RadOnc: An R Package for Analysis of Dose-Volume Histogram and Three-Dimensional Structural Data

Purpose/Objectives: Dose volume histogram (DVH) data are generally analyzed within the context of a treatment planning system (TPS) on a per-patient basis, with evaluation of single-plan or comparative dose distributions. However, TPS software generally cannot perform simultaneous comparative dosimetry among a cohort of patients. The same limitations apply to parallel analyses of three-dimensional structures and other clinical data. Materials/Methods: We developed a suite of tools ("RadOnc" package) using R statistical software to better compare pooled DVH data and empower analysis of structure data and clinical correlates. Representative patient data were identified among previously analyzed adult (n=13) and pediatric (n=1) cohorts and these data were used to demonstrate the performance and functionality of the RadOnc package. Results: The RadOnc package facilitates DVH data import from the TPS and includes automated methods for DVH visualization, dosimetric parameter extraction, statistical comparison among multiple DVHs, basic three-dimensional structural processing, and visualization tools to enable customizable production of publication-quality images. Conclusions: The RadOnc package provides a potent clinical research tool with the ability to integrate robust statistical software and dosimetric data from cohorts of patients. It is made freely available to the community for their current use and remains under active development

An Invertible Transform for Efficient String Matching in Labeled Digraphs

Let G = (V, E) be a digraph where each vertex is unlabeled, each edge is labeled by a character in some alphabet ?, and any two edges with both the same head and the same tail have different labels. The powerset construction gives a transform of G into a weakly connected digraph G\u27 = (V\u27, E\u27) that enables solving the decision problem of whether there is a walk in G matching an arbitrarily long query string q in time linear in |q| and independent of |E| and |V|. We show G is uniquely determined by G\u27 when for every v_? ? V, there is some distinct string s_? on ? such that v_? is the origin of a closed walk in G matching s_?, and no other walk in G matches s_? unless it starts and ends at v_?. We then exploit this invertibility condition to strategically alter any G so its transform G\u27 enables retrieval of all t terminal vertices of walks in the unaltered G matching q in O(|q| + t log |V|) time. We conclude by proposing two defining properties of a class of transforms that includes the Burrows-Wheeler transform and the transform presented here

A numerical study of the correspondence between paths in a causal set and geodesics in the continuum

This paper presents the results of a computational study related to the path-geodesic correspondence in causal sets. For intervals in flat spacetimes, and in selected curved spacetimes, we present evidence that the longest maximal chains (the longest paths) in the corresponding causal set intervals statistically approach the geodesic for that interval in the appropriate continuum limit.Comment: To the celebration of the 60th birthday of Rafael D. Sorki

Fully gapped superconductivity in Ni-pnictide superconductors BaNi2As2 and SrNi2P2

We have performed low-temperature specific heat $C$ and thermal conductivity $\kappa$ measurements on the Ni-pnictide superconductors BaNi$_2$As$_2$ ($T_\mathrm{c}$=0.7 K and SrNi$_2$P$_2$ ($T_\mathrm{c}$=1.4 K). The temperature dependences $C(T)$ and $\kappa(T)$ of the two compounds are similar to the results of a number of s-wave superconductors. Furthermore, the concave field responses of the residual $\kappa$ for BaNi$_2$As$_2$ rules out the presence of nodes on the Fermi surfaces. We postulate that fully gapped superconductivity could be universal for Ni-pnictide superconductors. Specific heat data on Ba$_{0.6}$La$_{0.4}$Ni$_2$As$_2$ shows a mild suppression of $T_\mathrm{c}$ and $H_\mathrm{c2}$ relative to BaNi$_2$As$_2$.Comment: 5 pages, 3 figures, to be published in J. Phys.: Conf. Se

Variable Stars in the Globular Cluster M5. Application of the Image Subtraction Method

We present $V$-band light curves of 61 variables from the core of the globular cluster M5 obtained using a newly developed image subtraction method (ISM). Four of these variables were previously unknown. Only 26 variables were found in the same field using photometry obtained with DoPHOT software. Fourier parameters of the ISM light curves have relative errors up to 20 times smaller than parameters measured from DoPHOT photometry. We conclude that the new method is very promising for searching for variable stars in the cores of the globular clusters and gives very accurate relative photometry with quality comparable to photometry obtained by HST. We also show that the variable V104 is not an eclipsing star as has been suggested, but is an RRc star showing non-radial pulsations.Comment: submitted to MNRAS, 9 pages, 4 figure

Cytosine Methylation Dysregulation in Neonates Following Intrauterine Growth Restriction

Perturbations of the intrauterine environment can affect fetal development during critical periods of plasticity, and can increase susceptibility to a number of age-related diseases (e.g., type 2 diabetes mellitus; T2DM), manifesting as late as decades later. We hypothesized that this biological memory is mediated by permanent alterations of the epigenome in stem cell populations, and focused our studies specifically on DNA methylation in CD34+ hematopoietic stem and progenitor cells from cord blood from neonates with intrauterine growth restriction (IUGR) and control subjects.Our epigenomic assays utilized a two-stage design involving genome-wide discovery followed by quantitative, single-locus validation. We found that changes in cytosine methylation occur in response to IUGR of moderate degree and involving a restricted number of loci. We also identify specific loci that are targeted for dysregulation of DNA methylation, in particular the hepatocyte nuclear factor 4alpha (HNF4A) gene, a well-known diabetes candidate gene not previously associated with growth restriction in utero, and other loci encoding HNF4A-interacting proteins.Our results give insights into the potential contribution of epigenomic dysregulation in mediating the long-term consequences of IUGR, and demonstrate the value of this approach to studies of the fetal origin of adult disease

Radio Astrometry Of The Triple Systems Algol And UX Arietis

We have used multi-epoch long-baseline radio interferometry to determine the proper motion and orbital elements of Algol and UX Arietis, two radio-bright, close binary stellar systems with distant tertiary components. For Algol, we refine the proper motion and outer orbit solutions, confirming the recent result of Zavala et al. (2010) that the inner orbit is retrograde. The radio centroid closely tracks the motion of the KIV secondary. In addition, the radio morphology varies from double-lobed at low flux level to crescent-shaped during active periods. These results are most easily interpreted as synchrotron emission from a large, co-rotating meridional loop centered on the K-star. If this is correct, it provides a radio-optical frame tie candidate with an uncertainty {\pm}0.5 mas. For UX Arietis, we find a outer orbit solution that accounts for previous VLBI observations of an acceleration term in the proper motion fit. The outer orbit solution is also consistent with previously published radial velocity curves and speckle observations of a third body. The derived tertiary mass, 0.75 solar masses, is consistent with the K1 main-sequence star detected spectroscopically. The inner orbit solution favors radio emission from the active K0IV primary only. The radio morphology, consisting of a single, partially resolved emission region, may be associated with the persistent polar spot observed using Doppler imaging

Gravitational wave radiometry: Mapping a stochastic gravitational wave background

The problem of the detection and mapping of a stochastic gravitational wave background (SGWB), either of cosmological or astrophysical origin, bears a strong semblance to the analysis of CMB anisotropy and polarization. The basic statistic we use is the cross-correlation between the data from a pair of detectors. In order to `point' the pair of detectors at different locations one must suitably delay the signal by the amount it takes for the gravitational waves (GW) to travel to both detectors corresponding to a source direction. Then the raw (observed) sky map of the SGWB is the signal convolved with a beam response function that varies with location in the sky. We first present a thorough analytic understanding of the structure of the beam response function using an analytic approach employing the stationary phase approximation. The true sky map is obtained by numerically deconvolving the beam function in the integral (convolution) equation. We adopt the maximum likelihood framework to estimate the true sky map that has been successfully used in the broadly similar, well-studied CMB map making problem. We numerically implement and demonstrate the method on simulated (unpolarized) SGWB for the radiometer consisting of the LIGO pair of detectors at Hanford and Livingston. We include `realistic' additive Gaussian noise in each data stream based on the LIGO-I noise power spectral density. The extension of the method to multiple baselines and polarized GWB is outlined. In the near future the network of GW detectors, including the Advanced LIGO and Virgo detectors that will be sensitive to sources within a thousand times larger spatial volume, could provide promising data sets for GW radiometry.Comment: 24 pages, 19 figures, pdflatex. Matched version published in Phys. Rev. D - minor change