Using Markov chain Monte Carlo methods for estimating parameters with gravitational radiation data

We present a Bayesian approach to the problem of determining parameters for coalescing binary systems observed with laser interferometric detectors. By applying a Markov Chain Monte Carlo (MCMC) algorithm, specifically the Gibbs sampler, we demonstrate the potential that MCMC techniques may hold for the computation of posterior distributions of parameters of the binary system that created the gravity radiation signal. We describe the use of the Gibbs sampler method, and present examples whereby signals are detected and analyzed from within noisy data.Comment: 21 pages, 10 figure

A Trial of a 7-Valent Pneumococcal Conjugate Vaccine in HIV-Infected Adults.

BACKGROUND: Streptococcus pneumoniae is a leading and serious coinfection in adults with human immunodeficiency virus (HIV) infection, particularly in Africa. Prevention of this disease by vaccination with the current 23-valent polysaccharide vaccine is suboptimal. Protein conjugate vaccines offer a further option for protection, but data on their clinical efficacy in adults are needed. METHODS: In this double-blind, randomized, placebo-controlled clinical efficacy trial, we studied the efficacy of a 7-valent conjugate pneumococcal vaccine in predominantly HIV-infected Malawian adolescents and adults who had recovered from documented invasive pneumococcal disease. Two doses of vaccine were given 4 weeks apart. The primary end point was a further episode of pneumococcal infection caused by vaccine serotypes or serotype 6A. RESULTS: From February 2003 through October 2007, we followed 496 patients (of whom 44% were male and 88% were HIV-seropositive) for 798 person-years of observation. There were 67 episodes of pneumococcal disease in 52 patients, all in the HIV-infected subgroup. In 24 patients, there were 19 episodes that were caused by vaccine serotypes and 5 episodes that were caused by the 6A serotype. Of these episodes, 5 occurred in the vaccine group and 19 in the placebo group, for a vaccine efficacy of 74% (95% confidence interval [CI], 30 to 90). There were 73 deaths from any cause in the vaccine group and 63 in the placebo group (hazard ratio in the vaccine group, 1.18; 95% CI, 0.84 to 1.66). The number of serious adverse events within 14 days after vaccination was significantly lower in the vaccine group than in the placebo group (3 vs. 17, P=0.002), and the number of minor adverse events was significantly higher in the vaccine group (41 vs. 13, P=0.003). CONCLUSIONS: The 7-valent pneumococcal conjugate vaccine protected HIV-infected adults from recurrent pneumococcal infection caused by vaccine serotypes or serotype 6A. (Current Controlled Trials number, ISRCTN54494731.) Copyright 2010 Massachusetts Medical Society

Gravitational-Wave Astronomy with Inspiral Signals of Spinning Compact-Object Binaries

Inspiral signals from binary compact objects (black holes and neutron stars) are primary targets of the ongoing searches by ground-based gravitational-wave interferometers (LIGO, Virgo, GEO-600 and TAMA-300). We present parameter-estimation simulations for inspirals of black-hole--neutron-star binaries using Markov-chain Monte-Carlo methods. For the first time, we have both estimated the parameters of a binary inspiral source with a spinning component and determined the accuracy of the parameter estimation, for simulated observations with ground-based gravitational-wave detectors. We demonstrate that we can obtain the distance, sky position, and binary orientation at a higher accuracy than previously suggested in the literature. For an observation of an inspiral with sufficient spin and two or three detectors we find an accuracy in the determination of the sky position of typically a few tens of square degrees.Comment: v2: major conceptual changes, 4 pages, 1 figure, 1 table, submitted to ApJ

HLA-A, -B, -C, -DRB1, DRB3, DRB4, DRB5 and DQB1 polymorphism detected by PCR-SSP in a semi-urban HIV-positive Ugandan population.

PCR-SSP was used to HLA-type a cohort of Ugandan HIV-positive individuals. The results represent a more comprehensive description of HLA in an African population than previously described and are in concordance with data from a general Black population. Substantial differences exist between this population and Caucasoid populations in which immunological responses to HIV have been investigated; this emphasises that the main HLA-restrictive elements for HIV-specific cytotoxic T lymphocytes will most likely be different for each population

Analyze This! A Cosmological Constraint Package for CMBEASY

We introduce a Markov Chain Monte Carlo simulation and data analysis package that extends the CMBEASY software. We have taken special care in implementing an adaptive step algorithm for the Markov Chain Monte Carlo in order to improve convergence. Data analysis routines are provided which allow to test models of the Universe against measurements of the cosmic microwave background, supernovae Ia and large scale structure. We present constraints on cosmological parameters derived from these measurements for a $\Lambda$CDM cosmology and discuss the impact of the different observational data sets on the parameters. The package is publicly available as part of the CMBEASY software at www.cmbeasy.org.Comment: Published version, JCAP style, 16 pages, 7 figures. The software is available at http://www.cmbeasy.or

Probing the Galactic Potential with Next-Generation Observations of Disk Stars

Near-future surveys promise a dramatic improvement in the number and precision of astrometric, photometric and spectroscopic measurements of stars in the Milky Way's disk. We examine the impact of such surveys on our understanding of the Galaxy by "observing" particle realizations of non-axisymmetric disk distributions orbiting in an axisymmetric halo with appropriate errors and then attempting to recover the underlying potential using a Markov Chain Monte Carlo (MCMC) approach. We demonstrate that the azimuthally averaged gravitational force field in the Galactic plane--and hence, to a lesser extent, the Galactic mass distribution--can be tightly constrained over a large range of radii using a variety of types of surveys so long as the error distribution of the measurements of the parallax, proper motion and radial velocity are well-understood and the disk is surveyed globally. One advantage of our method is that the target stars can be selected non-randomly in real or apparent-magnitude space to ensure just such a global sample without biasing the results. Assuming we can always measure the line-of-sight velocity of a star with at least 1 km/s precision, we demonstrate that the force field can be determined to better than ~1% for Galactocentric radii in the range R=4-20 kpc We conclude that near-future surveys, like SIM Lite, Gaia, and VERA, will provide the first precise mapping of the gravitational force field in the region of the Galactic disk.Comment: 41 pages and 10 figures, accepted for publication in Ap

BCL-2 Expression is Prognostic for Improved Survival in Non-small Cell Lung Cancer

ObjectiveWe used a large patient population to identify immunohistochemical biomarkers to enable improved prognostication in patients with non-small cell lung carcinoma (NSCLC).MethodsA tissue microarray was constructed using duplicate 0.6 mm cores of formalin-fixed paraffin-embedded tissue blocks from 609 patients with NSCLC. Immunohistochemical was used to detect 11 biomarkers including epidermal growth factor receptor, Her2, Her3, p53, p63, bcl-1, bcl-2, Thyroid transcription factor, carcinoembryonic antigen, chromogranin, and synaptophysin. A clinical database was generated prospectively at the time of tissue collection. Survival outcomes were obtained from a Provincial Cancer Registry database. Univariate and multivariate analyses were performed to look for a relationship between biomarker expression, smoking history, and survival.ResultsSurvival data for 535 cases were available. As of June 2005, 429 patients (80%) had died; of these 286 (54%) died of lung cancer, 117 (22%) died of other known causes, and for 26 (5%) the cause of death was not available. Univariate analysis revealed that bcl-2 (p = 0.007) was the only biomarker prognostic for improved overall survival (OS). bcl-2 (p = 0.021) and p63 (p = 0.025) were both found to be prognostic for improved disease-specific survival (DSS). Multivariate analysis (using age and biomarker expression) revealed that bcl-2 expression is prognostic for improved OS (p = 0.005) and DSS (p = 0.021).ConclusionsOur results suggest that bcl-2 expression is prognostic for improved OS and DSS in NSCLC. Testing for bcl-2 expression in a prospective study will help to determine its clinical relevance in prognostication

On the Inference of Thermal Inversions in Hot Jupiter Atmospheres

Several studies in the recent past have inferred the existence of thermal inversions in some transiting hot Jupiter atmospheres. Given the limited data available, the inference of a thermal inversion depends critically on the chemical composition assumed for the atmosphere. In this study, we explore the degeneracies between thermal inversions and molecular abundances in four highly irradiated hot Jupiter atmospheres, day-side observations of which were previously reported to be consistent with thermal inversions based on Spitzer photometry. The four systems are: HD 209458b, HAT-P-7b, TrES-4, and TrES-2. For each system, we explore the model parameter space with ~ 10^6 models using a Markov chain Monte Carlo routine. Our results primarily suggest that a thorough exploration of the model parameter space is necessary to identify thermal inversions in hot Jupiter atmospheres. We find that existing observations of TrES-4 and TrES-2 can both be fit very precisely with models with and without thermal inversions, and with a wide range in chemical composition. On the other hand, observations of HD 209458b and HAT-P-7b are better fit with thermal inversions than without, as has been reported before. We do not see a correlation between irradiation levels and thermal inversions, given current data. Before JWST becomes available, near-IR observations from ground and with HST, along with existing Spitzer observations, can potentially resolve thermal inversions in some systems.Comment: 16 pages in emulate ApJ format, 6 figures, 3 tables (Accepted in ApJ

Noisy Monte Carlo: Convergence of Markov chains with approximate transition kernels

Monte Carlo algorithms often aim to draw from a distribution $\pi$ by simulating a Markov chain with transition kernel $P$ such that $\pi$ is invariant under $P$. However, there are many situations for which it is impractical or impossible to draw from the transition kernel $P$. For instance, this is the case with massive datasets, where is it prohibitively expensive to calculate the likelihood and is also the case for intractable likelihood models arising from, for example, Gibbs random fields, such as those found in spatial statistics and network analysis. A natural approach in these cases is to replace $P$ by an approximation $\hat{P}$. Using theory from the stability of Markov chains we explore a variety of situations where it is possible to quantify how 'close' the chain given by the transition kernel $\hat{P}$ is to the chain given by $P$. We apply these results to several examples from spatial statistics and network analysis.Comment: This version: results extended to non-uniformly ergodic Markov chain

P53 IMMUNOHISTOCHEMISTRY AS A SURROGATE FOR TP53 MUTATIONAL ANALYSIS IN ENDOMETRIAL CANCER BIOPSIES

Meeting abstract from 17th Biennial Meeting of the International Gynecologic Cancer Society Kyoto, Japan September 14-16, 201