Finding the center reliably: robust patterns of developmental gene expression

We investigate a mechanism for the robust identification of the center of a developing biological system. We assume the existence of two morphogen gradients, an activator emanating from the anterior, and a co-repressor from the posterior. The co-repressor inhibits the action of the activator in switching on target genes. We apply this system to Drosophila embryos, where we predict the existence of a hitherto undetected posterior co-repressor. Using mathematical modelling, we show that a symmetric activator-co-repressor model can quantitatively explain the precise mid-embryo expression boundary of the hunchback gene, and the scaling of this pattern with embryo size.Comment: 4 pages, 3 figure

Linear formulation for the Maximum Expected Coverage Location Model with fractional coverage

Since ambulance providers are responsible for life-saving medical care at the scene in emergency situations and since response times are important in these situations, it is crucial that ambulances are located in such a way that good coverage is provided throughout the region. Most models that are developed to determine good base locations assume strict 0-1 coverage given a fixed base location and demand point. However, multiple applications require fractional coverage. Examples include stochastic, instead of fixed, response times and survival probabilities. Straightforward adaption of the well-studied MEXCLP to allow for coverage probabilities results in a non-linear formulation in integer variables, limiting the size of instances that can be solved by the model. In this paper, we present a linear integer programming formulation for the problem. We show that the computation time of the linear formulation is significantly shorter than that for the non-linear formulation. As a consequence, we are able to solve larger instances. Finally, we will apply the model, in the setting of stochastic response times, to the region of Amsterdam, the Netherlands

Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival

MiRNAs regulate gene expression at a post-transcriptional level and their dysregulation can play major roles in the pathogenesis of many different forms of cancer, including neuroblastoma, an often fatal paediatric cancer originating from precursor cells of the sympathetic nervous system. We have analyzed a set of neuroblastoma (n = 145) that is broadly representative of the genetic subtypes of this disease for miRNA expression (430 loci by stem-loop RT qPCR) and for DNA copy number alterations (array CGH) to assess miRNA involvement in disease pathogenesis. The tumors were stratified and then randomly split into a training set (n = 96) and a validation set (n = 49) for data analysis. Thirty-seven miRNAs were significantly over-or under-expressed in MYCN amplified tumors relative to MYCN single copy tumors, indicating a potential role for the MYCN transcription factor in either the direct or indirect dysregulation of these loci. In addition, we also determined that there was a highly significant correlation between miRNA expression levels and DNA copy number, indicating a role for large-scale genomic imbalances in the dysregulation of miRNA expression. In order to directly assess whether miRNA expression was predictive of clinical outcome, we used the Random Forest classifier to identify miRNAs that were most significantly associated with poor overall patient survival and developed a 15 miRNA signature that was predictive of overall survival with 72.7% sensitivity and 86.5% specificity in the validation set of tumors. We conclude that there is widespread dysregulation of miRNA expression in neuroblastoma tumors caused by both over-expression of the MYCN transcription factor and by large-scale chromosomal imbalances. MiRNA expression patterns are also predicative of clinical outcome, highlighting the potential for miRNA mediated diagnostics and therapeutics

The Evolution of Early-Type Galaxies in Distant Clusters III.: M/L_V Ratios in the z=0.33 Cluster CL1358+62

Keck spectroscopy and Hubble Space Telescope WFPC2 imaging over a 1.5x1.5 Mpc field of CL1358+62 at z=0.33 are used to study the Fundamental Plane of galaxies based on a new, large sample of 53 galaxies. First, we have constructed the Fundamental Plane for the 30 E and S0 galaxies and find that it has the following shape: r_e = sigma**(1.31+-0.13) * _e**(-0.86+-0.10), similar to that found locally. The 1-sigma intrinsic scatter about this plane is 14% in M/L(V), comparable to that observed in Coma. We conclude that these E and S0 galaxies are structurally mature and homogeneous, like those observed in nearby clusters. The M/L(V) ratios of these early-type galaxies are offset from the Coma Fundamental Plane by delta log M/L(V) = -0.13+- 0.03 (q0=0.1), indicative of mild luminosity evolution. This evolution suggests a formation epoch for the stars of z > 1. We have also analyzed the M/L(V) ratios of galaxies of type S0/a and later. These early-type spirals follow a different plane from the E and S0 galaxies, with a scatter that is twice as large as the scatter for the E/S0s. The difference in the tilt between the plane of the spirals and the plane of the E/S0s is shown to be due to a systematic correlation of velocity dispersion with residual from the plane of the early-type galaxies. These residuals also correlate with the residuals from the Color-Magnitude relation. Thus for spirals in clusters, we see a systematic variation in the luminosity-weighted mean properties of the stellar populations with central velocity dispersion. If this is a relative age trend, then luminosity-weighted age is positively correlated with dispersion. [abridged version]Comment: 18 pages, 8 figures; revised version, accepted by ApJ on 13 August 199

The Evolution of Early-Type Galaxies in Distant Clusters II: Internal Kinematics of 55 Galaxies in the z=0.33 Cluster CL1358+62

We define a large sample of galaxies for use in a study of the fundamental plane in the intermediate redshift cluster CL1358+62 at $z=0.33$. We have analyzed high resolution spectra for 55 members of the cluster. The data were acquired with the Low Resolution Imaging Spectrograph on the Keck I 10m telescope. A new algorithm for measuring velocity dispersions is presented and used to measure the internal kinematics of the galaxies. This algorithm has been tested against the Fourier Fitting method so the data presented here can be compared with those measured previously in nearby galaxies. We have measured central velocity dispersions suitable for use in a fundamental plane analysis. The data have high $S/N$ and the resulting random errors on the dispersions are very low, typically $<5$. Uncertainties due to mismatch of the stellar templates has been minimized through several tests and the total systematic error is of order \about 5%. Good seeing enabled us to measure velocity dispersion profiles and rotation curves for most of the sample and although a large fraction of the galaxies display a high level of rotation, the gradients of the total second moment of the kinematics are all very regular and similar to those in nearby galaxies. We conclude that the data therefore can be reliably corrected for aperture size in a manner consistent with nearby galaxy samples.Comment: 30 pages, 13 figures; for publication in the ApJ (accepted on 23 August 1999

Virgo cluster early-type dwarf galaxies with the Sloan Digital Sky Survey. II. Early-type dwarfs with central star formation

Despite the common picture of an early-type dwarf (dE) as a quiescent galaxy with no star formation and little gas, we identify 23 dEs that have blue central colors caused by recent or ongoing star formation in our sample of 476 Virgo cluster dEs. In addition, 14 objects that were mostly classified as (candidate) BCDs have similar properties. Among the certain cluster members, the dEs with blue centers reach a fraction of more than 15% of the dE population at brighter (B<=16) magnitudes. A spectral analysis of the centers of 16 galaxies reveals in all cases an underlying old population that dominates the mass, with M(old)>=90% for all but one object. Therefore the majority of these galaxies will appear like ordinary dEs within ~one Gigayear or less after the last episode of star formation. Their overall gas content is less than that of dwarf irregular galaxies, but higher than that of ordinary dEs. Their flattening distribution suggests the shape of a thick disk, similar to what has been found for dEs with disk features in Paper I of this series. Their projected spatial distribution shows no central clustering, and their distribution with projected local density follows that of irregular galaxies, indicative of an unrelaxed population. This is corroborated by their velocity distribution, which displays two side peaks characteristic of recent infall. We discuss possible formation mechanisms (ram-pressure stripping, tidally induced star formation, harassment) that might be able to explain both the disk shape and the central star formation of the dEs with blue centers.Comment: 16 pages + 15 figures. Accepted for publication in AJ. We recommend downloading the full resolution version from http://www.virgo-cluster.com/lisker2006b.ps.g

Suitability versus fidelity for rating single-photon guns

The creation of specified quantum states is important for most, if not all, applications in quantum computation and communication. The quality of the state preparation is therefore an essential ingredient in any assessment of a quantum-state gun. We show that the fidelity, under the standard definitions is not sufficient to assess quantum sources, and we propose a new measure of suitability that necessarily depends on the application for the source. We consider the performance of single-photon guns in the context of quantum key distribution (QKD) and linear optical quantum computation. Single-photon sources for QKD need radically different properties than sources for quantum computing. Furthermore, the suitability for single-photon guns is discussed explicitly in terms of experimentally accessible criteria.Comment: 4 pages, 2 figures Revised per referee suggestion

The Fundamental Plane at z=1.27: First Calibration of the Mass Scale of Red Galaxies at Redshifts z>1

We present results on the Fundamental Plane (FP) of early-type galaxies in the cluster RDCS J0848+4453 at z=1.27. Internal velocity dispersions of three K-selected early-type galaxies are determined from deep Keck spectra. Structural parameters are determined from HST NICMOS images. The galaxies show substantial offsets from the FP of the nearby Coma cluster, as expected from passive evolution of their stellar populations. The offsets from the FP can be expressed as offsets in M/L ratio. The M/L ratios of the two most massive galaxies are consistent with an extrapolation of results obtained at z=0.02-0.83. The evolution of early-type galaxies with masses >10^11 M_sun is well described by ln M/L(B) = (-1.06 +- 0.09) z, corresponding to passive evolution of -1.50 +- 0.13 mag at z=1.3. Ignoring selection effects, the best fitting stellar formation redshift is z*=2.6, corresponding to a luminosity weighted age at the epoch of observation of ~2 Gyr. The M/L ratios of these two galaxies are also in excellent agreement with predictions from models that include progenitor bias. The third galaxy is a factor ~10 less massive than the other two, shows strong Balmer absorption lines in its spectrum, and is offset from the Coma Fundamental Plane by 2.9 mag in rest-frame B. Despite their large range in M/L ratios, all three galaxies fall in the ``Extremely Red Object'' (ERO) class with I-H>3 and R-K>5, and our results show that it is hazardous to use simple models for converting luminosity to mass for these objects. Measurements of M/L ratios at high redshift can be considered first steps to empirically disentangle luminosity and mass evolution at the high mass end of the galaxy population, lifting an important degeneracy in the interpretation of evolution of the luminosity function. [SHORTENED]Comment: Accepted for publication in the Astrophysical Journa