Huffman Coding with Letter Costs: A Linear-Time Approximation Scheme

We give a polynomial-time approximation scheme for the generalization of Huffman Coding in which codeword letters have non-uniform costs (as in Morse code, where the dash is twice as long as the dot). The algorithm computes a (1+epsilon)-approximate solution in time O(n + f(epsilon) log^3 n), where n is the input size

Increased Risk for Aplastic Anemia and Myelodysplastic Syndrome in Individuals Lacking Glutathione S-Transferase Genes

BACKGROUND: Aplastic anemia (AA) and myelodysplastic syndrome (MDS) are marrow failure states that may be associated with chromosomal instability. An absence of the glutathione S-transferase (GST) enzyme may genetically predispose individuals to AA or MDS. PROCEDURE AND RESULTS: To test this hypothesis, we determined the GSTM1 and GSTT1 genotypes in a total of 196 patients using multiplex PCR. The GSTT1 null genotype was found to be overrepresented in Caucasian, Asian, and Hispanic patients with either AA or MDS. We confirmed a difference in the expected frequency of the GSTM1 null genotype in Caucasian MDS patients. The double null GSTM1/GSTT1 genotype was also overrepresented in Caucasian AA and MDS patients. In our population, 26% of AA patients and 40% of MDS patients had a chromosomal abnormality identified by karyotype or FISH analyses for chromosomes 7 and 8. Patients with AA and the GSTT1 null genotype had an increased frequency of chromosomal abnormalities (P = 0.003). CONCLUSION: There seems to be an increased risk for AA and MDS in individuals lacking GSTT1 or both GSTM1/GSTT1

Nonequilibrium work on spin glasses in longitudinal and transverse fields

We derive a number of exact relations between equilibrium and nonequilibrium quantities for spin glasses in external fields using the Jarzynski equality and gauge symmetry. For randomly-distributed longitudinal fields, a lower bound is established for the work done on the system in nonequilibrium processes, and identities are proven to relate equilibrium and nonequilibrium quantities. In the case of uniform transverse fields, identities are proven between physical quantities and exponentiated work done to the system at different parts of the phase diagram with the context of quantum annealing in mind. Additional relations are given, which relate the exponentiated work in quantum and simulated (classical) annealing. It is also suggested that the Jarzynski equality may serve as a guide to develop a method to perform quantum annealing under non-adiabatic conditions.Comment: 17 pages, 5 figures, submitted to JPS

On a Linear Program for Minimum-Weight Triangulation

Minimum-weight triangulation (MWT) is NP-hard. It has a polynomial-time constant-factor approximation algorithm, and a variety of effective polynomial- time heuristics that, for many instances, can find the exact MWT. Linear programs (LPs) for MWT are well-studied, but previously no connection was known between any LP and any approximation algorithm or heuristic for MWT. Here we show the first such connections: for an LP formulation due to Dantzig et al. (1985): (i) the integrality gap is bounded by a constant; (ii) given any instance, if the aforementioned heuristics find the MWT, then so does the LP.Comment: To appear in SICOMP. Extended abstract appeared in SODA 201

A Nearly Linear-Time PTAS for Explicit Fractional Packing and Covering Linear Programs

We give an approximation algorithm for packing and covering linear programs (linear programs with non-negative coefficients). Given a constraint matrix with n non-zeros, r rows, and c columns, the algorithm computes feasible primal and dual solutions whose costs are within a factor of 1+eps of the optimal cost in time O((r+c)log(n)/eps^2 + n).Comment: corrected version of FOCS 2007 paper: 10.1109/FOCS.2007.62. Accepted to Algorithmica, 201

Functional characterization of telomerase RNA variants found in patients with hematologic disorders

Human telomerase uses a specific cellular RNA, called hTERC, as the template to synthesize telomere repeats at chromosome ends. Approximately 10% to 15% of patients with aplastic anemia or other bone marrow failure syndromes are carriers of hTERC sequence variants whose functional significance, in most cases, is unknown. We screened 10 reported and 2 newly discovered hTERC variants from such patients and found that 10 of these negatively affected telomerase enzymatic function when they were used to reconstitute telomerase enzymatic function in human cells. Most functional deficits were due to perturbations of hTERC secondary structure and correlated well with the degrees of telomere shortening and reduced telomerase activity observed in peripheral blood lymphocytes of the representative patients. We also found no evidence of dominant-negative activity in any of the mutants. Therefore, loss of telomerase activity and of telomere maintenance resulting from inherited hTERC mutations may limit marrow stem cell renewal and predispose some patients to bone marrow failure. (Blood. 2005;105: 2332-2339

Discovery of a Low Mass Bipolar Molecular Outflow from L1014-IRS with the Submillimeter Array

Using the Submillimeter Array we report the discovery of a compact low mass bipolar molecular outflow from L1014-IRS and confirm its association with the L1014 dense core at 200 pc. Consequently, L1014-IRS is the lowest luminosity (L \~0.09 Lsun) and perhaps the lowest mass source known to be driving a bipolar molecular outflow, which is one of the smallest known in size (~500 AU), mass (< 10^{-4} Msun), and energetics (e.g., force < 10^{-7} Msun km/s/yr).Comment: 11 pages, 3 figures, to appear in ApJ Letter

The Bolocam Galactic Plane Survey: Survey Description and Data Reduction

We present the Bolocam Galactic Plane Survey (BGPS), a 1.1 mm continuum survey at 33" effective resolution of 170 square degrees of the Galactic Plane visible from the northern hemisphere. The survey is contiguous over the range -10.5 < l < 90.5, |b| < 0.5 and encompasses 133 square degrees, including some extended regions |b| < 1.5. In addition to the contiguous region, four targeted regions in the outer Galaxy were observed: IC1396, a region towards the Perseus Arm, W3/4/5, and Gem OB1. The BGPS has detected approximately 8400 clumps over the entire area to a limiting non-uniform 1-sigma noise level in the range 11 to 53 mJy/beam in the inner Galaxy. The BGPS source catalog is presented in a companion paper (Rosolowsky et al. 2010). This paper details the survey observations and data reduction methods for the images. We discuss in detail the determination of astrometric and flux density calibration uncertainties and compare our results to the literature. Data processing algorithms that separate astronomical signals from time-variable atmospheric fluctuations in the data time-stream are presented. These algorithms reproduce the structure of the astronomical sky over a limited range of angular scales and produce artifacts in the vicinity of bright sources. Based on simulations, we find that extended emission on scales larger than about 5.9' is nearly completely attenuated (> 90%) and the linear scale at which the attenuation reaches 50% is 3.8'. Comparison with other millimeter-wave data sets implies a possible systematic offset in flux calibration, for which no cause has been discovered. This presentation serves as a companion and guide to the public data release through NASA's Infrared Processing and Analysis Center (IPAC) Infrared Science Archive (IRSA). New data releases will be provided through IPAC IRSA with any future improvements in the reduction.Comment: Accepted for publication in Astrophysical Journal Supplemen