Morphological Classification of Galaxies by Shapelet Decomposition in the Sloan Digital Sky Survey II: Multiwavelength Classification

We describe the application of the `shapelet' linear decomposition of galaxy images to multi-wavelength morphological classification using the $u,g,r,i,$ and $z$-band images of 1519 galaxies from the Sloan Digital Sky Survey. We utilize elliptical shapelets to remove to first-order the effect of inclination on morphology. After decomposing the galaxies we perform a principal component analysis on the shapelet coefficients to reduce the dimensionality of the spectral morphological parameter space. We give a description of each of the first ten principal component's contribution to a galaxy's spectral morphology. We find that galaxies of different broad Hubble type separate cleanly in the principal component space. We apply a mixture of Gaussians model to the 2-dimensional space spanned by the first two principal components and use the results as a basis for classification. Using the mixture model, we separate galaxies into three classes and give a description of each class's physical and morphological properties. We find that the two dominant mixture model classes correspond to early and late type galaxies, respectively. The third class has, on average, a blue, extended core surrounded by a faint red halo, and typically exhibits some asymmetry. We compare our method to a simple cut on $u-r$ color and find the shapelet method to be superior in separating galaxies. Furthermore, we find evidence that the $u-r=2.22$ decision boundary may not be optimal for separation between early and late type galaxies, and suggest that the optimal cut may be $u-r \sim 2.4$.Comment: 42 pages, 18 figs, revised version in press at AJ. Some modification to the technique, more discussion, addition/deletion/modification of several figures, color figures have been added. A high resolution version may be obtained at http://bllac.as.arizona.edu/~bkelly/shapelets/shapelets_ugriz.ps.g

Distinct Bacterial Communities in Surficial Seafloor Sediments Following the 2010 Deepwater Horizon Blowout

A major fraction of the petroleum hydrocarbons discharged during the 2010 Macondo oil spill became associated with and sank to the seafloor as marine snow flocs. This sedimentation pulse induced the development of distinct bacterial communities. Between May 2010 and July 2011, full-length 16S rRNA gene clone libraries demonstrated bacterial community succession in oil-polluted sediment samples near the wellhead area. Libraries from early May 2010, before the sedimentation event, served as the baseline control. Freshly deposited oil-derived marine snow was collected on the surface of sediment cores in September 2010, and was characterized by abundantly detected members of the marine Roseobacter cluster within the Alphaproteobacteria. Samples collected in mid-October 2010 closest to the wellhead contained members of the sulfate-reducing, anaerobic bacterial families Desulfobacteraceae and Desulfobulbaceae within the Deltaproteobacteria, suggesting that the oil-derived sedimentation pulse triggered bacterial oxygen consumption and created patchy anaerobic microniches that favored sulfate-reducing bacteria. Phylotypes of the polycyclic aromatic hydrocarbon-degrading genus Cycloclasticus, previously found both in surface oil slicks and the deep hydrocarbon plume, were also found in oil-derived marine snow flocs sedimenting on the seafloor in September 2010, and in surficial sediments collected in October and November 2010, but not in any of the control samples. Due to the relative recalcitrance and stability of polycyclic aromatic compounds, Cycloclasticus represents the most persistent microbial marker of seafloor hydrocarbon deposition that we could identify in this dataset. The bacterial imprint of the DWH oil spill had diminished in late November 2010, when the bacterial communities in oil-impacted sediment samples collected near the Macondo wellhead began to resemble their pre-spill counterparts and spatial controls. Samples collected in summer of 2011 did not show a consistent bacterial community signature, suggesting that the bacterial community was no longer shaped by the DWH fallout of oil-derived marine snow, but instead by location-specific and seasonal factors

The recovery movement and its implications for policy, commissioning and practice

While a recovery approach is widespread and relatively unquestioned in the USA, its implementation in the UK and to a lesser extent in Australia has provoked a number of questions about what this means in practice and what some of the implications are for treatment. This is particularly important as there is growing interest in recovery in Western Europe with policy recognition in Belgium and the Netherlands, and increased interest in research issues around recovery. What this article sets out to do is to discuss the implications of a recovery model for commissioning and treatment systems, with a focus on where recovery approaches sit and what they can offer in terms of added value to treatment approaches

Cholesterol-Rich Membrane Microdomains Mediate Cell Cycle Arrest Induced by Actinobacillus Actinomycetemcomitans Cytolethal-Distending Toxin

We have previously shown that Actinobacillus actinomycetemcomitans cytolethal-distending toxin (Cdt) is a potent immunosuppressive agent that induces G2/M arrest in human lymphocytes. In this study, we explored the possibility that Cdt-mediated immunotoxicity involves lipid membrane microdomains. We first determined that following treatment of Jurkat cells with Cdt holotoxin all three Cdt subunits localize to these microdomains. Laser confocal microscopy was employed to colocalize the subunits with GM1-enriched membrane regions which are characteristic of membrane rafts. Western blot analysis of isolated lipid rafts also demonstrated the presence of Cdt peptides. Cholesterol depletion, using methyl β-cyclodextrin, protected cells from the ability of the Cdt holotoxin to induce G2 arrest. Moreover, cholesterol depletion reduced the ability of the toxin to associate with Jurkat cells. Thus, lipid raft integrity is vital to the action of Cdt on host cells. The implications of our observations with respect to Cdt mode of action are discussed

Applying the trigger review method after a brief educational intervention: potential for teaching and improving safety in GP specialty training?

<p>Background: The Trigger Review Method (TRM) is a structured approach to screening clinical records for undetected patient safety incidents (PSIs) and identifying learning and improvement opportunities. In Scotland, TRM participation can inform GP appraisal and has been included as a core component of the national primary care patient safety programme that was launched in March 2013. However, the clinical workforce needs up-skilled and the potential of TRM in GP training has yet to be tested. Current TRM training utilizes a workplace face-to-face session by a GP expert, which is not feasible. A less costly, more sustainable educational intervention is necessary to build capability at scale. We aimed to determine the feasibility and impact of TRM and a related training intervention in GP training.</p> Methods We recruited 25 west of Scotland GP trainees to attend a 2-hour TRM workshop. Trainees then applied TRM to 25 clinical records and returned findings within 4-weeks. A follow-up feedback workshop was held. <p>Results: 21/25 trainees (84%) completed the task. 520 records yielded 80 undetected PSIs (15.4%). 36/80 were judged potentially preventable (45%) with 35/80 classified as causing moderate to severe harm (44%). Trainees described a range of potential learning and improvement plans. Training was positively received and appeared to be successful given these findings. TRM was valued as a safety improvement tool by most participants.</p> <p>Conclusion: This small study provides further evidence of TRM utility and how to teach it pragmatically. TRM is of potential value in GP patient safety curriculum delivery and preparing trainees for future safety improvement expectations.</p&gt

Repeatability and reproducibility of multiparametric magnetic resonance imaging of the liver

As the burden of liver disease reaches epidemic levels, there is a high unmet medical need to develop robust, accurate and reproducible non-invasive methods to quantify liver tissue characteristics for use in clinical development and ultimately in clinical practice. This prospective cross-sectional study systematically examines the repeatability and reproducibility of iron-corrected T1 (cT1), T2*, and hepatic proton density fat fraction (PDFF) quantification with multiparametric MRI across different field strengths, scanner manufacturers and models. 61 adult participants with mixed liver disease aetiology and those without any history of liver disease underwent multiparametric MRI on combinations of 5 scanner models from two manufacturers (Siemens and Philips) at different field strengths (1.5T and 3T). We report high repeatability and reproducibility across different field strengths, manufacturers, and scanner models in standardized cT1 (repeatability CoV: 1.7%, bias -7.5ms, 95% LoA of -53.6 ms to 38.5 ms; reproducibility CoV 3.3%, bias 6.5 ms, 95% LoA of -76.3 to 89.2 ms) and T2* (repeatability CoV: 5.5%, bias -0.18 ms, 95% LoA -5.41 to 5.05 ms; reproducibility CoV 6.6%, bias -1.7 ms, 95% LoA -6.61 to 3.15 ms) in human measurements. PDFF repeatability (0.8%) and reproducibility (0.75%) coefficients showed high precision of this metric. Similar precision was observed in phantom measurements. Inspection of the ICC model indicated that most of the variance in cT1 could be accounted for by study participants (ICC = 0.91), with minimal contribution from technical differences. We demonstrate that multiparametric MRI is a non-invasive, repeatable and reproducible method for quantifying liver tissue characteristics across manufacturers (Philips and Siemens) and field strengths (1.5T and 3T)

Defining Components of the ßcatenin Destruction Complex and Exploring Its Regulation and Mechanisms of Action during Development

A subset of signaling pathways play exceptionally important roles in embryonic and post-embryonic development, and mis-regulation of these pathways occurs in most human cancers. One such pathway is the Wnt pathway. The primary mechanism keeping Wnt signaling off in the absence of ligand is regulated proteasomal destruction of the canonical Wnt effector ßcatenin (or its fly homolog Armadillo). A substantial body of evidence indicates that SCF(βTrCP) mediates βcat destruction, however, an essential role for Roc1 has not been demonstrated in this process, as would be predicted. In addition, other E3 ligases have also been proposed to destroy βcat, suggesting that βcat destruction may be regulated differently in different tissues.Here we used cultured Drosophila cells, human colon cancer cells, and Drosophila embryos and larvae to explore the machinery that targets Armadillo for destruction. Using RNAi in Drosophila S2 cells to examine which SCF components are essential for Armadillo destruction, we find that Roc1/Roc1a is essential for regulating Armadillo stability, and that in these cells the only F-box protein playing a detectable role is Slimb. Second, we find that while embryonic and larval Drosophila tissues use the same destruction complex proteins, the response of these tissues to destruction complex inactivation differs, with Armadillo levels more elevated in embryos. We provide evidence consistent with the possibility that this is due to differences in armadillo mRNA levels. Third, we find that there is no correlation between the ability of different APC2 mutant proteins to negatively regulate Armadillo levels, and their recently described function in positively-regulating Wnt signaling. Finally, we demonstrate that APC proteins lacking the N-terminal Armadillo-repeat domain cannot restore Armadillo destruction but retain residual function in negatively-regulating Wnt signaling.We use these data to refine our model for how Wnt signaling is regulated during normal development

Mutation detection in cholestatic patients using microarray resequencing of ATP8B1 and ABCB11

© 2013 McKay KE et al. Background: Neonatal cholestasis is a common presentation of childhood liver diseases and can be a feature of various conditions including disorders of bile acid biogenesis and transport, various inborn errors of metabolism and perinatal infections. Some inherited metabolic diseases can be easily screened using biochemical assays, however many can only be accurately diagnosed by DNA sequencing. Fluorescent capillary Sanger sequencing (FS) is the gold standard method used by clinical laboratories for genetic diagnosis of many inherited conditions; however, it does have limitations. Recently microarray resequencing (MR) has been introduced into research and clinical practice as an alternative method for genetic diagnosis of heterogeneous conditions. In this report we compared the accuracy of mutation detection for MR with FS in a group of patients with 'low-normal' gamma glutamyl transpeptidase (gGT) cholestasis without known molecular diagnoses. Methods: 29 patient DNA samples were tested for mutations in the ATP8B1 and ABCB11 genes using both FS and MR. Other known causes of "low gGT cholestasis such as ARC syndrome and bile acid biosynthesis disorders were excluded. Results: Mutations were identified in 13/29 samples. In 3/29 samples FS and MR gave discordant results: MR had a false positive rate of 3.4% and a false negative rate of 7%. Conclusions: The major advantage of MR over FS is that multiple genes can be screened in one experiment, allowing rapid and cost-effective diagnoses. However, we have demonstrated that MR technology is limited in sensitivity. We therefore recommend that MR be used as an initial evaluation, with FS deployed when genetic and clinical or histopathological findings are discordant

Functional limit theorems for random regular graphs

Consider d uniformly random permutation matrices on n labels. Consider the sum of these matrices along with their transposes. The total can be interpreted as the adjacency matrix of a random regular graph of degree 2d on n vertices. We consider limit theorems for various combinatorial and analytical properties of this graph (or the matrix) as n grows to infinity, either when d is kept fixed or grows slowly with n. In a suitable weak convergence framework, we prove that the (finite but growing in length) sequences of the number of short cycles and of cyclically non-backtracking walks converge to distributional limits. We estimate the total variation distance from the limit using Stein's method. As an application of these results we derive limits of linear functionals of the eigenvalues of the adjacency matrix. A key step in this latter derivation is an extension of the Kahn-Szemer\'edi argument for estimating the second largest eigenvalue for all values of d and n.Comment: Added Remark 27. 39 pages. To appear in Probability Theory and Related Field

Robust Optical Richness Estimation with Reduced Scatter

Reducing the scatter between cluster mass and optical richness is a key goal for cluster cosmology from photometric catalogs. We consider various modifications to the red-sequence matched filter richness estimator of Rozo et al. (2009), and evaluate their impact on the scatter in X-ray luminosity at fixed richness. Most significantly, we find that deeper luminosity cuts can reduce the recovered scatter, finding that sigma_lnLX|lambda=0.63+/-0.02 for clusters with M_500c >~ 1.6e14 h_70^-1 M_sun. The corresponding scatter in mass at fixed richness is sigma_lnM|lambda ~ 0.2-0.3 depending on the richness, comparable to that for total X-ray luminosity. We find that including blue galaxies in the richness estimate increases the scatter, as does weighting galaxies by their optical luminosity. We further demonstrate that our richness estimator is very robust. Specifically, the filter employed when estimating richness can be calibrated directly from the data, without requiring a-priori calibrations of the red-sequence. We also demonstrate that the recovered richness is robust to up to 50% uncertainties in the galaxy background, as well as to the choice of photometric filter employed, so long as the filters span the 4000 A break of red-sequence galaxies. Consequently, our richness estimator can be used to compare richness estimates of different clusters, even if they do not share the same photometric data. Appendix 1 includes "easy-bake" instructions for implementing our optimal richness estimator, and we are releasing an implementation of the code that works with SDSS data, as well as an augmented maxBCG catalog with the lambda richness measured for each cluster.Comment: Submitted to ApJ. 20 pages in emulateapj forma