Contemporary effective population size (Ne) can be estimated using linkage disequilibrium (LD) observed across pairs of loci presumed to be selectively neutral and unlinked. This method has been ...commonly applied to data sets containing 10-100 loci to inform conservation and study population demography. Performance of these Ne estimates could be improved by incorporating data from thousands of loci. However, these thousands of loci exist on a limited number of chromosomes, ensuring that some fraction will be physically linked. Linked loci have elevated LD due to limited recombination, which if not accounted for can cause Ne estimates to be downwardly biased. Here, we present results from coalescent and forward simulations designed to evaluate the bias of LD-based Ne estimates (Ncirc e). Contrary to common perceptions, increasing the number of loci does not increase the magnitude of linkage. Although we show it is possible to identify some pairs of loci that produce unusually large r(2) values, simply removing large r(2) values is not a reliable way to eliminate bias. Fortunately, the magnitude of bias in Ncirc e is strongly and negatively correlated with the process of recombination, including the number of chromosomes and their length, and this relationship provides a general way to adjust for bias. Additionally, we show that with thousands of loci, precision of Ncirc e is much lower than expected based on the assumption that each pair of loci provides completely independent information.
The thermodynamic state of star-forming gas determines its fragmentation behavior and thus plays a crucial role in determining the stellar initial mass function (IMF). We address the issue by ...studying the effects of a piecewise polytropic equation of state (EOS) on the formation of stellar clusters in turbulent, self-gravitating molecular clouds using three-dimensional, smoothed particle hydrodynamics simulations. In these simulations stars form via a process we call gravoturbulent fragmentation, i.e., gravitational fragmentation of turbulent gas. To approximate the results of published predictions of the thermal behavior of collapsing clouds, we increase the polytropic exponent γ from 0.7 to 1.1 at a critical density nc, which we estimated to be $2.5\times10^5\,\mathrm{cm^{-3}}$. The change of thermodynamic state at nc selects a characteristic mass scale for fragmentation Mch, which we relate to the peak of the observed IMF. A simple scaling argument based on the Jeans mass $M_\mathrm{J}$ at the critical density $n_\mathrm{c}$ leads to $M_{\mathrm{ch}}\propto n_{\mathrm{c}}^{-0.95}$. We perform simulations with $4.3\times10^4\,\mathrm{cm^{-3}} < n_{\mathrm{c}} < 4.3\times10^7\,\mathrm{cm^{-3}}$ to test this scaling argument. Our simulations qualitatively support this hypothesis, but we find a weaker density dependence of $M_{\mathrm{ch}} \propto n_{\mathrm{c}}^{-0.5\pm0.1}$. We also investigate the influence of additional environmental parameters on the IMF. We consider variations in the turbulent driving scheme, and consistently find $M_{\mathrm{J}}$ is decreasing with increasing $n_{\mathrm{c}}$. Our investigation generally supports the idea that the distribution of stellar masses depends mainly on the thermodynamic state of the star-forming gas. The thermodynamic state of interstellar gas is a result of the balance between heating and cooling processes, which in turn are determined by fundamental atomic and molecular physics and by chemical abundances. Given the abundances, the derivation of a characteristic stellar mass can thus be based on universal quantities and constants.
Acute liver failure (ALF) is classically defined by coagulopathy and hepatic encephalopathy (HE); however, acute liver injury (ALI), i.e., severe acute hepatocyte necrosis without HE, has not been ...carefully defined nor studied. Our aim is to describe the clinical course of specifically defined ALI, including the risk and clinical predictors of poor outcomes, namely progression to ALF, the need for liver transplantation (LT) and death.
386 subjects prospectively enrolled in the Acute Liver Failure Study Group registry between 1 September 2008 through 25 October 2013, met criteria for ALI: International Normalized Ratio (INR)≥2.0 and alanine aminotransferase (ALT)≥10 × elevated (irrespective of bilirubin level) for acetaminophen (N-acetyl-p-aminophenol, APAP) ALI, or INR≥2.0, ALT≥10x elevated, and bilirubin≥3.0 mg/dl for non-APAP ALI, both groups without any discernible HE. Subjects who progressed to poor outcomes (ALF, death, LT) were compared, by univariate analysis, with those who recovered. A model to predict poor outcome was developed using the random forest (RF) procedure.
Progression to a poor outcome occurred in 90/386 (23%), primarily in non-APAP (71/179, 40%) vs. only 14/194 (7.2%) in APAP patients comprising 52% of all cases (13 cases did not have an etiology assigned; 5 of whom had a poor outcome). Of 82 variables entered into the RF procedure: etiology, bilirubin, INR, APAP level and duration of jaundice were the most predictive of progression to ALF, LT, or death.
A majority of ALI cases are due to APAP, 93% of whom will improve rapidly and fully recover, while non-APAP patients have a far greater risk of poor outcome and should be targeted for early referral to a liver transplant center.
We present cosmological parameter constraints based on the final nine-year Wilkinson Microwave Anisotropy Probe (WMAP) data, in conjunction with a number of additional cosmological data sets. The ...WMAP data alone, and in combination, continue to be remarkably well fit by a six-parameter ?CDM model. We compare recent Planck measurements of the Sunyaev-Zel'dovich effect with our seven-year measurements, and show their mutual agreement. Our analysis of the polarization pattern around temperature extrema is updated. This confirms a fundamental prediction of the standard cosmological model and provides a striking illustration of acoustic oscillations and adiabatic initial conditions in the early universe.
We present the final nine-year maps and basic results from the Wilkinson Microwave Anisotropy Probe (WMAP) mission. The full nine-year analysis of the time-ordered data provides updated ...characterizations and calibrations of the experiment. We also provide new nine-year full sky temperature maps that were processed to reduce the asymmetry of the effective beams. Temperature and polarization sky maps are examined to separate cosmic microwave background (CMB) anisotropy from foreground emission, and both types of signals are analyzed in detail.We provide new point source catalogs as well as new diffuse and point source foreground masks. An updated template-removal process is used for cosmological analysis; new foreground fits are performed, and new foreground reduced are presented.We nowimplement an optimal C(exp -1)1 weighting to compute the temperature angular power spectrum. The WMAP mission has resulted in a highly constrained Lambda-CDM cosmological model with precise and accurate parameters in agreement with a host of other cosmological measurements. When WMAP data are combined with finer scale CMB, baryon acoustic oscillation, and Hubble constant measurements, we find that big bang nucleosynthesis is well supported and there is no compelling evidence for a non-standard number of neutrino species (N(sub eff) = 3.84 +/- 0.40). The model fit also implies that the age of the universe is (sub 0) = 13.772 +/- 0.059 Gyr, and the fit Hubble constant is H(sub 0) = 69.32 +/- 0.80 km/s/ Mpc. Inflation is also supported: the fluctuations are adiabatic, with Gaussian random phases; the detection of a deviation of the scalar spectral index from unity, reported earlier by the WMAP team, now has high statistical significance (n(sub s) = 0.9608+/-0.0080); and the universe is close to flat/Euclidean (Omega = −0.0027+0.0039/−0.0038). Overall, the WMAP mission has resulted in a reduction of the cosmological parameter volume by a factor of 68,000 for the standard six-parameter Lambda-CDM model, based on CMB data alone. For a model including tensors, the allowed seven-parameter volume has been reduced by a factor 117,000. Other cosmological observations are in accord with the CMB predictions, and the combined data reduces the cosmological parameter volume even further.With no significant anomalies and an adequate goodness of fit, the inflationary flat Lambda-CDM model and its precise and accurate parameters rooted in WMAP data stands as the standard model of cosmology.
The Wilkinson Microwave Anisotropy Probe (WMAP) 5-year data provide stringent limits on deviations from the minimal, six-parameter Lambda cold dark matter model. We report these limits and use them ...to constrain the physics of cosmic inflation via Gaussianity, adiabaticity, the power spectrum of primordial fluctuations, gravitational waves, and spatial curvature. We also constrain models of dark energy via its equation of state, parity-violating interaction, and neutrino properties, such as mass and the number of species. We detect no convincing deviations from the minimal model. The six parameters and the corresponding 68% uncertainties, derived from the WMAP data combined with the distance measurements from the Type Ia supernovae (SN) and the Baryon Acoustic Oscillations (BAO) in the distribution of galaxies, are: Omega b h 2 = 0.02267+0.00058 -0.00059, Omega c h 2 = 0.1131 ± 0.0034, Omega Lambda = 0.726 ± 0.015, ns = 0.960 ± 0.013, tau = 0.084 ± 0.016, and at k = 0.002 Mpc-1. From these, we derive sigma 8 = 0.812 ± 0.026, H 0 = 70.5 ± 1.3 km s-1 Mpc-1, Omega b = 0.0456 ± 0.0015, Omega c = 0.228 ± 0.013, Omega m h 2 = 0.1358+0.0037 -0.0036, z reion = 10.9 ± 1.4, and t 0 = 13.72 ± 0.12 Gyr. With the WMAP data combined with BAO and SN, we find the limit on the tensor-to-scalar ratio of r < 0.22(95%CL), and that ns > 1 is disfavored even when gravitational waves are included, which constrains the models of inflation that can produce significant gravitational waves, such as chaotic or power-law inflation models, or a blue spectrum, such as hybrid inflation models. We obtain tight, simultaneous limits on the (constant) equation of state of dark energy and the spatial curvature of the universe: -0.14 < 1 + w < 0.12(95%CL) and -0.0179 < Omega k < 0.0081(95%CL). We provide a set of 'WMAP distance priors,' to test a variety of dark energy models with spatial curvature. We test a time-dependent w with a present value constrained as -0.33 < 1 + w 0 < 0.21 (95% CL). Temperature and dark matter fluctuations are found to obey the adiabatic relation to within 8.9% and 2.1% for the axion-type and curvaton-type dark matter, respectively. The power spectra of TB and EB correlations constrain a parity-violating interaction, which rotates the polarization angle and converts E to B. The polarization angle could not be rotated more than -59 < Delta alpha < 24 (95% CL) between the decoupling and the present epoch. We find the limit on the total mass of massive neutrinos of capital sigma m Delta < 0.67 eV(95%CL), which is free from the uncertainty in the normalization of the large-scale structure data. The number of relativistic degrees of freedom (dof), expressed in units of the effective number of neutrino species, is constrained as N eff = 4.4 ± 1.5 (68%), consistent with the standard value of 3.04. Finally, quantitative limits on physically-motivated primordial non-Gaussianity parameters are -9 < f local NL < 111 (95% CL) and -151 < f equil NL < 253 (95% CL) for the local and equilateral models, respectively.
Ovarian cancer (OC) is the second most common gynecological malignancy and the fifth leading cause of death due to cancer in women in the United States mainly due to the late-stage diagnosis of this ...cancer. It is, therefore, critical to identify potential indicators to aid in early detection and diagnosis of this disease. We investigated the microbiome associated with OC and its potential role in detection, progression as well as prognosis of the disease. We identified a distinct OC microbiome with general enrichment of several microbial taxa, including Dialister, Corynebacterium, Prevotella, and Peptoniphilus in the OC cohort in all body sites excluding stool and omentum which were not sampled from the benign cohort. These taxa were, however, depleted in the advanced-stage and high-grade OC patients compared to early-stage and low-grade OC patients suggestive of decrease accumulation in advanced disease and could serve as potential indicators for early detection of OC. Similarly, we also observed the accumulation of these mainly pathogenic taxa in OC patients with adverse treatment outcomes compared to those without events and could also serve as potential indicators for predicting patients' responses to treatment. These findings provide important insights into the potential use of the microbiome as indicators in (1) early detection of and screening for OC and (2) predicting patients' response to treatment. Given the limited number of patients enrolled in the study, these results would need to be further investigated and confirmed in a larger study.
This paper focuses on cosmological constraints derived from analysis of WMAP data alone. A simple Lambda CDM cosmological model fits the five-year WMAP temperature and polarization data. The basic ...parameters of the model are consistent with the three-year data and now better constrained: Omega b h 2 = 0.02273 ± 0.00062, Omega c h 2 = 0.1099 ± 0.0062, Omega Lambda = 0.742 ± 0.030, ns = 0.963+0.014 -0.015, tau = 0.087 ± 0.017, and sigma 8 = 0.796 ± 0.036, with h = 0.719+0.026 -0.027. With five years of polarization data, we have measured the optical depth to reionization, tau >0, at 5 sigma significance. The redshift of an instantaneous reionization is constrained to be z reion = 11.0 ± 1.4 with 68% confidence. The 2 sigma lower limit is z reion > 8.2, and the 3 sigma limit is z reion > 6.7. This excludes a sudden reionization of the universe at z = 6 at more than 3.5 sigma significance, suggesting that reionization was an extended process. Using two methods for polarized foreground cleaning we get consistent estimates for the optical depth, indicating an error due to the foreground treatment of tau ~ 0.01. This cosmological model also fits small-scale cosmic microwave background (CMB) data, and a range of astronomical data measuring the expansion rate and clustering of matter in the universe. We find evidence for the first time in the CMB power spectrum for a nonzero cosmic neutrino background, or a background of relativistic species, with the standard three light neutrino species preferred over the best-fit Lambda CDM model with N eff = 0 at >99.5% confidence, and N eff > 2.3(95%confidence limit (CL)) when varied. The five-year WMAP data improve the upper limit on the tensor-to-scalar ratio, r < 0.43(95%CL), for power-law models, and halve the limit on r for models with a running index, r < 0.58(95%CL). With longer integration we find no evidence for a running spectral index, with dns /dln k = -0.037 ± 0.028, and find improved limits on isocurvature fluctuations. The current WMAP-only limit on the sum of the neutrino masses is capital sigma m Delta < 1.3 eV(95%CL), which is robust, to within 10%, to a varying tensor amplitude, running spectral index, or dark energy equation of state.
We present new full-sky temperature and polarization maps in five frequency bands from 23 to 94 GHz, based on data from the first five years of the Wilkinson Microwave Anisotropy Probe (WMAP) sky ...survey. The new maps are consistent with previous maps and are more sensitive. The five-year maps incorporate several improvements in data processing made possible by the additional years of data and by a more complete analysis of the instrument calibration and in-flight beam response. We present several new tests for systematic errors in the polarization data and conclude that W-band polarization data is not yet suitable for cosmological studies, but we suggest directions for further study. We do find that Ka-band data is suitable for use; in conjunction with the additional years of data, the addition of Ka band to the previously used Q- and V-band channels significantly reduces the uncertainty in the optical depth parameter, tau . Further scientific results from the five-year data analysis are presented in six companion papers and are summarized in Section 7 of this paper. With the five-year WMAP data, we detect no convincing deviations from the minimal six-parameter Lambda CDM model: a flat universe dominated by a cosmological constant, with adiabatic and nearly scale-invariant Gaussian fluctuations. Using WMAP data combined with measurements of Type Ia supernovae and Baryon Acoustic Oscillations in the galaxy distribution, we find (68% CL uncertainties): Omega b h 2 = 0.02267+0.00058 -0.00059, Omega c h 2 = 0.1131 ± 0.0034, Omega Lambda = 0.726 ± 0.015, ns = 0.960 ± 0.013, tau = 0.084 ± 0.016, and at k = 0.002 Mpc-1. From these we derive sigma 8 = 0.812 ± 0.026, H 0 = 70.5 ± 1.3 km s-1 Mpc-1, Omega b = 0.0456 ± 0.0015, Omega c = 0.228 ± 0.013, Omega m h 2 = 0.1358+0.0037 -0.0036, z reion = 10.9 ± 1.4, and t 0 = 13.72 ± 0.12 Gyr. The new limit on the tensor-to-scalar ratio is r < 0.22(95%CL), while the evidence for a running spectral index is insignificant, dns /dln k = -0.028 ± 0.020 (68% CL). We obtain tight, simultaneous limits on the (constant) dark energy equation of state and the spatial curvature of the universe: -0.14 < 1 + w < 0.12(95%CL) and -0.0179 < Omega k < 0.0081(95%CL). The number of relativistic degrees of freedom, expressed in units of the effective number of neutrino species, is found to be N eff = 4.4 ± 1.5 (68% CL), consistent with the standard value of 3.04. Models with N eff = 0 are disfavored at >99.5% confidence. Finally, new limits on physically motivated primordial non-Gaussianity parameters are -9 < f local NL < 111 (95% CL) and -151 < f equil NL < 253 (95% CL) for the local and equilateral models, respectively.
The combination of seven-year data from WMAP and improved astrophysical data rigorously tests the standard cosmological model and places new constraints on its basic parameters and extensions. By ...combining the WMAP data with the latest distance measurements from the baryon acoustic oscillations (BAO) in the distribution of galaxies and the Hubble constant (H 0) measurement, we determine the parameters of the simplest six-parameter Delta *LCDM model. The power-law index of the primordial power spectrum is ns = 0.968 ? 0.012 (68% CL) for this data combination, a measurement that excludes the Harrison-Zel'dovich-Peebles spectrum by 99.5% CL. The other parameters, including those beyond the minimal set, are also consistent with, and improved from, the five-year results. We find no convincing deviations from the minimal model. The seven-year temperature power spectrum gives a better determination of the third acoustic peak, which results in a better determination of the redshift of the matter-radiation equality epoch. Notable examples of improved parameters are the total mass of neutrinos, Delta *Sm Delta *n < 0.58 eV(95%CL), and the effective number of neutrino species, N eff = 4.34+0.86 --0.88 (68% CL), which benefit from better determinations of the third peak and H 0. The limit on a constant dark energy equation of state parameter from WMAP+BAO+H 0, without high-redshift Type Ia supernovae, is w = --1.10 ? 0.14 (68% CL). We detect the effect of primordial helium on the temperature power spectrum and provide a new test of big bang nucleosynthesis by measuring Yp = 0.326 ? 0.075 (68% CL). We detect, and show on the map for the first time, the tangential and radial polarization patterns around hot and cold spots of temperature fluctuations, an important test of physical processes at z = 1090 and the dominance of adiabatic scalar fluctuations. The seven-year polarization data have significantly improved: we now detect the temperature-E-mode polarization cross power spectrum at 21 Delta *s, compared with 13 Delta *s from the five-year data. With the seven-year temperature-B-mode cross power spectrum, the limit on a rotation of the polarization plane due to potential parity-violating effects has improved by 38% to (68% CL). We report significant detections of the Sunyaev-Zel'dovich (SZ) effect at the locations of known clusters of galaxies. The measured SZ signal agrees well with the expected signal from the X-ray data on a cluster-by-cluster basis. However, it is a factor of 0.5-0.7 times the predictions from 'universal profile' of Arnaud et al., analytical models, and hydrodynamical simulations. We find, for the first time in the SZ effect, a significant difference between the cooling-flow and non-cooling-flow clusters (or relaxed and non-relaxed clusters), which can explain some of the discrepancy. This lower amplitude is consistent with the lower-than-theoretically expected SZ power spectrum recently measured by the South Pole Telescope Collaboration.
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