Precision of diffuse 21-cm lensing

We study the limits of accuracy for weak lensing maps of dark matter using diffuse 21-cm radiation from the pre-reionization epoch using simulations. We improve on previous "optimal" quadratic lensing estimators by using shear and convergence instead of deflection angles. We find that non-Gaussianity provides a limit to the accuracy of weak lensing reconstruction, even if instrumental noise is reduced to zero. The best reconstruction result is equivalent to Gaussian sources with effectively independent cell of side length 2.0/h Mpc. Using a source full map from z=10-20, this limiting sensitivity allows mapping of dark matter at a Signal-to-Noise ratio (S/N) greater than 1 out to l < 6000, which is better than any other proposed technique for large area weak lensing mapping.Comment: 16 pages, 7 figures, submitted to MNRA

Towards optimal parallel PM N-body codes: PMFAST

We present a new parallel PM N-body code named PMFAST that is freely available to the public. PMFAST is based on a two-level mesh gravity solver where the gravitational forces are separated into long and short range components. The decomposition scheme minimizes communication costs and allows tolerance for slow networks. The code approaches optimality in several dimensions. The force computations are local and exploit highly optimized vendor FFT libraries. It features minimal memory overhead, with the particle positions and velocities being the main cost. The code features support for distributed and shared memory parallelization through the use of MPI and OpenMP, respectively. The current release version uses two grid levels on a slab decomposition, with periodic boundary conditions for cosmological applications. Open boundary conditions could be added with little computational overhead. We present timing information and results from a recent cosmological production run of the code using a 3712^3 mesh with 6.4 x 10^9 particles. PMFAST is cost-effective, memory-efficient, and is publicly available.Comment: 18 pages, 11 figure

Self calibration of photometric redshift scatter in weak lensing surveys

Photo-z errors, especially catastrophic errors, are a major uncertainty for precision weak lensing cosmology. We find that the shear-(galaxy number) density and density-density cross correlation measurements between photo-z bins, available from the same lensing surveys, contain valuable information for self-calibration of the scattering probabilities between the true-z and photo-z bins. The self-calibration technique we propose does not rely on cosmological priors nor parameterization of the photo-z probability distribution function, and preserves all of the cosmological information available from shear-shear measurement. We estimate the calibration accuracy through the Fisher matrix formalism. We find that, for advanced lensing surveys such as the planned stage IV surveys, the rate of photo-z outliers can be determined with statistical uncertainties of 0.01-1% for $z<2$ galaxies. Among the several sources of calibration error that we identify and investigate, the {\it galaxy distribution bias} is likely the most dominant systematic error, whereby photo-z outliers have different redshift distributions and/or bias than non-outliers from the same bin. This bias affects all photo-z calibration techniques based on correlation measurements. Galaxy bias variations of $O(0.1)$ produce biases in photo-z outlier rates similar to the statistical errors of our method, so this galaxy distribution bias may bias the reconstructed scatters at several-$\sigma$ level, but is unlikely to completely invalidate the self-calibration technique.Comment: v2: 19 pages, 10 figures. Added one figure. Expanded discussions. Accepted to MNRA

Out-of-Core Hydrodynamic Simulations for Cosmological Applications

We present an out-of-core hydrodynamic code for high resolution cosmological simulations that require terabytes of memory. Out-of-core computation refers to the technique of using disk space as virtual memory and transferring data in and out of main memory at high I/O bandwidth. The code is based on a two-level mesh scheme where short-range physics is solved on a high-resolution, localized mesh while long-range physics is captured on a lower resolution, global mesh. The two-level mesh gravity solver allows FFTs to operate on data stored entirely in memory, which is much faster than the alternative of computing the transforms out-of-core through non-sequential disk accesses. We also describe an out-of-core initial conditions generator that is used to prepare large data sets for cosmological simulations. The out-of-core code is accurate, cost-effective, and memory-efficient and the current version is implemented to run in parallel on shared-memory machines. I/O overhead is significantly reduced down to less than 10% by performing disk operations concurrently with numerical calculations. The current computational setup, which includes a 32 processor Alpha server and a 3 TB striped SCSI disk array, allows us to run cosmological simulations with up to 4000^3 grid cells and 2000^3 dark matter particles.Comment: 19 pages, 10 figures; accepted by New Astronom

The three dimensional power spectrum of dark and luminous matter from the VIRMOS-DESCART cosmic shear survey

We present the first optimal power spectrum estimation and three dimensional deprojections for the dark and luminous matter and their cross correlations. The results are obtained using a new optimal fast estimator (Pen 2003) deprojected using minimum variance and SVD techniques. We show the resulting 3-D power spectra for dark matter and galaxies, and their covariance for the VIRMOS-DESCART weak lensing shear and galaxy data. The survey is most sensitive to nonlinear scales k_NL ~ 1 h Mpc^-1. On these scales, our 3-D power spectrum of dark matter is in good agreement with the RCS 3-D power spectrum found by (Hoekstra et al 2002). Our galaxy power is similar to that found by the 2MASS survey, and larger than that of SDSS, APM and RCS, consistent with the expected difference in galaxy population. We find an average bias b=1.24+/-0.18 for the I selected galaxies, and a cross correlation coefficient r=0.75+/-0.23. Together with the power spectra, these results optimally encode the entire two point information about dark matter and galaxies, including galaxy-galaxy lensing. We address some of the implications regarding galaxy halos and mass-to-light ratios. The best fit ``halo'' parameter h=r/b=0.57+/-0.16, suggesting that dynamical masses estimated using galaxies systematically underestimate total mass. Ongoing surveys, such as the Canada-France-Hawaii-Telescope-Legacy survey will significantly improve on the dynamic range, and future photometric redshift catalogs will allow tomography along the same principles.Comment: 17 pages, 19 figures, submitted to mnra

Changes in Retinol-Binding Protein Concentrations and Thyroid Homeostasis with Nonoccupational Exposure to DDT

BACKGROUND: The insecticide dichlorodiphenyltrichloroethane (DDT) has been used for malaria vector control in the northern and eastern parts of the Vhembe District of Limpopo Province, South Africa, since 1945. Bioaccumulation of DDT raises concern because it reportedly affects thyroid function. OBJECTIVE: Our objective was to investigate the association between DDT uptake (as reflected in plasma concentrations) and thyroid homeostasis while considering related factors. METHODS: We compared dietary intake, serum retinol-binding protein (RBP), transthyretin (TTR) and albumin concentrations, and liver and thyroid function between cases with evidence of a body burden of DDT in the circulation (concentration of any DDT isomer ≥ 0.02 μg/g lipid; n = 278) and controls (concentration of all DDT isomers < 0.02 μg/g lipid; n = 40) in a cross-sectional study. Further analyses were performed to assess the relevance of changes in RBP status associated with DDT uptake. RESULTS: RBP concentrations below the reference range were more prevalent in cases (54% vs. 10% in controls; χ2 = 27.4; p < 0.001), which could not be explained by nutrient intake. We observed significantly lower thyroid hormone concentrations among cases (p ≤ 0.01). We also observed a significant linear trend for serum concentrations of free thyroxine and free triiodothyronine (p < 0.001) and a significant quadratic trend for serum thyroid-stimulating hormone (p = 0.025) and TTR (p < 0.001) across the control group and case groups with normal and relatively low RBP concentrations. Relatively low RBP concentrations were associated with significantly higher DDT and 1,1-dichloro-2,2-bis(p-chlorophenyl) ethylene (DDE) isomer concentrations and with a higher DDE/DDT ratio (p ≤ 0.01), which signifies long-term exposure. Inadequate intake of vitamin A and zinc were observed in 84% and 58%, respectively, of the total study population. CONCLUSION: RBP concentrations appear to decrease in the presence of long-term DDT uptake, which may have deleterious effects on thyroid function and vitamin A nutritional status. This is of major concern in a population with poor vitamin A and zinc intake

Limits on the ultra-bright Fast Radio Burst population from the CHIME Pathfinder

We present results from a new incoherent-beam Fast Radio Burst (FRB) search on the Canadian Hydrogen Intensity Mapping Experiment (CHIME) Pathfinder. Its large instantaneous field of view (FoV) and relative thermal insensitivity allow us to probe the ultra-bright tail of the FRB distribution, and to test a recent claim that this distribution's slope, $\alpha\equiv-\frac{\partial \log N}{\partial \log S}$, is quite small. A 256-input incoherent beamformer was deployed on the CHIME Pathfinder for this purpose. If the FRB distribution were described by a single power-law with $\alpha=0.7$, we would expect an FRB detection every few days, making this the fastest survey on sky at present. We collected 1268 hours of data, amounting to one of the largest exposures of any FRB survey, with over 2.4\,$\times$\,10$^5$\,deg$^2$\,hrs. Having seen no bursts, we have constrained the rate of extremely bright events to $<\!13$\,sky$^{-1}$\,day$^{-1}$ above $\sim$\,220$\sqrt{(\tau/\rm ms)}$ Jy\,ms for $\tau$ between 1.3 and 100\,ms, at 400--800\,MHz. The non-detection also allows us to rule out $\alpha\lesssim0.9$ with 95$\%$ confidence, after marginalizing over uncertainties in the GBT rate at 700--900\,MHz, though we show that for a cosmological population and a large dynamic range in flux density, $\alpha$ is brightness-dependent. Since FRBs now extend to large enough distances that non-Euclidean effects are significant, there is still expected to be a dearth of faint events and relative excess of bright events. Nevertheless we have constrained the allowed number of ultra-intense FRBs. While this does not have significant implications for deeper, large-FoV surveys like full CHIME and APERTIF, it does have important consequences for other wide-field, small dish experiments

First Detection of Cosmic Structure in the 21-cm Intensity Field

We present the first statistically significant detection of cosmic structure using broadly distributed hydrogen radio emission. This is accomplished using a cross correlation with optical galaxies. Statistical noise levels of $20 \mu$K are achieved, unprecedented in this frequency band. This lends support to the idea that large volumes of the universe can be rapidly mapped without the need to resolve individual faint galaxies, enabling precise constraints to dark energy models. We discuss strategies for improved intensity mapping.Comment: 5 pages, 4 figures, submitted to MNRA

Absolute estimation of initial concentrations of amplicon in a real-time RT-PCR process

<p>Abstract</p> <p>Background</p> <p>Since real time PCR was first developed, several approaches to estimating the initial quantity of template in an RT-PCR reaction have been tried. While initially only the early thermal cycles corresponding to exponential duplication were used, lately there has been an effort to use all of the cycles in a PCR. The efforts have included both fitting empirical sigmoid curves and more elaborate mechanistic models that explore the chemical reactions taking place during each cycle. The more elaborate mechanistic models require many more parameters than can be fit from a single amplification, while the empirical models provide little insight and are difficult to tailor to specific reactants.</p> <p>Results</p> <p>We directly estimate the initial amount of amplicon using a simplified mechanistic model based on chemical reactions in the annealing step of the PCR. The basic model includes the duplication of DNA with the digestion of Taqman probe and the re-annealing between previously synthesized DNA strands of opposite orientation. By modelling the amount of Taqman probe digested and matching that with the observed fluorescence, the conversion factor between the number of fluorescing dye molecules and observed fluorescent emission can be estimated, along with the absolute initial amount of amplicon and the rate parameter for re-annealing. The model is applied to several PCR reactions with known amounts of amplicon and is shown to work reasonably well. An expanded version of the model allows duplication of amplicon without release of fluorescent dye, by adding 1 more parameter to the model. The additional process is helpful in most cases where the initial primer concentration exceeds the initial probe concentration. Software for applying the algorithm to data may be downloaded at <url>http://www.niehs.nih.gov/research/resources/software/pcranalyzer/</url></p> <p>Conclusion</p> <p>We present proof of the principle that a mechanistically based model can be fit to observations from a single PCR amplification. Initial amounts of amplicon are well estimated without using a standard solution. Using the ratio of the predicted initial amounts of amplicon from 2 PCRs is shown to work well even when the absolute amounts of amplicon are underestimated in the individual PCRs.</p

Bone refilling in cortical bone multicellular units: Insights into tetracycline double labelling from a computational model

Bone remodelling is carried out by `bone multicellular units' (BMUs) in which active osteoclasts and active osteoblasts are spatially and temporally coupled. The refilling of new bone by osteoblasts towards the back of the BMU occurs at a rate that depends both on the number of osteoblasts and on their secretory activity. In cortical bone, a linear phenomenological relationship between matrix apposition rate (MAR) and BMU cavity radius is found experimentally. How this relationship emerges from the combination of complex, nonlinear regulations of osteoblast number and secretory activity is unknown. Here, we extend our previous mathematical model of cell development within a single BMU to investigate how osteoblast number and osteoblast secretory activity vary along the BMU's closing cone. MARs predicted by the model are compared with data from tetracycline double labelling experiments. We find that the linear phenomenological relationship observed in these experiments between MAR and BMU cavity radius holds for most of the refilling phase simulated by our model, but not near the start and end of refilling. This suggests that at a particular bone site undergoing remodelling, bone formation starts and ends rapidly. Our model also suggests that part of the observed cross-sectional variability in tetracycline data may be due to different bone sites being refilled by BMUs at different stages of their lifetime. The different stages of a BMU's lifetime depend on whether the cell populations within the BMU are still developing or have reached a quasi-steady state while travelling through bone. We find that due to their longer lifespan, active osteoblasts reach a quasi-steady distribution more slowly than active osteoclasts. We suggest that this fact may locally enlarge the Haversian canal diameter (due to a local lack of osteoblasts compared to osteoclasts) near the BMU's point of origin.Comment: 16 pages, 6 figures, 3 tables. V3: minor changes: added 2 paragraphs (BMU cavity in Section 2 and Model Robustness in Section 4), references [52,54