solar magnetohydrodynamical processes. In this paper, we provide a systematic study of the penetration of large-scale meridional flows from the convection zone into the radiative zone. In particular, we study the effects of the assumed boundary conditions applied at the convective-radiative interface on the deeper flows. Using simplified analytical models in conjunction with more complete numerical methods, we show that penetration of the convectively-driven meridional flows into the deeper interior is not necessarily limited to a shallow Ekman depth but can penetrate much deeper, depending on how the convective-radiative interface flows are modeled.Comment: 13 pages, 5 figures. Subitted to 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

Magnetic Reconnection with Radiative Cooling. I. Optically-Thin Regime

Magnetic reconnection, a fundamental plasma process associated with a rapid dissipation of magnetic energy, is believed to power many disruptive phenomena in laboratory plasma devices, the Earth magnetosphere, and the solar corona. Traditional reconnection research, geared towards these rather tenuous environments, has justifiably ignored the effects of radiation on the reconnection process. However, in many reconnecting systems in high-energy astrophysics (e.g., accretion-disk coronae, relativistic jets, magnetar flares) and, potentially, in powerful laser plasma and z-pinch experiments, the energy density is so high that radiation, in particular radiative cooling, may start to play an important role. This observation motivates the development of a theory of high-energy-density radiative magnetic reconnection. As a first step towards this goal, we present in this paper a simple Sweet--Parker-like theory of non-relativistic resistive-MHD reconnection with strong radiative cooling. First, we show how, in the absence of a guide magnetic field, intense cooling leads to a strong compression of the plasma in the reconnection layer, resulting in a higher reconnection rate. The compression ratio and the layer temperature are determined by the balance between ohmic heating and radiative cooling. The lower temperature in the radiatively-cooled layer leads to a higher Spitzer resistivity and hence to an extra enhancement of the reconnection rate. We then apply our general theory to several specific astrophysically important radiative processes (bremsstrahlung, cyclotron, and inverse-Compton) in the optically thin regime, for both the zero- and strong-guide-field cases. We derive specific expressions for key reconnection parameters, including the reconnection rate. We also discuss the limitations and conditions for applicability of our theory.Comment: 31 pages, 1 figur

Web-based phosphine fumigation monitoring with active sensor validation confirms lethality in stored grains: Presentation

The predominant measurement technologies for fumigation gases over the past 60 years include colorimetric tubes, photoionization detectors, and electrochemical sensors. Their limitations and inaccuracies are well documented. Spectros Instruments has shown non-dispersive infrared monitoring (NDIR) to be a superior analytical tool for the practical measurement of fumigation gases as shown in Table 1. Any compliant fumigation monitor must be accurate, reliable and affordable. Stored Product Protection has additional requirements in remote regions such as Central China and Western Australia. In these cases, the value of real time access via the internet to fumigation data collected with NDIR Technology from a remote location adds heretofore unknown benefits. Allocation of manpower and materials resources are optimized by access to information about fumigant gas levels in grain storages via the internet. Data is automatically transferred to a central database that can be accessed in real-time from any location with internet access. Intelligent monitors with built-in diagnostics tracking barometric pressure, temperature, sample flows and detector voltages are described. This data collection, data warehousing and reporting platform maintains measurement traceability to certified compliance with secure, encrypted electronic notebook format. Knowing REAL phosphine concentrations allows informed decisions to be made to achieve required CxT and avoid situations leading to target pest phosphine resistance.The predominant measurement technologies for fumigation gases over the past 60 years include colorimetric tubes, photoionization detectors, and electrochemical sensors. Their limitations and inaccuracies are well documented. Spectros Instruments has shown non-dispersive infrared monitoring (NDIR) to be a superior analytical tool for the practical measurement of fumigation gases as shown in Table 1. Any compliant fumigation monitor must be accurate, reliable and affordable. Stored Product Protection has additional requirements in remote regions such as Central China and Western Australia. In these cases, the value of real time access via the internet to fumigation data collected with NDIR Technology from a remote location adds heretofore unknown benefits. Allocation of manpower and materials resources are optimized by access to information about fumigant gas levels in grain storages via the internet. Data is automatically transferred to a central database that can be accessed in real-time from any location with internet access. Intelligent monitors with built-in diagnostics tracking barometric pressure, temperature, sample flows and detector voltages are described. This data collection, data warehousing and reporting platform maintains measurement traceability to certified compliance with secure, encrypted electronic notebook format. Knowing REAL phosphine concentrations allows informed decisions to be made to achieve required CxT and avoid situations leading to target pest phosphine resistance

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

X-point collapse and saturation in the nonlinear tearing mode reconnection

We study the nonlinear evolution of the resistive tearing mode in slab geometry in two dimensions. We show that, in the strongly driven regime (large Delta'), a collapse of the X-point occurs once the island width exceeds a certain critical value ~1/Delta'. A current sheet is formed and the reconnection is exponential in time with a growth rate ~eta^1/2, where eta is the resistivity. If the aspect ratio of the current sheet is sufficiently large, the sheet can itself become tearing-mode unstable, giving rise to secondary islands, which then coalesce with the original island. The saturated state depends on the value of Delta'. For small Delta', the saturation amplitude is ~Delta' and quantitatively agrees with the theoretical prediction. If Delta' is large enough for the X-point collapse to have occured, the saturation amplitude increases noticeably and becomes independent of Delta'.Comment: revtex4, 4 pages, 18 figure

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