Joint Bayesian Estimation of Quasar Continua and the Lyman-Alpha Forest Flux Probability Distribution Function

We present a new Bayesian algorithm making use of Markov Chain Monte Carlo sampling that allows us to simultaneously estimate the unknown continuum level of each quasar in an ensemble of high-resolution spectra, as well as their common probability distribution function (PDF) for the transmitted Ly$\alpha$ forest flux. This fully automated PDF regulated continuum fitting method models the unknown quasar continuum with a linear Principal Component Analysis (PCA) basis, with the PCA coefficients treated as nuisance parameters. The method allows one to estimate parameters governing the thermal state of the intergalactic medium (IGM), such as the slope of the temperature-density relation $\gamma-1$, while marginalizing out continuum uncertainties in a fully Bayesian way. Using realistic mock quasar spectra created from a simplified semi-numerical model of the IGM, we show that this method recovers the underlying quasar continua to a precision of $\simeq7\%$ and $\simeq10\%$ at $z=3$ and $z=5$, respectively. Given the number of principal component spectra, this is comparable to the underlying accuracy of the PCA model itself. Most importantly, we show that we can achieve a nearly unbiased estimate of the slope $\gamma-1$ of the IGM temperature-density relation with a precision of $\pm8.6\%$ at $z=3$, $\pm6.1\%$ at $z=5$, for an ensemble of ten mock high-resolution quasar spectra. Applying this method to real quasar spectra and comparing to a more realistic IGM model from hydrodynamical simulations would enable precise measurements of the thermal and cosmological parameters governing the IGM, albeit with somewhat larger uncertainties given the increased flexibility of the model.Comment: 21 pages (+ Appendix), accepted at Ap

Case of chronic indolent pheochromocytoma that caused medically controlled hypertension but treatment-resistant diabetes mellitus

No abstract available

The Fokker-Planck equation for bistable potential in the optimized expansion

The optimized expansion is used to formulate a systematic approximation scheme to the probability distribution of a stochastic system. The first order approximation for the one-dimensional system driven by noise in an anharmonic potential is shown to agree well with the exact solution of the Fokker-Planck equation. Even for a bistable system the whole period of evolution to equilibrium is correctly described at various noise intensities.Comment: 12 pages, LATEX, 3 Postscript figures compressed an

Switchable Membrane Remodeling and Antifungal Defense by Metamorphic Chemokine XCL1

Antimicrobial peptides (AMPs) are a class of molecules which generally kill pathogens via preferential cell membrane disruption. Chemokines are a family of signaling proteins that direct immune cell migration and share a conserved α–β tertiary structure. Recently, it was found that a subset of chemokines can also function as AMPs, including CCL20, CXCL4, and XCL1. It is therefore surprising that machine learning based analysis predicts that CCL20 and CXCL4’s α-helices are membrane disruptive, while XCL1’s helix is not. XCL1, however, is the only chemokine known to be a metamorphic protein which can interconvert reversibly between two distinct native structures (a β-sheet dimer and the α–β chemokine structure). Here, we investigate XCL1’s antimicrobial mechanism of action with a focus on the role of metamorphic folding. We demonstrate that XCL1 is a molecular “Swiss army knife” that can refold into different structures for distinct context-dependent functions: whereas the α–β chemokine structure controls cell migration by binding to G-Protein Coupled Receptors (GPCRs), we find using small angle X-ray scattering (SAXS) that only the β-sheet and unfolded XCL1 structures can induce negative Gaussian curvature (NGC) in membranes, the type of curvature topologically required for membrane permeation. Moreover, the membrane remodeling activity of XCL1’s β-sheet structure is strongly dependent on membrane composition: XCL1 selectively remodels bacterial model membranes but not mammalian model membranes. Interestingly, XCL1 also permeates fungal model membranes and exhibits anti-Candida activity in vitro, in contrast to the usual mode of antifungal defense which requires Th17 mediated cell-based responses. These observations suggest that metamorphic XCL1 is capable of a versatile multimodal form of antimicrobial defense

Switchable Membrane Remodeling and Antifungal Defense by Metamorphic Chemokine XCL1

Antimicrobial peptides (AMPs) are a class of molecules which generally kill pathogens via preferential cell membrane disruption. Chemokines are a family of signaling proteins that direct immune cell migration and share a conserved α–β tertiary structure. Recently, it was found that a subset of chemokines can also function as AMPs, including CCL20, CXCL4, and XCL1. It is therefore surprising that machine learning based analysis predicts that CCL20 and CXCL4’s α-helices are membrane disruptive, while XCL1’s helix is not. XCL1, however, is the only chemokine known to be a metamorphic protein which can interconvert reversibly between two distinct native structures (a β-sheet dimer and the α–β chemokine structure). Here, we investigate XCL1’s antimicrobial mechanism of action with a focus on the role of metamorphic folding. We demonstrate that XCL1 is a molecular “Swiss army knife” that can refold into different structures for distinct context-dependent functions: whereas the α–β chemokine structure controls cell migration by binding to G-Protein Coupled Receptors (GPCRs), we find using small angle X-ray scattering (SAXS) that only the β-sheet and unfolded XCL1 structures can induce negative Gaussian curvature (NGC) in membranes, the type of curvature topologically required for membrane permeation. Moreover, the membrane remodeling activity of XCL1’s β-sheet structure is strongly dependent on membrane composition: XCL1 selectively remodels bacterial model membranes but not mammalian model membranes. Interestingly, XCL1 also permeates fungal model membranes and exhibits anti-Candida activity in vitro, in contrast to the usual mode of antifungal defense which requires Th17 mediated cell-based responses. These observations suggest that metamorphic XCL1 is capable of a versatile multimodal form of antimicrobial defense

Prevalence and clinical features of patients with concurrent HBsAg and anti‐HBs: Evaluation of the hepatitis B research network cohort

The prevalence of concurrent HBsAg and anti‐HBs in plasma of persons with chronic hepatitis B virus (HBV) infection is variable and its clinical significance enigmatic. We examined the prevalence and clinical and virological features of concurrent HBsAg and anti‐HBs in children and adults with chronic HBV infection living in North America. A total of 1462 HBsAg positive participants in the Hepatitis B Research Network paediatric and adult cohorts were included (median age 41 (range 4‐80) years, 48% female, 11% white, 13% black, 73% Asians). Only 18 (1.2%) were found to be anti‐HBs positive (≥10 mIU/mL) at initial study evaluation. Distributions of sex, race, HBV genotype and ALT were similar between participants with and without concurrent anti‐HBs. Those who were anti‐HBs positive appeared to be older (median age 50 vs 41 years, P = .06), have lower platelet counts (median 197 vs 222 × 103/mm3, P = .07) and have higher prevalence of HBeAg (44% vs 26%, P = .10). They also had lower HBsAg levels (median 2.0 vs 3.5 log10 IU/mL, P = .02). Testing of follow‐up samples after a median of 4 years (range 1‐6) in 12 of the 18 participants with initial concurrent anti‐HBs showed anti‐HBs became undetectable in 6, decreased to <10 mIU/mL in 1 and remained positive in 5 participants. Two patients lost HBsAg during follow‐up. In conclusion, prevalence of concurrent HBsAg and anti‐HBs was low at 1.2%, with anti‐HBs disappearing in some during follow‐up, in this large cohort of racially diverse children and adults with chronic HBV infection living in North America. Presence of concurrent HBsAg and anti‐HBs did not identify a specific phenotype of chronic hepatitis B, nor did it appear to affect clinical outcomes.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/156489/3/jvh13312.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156489/2/jvh13312-sup-0001-FigS1-S3.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156489/1/jvh13312_am.pd

The Chemical Compositions of Very Metal-Poor Stars HD 122563 and HD 140283; A View From the Infrared

From high resolution (R = 45,000), high signal-to-noise (S/N > 400) spectra gathered with the Immersion Grating Infrared Spectrograph (IGRINS) in the H and K photometric bands, we have derived elemental abundances of two bright, well-known metal-poor halo stars: the red giant HD 122563 and the subgiant HD 140283. Since these stars have metallicities approaching [Fe/H] = -3, their absorption features are generally very weak. Neutral-species lines of Mg, Si, S and Ca are detectable, as well as those of the light odd-Z elements Na and Al. The derived IR-based abundances agree with those obtained from optical-wavelength spectra. For Mg and Si the abundances from the infrared transitions are improvements to those derived from shorter wavelength data. Many useful OH and CO lines can be detected in the IGRINS HD 122563 spectrum, from which derived O and C abundances are consistent to those obtained from the traditional [O I] and CH features. IGRINS high resolutions H- and K-band spectroscopy offers promising ways to determine more reliable abundances for additional metal-poor stars whose optical features are either not detectable, or too weak, or are based on lines with analytical difficulties.Comment: Accepted for publication in ApJ (28 pages, 4 tables, 6 figures

The impact of the mixing properties within the Antarctic stratospheric vortex on ozone loss in spring

Calculations of equivalent length from an artificial advected tracer provide new insight into the isentropic transport processes occurring within the Antarctic stratospheric vortex. These calculations show two distinct regions of approximately equal area: a strongly mixed vortex core and a broad ring of weakly mixed air extending out to the vortex boundary. This broad ring of vortex air remains isolated from the core between late winter and midspring. Satellite measurements of stratospheric H2O confirm that the isolation lasts until at least mid-October. A three-dimensional chemical transport model simulation of the Antarctic ozone hole quantifies the ozone loss within this ring and demonstrates its isolation. In contrast to the vortex core, ozone loss in the weakly mixed broad ring is not complete. The reasons are twofold. First, warmer temperatures in the broad ring prevent continuous polar stratospheric cloud (PSC) formation and the associated chemical processing (i.e., the conversion of unreactive chlorine into reactive forms). Second, the isolation prevents ozone-rich air from the broad ring mixing with chemically processed air from the vortex core. If the stratosphere continues to cool, this will lead to increased PSC formation and more complete chemical processing in the broad ring. Despite the expected decline in halocarbons, sensitivity studies suggest that this mechanism will lead to enhanced ozone loss in the weakly mixed region, delaying the future recovery of the ozone hole

Asymptotically hyperbolic manifolds with small mass

For asymptotically hyperbolic manifolds of dimension $n$ with scalar curvature at least equal to $-n(n-1)$ the conjectured positive mass theorem states that the mass is non-negative, and vanishes only if the manifold is isometric to hyperbolic space. In this paper we study asymptotically hyperbolic manifolds which are also conformally hyperbolic outside a ball of fixed radius, and for which the positive mass theorem holds. For such manifolds we show that the conformal factor tends to one as the mass tends to zero

Predictive response-relevant clustering of expression data provides insights into disease processes

This article describes and illustrates a novel method of microarray data analysis that couples model-based clustering and binary classification to form clusters of ;response-relevant' genes; that is, genes that are informative when discriminating between the different values of the response. Predictions are subsequently made using an appropriate statistical summary of each gene cluster, which we call the ;meta-covariate' representation of the cluster, in a probit regression model. We first illustrate this method by analysing a leukaemia expression dataset, before focusing closely on the meta-covariate analysis of a renal gene expression dataset in a rat model of salt-sensitive hypertension. We explore the biological insights provided by our analysis of these data. In particular, we identify a highly influential cluster of 13 genes-including three transcription factors (Arntl, Bhlhe41 and Npas2)-that is implicated as being protective against hypertension in response to increased dietary sodium. Functional and canonical pathway analysis of this cluster using Ingenuity Pathway Analysis implicated transcriptional activation and circadian rhythm signalling, respectively. Although we illustrate our method using only expression data, the method is applicable to any high-dimensional datasets