Optimal Moments for the Analysis of Peculiar Velocity Surveys

We present a new method for the analysis of peculiar velocity surveys which removes contributions to velocities from small scale, nonlinear velocity modes while retaining information about large scale motions. Our method utilizes Karhunen--Lo\`eve methods of data compression to construct a set of moments out of the velocities which are minimally sensitive to small scale power. The set of moments are then used in a likelihood analysis. We develop criteria for the selection of moments, as well as a statistic to quantify the overall sensitivity of a set of moments to small scale power. Although we discuss our method in the context of peculiar velocity surveys, it may also prove useful in other situations where data filtering is required.Comment: 25 Pages, 3 figures. Submitted to Ap

Optimal Moments for the Analysis of Peculiar Velocity Surveys II: Testing

Analyses of peculiar velocity surveys face several challenges, including low signal--to--noise in individual velocity measurements and the presence of small--scale, nonlinear flows. This is the second in a series of papers in which we describe a new method of overcoming these problems by using data compression as a filter with which to separate large--scale, linear flows from small--scale noise that can bias results. We demonstrate the effectiveness of our method using realistic catalogs of galaxy velocities drawn from N--body simulations. Our tests show that a likelihood analysis of simulated catalogs that uses all of the information contained in the peculiar velocities results in a bias in the estimation of the power spectrum shape parameter $\Gamma$ and amplitude $\beta$, and that our method of analysis effectively removes this bias. We expect that this new method will cause peculiar velocity surveys to re--emerge as a useful tool to determine cosmological parameters.Comment: 28 pages, 9 figure

Preliminary Results from an Experimental Assessment of a Natural Laminar Flow Design Method

A 5.2% scale semispan model of the new Common Research Model with Natural Laminar Flow (CRM-NLF) was tested in the National Transonic Facility (NTF) at the NASA Langley Research Center. The model was tested at transonic cruise flight conditions with Reynolds numbers based on mean aerodynamic chord ranging from 10 to 30 million. The goal of the test was to experimentally validate a new design method, referred to as Crossflow Attenuated NLF (CATNLF), which shapes airfoils to have pressure distributions that delay transition on wings with high sweep and Reynolds numbers. Additionally, the test aimed to characterize the NTF laminar flow testing capabilities, as well as establish best practices for laminar flow wind tunnel testing. Preliminary results regarding the first goal of validating the new design method are presented in this paper. Experimental data analyzed in this assessment include surface pressure data and transition images. The surface pressure data acquired during the test agree well with computational fluid dynamics (CFD) results. Transition images at a variety of Reynolds numbers and angles of attack are presented and compared to computational transition predictions. The experimental data are used to assess transition due to a turbulent attachment line, as well as crossflow and Tollmien-Schlichting modal instabilities. Preliminary results suggest the CATNLF design method is successful at delaying transition on wings with high sweep. Initial analysis of the transition front images showed transition Reynolds numbers that exceed historic experimental values at similar sweep angles. , section lif

Hubble flow variance and the cosmic rest frame

We characterize the radial and angular variance of the Hubble flow in the COMPOSITE sample of 4534 galaxies, on scales in which much of the flow is in the nonlinear regime. With no cosmological assumptions other than the existence of a suitably averaged linear Hubble law, we find with decisive Bayesian evidence (ln B >> 5) that the Hubble constant averaged in independent spherical radial shells is closer to its asymptotic value when referred to the rest frame of the Local Group, rather than the standard rest frame of the Cosmic Microwave Background. An exception occurs for radial shells in the range 40/h-60/h Mpc. Angular averages reveal a dipole structure in the Hubble flow, whose amplitude changes markedly over the range 32/h-62/h Mpc. Whereas the LG frame dipole is initially constant and then decreases significantly, the CMB frame dipole initially decreases but then increases. The map of angular Hubble flow variation in the LG rest frame is found to coincide with that of the residual CMB temperature dipole, with correlation coefficient -0.92. These results are difficult to reconcile with the standard kinematic interpretation of the motion of the Local Group in response to the clustering dipole, but are consistent with a foreground non-kinematic anisotropy in the distance-redshift relation of 0.5% on scales up to 65/h Mpc. Effectively, the differential expansion of space produced by nearby nonlinear structures of local voids and denser walls and filaments cannot be reduced to a local boost. This hypothesis suggests a reinterpretation of bulk flows, which may potentially impact on calibration of supernovae distances, anomalies associated with large angles in the CMB anisotropy spectrum, and the dark flow inferred from the kinematic Sunyaev-Zel'dovich effect. It is consistent with recent studies that find evidence for a non-kinematic dipole in the distribution of distant radio sources.Comment: 37 pages, 9 tables, 13 figures; v2 adds extensive new analysis (including additional subsections, tables, figures); v3 adds a Monte Carlo analysis (with additional table, figure) which further tightens the statistical robustness of the dipole results; v4 adds further clarifications, small corrections, references and discussion of Planck satellite results; v5 typos fixed, matches published versio

In vivo analysis of Nef’s role in HIV-1 replication, systemic T cell activation and CD4+ T cell loss

Background Nef is a multifunctional HIV-1 protein critical for progression to AIDS. Humans infected with nef(−) HIV-1 have greatly delayed or no disease consequences. We have contrasted nef(−) and nef(+) infection of BLT humanized mice to better characterize Nef’s pathogenic effects. Results Mice were inoculated with CCR5-tropic HIV-1JRCSF (JRCSF) or JRCSF with an irreversibly inactivated nef (JRCSFNefdd). In peripheral blood (PB), JRCSF exhibited high levels of viral RNA (peak viral loads of 4.71 × 106 ± 1.23 × 106 copies/ml) and a progressive, 75% loss of CD4+ T cells over 17 weeks. Similar losses were observed in CD4+ T cells from bone marrow, spleen, lymph node, lung and liver but thymocytes were not significantly decreased. JRCSFNefdd also had high peak viral loads (2.31 × 106 ± 1.67 × 106) but induced no loss of PB CD4+ T cells. In organs, JRCSFNefdd produced small, but significant, reductions in CD4+ T cell levels and did not affect the level of thymocytes. Uninfected mice have low levels of HLA-DR+CD38+CD8+ T cells in blood (1–2%). Six weeks post inoculation, JRCSF infection resulted in significantly elevated levels of activated CD8+ T cells (6.37 ± 1.07%). T cell activation coincided with PB CD4+ T cell loss which suggests a common Nef-dependent mechanism. At 12 weeks, in JRCSF infected animals PB T cell activation sharply increased to 19.7 ± 2.9% then subsided to 5.4 ± 1.4% at 14 weeks. HLA-DR+CD38+CD8+ T cell levels in JRCSFNefdd infected mice did not rise above 1–2% despite sustained high levels of viremia. Interestingly, we also noted that in mice engrafted with human tissue expressing a putative protective HLA-B allele (B42:01), JRCSFNefdd exhibited a substantial (200-fold) reduced viral load compared to JRCSF. Conclusions Nef expression was necessary for both systemic T cell activation and substantial CD4+ T cell loss from blood and tissues. JRCSFNefdd infection did not activate CD8+ T cells or reduce the level of CD4+ T cells in blood but did result in a small Nef-independent decrease in CD4+ T cells in organs. These observations strongly support the conclusion that viral pathogenicity is mostly driven by Nef. We also observed for the first time substantial host-specific suppression of HIV-1 replication in a small animal infection model

Nef functions in BLT mice to enhance HIV-1 replication and deplete CD4+CD8+ thymocytes

Background: The outcome of untreated HIV-1 infection is progression to AIDS and death in nearly all cases. Some important exceptions are the small number of patients infected with HIV-1 deleted for the accessory gene, nef. With these infections, disease progression is entirely suppressed or greatly delayed. Whether Nef is critical for high levels of replication or is directly cytotoxic remains controversial. The major problem in determining the role of Nef in HIV/AIDS has been the lack of tractable in vivo models where Nef’s complex pathogenic phenotype can be recapitulated. Results: Intravenous inoculation (3000 to 600,000 TCIU) of BLT humanized mice with HIV-1LAI reproducibly establishes a systemic infection. HIV-1LAI (LAI) replicates to high levels (peak viral load in blood 8,200,000 ± 1,800,000 copies of viral RNA/ml, range 3,600,000 to 20,400,000; n = 9) and exhaustively depletes CD4+ T cells in blood and tissues. CD4+CD8+ thymocytes were also efficiently depleted but CD4+CD8- thymocytes were partially resistant to cell killing by LAI. Infection with a nef-deleted LAI (LAINefdd) gave lower peak viral loads (1,220,000 ± 330,000, range 27,000 to 4,240,000; n = 17). For fourteen of seventeen LAINefdd-infected mice, there was little to no loss of either CD4+ T cells or thymocytes. Both LAIand LAINefdd-infected mice had about 8% of total peripheral blood CD8+ T cells that were CD38+HLA-DR+ compared \u3c1% for uninfected mice. Three exceptional LAINefdd-infected mice that lost CD4+ T cells received 600,000 TCIU. All three exhibited peak viral loads over 3,000,000 copies of LAINefdd RNA/ml. Over an extended time course, substantial systemic CD4+ T cell loss was observed for the three mice, but there was no loss of CD4+CD8+ or CD4+CD8- thymocytes. Conclusion: We conclude Nef is necessary for elevated viral replication and as a result indirectly contributes to CD4+ T cell killing. Further, Nef was not necessary for the activation of peripheral blood CD8+ T cells following infection. However, CD4+CD8+ thymocyte killing was dependent on Nef even in cases of elevated LAINefdd replication and T cell loss. This depletion of thymic T cell precursors may be a significant factor in the elevated pathogenicity of CXCR4 trophic HIV-1

Using organic phosphorus to sustain pasture productivity: A perspective

Organic phosphorus (P) in grazed pastures/grasslands could sustain production systems that historically relied on inorganic P fertiliser. Interactions between inorganic P, plants and soils have been studied extensively. However, less is known about the transformation of organic P to inorganic orthophosphate. This paper investigates what is known about organic P in pasture/grassland soils used for agriculture, as well as the research needed to utilise organic P for sustainable plant production. Organic P comprises > 50% of total soil P in agricultural systems depending on location, soil type and land use. Organic P hydrolysis and release of orthophosphate by phosphatase enzymatic activity is affected by a range of factors including: (a) the chemical nature of the organic P and its ability to interact with the soil matrix; (b) microorganisms that facilitate mineralisation; (c) soil mineralogy; (d) soil water electrolytes; and (e) soil physicochemical properties. Current biogeochemical knowledge of organic P processing in soil limits our ability to develop management strategies that promote the use of organic P in plant production. Information is particularly needed on the types and sources of organic P in grassland systems and the factors affecting the activity of enzymes that mineralise organic P. Integrated approaches analysing the soil matrix, soil water and soil biology are suggested to address this knowledge gap