Second-generation PLINK: rising to the challenge of larger and richer datasets

PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for even faster and more scalable implementations of key functions. In addition, GWAS and population-genetic data now frequently contain probabilistic calls, phase information, and/or multiallelic variants, none of which can be represented by PLINK 1's primary data format. To address these issues, we are developing a second-generation codebase for PLINK. The first major release from this codebase, PLINK 1.9, introduces extensive use of bit-level parallelism, O(sqrt(n))-time/constant-space Hardy-Weinberg equilibrium and Fisher's exact tests, and many other algorithmic improvements. In combination, these changes accelerate most operations by 1-4 orders of magnitude, and allow the program to handle datasets too large to fit in RAM. This will be followed by PLINK 2.0, which will introduce (a) a new data format capable of efficiently representing probabilities, phase, and multiallelic variants, and (b) extensions of many functions to account for the new types of information. The second-generation versions of PLINK will offer dramatic improvements in performance and compatibility. For the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use.Comment: 2 figures, 1 additional fil

Charge distribution and electroluminescence in cross-linked polyethylene under dc field

The intent of this paper is to cross-correlate the information obtained by space charge distribution analysis and electroluminescence (EL) detection in cross-linked polyethylene samples submitted to dc fields, with the objective to make a link between space charge phenomena and energy release as revealed by the detection of visible photons. Space charge measurements carried out at different field levels by the pulsed electro-acoustic method show the presence of a low-field threshold, close to 15-20 kV mm-1, above which considerable space charge begins to accumulate in the insulation. Charges are seen to cross the insulation thickness through a packet-like behaviour at higher fields, starting at about 60-70 kV mm-1. EL measurements show the existence of two distinct thresholds, one related to the continuous excitation of EL under voltage, the other being transient EL detected upon specimen short circuit. The former occurs at values of field corresponding to charge packet formation and the latter to the onset of space charge accumulation. The correspondence between pertinent values of the electric field obtained through space charge and EL analyses provides support for the existence of degradation thresholds in insulating materials. Special emphasis is given to the relationship between charge packet formation and propagation, and EL. Although the two phenomena are observed in the same field range, it is found that the onset of continuous EL follows the formation at the electrodes of positive and negative space charge regions that extend into the bulk prior to the propagation of charge packets. Charge recombination appears to be the excitation process of EL since oppositely charged domains meet in the material bulk. To gain an insight into specific light-excitation processes associated with charge packet propagation, EL has been recorded for several hours under fields at which charge packet dynamics were evidenced. It is shown that current and luminescence oscillations are detected during charge packet propagation, and that they are in phase. The mechanisms underlying EL and charge packets are further considered on the basis of these results

VLBA determination of the distance to nearby star-forming regions II. Hubble 4 and HDE 283572 in Taurus

The non-thermal 3.6 cm radio continuum emission from the naked T Tauri stars Hubble 4 and HDE 283572 in Taurus has been observed with the Very Long Baseline Array (VLBA) at 6 epochs between September 2004 and December 2005 with a typical separation between successive observations of 3 months. Thanks to the remarkably accurate astrometry delivered by the VLBA, the trajectory described by both stars on the plane of the sky could be traced very precisely, and modeled as the superposition of their trigonometric parallax and uniform proper motion. The best fits yield distances to Hubble 4 and HDE 283572 of 132.8 +/- 0.5 and 128.5 +/- 0.6 pc, respectively. Combining these results with the other two existing VLBI distance determinations in Taurus, we estimate the mean distance to the Taurus association to be 137 pc with a dispersion (most probably reflecting the depth of the complex) of about 20 pc.Comment: 21 pages, 4 figues, accepted in ApJ (Dec 20, 2007 issue

Isochoric, isobaric and ultrafast conductivities of aluminum, lithium and carbon in the warm dense matter (WDM) regime

We study the conductivities $\sigma$ of (i) the equilibrium isochoric state ($\sigma_{\rm is}$), (ii) the equilibrium isobaric state ($\sigma_{\rm ib}$), and also the (iii) non-equilibrium ultrafast matter (UFM) state ($\sigma_{\rm uf}$) with the ion temperature $T_i$ less than the the electron temperature $T_e$. Aluminum, lithium and carbon are considered, being increasingly complex warm dense matter (WDM) systems, with carbon having transient covalent bonds. First-principles calculations, i.e., neutral-pseudoatom (NPA) calculations and density-functional theory (DFT) with molecular-dynamics (MD) simulations, are compared where possible with experimental data to characterize $\sigma_{\rm ic}, \sigma_{\rm ib}$ and $\sigma_{\rm uf}$. The NPA $\sigma_{\rm ib}$ are closest to the available experimental data when compared to results from DFT+MD, where simulations of about 64-125 atoms are typically used. The published conductivities for Li are reviewed and the value at a temperature of 4.5 eV is examined using supporting X-ray Thomson scattering calculations. A physical picture of the variations of $\sigma$ with temperature and density applicable to these materials is given. The insensitivity of $\sigma$ to $T_e$ below 10 eV for carbon, compared to Al and Li, is clarified.Comment: 10 figure

Spectral state dependence of the 0.4-2 MeV polarized emission in Cygnus X-1 seen with INTEGRAL/IBIS, and links with the AMI radio data

Polarization of the >~400 keV hard tail of the microquasar Cygnus X-1 has been independently reported by INTEGRAL/IBIS, and INTEGRAL/SPI and interpreted as emission from a compact jet. These conclusions were, however, based on the accumulation of all INTEGRAL data regardless of the spectral state. We utilize additional INTEGRAL exposure accumulated until December 2012, and include the AMI/Ryle (15 GHz) radio data in our study. We separate the observations into hard, soft, and intermediate/transitional states and detect radio emission from a compact jet in hard and intermediate states, but not in the soft. The 10-400 keV INTEGRAL (JEM-X and IBIS) state resolved spectra are well modeled with thermal Comptonization and reflection components. We detect a hard tail in the 0.4-2 MeV range for the hard state only. We extract the state dependent polarigrams of Cyg X-1, which all are compatible to no or undetectable level of polarization except in 400-2000 keV range in the hard state where the polarization fraction is 75$\pm$32 % and the polarization angle 40.0 +-14 deg. An upper limit on the 0.4-2 MeV soft state polarization fraction is 70%. Due to the short exposure, we obtain no meaningful constraint for the intermediate state. The likely detection of a >400 keV polarized tail in the hard state, together with the simultaneous presence of a radio jet, reinforce the notion of a compact jet origin of the 400 keV emission.Comment: 13 pages, 5 figures, accepted for publication in Ap

A heterotic sigma model with novel target geometry

We construct a (1,2) heterotic sigma model whose target space geometry consists of a transitive Lie algebroid with complex structure on a Kaehler manifold. We show that, under certain geometrical and topological conditions, there are two distinguished topological half--twists of the heterotic sigma model leading to A and B type half--topological models. Each of these models is characterized by the usual topological BRST operator, stemming from the heterotic (0,2) supersymmetry, and a second BRST operator anticommuting with the former, originating from the (1,0) supersymmetry. These BRST operators combined in a certain way provide each half--topological model with two inequivalent BRST structures and, correspondingly, two distinct perturbative chiral algebras and chiral rings. The latter are studied in detail and characterized geometrically in terms of Lie algebroid cohomology in the quasiclassical limit.Comment: 83 pages, no figures, 2 references adde