UNIT project: Universe NN-body simulations for the Investigation of Theoretical models from galaxy surveys

We present the UNIT $N$-body cosmological simulations project, designed to provide precise predictions for nonlinear statistics of the galaxy distribution. We focus on characterizing statistics relevant to emission line and luminous red galaxies in the current and upcoming generation of galaxy surveys. We use a suite of precise particle mesh simulations (FastPM) as well as with full $N$-body calculations with a mass resolution of $\sim 1.2\times10^9\,h^{-1}$M$_{\odot}$ to investigate the recently suggested technique of Angulo & Pontzen 2016 to suppress the variance of cosmological simulations We study redshift space distortions, cosmic voids, higher order statistics from $z=2$ down to $z=0$. We find that both two- and three-point statistics are unbiased. Over the scales of interest for baryon acoustic oscillations and redshift-space distortions, we find that the variance is greatly reduced in the two-point statistics and in the cross correlation between halos and cosmic voids, but is not reduced significantly for the three-point statistics. We demonstrate that the accuracy of the two-point correlation function for a galaxy survey with effective volume of 20 ($h^{-1}$Gpc)$^3$ is improved by about a factor of 40, indicating that two pairs of simulations with a volume of 1 ($h^{-1}$Gpc)$^3$ lead to the equivalent variance of $\sim$150 such simulations. The $N$-body simulations presented here thus provide an effective survey volume of about seven times the effective survey volume of DESI or Euclid. The data from this project, including dark matter fields, halo catalogues, and their clustering statistics, are publicly available at http://www.unitsims.org.Comment: 12 pages, 9 figures. This version matches the one accepted by MNRAS. The data from this project are publicly available at: http://www.unitsims.or

A model-based circular binary segmentation algorithm for the analysis of array CGH data

<p>Abstract</p> <p>Background</p> <p>Circular Binary Segmentation (CBS) is a permutation-based algorithm for array Comparative Genomic Hybridization (aCGH) data analysis. CBS accurately segments data by detecting change-points using a maximal-<it>t </it>test; but extensive computational burden is involved for evaluating the significance of change-points using permutations. A recent implementation utilizing a hybrid method and early stopping rules (hybrid CBS) to improve the performance in speed was subsequently proposed. However, a time analysis revealed that a major portion of computation time of the hybrid CBS was still spent on permutation. In addition, what the hybrid method provides is an approximation of the significance upper bound or lower bound, not an approximation of the significance of change-points itself.</p> <p>Results</p> <p>We developed a novel model-based algorithm, extreme-value based CBS (eCBS), which limits permutations and provides robust results without loss of accuracy. Thousands of aCGH data under null hypothesis were simulated in advance based on a variety of non-normal assumptions, and the corresponding maximal-<it>t </it>distribution was modeled by the Generalized Extreme Value (GEV) distribution. The modeling results, which associate characteristics of aCGH data to the GEV parameters, constitute lookup tables (eXtreme model). Using the eXtreme model, the significance of change-points could be evaluated in a constant time complexity through a table lookup process.</p> <p>Conclusions</p> <p>A novel algorithm, eCBS, was developed in this study. The current implementation of eCBS consistently outperforms the hybrid CBS 4× to 20× in computation time without loss of accuracy. Source codes, supplementary materials, supplementary figures, and supplementary tables can be found at <url>http://ntumaps.cgm.ntu.edu.tw/eCBSsupplementary</url>.</p

Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing

Number of misassemblies for different assembly strategies. Number of misassemblies for the de novo assembly results for E. coli DH1 and S. Parasanguinis FW213 are shown together with their standard errors of the mean. Group A [PE] and Group A [SE] represent all reads assembled as paired-end reads and single end reads, respectively. Group A [PE + SE] represents all the non-overlapped paired-end reads assembled together with merged reads. Group M [PE] and Group M [SE] represent Group M reads assembled as paired-end reads and single end reads, respectively. The numbers of misassemblies fluctuate a lot when depths of read number are low and gradually decreases until they reach a steady number. The paired-end reads (Group A [PE] and Group M [PE]) in S. Parasanguinis FW213 gave the lowest number of misassemblies when depths of read number are high. (TIFF 669 kb

Pressure tunable quantum anomalous Hall states in a topological antiferromagnet

Mechanical modulation of the lattice parameter can modify the electronic structure and manipulate the magnetic coupling of a material without introducing impurities. Inspired by success in pressure-controlled magnetism, we investigate the effect of hydrostatic pressure on quantized Chern states in the antiferromagnetic topological insulator MnBi2Te4, using transport as a probe. We show that pressure can enhance the robustness of quantum anomalous Hall (QAH) phases that are otherwise delicate in 7SL MnBi2Te4 and in the spin-flop (SF) state of 8SL MnBi2Te4. We explain our findings using a coupled Dirac cone model of MnBi2Te4, which identifies stronger hybridization between van der Waals layers as the driver of topological states. We further demonstrate that moderate pressures readily available in laboratory systems can provide reversible control of magnetic and topological phases. Our results reveal a strong connection between the mechanical engineering of band topology and magnetism.Comment: 11 pages, 4 figure

Covariance matrices for variance-suppressed simulations

Cosmological $N$-body simulations provide numerical predictions of the structure of the universe against which to compare data from ongoing and future surveys. The growing volume of the surveyed universe, however, requires increasingly large simulations. It was recently proposed to reduce the variance in simulations by adopting fixed-amplitude initial conditions. This method has been demonstrated not to introduce bias in various statistics, including the two-point statistics of galaxy samples typically used for extracting cosmological parameters from galaxy redshift survey data. However, we must revisit current methods for estimating covariance matrices for these simulations to be sure that we can properly use them. In this work, we find that it is not trivial to construct the covariance matrix analytically, but we demonstrate that EZmock, the most efficient method for constructing mock catalogues with accurate two- and three-point statistics, provides reasonable covariance matrix estimates for variance-suppressed simulations. We further investigate the behavior of the variance suppression by varying galaxy bias, three-point statistics, and small-scale clustering.Comment: 9 pages, 7 figure

Deep ultraviolet laser direct write for patterning sol-gel InGaZnO semiconducting micro/nanowires and improving field-effect mobility

Deep-UV (DUV) laser was used to directly write indium-gallium-zinc-oxide (IGZO) precursor solution and form micro and nanoscale patterns. The directional DUV laser beam avoids the substrate heating and suppresses the diffraction effect. A IGZO precursor solution was also developed to fulfill the requirements for direct photopatterning and for achieving semi-conducting properties with thermal annealing at moderate temperature. The DUV-induced crosslinking of the starting material allows direct write of semi-conducting channels in thin-film transistors but also it improves the field-effect mobility and surface roughness. Material analysis has been carried out by XPS, FTIR, spectroscopic ellipsometry and AFM and the effect of DUV on the final material structure is discussed. The DUV irradiation step results in photolysis and a partial condensation of the inorganic network that freezes the sol-gel layer in a homogeneous distribution, lowering possibilities of thermally induced reorganization at the atomic scale. Laser irradiation allows high-resolution photopatterning and high-enough field-effect mobility, which enables the easy fabrication of oxide nanowires for applications in solar cell, display, flexible electronics, and biomedical sensors

Erratum to: Erythropoietin improves long-term neurological outcome in acute ischemic stroke patients: a randomized, prospective, placebo-controlled clinical trial.

This article is freely available via Open Access. Click on the 'Additional Link' above to access the full-text via the publisher's site.Publishe

Seroprevalence and Severity of 2009 Pandemic Influenza A H1N1 in Taiwan

BACKGROUND: This study is to determine the seroprevalence of the pandemic influenza A H1N1 virus (pH1N1) in Taiwan before and after the 2009 pandemic, and to estimate the relative severity of pH1N1 infections among different age groups. METHODOLOGY/PRINCIPAL FINDINGS: A total of 1544 and 1558 random serum samples were collected from the general population in Taiwan in 2007 and 2010, respectively. Seropositivity was defined by a hemagglutination inhibition titer to pH1N1 (A/Taiwan/126/09) ≥1:40. The seropositivity rate of pH1N1 among the unvaccinated subjects and national surveillance data were used to compare the proportion of infections that led to severe diseases and fatalities among different age groups. The overall seroprevalence of pH1N1 was 0.91% (95% confidence interval [CI] 0.43-1.38) in 2007 and significantly increased to 29.9% (95% CI 27.6-32.2) in 2010 (p<0.0001), with the peak attack rate (55.4%) in 10-17 year-old adolescents, the lowest in elderly ≥65 years (14.1%). The overall attack rates were 20.6% (188/912) in unvaccinated subjects. Among the unvaccinated but infected populations, the estimated attack rates of severe cases per 100,000 infections were significantly higher in children aged 0-5 years (54.9 cases, odds ratio [OR] 4.23, 95% CI 3.04-5.90) and elderly ≥ 65 years (22.4 cases, OR 2.76, 95% CI 1.99-3.83) compared to adolescents aged 10-17 years (13.0 cases). The overall case-fatality rate was 0.98 per 100,000 infections without a significant difference in different age groups. CONCLUSIONS/SIGNIFICANCE: Pre-existing immunity against pH1N1 was rarely identified in Taiwanese at any age in 2007. Young children and elderly--the two most lower seroprotection groups showed the greatest vulnerability to clinical severity after the pH1N1 infections. These results imply that both age groups should have higher priority for immunization in the coming flu season