Robust Machine Learning Applied to Astronomical Datasets I: Star-Galaxy Classification of the SDSS DR3 Using Decision Trees

We provide classifications for all 143 million non-repeat photometric objects in the Third Data Release of the Sloan Digital Sky Survey (SDSS) using decision trees trained on 477,068 objects with SDSS spectroscopic data. We demonstrate that these star/galaxy classifications are expected to be reliable for approximately 22 million objects with r < ~20. The general machine learning environment Data-to-Knowledge and supercomputing resources enabled extensive investigation of the decision tree parameter space. This work presents the first public release of objects classified in this way for an entire SDSS data release. The objects are classified as either galaxy, star or nsng (neither star nor galaxy), with an associated probability for each class. To demonstrate how to effectively make use of these classifications, we perform several important tests. First, we detail selection criteria within the probability space defined by the three classes to extract samples of stars and galaxies to a given completeness and efficiency. Second, we investigate the efficacy of the classifications and the effect of extrapolating from the spectroscopic regime by performing blind tests on objects in the SDSS, 2dF Galaxy Redshift and 2dF QSO Redshift (2QZ) surveys. Given the photometric limits of our spectroscopic training data, we effectively begin to extrapolate past our star-galaxy training set at r ~ 18. By comparing the number counts of our training sample with the classified sources, however, we find that our efficiencies appear to remain robust to r ~ 20. As a result, we expect our classifications to be accurate for 900,000 galaxies and 6.7 million stars, and remain robust via extrapolation for a total of 8.0 million galaxies and 13.9 million stars. [Abridged]Comment: 27 pages, 12 figures, to be published in ApJ, uses emulateapj.cl

In vitro culture of embryonic mouse intestinal epithelium: cell differentiation and introduction of reporter genes

BACKGROUND: Study of the normal development of the intestinal epithelium has been hampered by a lack of suitable model systems, in particular ones that enable the introduction of exogenous genes. Production of such a system would advance our understanding of normal epithelial development and help to shed light on the pathogenesis of intestinal neoplasia. The criteria for a reliable culture system include the ability to perform real time observations and manipulations in vitro, the preparation of wholemounts for immunostaining and the potential for introducing genes. RESULTS: The new culture system involves growing mouse embryo intestinal explants on fibronectin-coated coverslips in basal Eagle's medium+20% fetal bovine serum. Initially the cultures maintain expression of the intestinal transcription factor Cdx2 together with columnar epithelial (cytokeratin 8) and mesenchymal (smooth muscle actin) markers. Over a few days of culture, differentiation markers appear characteristic of absorptive epithelium (sucrase-isomaltase), goblet cells (Periodic Acid Schiff positive), enteroendocrine cells (chromogranin A) and Paneth cells (lysozyme). Three different approaches were tested to express genes in the developing cultures: transfection, electroporation and adenoviral infection. All could introduce genes into the mesenchyme, but only to a small extent into the epithelium. However the efficiency of adenovirus infection can be greatly improved by a limited enzyme digestion, which makes accessible the lateral faces of cells bearing the Coxsackie and Adenovirus Receptor. This enables reliable delivery of genes into epithelial cells. CONCLUSION: We describe a new in vitro culture system for the small intestine of the mouse embryo that recapitulates its normal development. The system both provides a model for studying normal development of the intestinal epithelium and also allows for the manipulation of gene expression. The explants can be cultured for up to two weeks, they form the full repertoire of intestinal epithelial cell types (enterocytes, goblet cells, Paneth cells and enteroendocrine cells) and the method for gene introduction into the epithelium is efficient and reliable

Randomized Reference Classifier with Gaussian Distribution and Soft Confusion Matrix Applied to the Improving Weak Classifiers

In this paper, an issue of building the RRC model using probability distributions other than beta distribution is addressed. More precisely, in this paper, we propose to build the RRR model using the truncated normal distribution. Heuristic procedures for expected value and the variance of the truncated-normal distribution are also proposed. The proposed approach is tested using SCM-based model for testing the consequences of applying the truncated normal distribution in the RRC model. The experimental evaluation is performed using four different base classifiers and seven quality measures. The results showed that the proposed approach is comparable to the RRC model built using beta distribution. What is more, for some base classifiers, the truncated-normal-based SCM algorithm turned out to be better at discovering objects coming from minority classes.Comment: arXiv admin note: text overlap with arXiv:1901.0882

Dynamical Evolution of Elliptical Galaxies with Central Singularities

We study the effect of a massive central singularity on the structure of a triaxial galaxy using N-body simulations. Starting from a single initial model, we grow black holes with various final masses Mh and at various rates, ranging from impulsive to adiabatic. In all cases, the galaxy achieves a final shape that is nearly spherical at the center and close to axisymmetric throughout. However, the rate of change of the galaxy's shape depends strongly on the ratio Mh/Mg of black hole mass to galaxy mass. When Mh/Mg < 0.3%, the galaxy evolves in shape on a timescale that exceeds 100 orbital periods, or roughly a galaxy lifetime. When Mh/Mg > 2%, the galaxy becomes axisymmetric in little more than a crossing time. We propose that the rapid evolution toward axisymmetric shapes that occurs when Mh/Mg > 2% provides a negative feedback mechanism which limits the mass of central black holes by cutting off their supply of fuel.Comment: 27 Latex pages, 9 Postscript figures, uses aastex.sty. Accepted for Publication in The Astrophysical Journal, Nov. 26, 199

Shaping electron wave functions in a carbon nanotube with a parallel magnetic field

A magnetic field, through its vector potential, usually causes measurable changes in the electron wave function only in the direction transverse to the field. Here we demonstrate experimentally and theoretically that in carbon nanotube quantum dots, combining cylindrical topology and bipartite hexagonal lattice, a magnetic field along the nanotube axis impacts also the longitudinal profile of the electronic states. With the high (up to 17T) magnetic fields in our experiment the wave functions can be tuned all the way from "half-wave resonator" shape, with nodes at both ends, to "quarter-wave resonator" shape, with an antinode at one end. This in turn causes a distinct dependence of the conductance on the magnetic field. Our results demonstrate a new strategy for the control of wave functions using magnetic fields in quantum systems with nontrivial lattice and topology.Comment: 5 figure

Observational evidence for self-interacting cold dark matter

Cosmological models with cold dark matter composed of weakly interacting particles predict overly dense cores in the centers of galaxies and clusters and an overly large number of halos within the Local Group compared to actual observations. We propose that the conflict can be resolved if the cold dark matter particles are self-interacting with a large scattering cross-section but negligible annihilation or dissipation. In this scenario, astronomical observations may enable us to study dark matter properties that are inaccessible in the laboratoryComment: 4 pages, no figures; added references, pedagogical improvements, to appear in PR

VAST: An ASKAP Survey for Variables and Slow Transients

The Australian Square Kilometre Array Pathfinder (ASKAP) will give us an unprecedented opportunity to investigate the transient sky at radio wavelengths. In this paper we present VAST, an ASKAP survey for Variables and Slow Transients. VAST will exploit the wide-field survey capabilities of ASKAP to enable the discovery and investigation of variable and transient phenomena from the local to the cosmological, including flare stars, intermittent pulsars, X-ray binaries, magnetars, extreme scattering events, interstellar scintillation, radio supernovae and orphan afterglows of gamma ray bursts. In addition, it will allow us to probe unexplored regions of parameter space where new classes of transient sources may be detected. In this paper we review the known radio transient and variable populations and the current results from blind radio surveys. We outline a comprehensive program based on a multi-tiered survey strategy to characterise the radio transient sky through detection and monitoring of transient and variable sources on the ASKAP imaging timescales of five seconds and greater. We also present an analysis of the expected source populations that we will be able to detect with VAST.Comment: 29 pages, 8 figures. Submitted for publication in Pub. Astron. Soc. Australi

Complex spectrum of phenobarbital effects in a mouse model of neonatal hypoxia-induced seizures

Seizures in neonates, mainly caused by hypoxic-ischemic encephalopathy, are thought to be harmful to the brain. Phenobarbital remains the first line drug therapy for the treatment of suspected neonatal seizures but concerns remain with efficacy and safety. Here we explored the short- and long-term outcomes of phenobarbital treatment in a mouse model of hypoxia-induced neonatal seizures. Seizures were induced in P7 mice by exposure to 5% O-2 for 15 minutes. Immediately after hypoxia, pups received a single dose of phenobarbital (25 mg.kg(-1)) or saline. We observed that after administration of phenobarbital seizure burden and number of seizures were reduced compared to the hypoxic period; however, PhB did not suppress acute histopathology. Behavioural analysis of mice at 5 weeks of age previously subjected to hypoxia-seizures revealed an increase in anxiety-like behaviour and impaired memory function compared to control littermates, and these effects were not normalized by phenobarbital. In a seizure susceptibility test, pups previously exposed to hypoxia, with or without phenobarbital, developed longer and more severe seizures in response to kainic acid injection compared to control mice. Unexpectedly, mice treated with phenobarbital developed less hippocampal damage after kainic acid than untreated counterparts. The present study suggests phenobarbital treatment in immature mice does not improve the long lasting functional deficits induces by hypoxia-induced seizures but, unexpectedly, may reduce neuronal death caused by exposure to a second seizure event in later life

MAGE-A cancer/testis antigens inhibit MDM2 ubiquitylation function and promote increased levels of MDM4

Melanoma antigen A (MAGE-A) proteins comprise a structurally and biochemically similar sub-family of Cancer/Testis antigens that are expressed in many cancer types and are thought to contribute actively to malignancy. MAGE-A proteins are established regulators of certain cancer-associated transcription factors, including p53, and are activators of several RING finger-dependent ubiquitin E3 ligases. Here, we show that MAGE-A2 associates with MDM2, a ubiquitin E3 ligase that mediates ubiquitylation of more than 20 substrates including mainly p53, MDM2 itself, and MDM4, a potent p53 inhibitor and MDM2 partner that is structurally related to MDM2. We find that MAGE-A2 interacts with MDM2 via the N-terminal p53-binding pocket and the RING finger domain of MDM2 that is required for homo/hetero-dimerization and for E2 ligase interaction. Consistent with these data, we show that MAGE-A2 is a potent inhibitor of the E3 ubiquitin ligase activity of MDM2, yet it does not have any significant effect on p53 turnover mediated by MDM2. Strikingly, however, increased MAGE-A2 expression leads to reduced ubiquitylation and increased levels of MDM4. Similarly, silencing of endogenous MAGE-A expression diminishes MDM4 levels in a manner that can be rescued by the proteasomal inhibitor, bortezomid, and permits increased MDM2/MDM4 association. These data suggest that MAGE-A proteins can: (i) uncouple the ubiquitin ligase and degradation functions of MDM2; (ii) act as potent inhibitors of E3 ligase function; and (iii) regulate the turnover of MDM4. We also find an association between the presence of MAGE-A and increased MDM4 levels in primary breast cancer, suggesting that MAGE-A-dependent control of MDM4 levels has relevance to cancer clinically