Physics and chemistry of gas in discs

Protoplanetary discs set the initial conditions for planet formation. By combining observations with detailed modelling, it is possible to constrain the physics and chemistry in such discs. I have used the detailed thermo-chemical disc model ProDiMo to explore the characteristics of the gas in protoplanetary discs, particularly in Herbig Ae objects. I have assessed the ability of various observational data to trace the disc properties. This has involved a number of different approaches. Firstly I compute a series of disc models with increasing mass, in order to test the diagnostic powers of various emission lines, in particular as gas mass tracers. This approach is then expanded to a large multiparameter grid of ~ 10 5 disc models. I have helped to develop a tool for analysing and plotting the huge quantity of data presented by such a model grid. Following this approach I move on to a detailed study of the Herbig Ae star HD 163296, attempting to fit the large wealth of available observations simultaneously. These include new Herschel observations of the far-infrared emission lines, as well as interferometric CO observations and a large number of continuum data. This study addresses the topical issues of the disc gas/dust ratio, and the treatment of the disc outer edge. It explores the effects of dust settling, UV variability and stellar X-ray emission on the disc chemistry and line emission. There is possible evidence for gas-depletion in the disc of HD 163296, with the line emission enhanced by dust settling, which would indicate a later evolutionary stage for this disc than suggested by other studies. Finally, I work to improve the treatment of the gas heating/cooling balance in ProDiMo, by introducing a non-LTE treatment of the atomic hydrogen line transitions and bound-free continuum transitions. I explore the effects of this on the disc chemical and thermal structure, and assess its impact in terms of the observable quantities

Continuum and line modelling of discs around young stars. I. 300000 disc models for Herschel/GASPS

We have combined the thermo-chemical disc code ProDiMo with the Monte Carlo radiative transfer code MCFOST to calculate a grid of ~300000 circumstellar disc models, systematically varying 11 stellar, disc and dust parameters including the total disc mass, several disc shape parameters and the dust-to-gas ratio. For each model, dust continuum and line radiative transfer calculations are carried out for 29 far IR, sub-mm and mm lines of [OI], [CII], 12CO and o/p-H2O under 5 inclinations. The grid allows to study the influence of the input parameters on the observables, to make statistical predictions for different types of circumstellar discs, and to find systematic trends and correlations between the parameters, the continuum fluxes, and the line fluxes. The model grid, comprising the calculated disc temperatures and chemical structures, the computed SEDs, line fluxes and profiles, will be used in particular for the data interpretation of the Herschel open time key programme GASPS. The calculated line fluxes show a strong dependence on the assumed UV excess of the central star, and on the disc flaring. The fraction of models predicting [OI] and [CII] fine-structure lines fluxes above Herschel/PACS and Spica/SAFARI detection limits are calculated as function of disc mass. The possibility of deriving the disc gas mass from line observations is discussed.Comment: accepted by MNRAS. 5 pages, 4 figures, 3 table

Joint modelling rationale for chained equations.

BACKGROUND: Chained equations imputation is widely used in medical research. It uses a set of conditional models, so is more flexible than joint modelling imputation for the imputation of different types of variables (e.g. binary, ordinal or unordered categorical). However, chained equations imputation does not correspond to drawing from a joint distribution when the conditional models are incompatible. Concurrently with our work, other authors have shown the equivalence of the two imputation methods in finite samples. METHODS: Taking a different approach, we prove, in finite samples, sufficient conditions for chained equations and joint modelling to yield imputations from the same predictive distribution. Further, we apply this proof in four specific cases and conduct a simulation study which explores the consequences when the conditional models are compatible but the conditions otherwise are not satisfied. RESULTS: We provide an additional "non-informative margins" condition which, together with compatibility, is sufficient. We show that the non-informative margins condition is not satisfied, despite compatible conditional models, in a situation as simple as two continuous variables and one binary variable. Our simulation study demonstrates that as a consequence of this violation order effects can occur; that is, systematic differences depending upon the ordering of the variables in the chained equations algorithm. However, the order effects appear to be small, especially when associations between variables are weak. CONCLUSIONS: Since chained equations is typically used in medical research for datasets with different types of variables, researchers must be aware that order effects are likely to be ubiquitous, but our results suggest they may be small enough to be negligible

Early and Prolonged Antiretroviral Therapy Is Associated with an HIV-1-Specific T-Cell Profile Comparable to That of Long-Term Non-Progressors

Background: Intervention with antiretroviral treatment (ART) and control of viral replication at the time of HIV-1 seroconversion may curtail cumulative immunological damage. We have therefore hypothesized that ART maintenance over a very prolonged period in HIV-1 seroconverters could induce an immuno-virological status similar to that of HIV-1 long-term non-progressors (LTNPs).Methodology/Principal Findings: We have investigated a cohort of 20 HIV-1 seroconverters on long-term ART (LTTS) and compared it to one of 15 LTNPs. Residual viral replication and reservoirs in peripheral blood, as measured by cell-associated HIV-1 RNA and DNA, respectively, were demonstrated to be similarly low in both cohorts. These two virologically matched cohorts were then comprehensively analysed by polychromatic flow cytometry for HIV-1-specific CD4(+) and CD8(+) T-cell functional profile in terms of cytokine production and cytotoxic capacity using IFN-gamma, IL-2, TNF-alpha production and perforin expression, respectively. Comparable levels of highly polyfunctional HIV-1-specific CD4(+) and CD8(+) T-cells were found in LTTS and LTNPs, with low perforin expression on HIV-1-specific CD8+ T-cells, consistent with a polyfunctional/non-cytotoxic profile in a context of low viral burden.Conclusions: Our results indicate that prolonged ART initiated at the time of HIV-1 seroconversion is associated with immuno-virological features which resemble those of LTNPs, strengthening the recent emphasis on the positive impact of early treatment initiation and paving the way for further interventions to promote virological control after treatment interruption

Telomere length and physical performance at older ages: an individual participant meta-analysis

BACKGROUND: Telomeres are involved in cellular ageing and shorten with increasing age. If telomere length is a valuable biomarker of ageing, then telomere shortening should be associated with worse physical performance, an ageing trait, but evidence for such an association is lacking. The purpose of this study was to examine whether change in telomere length is associated with physical performance.METHODS: Using data from four UK adult cohorts (ages 53-80 years at baseline), we undertook cross-sectional and longitudinal analyses. We analysed each study separately and then used meta-analytic methods to pool the results. Physical performance was measured using walking and chair rise speed, standing balance time and grip strength. Telomere length was measured by quantitative real-time polymerase chain reaction (PCR) in whole blood at baseline and follow-up (time 1, time 2).RESULTS: Total sample sizes in meta-analyses ranged from 1,217 to 3,707. There was little evidence that telomere length was associated with walking speed, balance or grip strength, though weak associations were seen with chair rise speed and grip strength at baseline (p = 0.02 and 0.01 respectively). Faster chair rise speed at follow-up, was associated with a smaller decline in telomere length between time 1 and time 2 (standardised coefficient per SD increase 0.061, 95% CI 0.006, 0.115, p = 0.03) but this was consistent with chance (p =0.08) after further adjustment.CONCLUSIONS: Whereas shortening of leukocyte telomeres might be an important measure of cellular ageing, there is little evidence that it is a strong biomarker for physical performance

Experimental game theory and its application in sociology and political science

This is an open access special issue distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.The aim of this special issue is to encourage original research that seeks to study sociological or political phenomena using laboratory experiments that are based on game-theoretical benchmarks and, vice versa, that seeks mathematical modeling of game theoretical arguments to inspire experiments in the fields of Sociology and Political Science. We received 14 papers from authors in varies countries all over the world, of which 5 high-quality papers emerged for publication in the special issue after a strict review process. In the first research article of the special issue, G. Bravo, F. Squazzoni, and K. Takács experimentally study whether intermediaries can positively influence cooperation between a trustor and a trustee in an investment or trust game. The second article by L. A. Palacio, A. Cortés-Aguilar, and M. Muñoz-Herrera develops a game theoretical foundation for experimental investigations of the strategic role in games with nonbinding communication. In the third article, L. Corazzini and M. Tyszler employ quantal response equilibrium (QRE) to find out the extent of confusion and efficiency motives of laboratory participants in their decisions to contribute to a public good. The fourth article by S. A. Tulman utilizes QRE (i.e., noisy decision-making) and altruism-motivated players to investigate the “paradox of voter turnout” in a participation game experiment. Finally, in the fifth article B. Kittel, F. Paetzel, and S. Traub present a laboratory study in which they examine the role of the middle class on income distribution within the framework of a contest game.-- Experimental Game Theory and Its Application in Sociology and Political Science, Arthur Schram, Vincent Buskens, Klarita Gërxhani, and Jens Großer - Editorial (2 pages), Article ID 280789 -- The Strategic Role of Nonbinding Communication, Luis A. Palacio, Alexandra Cortés-Aguilar, and Manuel Muñoz-Herrera (11 pages), Article ID 910614 -- Intermediaries in Trust: Indirect Reciprocity, Incentives, and Norms, Giangiacomo Bravo, Flaminio Squazzoni, and Károly Takács (12 pages), Article ID 234528 -- Altruism, Noise, and the Paradox of Voter Turnout: An Experimental Study, Sarah A. Tulman (22 pages), Article ID 972753 -- Preference for Efficiency or Confusion? A Note on a Boundedly Rational Equilibrium Approach to Individual Contributions in a Public Good Game, Luca Corazzini and Marcelo Tyszler (8 pages), Article ID 961930 -- Competition, Income Distribution, and the Middle Class: An Experimental Study, Bernhard Kittel, Fabian Paetzel, and Stefan Traub (15 pages), Article ID 30391

The Stata Journal

Estimating adjusted associations between random effects from multilevel models : the reffadjust package. Stata Journal, Volume 14 (Number 1). pp. 119-140. Permanent WRAP url: http://wrap.warwick.ac.uk/60030 Copyright and reuse: The Warwick Research Archive Portal (WRAP) makes this work of researchers of the University of Warwick available open access under the following conditions. Copyright © and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners. To the extent reasonable and practicable the material made available in WRAP has been checked for eligibility before being made available. Copies of full items can be used for personal research or study, educational, or not-forprofit purposes without prior permission or charge. Provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way. Publisher's statement: http://www.stata-journal.com. A note on versions: The version presented in WRAP is the published version or, version of record, and may be cited as it appears here. The Stata Journal publishes reviewed papers together with shorter notes or comments, regular columns, book reviews, and other material of interest to Stata users. Examples of the types of papers include 1) expository papers that link the use of Stata commands or programs to associated principles, such as those that will serve as tutorials for users first encountering a new field of statistics or a major new technique; 2) papers that go "beyond the Stata manual" in explaining key features or uses of Stata that are of interest to intermediate or advanced users of Stata; 3) papers that discuss new commands or Stata programs of interest either to a wide spectrum of users (e.g., in data management or graphics) or to some large segment of Stata users (e.g., in survey statistics, survival analysis, panel analysis, or limited dependent variable modeling); 4) papers analyzing the statistical properties of new or existing estimators and tests in Stata; 5) papers that could be of interest or usefulness to researchers, especially in fields that are of practical importance but are not often included in texts or other journals, such as the use of Stata in managing datasets, especially large datasets, with advice from hard-won experience; and 6) papers of interest to those who teach, including Stata with topics such as extended examples of techniques and interpretation of results, simulations of statistical concepts, and overviews of subject areas. Copyright c 2014 by StataCorp LP Copyright Statement: The Stata Journal and the contents of the supporting files (programs, datasets, and help files) are copyright c by StataCorp LP. The contents of the supporting files (programs, datasets, and help files) may be copied or reproduced by any means whatsoever, in whole or in part, as long as any copy or reproduction includes attribution to both (1) the author and (2) the Stata Journal. The articles appearing in the Stata Journal may be copied or reproduced as printed copies, in whole or in part, as long as any copy or reproduction includes attribution to both (1) the author and (2) the Stata Journal. Written permission must be obtained from StataCorp if you wish to make electronic copies of the insertions. This precludes placing electronic copies of the Stata Journal, in whole or in part, on publicly accessible websites, fileservers, or other locations where the copy may be accessed by anyone other than the subscriber. Users of any of the software, ideas, data, or other materials published in the Stata Journal or the supporting files understand that such use is made without warranty of any kind, by either the Stata Journal, the author, or StataCorp. In particular, there is no warranty of fitness of purpose or merchantability, nor for special, incidental, or consequential damages such as loss of profits. Abstract. We describe a method to estimate associations between random effects from multilevel models. We provide two new postestimation commands, reffadjustsim and reffadjust4nlcom, which are distributed as the reffadjust package. These commands produce the estimates and their associated confidence intervals. The commands are used after official Stata multilevel model estimation commands mixed, meqrlogit, and meqrpoisson (formerly named xtmixed, xtmelogit, and xtmepoisson, respectively, before Stata 13) and with models fit in the MLwiN statistical software package via the runmlwin command. We demonstrate our commands with several simulated datasets and for a bivariate outcome model investigating the relationship between weight and mean arterial pressure in pregnant women using data from the Avon Longitudinal Study of Parents and Children. Our method and commands help to improve the interpretability of estimated random-effects variance components from multilevel models