A Decomposition of the Pure Parsimony Problem

We partially order a collection of genotypes so that we can represent the problem of inferring the least number of haplotypes in terms of substructures we call g-lattices. This representation allows us to prove that if the genotypes partition into chains with certain structure, then the NP-Hard problem can be solved efficiently. Even without the specified structure, the decomposition shows how to separate the underlying integer programming model into smaller models

Measuring galaxy cluster masses with CMB lensing using a Maximum Likelihood estimator: Statistical and systematic error budgets for future experiments

We develop a Maximum Likelihood estimator (MLE) to measure the masses of galaxy clusters through the impact of gravitational lensing on the temperature and polarization anisotropies of the cosmic microwave background (CMB). We show that, at low noise levels in temperature, this optimal estimator outperforms the standard quadratic estimator by a factor of two. For polarization, we show that the Stokes Q/U maps can be used instead of the traditional E- and B-mode maps without losing information. We test and quantify the bias in the recovered lensing mass for a comprehensive list of potential systematic errors. Using realistic simulations, we examine the cluster mass uncertainties from CMB-cluster lensing as a function of an experiment's beam size and noise level. We predict the cluster mass uncertainties will be 3 - 6% for SPT-3G, AdvACT, and Simons Array experiments with 10,000 clusters and less than 1% for the CMB-S4 experiment with a sample containing 100,000 clusters. The mass constraints from CMB polarization are very sensitive to the experimental beam size and map noise level: for a factor of three reduction in either the beam size or noise level, the lensing signal-to-noise improves by roughly a factor of two.Comment: 28 pages, 5 figures: figs 2, 3 updated, references added: accepted for publication in JCA

The polarizability model for ferroelectricity in perovskite oxides

This article reviews the polarizability model and its applications to ferroelectric perovskite oxides. The motivation for the introduction of the model is discussed and nonlinear oxygen ion polarizability effects and their lattice dynamical implementation outlined. While a large part of this work is dedicated to results obtained within the self-consistent-phonon approximation (SPA), also nonlinear solutions of the model are handled which are of interest to the physics of relaxor ferroelectrics, domain wall motions, incommensurate phase transitions. The main emphasis is to compare the results of the model with experimental data and to predict novel phenomena.Comment: 55 pages, 35 figure

ISCEV standard for clinical pattern electroretinography—2007 update

The pattern electroretinogram (PERG) is a retinal response evoked by viewing a temporally alternating pattern, usually a black and white checkerboard or grating. The PERG is important in clinical and research applications because it provides information both about retinal ganglion cell function and, because the stimulus is customarily viewed with central fixation, the function of the macula. The PERG can therefore facilitate interpretation of an abnormal pattern VEP by revealing the retinal responses to a similar stimulus to that used for the VEP. However, practitioners may have difficulty choosing between the different techniques for recording the PERG that have been described in the literature. The International Society for Clinical Electrophysiology of Vision published a standard for clinical PERG recording in 2000 to assist practitioners in obtaining good quality reliable responses and to facilitate inter-laboratory communication and comparison. This document is the scheduled revision of that standard

Constraints on the Neutrino Mass from SZ Surveys

Statistical measures of galaxy clusters are sensitive to neutrino masses in the sub-eV range. We explore the possibility of using cluster number counts from the ongoing PLANCK/SZ and future cosmic-variance-limited surveys to constrain neutrino masses from CMB data alone. The precision with which the total neutrino mass can be determined from SZ number counts is limited mostly by uncertainties in the cluster mass function and intracluster gas evolution; these are explicitly accounted for in our analysis. We find that projected results from the PLANCK/SZ survey can be used to determine the total neutrino mass with a (1\sigma) uncertainty of 0.06 eV, assuming it is in the range 0.1-0.3 eV, and the survey detection limit is set at the 5\sigma significance level. Our results constitute a significant improvement on the limits expected from PLANCK/CMB lensing measurements, 0.15 eV. Based on expected results from future cosmic-variance-limited (CVL) SZ survey we predict a 1\sigma uncertainty of 0.04 eV, a level comparable to that expected when CMB lensing extraction is carried out with the same experiment. A few percent uncertainty in the mass function parameters could result in up to a factor \sim 2-3 degradation of our PLANCK and CVL forecasts. Our analysis shows that cluster number counts provide a viable complementary cosmological probe to CMB lensing constraints on the total neutrino mass.Comment: Replaced with a revised version to match the MNRAS accepted version. arXiv admin note: text overlap with arXiv:1009.411

Neutrino Mass Inference from SZ Surveys

The growth of structure in the universe begins at the time of radiation-matter equality, which corresponds to energy scales of $\sim 0.4 eV$. All tracers of dark matter evolution are expected to be sensitive to neutrino masses on this and smaller scales. Here we explore the possibility of using cluster number counts and power spectrum obtained from ongoing SZ surveys to constrain neutrino masses. Specifically, we forecast the capability of ongoing measurements with the PLANCK satellite and the ground-based SPT experiment, as well as measurements with the proposed EPIC satellite, to set interesting bounds on neutrino masses from their respective SZ surveys. We also consider an ACT-like CMB experiment that covers only a few hundred ${\rm deg^{2}}$ also to explore the tradeoff between the survey area and sensitivity and what effect this may have on inferred neutrino masses. We find that for such an experiment a shallow survey is preferable over a deep and low-noise scanning scheme. We also find that projected results from the PLANCK SZ survey can, in principle, be used to determine the total neutrino mass with a ($1\sigma$) uncertainty of $0.28 eV$, if the detection limit of a cluster is set at the $5\sigma$ significance level. This is twice as large as the limits expected from PLANCK CMB lensing measurements. The corresponding limits from the SPT and EPIC surveys are $\sim 0.44 eV$ and $\sim 0.12 eV$, respectively. Mapping an area of 200 deg$^{2}$, ACT measurements are predicted to attain a $1\sigma$ uncertainty of 0.61 eV; expanding the observed area to 4,000 deg$^{2}$ will decrease the uncertainty to 0.36 eV.Comment: 14 pages, 1 figure, 6 table

LoCuSS: A Comparison of Sunyaev-Zel'dovich Effect and Gravitational Lensing Measurements of Galaxy Clusters

We present the first measurement of the relationship between the Sunyaev-Zel'dovich effect signal and the mass of galaxy clusters that uses gravitational lensing to measure cluster mass, based on 14 X-ray luminous clusters at z~0.2 from the Local Cluster Substructure Survey. We measure the integrated Compton y-parameter, Y, and total projected mass of the clusters (M_GL) within a projected clustercentric radius of 350 kpc, corresponding to mean overdensities of 4000-8000 relative to the critical density. We find self-similar scaling between M_GL and Y, with a scatter in mass at fixed Y of 32%. This scatter exceeds that predicted from numerical cluster simulations, however, it is smaller than comparable measurements of the scatter in mass at fixed T_X. We also find no evidence of segregation in Y between disturbed and undisturbed clusters, as had been seen with T_X on the same physical scales. We compare our scaling relation to the Bonamente et al. relation based on mass measurements that assume hydrostatic equilibrium, finding no evidence for a hydrostatic mass bias in cluster cores (M_GL = 0.98+/-0.13 M_HSE), consistent with both predictions from numerical simulations and lensing/X-ray-based measurements of mass-observable scaling relations at larger radii. Overall our results suggest that the Sunyaev-Zel'dovich effect may be less sensitive than X-ray observations to the details of cluster physics in cluster cores.Comment: Minor changes to match published version: 2009 ApJL 701:114-11

CMB-S4 Science Book, First Edition

This book lays out the scientific goals to be addressed by the next-generation ground-based cosmic microwave background experiment, CMB-S4, envisioned to consist of dedicated telescopes at the South Pole, the high Chilean Atacama plateau and possibly a northern hemisphere site, all equipped with new superconducting cameras. CMB-S4 will dramatically advance cosmological studies by crossing critical thresholds in the search for the B-mode polarization signature of primordial gravitational waves, in the determination of the number and masses of the neutrinos, in the search for evidence of new light relics, in constraining the nature of dark energy, and in testing general relativity on large scales

A novel insertion mutation in the cartilage-derived morphogenetic protein-1 (CDMP1) gene underlies Grebe-type chondrodysplasia in a consanguineous Pakistani family

<p>Abstract</p> <p>Background</p> <p>Grebe-type chondrodysplasia (GCD) is a rare autosomal recessive syndrome characterized by severe acromesomelic limb shortness with non-functional knob like fingers resembling toes. Mutations in the cartilage-derived morphogenetic protein 1 (<it>CDMP1</it>) gene cause Grebe-type chondrodysplasia.</p> <p>Methods</p> <p>Genotyping of six members of a Pakistani family with Grebe-type chondrodysplasia, including two affected and four unaffected individuals, was carried out by using polymorphic microsatellite markers, which are closely linked to <it>CDMP1 </it>locus on chromosome 20q11.22. To screen for a mutation in <it>CDMP1 </it>gene, all of its coding exons and splice junction sites were PCR amplified from genomic DNA of affected and unaffected individuals of the family and sequenced directly in an ABI Prism 310 automated DNA sequencer.</p> <p>Results</p> <p>Genotyping results showed linkage of the family to <it>CDMP1 </it>locus. Sequence analysis of the <it>CDMP1 </it>gene identified a novel four bases insertion mutation (1114insGAGT) in exon 2 of the gene causing frameshift and premature termination of the polypeptide.</p> <p>Conclusion</p> <p>We describe a 4 bp novel insertion mutation in <it>CDMP1 </it>gene in a Pakistani family with Grebe-type chondrodysplasia. Our findings extend the body of evidence that supports the importance of <it>CDMP1 </it>in the development of limbs.</p