Peptide mass fingerprinting using field-programmable gate arrays

The reconfigurable computing paradigm, which exploits the flexibility and versatility of field-programmable gate arrays (FPGAs), has emerged as a powerful solution for speeding up time-critical algorithms. This paper describes a reconfigurable computing solution for processing raw mass spectrometric data generated by MALDI-TOF instruments. The hardware-implemented algorithms for denoising, baseline correction, peak identification, and deisotoping, running on a Xilinx Virtex-2 FPGA at 180 MHz, generate a mass fingerprint that is over 100 times faster than an equivalent algorithm written in C, running on a Dual 3-GHz Xeon server. The results obtained using the FPGA implementation are virtually identical to those generated by a commercial software package MassLynx

Inside loops: Developmental premises of self-ascriptions

Self-ascriptions of thoughts and attitudes depend on a sense of the intentionality of one's own mental states, which develops later than, and independently of, the sense of the intentionality of the thoughts and attitudes of others. This sense of the self-intentionality of one's own mental states grows initially out of executive developments that enable one to simulate one's own actions and perceptions, as genuine off-line thoughts, and to regulate such simulations. © 2007 Springer Science+Business Media B.V

Three Dimensional MHD Wave Propagation and Conversion to Alfven Waves near the Solar Surface. I. Direct Numerical Solution

The efficacy of fast/slow MHD mode conversion in the surface layers of sunspots has been demonstrated over recent years using a number of modelling techniques, including ray theory, perturbation theory, differential eigensystem analysis, and direct numerical simulation. These show that significant energy may be transferred between the fast and slow modes in the neighbourhood of the equipartition layer where the Alfven and sound speeds coincide. However, most of the models so far have been two dimensional. In three dimensions the Alfven wave may couple to the magneto-acoustic waves with important implications for energy loss from helioseismic modes and for oscillations in the atmosphere above the spot. In this paper, we carry out a numerical ``scattering experiment'', placing an acoustic driver 4 Mm below the solar surface and monitoring the acoustic and Alfvenic wave energy flux high in an isothermal atmosphere placed above it. These calculations indeed show that energy conversion to upward travelling Alfven waves can be substantial, in many cases exceeding loss to slow (acoustic) waves. Typically, at penumbral magnetic field strengths, the strongest Alfven fluxes are produced when the field is inclined 30-40 degrees from the vertical, with the vertical plane of wave propagation offset from the vertical plane containing field lines by some 60-80 degrees.Comment: Accepted for the HELAS II/ SOHO 19/ GONG 2007 Topical Issue of Solar Physic

Multiwavelength studies of MHD waves in the solar chromosphere: An overview of recent results

The chromosphere is a thin layer of the solar atmosphere that bridges the relatively cool photosphere and the intensely heated transition region and corona. Compressible and incompressible waves propagating through the chromosphere can supply significant amounts of energy to the interface region and corona. In recent years an abundance of high-resolution observations from state-of-the-art facilities have provided new and exciting ways of disentangling the characteristics of oscillatory phenomena propagating through the dynamic chromosphere. Coupled with rapid advancements in magnetohydrodynamic wave theory, we are now in an ideal position to thoroughly investigate the role waves play in supplying energy to sustain chromospheric and coronal heating. Here, we review the recent progress made in characterising, categorising and interpreting oscillations manifesting in the solar chromosphere, with an impetus placed on their intrinsic energetics.Comment: 48 pages, 25 figures, accepted into Space Science Review

Does centrality in a cross-sectional network suggest intervention targets for social anxiety disorder?

Objective: Network analysis allows us to identify the most interconnected (i.e., central) symptoms, and multiple authors have suggested that these symptoms might be important treatment targets. This is because change in central symptoms (relative to others) should have greater impact on change in all other symptoms. It has been argued that networks derived from cross-sectional data may help identify such important symptoms. We tested this hypothesis in social anxiety disorder. Method: We first estimated a state-of-the-art regularized partial correlation network based on participants with social anxiety disorder (n = 910) to determine which symptoms were more central. Next, we tested whether change in these central symptoms were indeed more related to overall symptom change in a separate dataset of participants with social anxiety disorder who underwent a variety of treatments (n = 244). We also tested whether relatively superficial item properties (infrequency of endorsement and variance of items) might account for any effects shown for central symptoms. Results: Centrality indices successfully predicted how strongly changes in items correlated with change in the remainder of the items. Findings were limited to the measure used in the network and did not generalize to three other measures related to social anxiety severity. In contrast, infrequency of endorsement showed associations across all measures. Conclusions: The transfer of recently published results from cross-sectional network analyses to treatment data is unlikely to be straightforward. (PsycINFO Database Record (c) 2018 APA, all rights reserved)FSW – Publicaties zonder aanstelling Universiteit Leide

Modeling the Subsurface Structure of Sunspots

While sunspots are easily observed at the solar surface, determining their subsurface structure is not trivial. There are two main hypotheses for the subsurface structure of sunspots: the monolithic model and the cluster model. Local helioseismology is the only means by which we can investigate subphotospheric structure. However, as current linear inversion techniques do not yet allow helioseismology to probe the internal structure with sufficient confidence to distinguish between the monolith and cluster models, the development of physically realistic sunspot models are a priority for helioseismologists. This is because they are not only important indicators of the variety of physical effects that may influence helioseismic inferences in active regions, but they also enable detailed assessments of the validity of helioseismic interpretations through numerical forward modeling. In this paper, we provide a critical review of the existing sunspot models and an overview of numerical methods employed to model wave propagation through model sunspots. We then carry out an helioseismic analysis of the sunspot in Active Region 9787 and address the serious inconsistencies uncovered by \citeauthor{gizonetal2009}~(\citeyear{gizonetal2009,gizonetal2009a}). We find that this sunspot is most probably associated with a shallow, positive wave-speed perturbation (unlike the traditional two-layer model) and that travel-time measurements are consistent with a horizontal outflow in the surrounding moat.Comment: 73 pages, 19 figures, accepted by Solar Physic

Large-scale transcriptome-wide association study identifies new prostate cancer risk regions

Although genome-wide association studies (GWAS) for prostate cancer (PrCa) have identified more than 100 risk regions, most of the risk genes at these regions remain largely unknown. Here we integrate the largest PrCa GWAS (N = 142,392) with gene expression measured in 45 tissues (N = 4458), including normal and tumor prostate, to perform a multi-tissue transcriptome-wide association study (TWAS) for PrCa. We identify 217 genes at 84 independent 1 Mb regions associated with PrCa risk, 9 of which are region

The philosophy and practice of interpretivist research in entrepreneurship: Quality, validation and trust

Knowledge production in entrepreneurship requires inclusivity as well as diversity and pluralism in research perspectives and approaches. In this article, the authors address concerns about interpretivist research regarding validity, reliability, objectivity, generalizability, and communicability of results that militate against its more widespread acceptance. Following the nonfoundationalist argument that all observation is theory-laden, context specific, and that there are no external criteria against which to assess research design and execution and the data produced, the authors propose that quality must be internalized within the underlying research philosophy rather than something to be tested upon completion. This requires a shift from the notion of validity as an outcome to validation as a process. To elucidate this, they provide a guiding framework and present a case illustration that will assist an interpretivist entrepreneurship researcher to establish and demonstrate the quality of their work