Statistical analysis of network data and evolution on GPUs: High-performance statistical computing

Network analysis typically involves as set of repetitive tasks that are particularly amenable to poor-man's parallelization. This is therefore an ideal application are for GPU architectures, which help to alleviate the tedium inherent to statistically sound analysis of network data. Here we will illustrate the use of GPUs in a range of applications, which include percolation processes on networks, the evolution of protein-protein interaction networks, and the fusion of different types of biomedical and disease data in the context of molecular interaction networks. We will pay particular attention to the numerical performance of different routines that are frequently invoked in network analysis problems. We conclude with a review over recent developments in the generation of random numbers that address the specific requirements posed by GPUs and high-performance computing needs

John Wheeler, relativity, and quantum information

In spring 1952, as John Wheeler neared the end of design work for the first thermonuclear explosion, he plotted a radical change of research direction: from particles and atomic nuclei to general relativity

Estimating the spatial and temporal distribution of species richness within Sequoia and Kings Canyon National Parks.

Evidence for significant losses of species richness or biodiversity, even within protected natural areas, is mounting. Managers are increasingly being asked to monitor biodiversity, yet estimating biodiversity is often prohibitively expensive. As a cost-effective option, we estimated the spatial and temporal distribution of species richness for four taxonomic groups (birds, mammals, herpetofauna (reptiles and amphibians), and plants) within Sequoia and Kings Canyon National Parks using only existing biological studies undertaken within the Parks and the Parks' long-term wildlife observation database. We used a rarefaction approach to model species richness for the four taxonomic groups and analyzed those groups by habitat type, elevation zone, and time period. We then mapped the spatial distributions of species richness values for the four taxonomic groups, as well as total species richness, for the Parks. We also estimated changes in species richness for birds, mammals, and herpetofauna since 1980. The modeled patterns of species richness either peaked at mid elevations (mammals, plants, and total species richness) or declined consistently with increasing elevation (herpetofauna and birds). Plants reached maximum species richness values at much higher elevations than did vertebrate taxa, and non-flying mammals reached maximum species richness values at higher elevations than did birds. Alpine plant communities, including sagebrush, had higher species richness values than did subalpine plant communities located below them in elevation. These results are supported by other papers published in the scientific literature. Perhaps reflecting climate change: birds and herpetofauna displayed declines in species richness since 1980 at low and middle elevations and mammals displayed declines in species richness since 1980 at all elevations

Hydromagnetic and gravitomagnetic crust-core coupling in a precessing neutron star

We consider two types of mechanical coupling between the crust and the core of a precessing neutron star. First, we find that a hydromagnetic (MHD) coupling between the crust and the core strongly modifies the star's precessional modes when $t_a\le\sim (T_s\times T_p)^{1/2}$; here $t_a$ is the Alfven crossing timescale, and $T_s$ and $T_p$ are the star's spin and precession periods, respectively. We argue that in a precessing pulsar PSR B1828-11 the restoring MHD stress prevents a free wobble of the crust relative to the non-precessing core. Instead, the crust and the proton-electron plasma in the core must precess in unison, and their combined ellipticity determines the period of precession. Link has recently shown that the neutron superfluid vortices in the core of PSR B1828-11 cannot be pinned to the plasma; he has also argued that this lack of pinning is expected if the proton Fermi liquid in the core is type-I superconductor. In this case, the neutron superfluid is dynamically decoupled from the precessing motion. The pulsar's precession decays due to the mutual friction between the neutron superfluid and the plasma in the core. The decay is expected to occur over tens to hundreds of precession periods and may be measurable over a human lifetime. Such a measurement would provide information about the strong n-p interaction in the neutron-star core. Second, we consider the effect of gravitomagnetic coupling between the neutron superfluid in the core and the rest of the star and show that this coupling changes the rate of precession by about 10%. The general formalism developed in this paper may be useful for other applications.Comment: 6 page

Modelling Livestock Component in FSSIM

This document summarises the development of a ruminant livestock component for the Farm System Simulator (FSSIM). This includes treatments of energy and protein transactions in ruminant livestock that have been used as a basis for the biophysical simulations that will generate the input production parameters for FSSIM. The treatments are derived principally from the “French” feed evaluation and rationing system for protein and energy. Currently, we have constructed routines that are capable of simulating input-output relationships for energy and protein in the following representative systems; dairy cattle; suckler cows; growing and finishing cattle; sheep and goats. The calculations of energy and protein requirements for these classes of livestock are described in detail in this documen

Dynamical fluctuations in mode locking experiments on vortices moving through mesoscopic channels

We have studied the flow properties of vortices driven through easy flow mesoscopic channels by means of the mode locking (ML) technique. We observe a ML jump with large voltage broadening in the real part of the rf-impedance. Upon approaching the pure dc flow by reducing the rf amplitude, the ML jump is smeared out via a divergence of the voltage width. This indicates a large spread in internal frequencies and lack of temporal coherence in the dc-driven state.Comment: 2 pages, 2 figures, contribution to M2S-HTSC 2003, Ri

In-Chain Tunneling Through Charge-Density Wave Nanoconstrictions and Break-Junctions

We have fabricated longitudinal nanoconstrictions in the charge-density wave conductor (CDW) NbSe$_{3}$ using a focused ion beam and using a mechanically controlled break-junction technique. Conductance peaks are observed below the T$_{P1}$$=145$K and T$_{P2}$$=59$K CDW transitions, which correspond closely with previous values of the full CDW gaps $2\Delta_{1}$ and $2\Delta_{2}$ obtained from photo-emission. These results can be explained by assuming CDW-CDW tunneling in the presence of an energy gap corrugation $\epsilon_{2}$ comparable to $\Delta_{2}$, which eliminates expected peak at $\Delta_{1}+\Delta_{2}$. The nanometer length-scales our experiments imply indicate that an alternative explanation based on tunneling through back-to-back CDW-normal junctions is unlikely.Comment: 5 pages, 3 figures, submitted to physical review letter

Tidal coupling of a Schwarzschild black hole and circularly orbiting moon

We describe the possibility of using LISA's gravitational-wave observations to study, with high precision, the response of a massive central body to the tidal gravitational pull of an orbiting, compact, small-mass object. Motivated by this application, we use first-order perturbation theory to study tidal coupling for an idealized case: a massive Schwarzschild black hole, tidally perturbed by a much less massive moon in a distant, circular orbit. We investigate the details of how the tidal deformation of the hole gives rise to an induced quadrupole moment in the hole's external gravitational field at large radii. In the limit that the moon is static, we find, in Schwarzschild coordinates and Regge-Wheeler gauge, the surprising result that there is no induced quadrupole moment. We show that this conclusion is gauge dependent and that the static, induced quadrupole moment for a black hole is inherently ambiguous. For the orbiting moon and the central Schwarzschild hole, we find (in agreement with a recent result of Poisson) a time-varying induced quadrupole moment that is proportional to the time derivative of the moon's tidal field. As a partial analog of a result derived long ago by Hartle for a spinning hole and a stationary distant companion, we show that the orbiting moon's tidal field induces a tidal bulge on the hole's horizon, and that the rate of change of the horizon shape leads the perturbing tidal field at the horizon by a small angle.Comment: 14 pages, 0 figures, submitted to Phys. Rev.

Neonatal deaths among infants born to women living with HIV in the UK and Ireland 1998–2017

OBJECTIVES: To estimate the incidence of neonatal mortality among infants born to women living with HIV in the UK and Ireland in 1998-2017, describe causes of neonatal death (NND) and examine risk factors. DESIGN: Population-based surveillance of pregnancies in diagnosed women living with HIV and their infants in the UK and Ireland. METHODS: Estimated yearly incidence of NND was reported for 1998-2017 and causes coded using the World Health Organization International Classification of Perinatal Mortality. Risk factor analyses used multivariable logistic regression, including delivery year, maternal origin, maternal age, delivery CD4 count and viral load (VL), antiretroviral therapy (ART) at conception, preterm delivery (PTD), injecting drug use and infant sex. RESULTS: There were 20,012 live-born infants delivered to 12,684 mothers in 19,601 pregnancies. The overall neonatal mortality rate was 4.10 per 1000 livebirths (95%CI, 3.2-5.0), which was higher than that of the general population. Prematurity was the leading cause of death followed by congenital abnormality. Most NND occurred on the first day of life. ART at conception was associated with significantly reduced NND risk. In a restricted 2007-2017 analysis including VL, PTD and detectable maternal VL were associated with significantly increased NND risk. CONCLUSIONS: The vertical transmission rate in the UK, at 3 per 1000, is now lower than the neonatal mortality rate among infants born to women with HIV. More research is needed to investigate the complex relationship between ART, preterm delivery and neonatal death in order to improve all perinatal outcomes