Robust testing of haplotype/disease association

Haplotypes, the combination of closely linked alleles that fall on the same chromosome, show great promise for studying the genetic components of complex diseases. However, when only multilocus genotype data are available, statistical approaches need to be employed to resolve haplotype phase ambiguity. Recently, we have proposed an approach to testing and estimating haplotype/disease association that is invariant to any existing genetic structure in the population. Here we evaluate this approach by applying it to the Genetic Analysis Workshop 14 simulated data

Accretion onto the Supermassive Black Hole in M87

Chandra X-ray observations of the giant elliptical galaxy M87 resolve the thermal state of the hot interstellar medium into the accretion (Bondi) radius of its central 3 10^9 Msun black hole. We measure the X-ray gas temperature and density profiles and calculate the Bondi accretion rate, Mdot_Bondi \sim 0.1 Msun/yr. The X-ray luminosity of the active nucleus of M87 observed with Chandra is L_{x, 0.5-7 \keV} \sim 7 \times 10^{40}erg/s. This value is much less than the predicted nuclear luminosity, L_{Bondi} \sim 5 \times 10^{44} erg/s, for accretion at the Bondi rate with a canonical accretion radiative efficiency of 10%. If the black hole in M87 accretes at this rate it must do so at a much lower radiative efficiency than the canonical value. The multiwavelength spectrum of the nucleus is consistent with that predicted by an advection-dominated flow. However, as is likely, the X-ray nucleus is dominated by jet emission then the properties of flow must be modified, possibly by outflows. We show that the overall energetics of the system are just consistent with the predicted Bondi nuclear power. This suggests that either most of the accretion energy is released in the relativistic jet or that the central engine of M87 undergoes on-off activity cycles. We show that, at present, the energy dumped into the ISM by the jet may reduce the accretion rate onto the black hole by a factor \propto (v_j/c_s)^{-2}, where v_j is the jet velocity and c_s the ISM sound speed, and that this is sufficient to account for the low nuclear luminosity.Comment: emulateapj.sty, revised version, accepted by Ap

Application of the level-set method to the implicit solvation of nonpolar molecules

A level-set method is developed for numerically capturing the equilibrium solute-solvent interface that is defined by the recently proposed variational implicit solvent model (Dzubiella, Swanson, and McCammon, Phys. Rev. Lett. {\bf 104}, 527 (2006) and J. Chem.\Phys. {\bf 124}, 084905 (2006)). In the level-set method, a possible solute-solvent interface is represented by the zero level-set (i.e., the zero level surface) of a level-set function and is eventually evolved into the equilibrium solute-solvent interface. The evolution law is determined by minimization of a solvation free energy {\it functional} that couples both the interfacial energy and the van der Waals type solute-solvent interaction energy. The surface evolution is thus an energy minimizing process, and the equilibrium solute-solvent interface is an output of this process. The method is implemented and applied to the solvation of nonpolar molecules such as two xenon atoms, two parallel paraffin plates, helical alkane chains, and a single fullerene $C_{60}$. The level-set solutions show good agreement for the solvation energies when compared to available molecular dynamics simulations. In particular, the method captures solvent dewetting (nanobubble formation) and quantitatively describes the interaction in the strongly hydrophobic plate system

The Relationship Between Meaning and Morphological Productivity

Proceedings of the Fifth Annual Meeting of the Berkeley Linguistics Society (1979), pp. 453-46

The Leader Verb as a Mechanism of Morphological Change

Proceedings of the Eighth Annual Meeting of the Berkeley Linguistics Society (1982

Ecological interactions disrupted by habitat alteration in the Neotropics

Ecological interactions help determine the distribution of species across landscapes and play crucial roles in ecosystem services such as pollination, seed dispersal, and pest control1. Human disturbances, particularly habitat alteration, have the potential to modify or erase ecological interactions2,3 and so jeopardise the processes they control. While examples of interactions becoming rewired under human influence have been recorded, studies of this process for speciose assemblages at regional to continental scales are uncommon4 and obstructed by logistical difficulties2. The consequences for ecological communities and people are therefore poorly understood. Here we show that human habitat alteration is associated with a decrease in the spatial aggregation of Neotropical bat pairs and bird pairs that share similar dietary requirements. We find that groups of species pairs with similar vs. different diets have positive spatial associations on average, but pairs within dietary guilds have stronger associations than pairs with disparate diets when habitats are relatively intact. Our results suggest that species with similar resource requirements typically coexist in relatively intact natural settings. By contrast, exclusion becomes more common (though not dominant) when habitats are altered. Altered habitats thus fail to support the coexistence of diverse competitive interactions, reversing patterns observed in the wild

NASA ISS Portable Fan Assembly Acoustics

The Portable Fan Assembly (PFA) is a variable speed fan that can be used to provide additional ventilation inside International Space Station (ISS) modules as needed for crew comfort or for enhanced mixing of the ISS atmosphere. This fan can also be configured with a Shuttle era lithium hydroxide (LiOH) canister for CO2 removal in confined areas partially of fully isolated from the primary Environmental Control and Life Support System (ECLSS) on ISS which is responsible for CO2 removal. This report documents noise emission levels of the PFA at various speed settings and configurations. It also documents the acoustic attenuation effects realized when circulating air through the PFA inlet and outlet mufflers and when operating in its CO2 removal configuration (CRK) with a LiOH canister (sorbent bed) installed over the fan outlet

Development of a low-maintenance measurement approach to continuously estimate methane emissions: a case study

The chemical breakdown of organic matter in landfills represents a significant source of methane gas (CH4). Current estimates suggest that landfills are responsible for between 3% and 19% of global anthropogenic emissions. The net CH4 emissions resulting from biogeochemical processes and their modulation by microbes in landfills are poorly constrained by imprecise knowledge of environmental constraints. The uncertainty in absolute CH4 emissions from landfills is therefore considerable. This study investigates a new method to estimate the temporal variability of CH4 emissions using meteorological and CH4 concentration measurements downwind of a landfill site in Suffolk, UK from July to September 2014, taking advantage of the statistics that such a measurement approach offers versus shorter-term, but more complex and instantaneously accurate, flux snapshots. Methane emissions were calculated from CH4 concentrations measured 700 m from the perimeter of the landfill with observed concentrations ranging from background to 46.4 ppm. Using an atmospheric dispersion model, we estimate a mean emission flux of 709 μg m−2 s−1 over this period, with a maximum value of 6.21 mg m−2 s−1, reflecting the wide natural variability in biogeochemical and other environmental controls on net site emission. The emissions calculated suggest that meteorological conditions have an influence on the magnitude of CH4 emissions. We also investigate the factors responsible for the large variability observed in the estimated CH4 emissions, and suggest that the largest component arises from uncertainty in the spatial distribution of CH4 emissions within the landfill area. The results determined using the low-maintenance approach discussed in this paper suggest that a network of cheaper, less precise CH4 sensors could be used to measure a continuous CH4 emission time series from a landfill site, something that is not practical using far-field approaches such as tracer release methods. Even though there are limitations to the approach described here, this easy, low-maintenance, low-cost method could be used by landfill operators to estimate time-averaged CH4 emissions and their impact downwind by simultaneously monitoring plume advection and CH4 concentrations