19,458 research outputs found
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
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