Visualization, Exploration and Data Analysis of Complex Astrophysical Data

In this paper we show how advanced visualization tools can help the researcher in investigating and extracting information from data. The focus is on VisIVO, a novel open source graphics application, which blends high performance multidimensional visualization techniques and up-to-date technologies to cooperate with other applications and to access remote, distributed data archives. VisIVO supports the standards defined by the International Virtual Observatory Alliance in order to make it interoperable with VO data repositories. The paper describes the basic technical details and features of the software and it dedicates a large section to show how VisIVO can be used in several scientific cases.Comment: 32 pages, 15 figures, accepted by PAS

Particle Induced X-Ray Emission Microanalysis of Root Samples from Beech (Fagus sylvatica)

Beech seedlings (Fagus Sylvatica) were grown in a nutrient solution to which AlCl3 had been added. The experiments were designed to evaluate the effect of aluminum on the localization of elements in plant root tissue. Cross-sections of roots were analyzed with micro-PIXE (particle induced X-ray emission) and Rutherford backscattering (RBS) simultaneously. A proton beam of either 30x30 μm2 or 5x5 μm2 was scanned over the samples, and quantitative elemental maps were created. Aluminum was found to accumulate in high concentrations (percent levels) in the epidermis and the outer layer of the cortex, when the nutrient solution held 1.0 mM AlCl3. It was also obvious that calcium was depleted where aluminum accumulated. The distribution of aluminum was inhomogeneous, and therefore, it was necessary to analyze the total area of the cross-section and not only look at a small part of it, for example along a diametrical line

Determinants of guideline use in primary care physical therapy: a cross-sectional survey of attitudes, knowledge, and behavior

Background Understanding of attitudes, knowledge, and behavior related to evidence-based practice (EBP) and use of evidence-based clinical practice guidelines in primary care physical therapy is limited. Objectives The objectives of this study were: (1) to investigate self-reported attitudes, knowledge, behavior, prerequisites, and barriers related to EBP and guideline use among physical therapists in primary care and (2) to explore associations of self-reported use of guidelines with these social cognitive factors along with demographic and workplace characteristics. Design This was a cross-sectional survey. Methods A web-based survey of 419 physical therapists in primary care in western Sweden was performed. Multiple logistic regression analysis was performed to examine factors associated with guideline use. Results The response rate was 64.7%. Most respondents had positive attitudes toward EBP and guidelines: 90% considered EBP necessary, and 96% considered guidelines important. Approximately two thirds reported confidence in finding and using evidence. One third reported being aware of guidelines. Thirteen percent knew where to find guidelines, and only 9% reported having easy access to guidelines. Fewer than half reported using guidelines frequently. The most important barriers to using guidelines were lack of time, poor availability, and limited access to guidelines. Young age and brief work experience were associated with positive attitudes toward EBP. A postgraduate degree was associated with higher application of EBP. Positive attitudes, awareness of guidelines, considering guidelines to facilitate practice, and knowing how to integrate patient preferences with guideline use were associated with frequent use of guidelines. Limitations Data were self-reported, which may have increased the risk of social desirability bias. Conclusions Use of guidelines was not as frequent as could be expected in view of the positive attitudes toward EBP and guidelines among physical therapists. Awareness of and perceived access to guidelines were limited. The identified determinants can be addressed when developing guideline implementation strategies

Resolving the shocked gas in HH54 with Herschel: CO line mapping at high spatial and spectral resolution

The HH54 shock is a Herbig-Haro object, located in the nearby Chamaeleon II cloud. Observed CO line profiles are due to a complex distribution in density, temperature, velocity, and geometry. Resolving the HH54 shock wave in the far-infrared cooling lines of CO constrain the kinematics, morphology, and physical conditions of the shocked region. We used the PACS and SPIRE instruments on board the Herschel space observatory to map the full FIR spectrum in a region covering the HH54 shock wave. Complementary Herschel-HIFI, APEX, and Spitzer data are used in the analysis as well. The observed features in the line profiles are reproduced using a 3D radiative transfer model of a bow-shock, constructed with the Line Modeling Engine code (LIME). The FIR emission is confined to the HH54 region and a coherent displacement of the location of the emission maximum of CO with increasing J is observed. The peak positions of the high-J CO lines are shifted upstream from the lower J CO lines and coincide with the position of the spectral feature identified previously in CO(10-9) profiles with HIFI. This indicates a hotter molecular component in the upstream gas with distinct dynamics. The coherent displacement with increasing J for CO is consistent with a scenario where IRAS12500-7658 is the exciting source of the flow, and the 180 K bow-shock is accompanied by a hot (800 K) molecular component located upstream from the apex of the shock and blueshifted by -7 km s$^{-1}$. The spatial proximity of this knot to the peaks of the atomic fine-structure emission lines observed with Spitzer and PACS ([OI]63, 145 $\mu$m) suggests that it may be associated with the dissociative shock as the jet impacts slower moving gas in the HH54 bow-shock.Comment: 6 pages, 5 figure

A Model Analysis of Mechanisms for Radial Microtubular Patterns at Root Hair Initiation Sites

Plant cells have two main modes of growth generating anisotropic structures. Diffuse growth where whole cell walls extend in specific directions, guided by anisotropically positioned cellulose fibers, and tip growth, with inhomogeneous addition of new cell wall material at the tip of the structure. Cells are known to regulate these processes via molecular signals and the cytoskeleton. Mechanical stress has been proposed to provide an input to the positioning of the cellulose fibers via cortical microtubules in diffuse growth. In particular, a stress feedback model predicts a circumferential pattern of fibers surrounding apical tissues and growing primordia, guided by the anisotropic curvature in such tissues. In contrast, during the initiation of tip growing root hairs, a star-like radial pattern has recently been observed. Here, we use detailed finite element models to analyze how a change in mechanical properties at the root hair initiation site can lead to star-like stress patterns in order to understand whether a stress-based feedback model can also explain the microtubule patterns seen during root hair initiation. We show that two independent mechanisms, individually or combined, can be sufficient to generate radial patterns. In the first, new material is added locally at the position of the root hair. In the second, increased tension in the initiation area provides a mechanism. Finally, we describe how a molecular model of Rho-of-plant (ROP) GTPases activation driven by auxin can position a patch of activated ROP protein basally along a 2D root epidermal cell plasma membrane, paving the way for models where mechanical and molecular mechanisms cooperate in the initial placement and outgrowth of root hairs.This work was funded by the Knut and Alice Wallenberg Foundation via grant ShapeSystems (KAW 2012.0050) to MG and HJ, the Swedish Research Council (VR2013-4632) to HJ, and the Gatsby Charitable Foundation (GAT3395/PR4) to HJ

Improved predictions by Pcons.net using multiple templates

Summary: Multiple templates can often be used to build more accurate homology models than models built from a single template. Here we introduce PconsM, an automated protocol that uses multiple templates to build protein models. PconsM has been among the top-performing methods in the recent CASP experiments and consistently perform better than the single template models used in Pcons.net. In particular for the easier targets with many alternative templates with a high degree of sequence identity, quality is readily improved with a few percentages over the highest ranked model built on a single template. PconsM is available as an additional pipeline within the Pcons.net protein structure prediction server

Detection of interstellar hydrogen peroxide

The molecular species hydrogen peroxide, HOOH, is likely to be a key ingredient in the oxygen and water chemistry in the interstellar medium. Our aim with this investigation is to determine how abundant HOOH is in the cloud core {\rho} Oph A. By observing several transitions of HOOH in the (sub)millimeter regime we seek to identify the molecule and also to determine the excitation conditions through a multilevel excitation analysis. We have detected three spectral lines toward the SM1 position of {\rho} Oph A at velocity-corrected frequencies that coincide very closely with those measured from laboratory spectroscopy of HOOH. A fourth line was detected at the 4{\sigma} level. We also found through mapping observations that the HOOH emission extends (about 0.05 pc) over the densest part of the {\rho} Oph A cloud core. We derive an abundance of HOOH relative to that of H_2 in the SM1 core of about 1\times10^(-10). To our knowledge, this is the first reported detection of HOOH in the interstellar medium.Comment: 5 pages, 4 figures, accepted for publication in Astronomy & Astrophysics, new version corrects a typo in Table 1 (and consequently in Fig 4

Evolution of dust and ice features around FU Orionis objects

(abridged) We present spectroscopy data for a sample of 14 FUors and 2 TTauri stars observed with the Spitzer Space Telescope or with the Infrared Space Observatory (ISO). Based on the appearance of the 10 micron silicate feature we define 2 categories of FUors. Objects showing the silicate feature in absorption (Category 1) are still embedded in a dusty and icy envelope. The shape of the 10 micron silicate absorption bands is compared to typical dust compositions of the interstellar medium and found to be in general agreement. Only one object (RNO 1B) appears to be too rich in amorphous pyroxene dust, but a superposed emission feature can explain the observed shape. We derive optical depths and extinction values from the silicate band and additional ice bands at 6.0, 6.8 and 15.2 micron. In particular the analysis of the CO_2 ice band at 15.2 micron allows us to search for evidence for ice processing and constrains whether the absorbing material is physically linked to the central object or in the foreground. For objects showing the silicate feature in emission (Category 2), we argue that the emission comes from the surface layer of accretion disks. Analyzing the dust composition reveals that significant grain growth has already taken place within the accretion disks, but no clear indications for crystallization are present. We discuss how these observational results can be explained in the picture of a young, and highly active accretion disk. Finally, a framework is proposed as to how the two categories of FUors can be understood in a general paradigm of the evolution of young, low-mass stars. Only one object (Parsamian 21) shows PAH emission features. Their shapes, however, are often seen toward evolved stars and we question the object's status as a FUor and discuss other possible classifications.Comment: accepted for publication in ApJ; 63 pages preprint style including 8 tables and 24 figure

Quantitative characterization of machining-induced white layers in Ti–6Al–4V

Machining-induced white layers can affect the functional performance of engineered components, due to the resulting mechanical and microstructural properties. Destructive inspection methods such as cross-sectional microscopy are typically used to identify white layers, however, these methods are inherently costly and time-consuming. It is, therefore, desirable to detect this anomalous surface feature using non-destructive methods which requires improved knowledge around the characteristics of white layers. The present paper reports on the characterization of white layers formed during machining of Ti–6Al–4V, to aid future development of a reliable non-destructive assessment method. The microstructure of the material in the white layer was found to have a basal α-hexagonal close packed texture and there was no evidence of an α→β phase transformation during white layer formation. The white layer has a highly refined grain structure with an increased nanohardness of up to 15% compared with the bulk material. It is proposed that white layers in Ti–6Al–4V are formed by continuous dynamic recrystallization driven by severe plastic deformation during machining. According to the measured micro-mechanical properties of the white layer, suitable non-destructive testing methods are suggested for the detection of this surface feature