Probabilities of spurious connections in gene networks: Application to expression time series

Motivation: The reconstruction of gene networks from gene expression microarrays is gaining popularity as methods improve and as more data become available. The reliability of such networks could be judged by the probability that a connection between genes is spurious, resulting from chance fluctuations rather than from a true biological relationship. Results: Unlike the false discovery rate and positive false discovery rate, the decisive false discovery rate (dFDR) is exactly equal to a conditional probability without assuming independence or the randomness of hypothesis truth values. This property is useful not only in the common application to the detection of differential gene expression, but also in determining the probability of a spurious connection in a reconstructed gene network. Estimators of the dFDR can estimate each of three probabilities: 1. The probability that two genes that appear to be associated with each other lack such association. 2. The probability that a time ordering observed for two associated genes is misleading. 3. The probability that a time ordering observed for two genes is misleading, either because they are not associated or because they are associated without a lag in time. The first probability applies to both static and dynamic gene networks, and the other two only apply to dynamic gene networks. Availability: Cross-platform software for network reconstruction, probability estimation, and plotting is free from http://www.davidbickel.com as R functions and a Java application.Comment: Like q-bio.GN/0404032, this was rejected in March 2004 because it was submitted to the math archive. The only modification is a corrected reference to q-bio.GN/0404032, which was not modified at al

A Look At Three Different Scenarios for Bulge Formation

In this paper, we present three qualitatively different scenarios for bulge formation: a secular evolution model in which bulges form after disks and undergo several central starbursts, a primordial collapse model in which bulges and disks form simultaneously, and an early bulge formation model in which bulges form prior to disks. We normalize our models to the local z=0 observations of de Jong & van der Kruit (1994) and Peletier & Balcells (1996) and make comparisons with high redshift observations. We consider model predictions relating directly to bulge-to-disk properties. As expected, smaller bulge-to-disk ratios and bluer bulge colors are predicted by the secular evolution model at all redshifts, although uncertainties in the data are currently too large to differentiate strongly between the models.Comment: 19 pages, 6 figures, accepted for publication in the Astrophysical Journa

The Trouble with Hubble Types in the Virgo Cluster

Quantitative measures of central light concentration and star formation activity are derived from R and Halpha surface photometry of 84 bright S0-Scd Virgo Cluster and isolated spiral galaxies. For isolated spirals, there is a good correlation between these two parameters and assigned Hubble types. In the Virgo Cluster, the correlation between central light concentration and star formation activity is significantly weaker. Virgo Cluster spirals have systematically reduced global star formation with respect to isolated spirals, with severe reduction in the outer disk, but normal or enhanced activity in the inner disk. Assigned Hubble types are thus inadequate to describe the range in morphologies of bright Virgo Cluster spirals. In particular, spirals with reduced global star formation activity are often assigned misleading early-type classifications, irrespective of their central light concentrations. 45+-25% of the galaxies classified as Sa in the Virgo Cluster sample have central light concentrations more characteristic of isolated Sb-Sc galaxies. The misleading classification of low concentration galaxies with low star formation rates as early-type spirals may account for part of the excess of `early-type' spiral galaxies in clusters. Thus the morphology-density relationship is not all due to a systematic increase in the bulge-to-disk ratio with environmental density.Comment: Accepted for publication in ApJ Letters. Latex aaspp4.sty, 9 pages, 2 Postscript (embedded) figures. Also available at http://www.astro.yale.edu/koopmann/preprint.htm

Dark and Baryonic Matter in Bright Spiral Galaxies: I.Near-infrared and Optical Broadband Surface Photometry of 30 Galaxies

We present photometrically calibrated images and surface photometry in the B, V, R, J, H, and K-bands of 25, and in the g, r, and K-bands of 5 nearby bright (Bo_T<12.5 mag) spiral galaxies with inclinations between 30-65 degrees spanning the Hubble Sequence from Sa to Scd. Data are from The Ohio State University Bright Spiral Galaxy Survey, the Two Micron All Sky Survey, and the Sloan Digital Sky Survey Second Data Release. Radial surface brightness profiles are extracted, and integrated magnitudes are measured from the profiles. Axis ratios, position angles, and scale lengths are measured from the near-infrared images. A 1-dimensional bulge/disk decomposition is performed on the near-infrared images of galaxies with a non-negligible bulge component, and an exponential disk is fit to the radial surface brightness profiles of the remaining galaxies.Comment: 28 page

Morphological Evolution of Distant Galaxies from Adaptive Optics Imaging

We report here on a sample of resolved, infrared images of galaxies at z~0.5 taken with the 10-m Keck Telescope's Adaptive Optics (AO) system. We regularly achieve a spatial resolution of 0.05'' and are thus able to resolve both the disk and bulge components. We have extracted morphological information for ten galaxies and compared their properties to those of a local sample. The selection effects of both samples were explicitly taken into account in order to derive the unbiased result that disks at z~0.5 are ~0.6 mag arcsec^-2 brighter than, and about the same size as, local disks. The no-luminosity-evolution case is ruled out at 90% confidence. We also find, in a more qualitative analysis, that the bulges of these galaxies have undergone a smaller amount of surface brightness evolution and have also not changed significantly in size from z~0.5 to today. This is the first time this type of morphological evolution has been measured in the infrared and it points to the unique power of AO in exploring galaxy evolution.Comment: 27 pages, 7figures, 2 tables. Accepted for publication in the Astrophysical Journa

Structure of Disk Dominated Galaxies I. Bulge/Disk Parameters, Simulations, and Secular Evolution

(Abridged) A robust analysis of galaxy structural parameters, based on the modeling of bulge and disk brightnesses in the BVRH bandpasses, is presented for 121 face-on and moderately inclined late-type spirals. Each surface brightness (SB) profile is decomposed into a sum of a generalized Sersic bulge and an exponential disk. The reliability and limitations of our bulge-to-disk (B/D) decompositions are tested with extensive simulations of galaxy brightness profiles (1D) and images (2D). Galaxy types are divided into 3 classes according to their SB profile shapes; Freeman Type-I and Type-II, and a third ``Transition'' class for galaxies whose profiles change from Type-II in the optical to Type-I in the infrared. We discuss possible interpretations of Freeman Type-II profiles. The Sersic bulge shape parameter for nearby Type-I late-type spirals shows a range between n=0.1-2 but, on average, the underlying surface density profile for the bulge and disk of these galaxies is adequately described by a double-exponential distribution. We confirm a coupling between the bulge and disk with a scale length ratio r_e/h=0.22+/-0.09, or h_bulge/h_disk=0.13+/-0.06 for late-type spirals, in agreement with recent N-body simulations of disk formation and models of secular evolution. This ratio increases from ~0.20 for late-type spirals to ~0.24 for earlier types. The similar scaling relations for early and late-type spirals suggest comparable formation and/or evolution scenarios for disk galaxies of all Hubble types.Comment: 78 pages with 23 embedded color figures + tables of galaxy structural parameters. Accepted for publication in the Astrophysical Journal. The interested reader is strongly encouraged to ignore some of the low res figures within; instead, download the high resolution version from http://www.astro.ubc.ca/people/courteau/public/macarthur02_disks.ps.g

Stabilizing nuclear spins around semiconductor electrons via the interplay of optical coherent population trapping and dynamic nuclear polarization

We experimentally demonstrate how coherent population trapping (CPT) for donor-bound electron spins in GaAs results in autonomous feedback that prepares stabilized states for the spin polarization of nuclei around the electrons. CPT was realized by excitation with two lasers to a bound-exciton state. Transmission studies of the spectral CPT feature on an ensemble of electrons directly reveal the statistical distribution of prepared nuclear spin states. Tuning the laser driving from blue to red detuned drives a transition from one to two stable states. Our results have importance for ongoing research on schemes for dynamic nuclear spin polarization, the central spin problem and control of spin coherence.Comment: 5 pages, 4 figure

The Potential Of High-Resolution BAC-FISH In Banana Breeding

Abstract The genetic complexity in the genus Musa has been subject of study in many breeding programs worldwide. Parthenocarpy, female sterility, polyploidy in different cultivars and limited amount of genetic and genomic information make the production of new banana cultivars difficult and time consuming. In addition, it is known that part of the cultivars and related wild species in the genus contain numerous chromosomal rearrangements. In order to produce new cultivars more effectively breeders must better understand the genetic differences of the potential crossing parents for introgression hybridization, but extensive genetic information is lacking. As an alternative to achieve information on genetic collinearity we make use of modern chromosome map technology known as high-resolution fluorescent in situ hybridization (FISH). This article presents the technical aspects and applications of such a technology in Musa species. The technique deals with BAC clone positioning on pachytene chromosomes of Calcutta 4 (Musa acuminata ssp. burmanicoides, A genome group, section Eumusa) and M. velutina (section Rodochlamys). Pollen mother cells digestion with pectolytic enzymes and maceration with acetic acid were optimized for making cell spread preparations appropriate for FISH. As an example of this approach we chose BAC clones that contain markers to known resistance genes and hybridize them for establishing their relative positions on the two species. Technical challenges for adapting existing protocols to the banana cells are presented. We also discuss how this technique can be instrumental for validating collinearity between potential crossing parents and how the method can be helpful in future mapping initiatives, and how this method allows identification of chromosomal rearrangements between related Musa species and cultivar

The Spitzer View of Low-Metallicity Star Formation: II. Mrk 996, a Blue Compact Dwarf Galaxy with an Extremely Dense Nucleus

(abridged) We present new Spitzer, UKIRT and MMT observations of the blue compact dwarf galaxy (BCD) Mrk 996, with an oxygen abundance of 12+log(O/H)=8.0. This galaxy has the peculiarity of possessing an extraordinarily dense nuclear star-forming region, with a central density of ~10^6 cm^{-3}. The nuclear region of Mrk 996 is characterized by several unusual properties: a very red color J-K = 1.8, broad and narrow emission-line components, and ionizing radiation as hard as 54.9 eV, as implied by the presence of the OIV 25.89 micron line. The nucleus is located within an exponential disk with colors consistent with a single stellar population of age >1 Gyr. The infrared morphology of Mrk 996 changes with wavelength. The IRS spectrum shows strong narrow Polycyclic Aromatic Hydrocarbon (PAH) emission, with narrow line widths and equivalent widths that are high for the metallicity of Mrk 996. Gaseous nebular fine-structure lines are also seen. A CLOUDY model requires that they originate in two distinct HII regions: a very dense HII region of radius ~580 pc with densities declining from ~10^6 at the center to a few hundreds cm^{-3} at the outer radius, where most of the optical lines arise; and a HII region with a density of ~300 cm^{-3} that is hidden in the optical but seen in the MIR. We suggest that the infrared lines arise mainly in the optically obscured HII region while they are strongly suppressed by collisional deexcitation in the optically visible one. The hard ionizing radiation needed to account for the OIV 25.89 micron line is most likely due to fast radiative shocks propagating in an interstellar medium. A hidden population of Wolf-Rayet stars of type WNE-w or a hidden AGN as sources of hard ionizing radiation are less likely possibilities.Comment: 48 pages, 13 figures, accepted for publication in the Astrophysical Journa