Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test

BACKGROUND: Determining interacting SNPs in genome-wide association studies is computationally expensive yet of considerable interest in genomics. FINDINGS: We present a program Chi8 that calculates the Chi-square 8 degree of freedom test between all pairs of SNPs in a brute force manner on a Graphics Processing Unit. We analyze each of the seven WTCCC genome-wide association studies that have about 5000 total case and controls and 400,000 SNPs in an average of 9.6 h on a single GPU. We also study the power, false positives, and area under curve of our program on simulated data and provide a comparison to the GBOOST program. Our program source code is freely available from http://www.cs.njit.edu/usman/Chi8

Antiferromagnetic ordering in the Kondo lattice system Yb2_2Fe3_3Si5_5

Compounds belonging to the R$_2$Fe$_3$Si$_5$ series exhibit unusual superconducting and magnetic properties. Although a number of studies have been made on the first reentrant antiferromagnet superconductor Tm$_2$Fe$_3$Si$_5$, the physical properties of Yb$_2$Fe$_3$Si$_5$ are largely unexplored. In this work, we attempt to provide a comprehensive study of bulk properties such as, resistivity, susceptibility and heat-capacity of a well characterized polycrystalline Yb$_2$Fe$_3$Si$_5$. Our measurements indicate that Yb$^{3+}$ moments order antiferromagnetically below 1.7 K. Moreover, the system behaves as a Kondo lattice with large Sommerfeld coefficient ($\gamma$) of 0.5~J/Yb mol K$^{2}$ at 0.3 K, which is well below T$_N$. The absence of superconductivity in Yb$_2$Fe$_3$Si$_5$ down to 0.3 K at ambient pressure is attributed to the presence of the Kondo effect.Comment: 10 pages, 3 figures, tex document. A fuller version has appeared in PRB. Here we have omitted the figures showing the crystal structure and the fitting of the X-ray pattern. Also the table with the lattice parameters obtained from fitting has been remove

Vitamins and Perinatal Outcomes Among HIV-Negative Women in Tanzania.

Prematurity and low birth weight are associated with high perinatal and infant mortality, especially in developing countries. Maternal micronutrient deficiencies may contribute to these adverse outcomes. In a double-blind trial in Dar es Salaam, Tanzania, we randomly assigned 8468 pregnant women (gestational age of fetus, 12 to 27 weeks) who were negative for human immunodeficiency virus infection to receive daily multivitamins (including multiples of the recommended dietary allowance) or placebo. All the women received prenatal supplemental iron and folic acid. The primary outcomes were low birth weight (<2500 g), prematurity, and fetal death. The incidence of low birth weight was 7.8% among the infants in the multivitamin group and 9.4% among those in the placebo group (relative risk, 0.82; 95% confidence interval [CI], 0.70 to 0.95; P=0.01). The mean difference in birth weight between the groups was modest (67 g, P<0.001). The rates of prematurity were 16.9% in the multivitamin group and 16.7% in the placebo group (relative risk, 1.01; 95% CI, 0.91 to 1.11; P=0.87), and the rates of fetal death were 4.3% and 5.0%, respectively (relative risk, 0.87; 95% CI, 0.72 to 1.05; P=0.15). Supplementation reduced both the risk of a birth size that was small for gestational age (<10th percentile; 10.7% in the multivitamin group vs. 13.6% in the placebo group; relative risk, 0.77; 95% CI, 0.68 to 0.87; P<0.001) and the risk of maternal anemia (hemoglobin level, <11 g per deciliter; relative risk, 0.88; 95% CI, 0.80 to 0.97; P=0.01), although the difference in the mean hemoglobin levels between the groups was small (0.2 g per deciliter, P<0.001). Multivitamin supplementation reduced the incidence of low birth weight and small-for-gestational-age births but had no significant effects on prematurity or fetal death. Multivitamins should be considered for all pregnant women in developing countries. (ClinicalTrials.gov number, NCT00197548 [ClinicalTrials.gov].)

A Pathwise Ergodic Theorem for Quantum Trajectories

If the time evolution of an open quantum system approaches equilibrium in the time mean, then on any single trajectory of any of its unravelings the time averaged state approaches the same equilibrium state with probability 1. In the case of multiple equilibrium states the quantum trajectory converges in the mean to a random choice from these states.Comment: 8 page

Crystal Symmetry Lowering in Chiral Multiferroic Ba3_3TaFe3_3Si2_2O14_{14} observed by X-Ray Magnetic Scattering

Chiral multiferroic langasites have attracted attention due to their doubly-chiral magnetic ground state within an enantiomorphic crystal. We report on a detailed resonant soft X-ray diffraction study of the multiferroic Ba$_3$TaFe$_3$Si$_2$O$_{14}$ at the Fe $L_{2,3}$ and oxygen $K$ edges. Below $T_N$ ($\approx27K$) we observe the satellite reflections $(0,0,\tau)$, $(0,0,2\tau)$, $(0,0,3\tau)$ and $(0,0,1-3\tau)$ where $\tau \approx 0.140 \pm 0.001$. The dependence of the scattering intensity on X-ray polarization and azimuthal angle indicate that the odd harmonics are dominated by the out-of-plane ($\mathbf{\hat{c}}$-axis) magnetic dipole while the $(0,0,2\tau)$ originates from the electron density distortions accompanying magnetic order. We observe dissimilar energy dependences of the diffraction intensity of the purely magnetic odd-harmonic satellites at the Fe $L_3$ edge. Utilizing first-principles calculations, we show that this is a consequence of the loss of threefold crystal symmetry in the multiferroic phase

Personalisation and recommender systems in digital libraries

Widespread use of the Internet has resulted in digital libraries that are increasingly used by diverse communities of users for diverse purposes and in which sharing and collaboration have become important social elements. As such libraries become commonplace, as their contents and services become more varied, and as their patrons become more experienced with computer technology, users will expect more sophisticated services from these libraries. A simple search function, normally an integral part of any digital library, increasingly leads to user frustration as user needs become more complex and as the volume of managed information increases. Proactive digital libraries, where the library evolves from being passive and untailored, are seen as offering great potential for addressing and overcoming these issues and include techniques such as personalisation and recommender systems. In this paper, following on from the DELOS/NSF Working Group on Personalisation and Recommender Systems for Digital Libraries, which met and reported during 2003, we present some background material on the scope of personalisation and recommender systems in digital libraries. We then outline the working group’s vision for the evolution of digital libraries and the role that personalisation and recommender systems will play, and we present a series of research challenges and specific recommendations and research priorities for the field

Catch, abundance and some aspects of biology of deep sea fish in the southeastern Arabian Sea

The bottom trawls operated by FORV Sagar Sampada in the southeastern Arabian Sea revealed the existence of grounds with potentially rich unexploited deep sea finfish resources. Chlorophthalmus sp. formed the most dominant species with catch rates of 4.6 tonne/hr at lat. 8°56' N long. 73° 35' E and 4.2 tonne/hr at lat. 8°55' N, long. 73°35'E. Cubiceps rmtalensis with catch rates of 2.8 t forms the next important species. Maximum catch rate of deep sea fish was observed at depths ranging from 300 to 350 m. The other major exploitable species include Neopinnula orientalis, Pseneopsis cyanea, Chascanopsetta lugubris, Priacanthus hamrur and Chlorophthalmus bicomis. Information on some aspects of biology of fishes landed in fairly good quantity are also dealt with. Concentrations of deep sea fish resources are found in comparatively shallower depths in the northern latitudes whereas a wider distribution is seen in the southern latitudes

Crystal symmetry lowering in chiral multiferroic Ba3TaFe3Si2O14{\mathrm{Ba}}_{3}{\mathrm{TaFe}}_{3}{\mathrm{Si}}_{2}{\mathrm{O}}_{14} observed by x-ray magnetic scattering

Chiral multiferroic langasites have attracted attention due to their doubly chiral magnetic ground state within an enantiomorphic crystal. We report on a detailed resonant soft x-ray diffraction study of the multiferroic Ba3TaFe3Si2O14 at the Fe L2,3 and oxygen K edges. Below TN (≈27K) we observe the satellite reflections (0,0,τ), (0,0,2τ), (0,0,3τ), and (0,0,1−3τ) where τ≈0.140±0.001. The dependence of the scattering intensity on x-ray polarization and azimuthal angle indicate that the odd harmonics are dominated by the out-of-plane (ˆc axis) magnetic dipole while the (0,0,2τ) originates from the electron density distortions accompanying magnetic order. We observe dissimilar energy dependencies of the diffraction intensity of the purely magnetic odd-harmonic satellites at the Fe L3 edge. Utilizing first-principles calculations, we show that this is a consequence of the loss of threefold crystal symmetry in the multiferroic phase