Examining alternatives to wavelet de-noising for astronomical source finding

The Square Kilometre Array and its pathfinders ASKAP and MeerKAT will produce prodigious amounts of data that necessitate automated source finding. The performance of automated source finders can be improved by pre-processing a dataset. In preparation for the WALLABY and DINGO surveys, we have used a test HI datacube constructed from actual Westerbork Telescope noise and WHISP HI galaxies to test the real world improvement of linear smoothing, the {\sc Duchamp} source finder's wavelet de-noising, iterative median smoothing and mathematical morphology subtraction, on intensity threshold source finding of spectral line datasets. To compare these pre-processing methods we have generated completeness-reliability performance curves for each method and a range of input parameters. We find that iterative median smoothing produces the best source finding results for ASKAP HI spectral line observations, but wavelet de-noising is a safer pre-processing technique. In this paper we also present our implementations of iterative median smoothing and mathematical morphology subtraction.Comment: 7 pages, 4 figures, 3 colour figures. Accepted as part of the Publications of the Astronomical Society of Australia's special issue on source finding and visualisatio

Imaging atom-clusters by hard x-ray free electron lasers

The ingenious idea of single molecule imaging by hard x-ray Free Electron Laser (X-FEL) pulses was recently proposed by Neutze et al. [Nature,406,752(2000)]. However, in their numerical modelling of the Coulomb explosion several interactions were neglected and no reconstruction of the atomic structure was given. In this work we carried out improved molecular dynamics calculations including all quantum processes which affect the explosion. Based on this time evolution we generated composite elastic scattering patterns, and by using Fienup's algorithm successfully reconstructed the original atomic structure. The critical evaluation of these results gives guidelines and sets important conditions for future experiments aiming single molecule structure solution.Comment: 8 pages, 4 figures, submitted to Europhysics Letter

Hydrodynamic model for expansion and collisional relaxation of x-ray laser-excited multi-component nanoplasma

The irradiation of an atomic cluster with a femtosecond x-ray free-electron laser pulse results in a nanoplasma formation. This typically occurs within a few hundreds femtoseconds. By this time the x-ray pulse is over, and the direct photoinduced processes no longer contributing. All created electrons within the nanoplasma are thermalized. The nanoplasma thus formed is a mixture of atoms, electrons and ions of various charges. While expanding, it is undergoing electron impact ionization and three-body recombination. Below we present a hydrodynamic model to describe the dynamics of such multi-component nanoplasma. The model equations are derived by taking the moments of the corresponding Boltzmann kinetic equations. We include the equations obtained, together with the source terms due to electron impact ionization and three-body recombination, in our hydrodynamic solver. Model predictions for a test case: expanding spherical Ar nanoplasma are obtained. With this model we complete the two-step approach to simulate x-ray created nanoplasmas, enabling computationally efficient simulations of their picosecond dynamics. Moreover, the hydrodynamic framework including collisional processes can be easily extended for other source terms and then applied to follow relaxation of any finite non-isothermal multi-component nanoplasma with its components relaxed into local thermodynamic equilibrium.Comment: 12 pages, 4 figures. This article has been accepted by Physics of Plasmas. After it is published, it will be found at http://scitation.aip.org/content/aip/journal/po

Using negative detections to estimate source finder reliability

We describe a simple method to determine the reliability of source finders based on the detection of sources with both positive and negative total flux. Under the assumption that the noise is symmetric and that real sources have positive total flux, negative detections can be used to assign to each positive detection a probability of being real. We discuss this method in the context of upcoming, interferometric HI surveys.Comment: Accepted for publication on the 2012 PASA source finding special issu

The Characterised Noise Hi source finder: Detecting Hi galaxies using a novel implementation of matched filtering

The spectral line datacubes obtained from the Square Kilometre Array (SKA) and its precursors, such as the Australian SKA Pathfinder (ASKAP), will be sufficiently large to necessitate automated detection and parametrisation of sources. Matched filtering is widely acknowledged as the best possible method for the automated detection of sources. This paper presents the Characterised Noise Hi (CNHI) source finder, which employs a novel implementation of matched filtering. This implementation is optimised for the 3-D nature of the planned Wide-field ASKAP Legacy L-band All- sky Blind surveY's (WALLABY) Hi spectral line observations. The CNHI source finder also employs a novel sparse representation of 3-D objects, with a high compression rate, to implement Lutz one-pass algorithm on datacubes that are too large to process in a single pass. WALLABY will use ASKAP's phenomenal 30 square degree field of view to image \sim 70% of the sky. It is expected that WALLABY will find 500 000 Hi galaxies out to z \sim 0.2.Comment: Part of the 2012 PASA Source Finding Special Issue, 10 figure

Optimizing adipogenic transdifferentiation of bovine mesenchymal stem cells: a prominent role of ascorbic acid in FABP4 induction

Adipocyte differentiation of bovine adipose-derived stem cells (ASC) was induced by foetal bovine serum (FBS), biotin, pantothenic acid, insulin, rosiglitazone, dexamethasone and 3-isobutyl-1-methylxanthine, followed by incubation in different media to test the influence of ascorbic acid (AsA), bovine serum lipids (BSL), FBS, glucose and acetic acid on transdifferentiation into functional adipocytes. Moreover, different culture plate coatings (collagen-A, gelatin-A or poly-L-lysine) were tested. The differentiated ASC were subjected to Nile red staining, DAPI staining, immunocytochemistry and quantitative reverse transcription PCR (for NT5E, THY1, ENG, PDGFRα, FABP4, PPARγ, LPL, FAS, GLUT4). Nile red quantification showed a significant increase in the development of lipid droplets in treatments with AsA and BSL without FBS. The presence of BSL induced a prominent increase in FABP4 mRNA abundance and in FABP4 immunofluorescence signals in coincubation with AsA. The abundance of NT5E, ENG and THY1 mRNA decreased or tended to decrease in the absence of FBS, and ENG was additionally suppressed by AsA. DAPI fluorescence was higher in cells cultured in poly-L-lysine or gelatin-A coated wells. In additional experiments, the multi-lineage differentiation potential to osteoblasts was verified in medium containing ß-glycerophosphate, dexamethasone and 1,25-dihydroxyvitamin D3 using alizarin red staining. In conclusion, bovine ASC are capable of multi-lineage differentiation. Poly-L-lysine or gelatin-A coating, the absence of FBS, and the presence of BSL and AsA favour optimal transdifferentiation into adipocytes. AsA supports transdifferentiation via a unique role in FABP4 induction, but this is not linearly related to the primarily BSL-driven lipid accumulation

Biomolecular imaging and electronic damage using X-ray free-electron lasers

Proposals to determine biomolecular structures from diffraction experiments using femtosecond X-ray free-electron laser (XFEL) pulses involve a conflict between the incident brightness required to achieve diffraction-limited atomic resolution and the electronic and structural damage induced by the illumination. Here we show that previous estimates of the conditions under which biomolecular structures may be obtained in this manner are unduly restrictive, because they are based on a coherent diffraction model that is not appropriate to the proposed interaction conditions. A more detailed imaging model derived from optical coherence theory and quantum electrodynamics is shown to be far more tolerant of electronic damage. The nuclear density is employed as the principal descriptor of molecular structure. The foundations of the approach may also be used to characterize electrodynamical processes by performing scattering experiments on complex molecules of known structure.Comment: 16 pages, 2 figure

Can holography reproduce the QCD Wilson line?

Recently a remarkable agreement was found between lattice simulations of long Wilson lines and behavior of the Nambu Goto string in flat space-time. However, the latter fails to fit the short distance behavior since it admits a tachyonic mode for a string shorter than a critical length. In this paper we examine the question of whether a classical holographic Wilson line can reproduce the lattice results for Wilson lines of any length. We determine the condition on the the gravitational background to admit a Coulombic potential at short distances. We analyze the system using three different renormalization schemes. We perform an explicit best fit comparison of the lattice results with the holographic models based on near extremal D3 and D4 branes, non-critical near extremal AdS6 model and the Klebanov Strassler model. We find that all the holographic models examined admit after renormalization a constant term in the potential. We argue that the curves of the lattice simulation also have such a constant term and we discuss its physical interpretation