INTEREST: INteractive Tool for Exploring REsults from Simulation sTudies

Simulation studies allow us to explore the properties of statistical methods. They provide a powerful tool with a multiplicity of aims; among others: evaluating and comparing new or existing statistical methods, assessing violations of modelling assumptions, helping with the understanding of statistical concepts, and supporting the design of clinical trials. The increased availability of powerful computational tools and usable software has contributed to the rise of simulation studies in the current literature. However, simulation studies involve increasingly complex designs, making it difficult to provide all relevant results clearly. Dissemination of results plays a focal role in simulation studies: it can drive applied analysts to use methods that have been shown to perform well in their settings, guide researchers to develop new methods in a promising direction, and provide insights into less established methods. It is crucial that we can digest relevant results of simulation studies. Therefore, we developed INTEREST: an INteractive Tool for Exploring REsults from Simulation sTudies. The tool has been developed using the Shiny framework in R and is available as a web app or as a standalone package. It requires uploading a tidy format dataset with the results of a simulation study in R, Stata, SAS, SPSS, or comma-separated format. A variety of performance measures are estimated automatically along with Monte Carlo standard errors; results and performance summaries are displayed both in tabular and graphical fashion, with a wide variety of available plots. Consequently, the reader can focus on simulation parameters and estimands of most interest. In conclusion, INTEREST can facilitate the investigation of results from simulation studies and supplement the reporting of results, allowing researchers to share detailed results from their simulations and readers to explore them freely

SwSt 1: an O-rich planetary nebula around a C-rich central star

The hydrogen-deficient [WCL] type central star HD 167362 and its planetary nebula (PN) SwSt 1 are investigated. The central star has a carbon-rich emission-line spectrum, and yet the nebula exhibits a 10-μm emission feature from warm silicate dust, perhaps indicating a recent origin for the carbon-rich stellar spectrum. Its stellar and nebular properties might therefore provide further understanding as to the origin of the [WCL] central star class. The central star optical and UV spectra are modelled with state-of-the art non-LTE codes for expanding atmospheres, from which the stellar parameters are determined. Using the Sobolev approximation code ISA-Wind, we find graphic, graphic, graphic (for a distance of 2.0 kpc), and graphic. The abundance mass fractions for helium, carbon and oxygen are determined to be 37, 51 and 12 per cent, respectively. From this we derive graphic (by mass), confirming that the star suffered efficient third dredge-up. The nitrogen abundance is close to zero, while an upper limit of <10 per cent by mass is established for H. The model uses a composite beta velocity law which allows us to reproduce the optical line profiles. The overall shape of the dereddened spectrum agrees with the V-scaled [graphic, graphic] model atmosphere, showing the nebular-derived reddening to be consistent with the reddening indicated by the stellar analysis. We confirm our model results by using the comoving frame code CMFGEN, although a few differences remain. The PN has a high electron density graphic and a small ionized radius (0.65 arcsec – measured from the HST-WF/PC Hβ images), indicating a young object. Its nebular abundances are not peculiar. The nebular C/O ratio is close to solar, confirming the PN as an O-rich nebula. The nebular N/O ratio of 0.08 is not indicative of a Type-I PN, although the high stellar luminosity points to a relatively high stellar mass. Near-IR spectroscopy is presented and fitted together with IRAS fluxes by using two blackbody curves with temperatures of 1200 and 230 K, indicating the presence of hot dust. We also report the first detection of H2 in this young and compact PN. All of the published spectroscopy since the discovery of SwSt 1 in 1895 has been re-examined, and it is concluded that no clear spectral variability is seen, in contrast to claims in some previously published studies. If an event occurred that has turned it into a hydrogen-deficient central star, it did not happen in the last 100 years

Using simulation studies to evaluate statistical methods

Simulation studies are computer experiments that involve creating data by pseudo‐random sampling. A key strength of simulation studies is the ability to understand the behavior of statistical methods because some “truth” (usually some parameter/s of interest) is known from the process of generating the data. This allows us to consider properties of methods, such as bias. While widely used, simulation studies are often poorly designed, analyzed, and reported. This tutorial outlines the rationale for using simulation studies and offers guidance for design, execution, analysis, reporting, and presentation. In particular, this tutorial provides a structured approach for planning and reporting simulation studies, which involves defining aims, data‐generating mechanisms, estimands, methods, and performance measures (“ADEMP”); coherent terminology for simulation studies; guidance on coding simulation studies; a critical discussion of key performance measures and their estimation; guidance on structuring tabular and graphical presentation of results; and new graphical presentations. With a view to describing recent practice, we review 100 articles taken from Volume 34 of Statistics in Medicine, which included at least one simulation study and identify areas for improvement

Far Ultraviolet Spectroscopic Explorer Spectroscopy of the O VI Resonance Doublet in Sand 2 (WO)

We present Far Ultraviolet Spectroscopic Explorer spectroscopy of Sand 2, an LMC WO-type Wolf-Rayet star, revealing the O VI resonance P Cygni doublet at 1032-1038 Å. These data are combined with Hubble Space Telescope Faint Object Spectrograph ultraviolet and Mount Stromlo 2.3 m optical spectroscopy and analyzed using a spherical, non-LTE, line-blanketed code. Our study reveals exceptional stellar parameters: T* ~ 150,000 K, v∞ = 4100 km s-1, log(L/L☉) = 5.3, andimg1.gif = 1 × 10-5 M☉ yr-1, if we adopt a volume filling factor of 10%. Elemental abundances of C/He ~ 0.7 ± 0.2 and O/He ~ 0.15img2.gif by number qualitatively support previous recombination line studies. We confirm that Sand 2 is more chemically enriched in carbon than LMC WC stars and that it is expected to undergo a supernova explosion within the next 5 × 104 yr

Stellar winds from Massive Stars

We review the various techniques through which wind properties of massive stars - O stars, AB supergiants, Luminous Blue Variables (LBVs), Wolf-Rayet (WR) stars and cool supergiants - are derived. The wind momentum-luminosity relation (e.g. Kudritzki et al. 1999) provides a method of predicting mass-loss rates of O stars and blue supergiants which is superior to previous parameterizations. Assuming the theoretical sqrt(Z) metallicity dependence, Magellanic Cloud O star mass-loss rates are typically matched to within a factor of two for various calibrations. Stellar winds from LBVs are typically denser and slower than equivalent B supergiants, with exceptional mass-loss rates during giant eruptions Mdot=10^-3 .. 10^-1 Mo/yr (Drissen et al. 2001). Recent mass-loss rates for Galactic WR stars indicate a downward revision of 2-4 relative to previous calibrations due to clumping (e.g. Schmutz 1997), although evidence for a metallicity dependence remains inconclusive (Crowther 2000). Mass-loss properties of luminous (> 10^5 Lo) yellow and red supergiants from alternative techniques remain highly contradictory. Recent Galactic and LMC results for RSG reveal a large scatter such that typical mass-loss rates lie in the range 10^-6 .. 10^-4 Mo/yr, with a few cases exhibiting 10^-3 Mo/yr.Comment: 16 pages, 2 figures, Review paper to appear in Proc `The influence of binaries on stellar population studies', Brussels, Aug 2000 (D. Vanbeveren ed.), Kluwe

Phenotypic Screens, Chemical Genomics, and Antimalarial Lead Discovery

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Patent Human Infections with the Whipworm, Trichuris trichiura, Are Not Associated with Alterations in the Faecal Microbiota

Background: The soil-transmitted helminth (STH), Trichuris trichiura colonises the human large intestine where it may modify inflammatory responses, an effect possibly mediated through alterations in the intestinal microbiota. We hypothesised that patent T. trichiura infections would be associated with altered faecal microbiota and that anthelmintic treatment would induce a microbiota resembling more closely that observed in uninfected individuals. Materials and Methods: School children in Ecuador were screened for STH infections and allocated to 3 groups: uninfected, T. trichiura only, and mixed infections with T. trichiura and Ascaris lumbricoides. A sample of uninfected children and those with T. trichiura infections only were given anthelmintic treatment. Bacterial community profiles in faecal samples were studied by 454 pyrosequencing of 16 S rRNA genes. Results: Microbiota analyses of faeces were done for 97 children: 30 were uninfected, 17 were infected with T. trichiura, and 50 with T. trichiura and A. lumbricoides. Post-treatment samples were analyzed for 14 children initially infected with T. trichiura alone and for 21 uninfected children. Treatment resulted in 100% cure of STH infections. Comparisons of the microbiota at different taxonomic levels showed no statistically significant differences in composition between uninfected children and those with T. trichiura infections. We observed a decreased proportional abundance of a few bacterial genera from the Clostridia class of Firmicutes and a reduced bacterial diversity among children with mixed infections compared to the other two groups, indicating a possible specific effect of A. lumbricoides infection. Anthelmintic treatment of children with T. trichiura did not alter faecal microbiota composition. Discussion: Our data indicate that patent human infections with T. trichiura may have no effect on faecal microbiota but that A. lumbricoides colonisation might be associated with a disturbed microbiota. Our results also catalogue the microbiota of rural Ecuadorians and indicate differences with individuals from more urban industrialised societies

Multi-slice ptychographic tomography

Ptychography is a form of Coherent Diffractive Imaging, where diffraction patterns are processed by iterative algorithms to recover an image of a specimen. Although mostly applied in two dimensions, ptychography can be extended to produce three dimensional images in two ways: via multi-slice ptychography or ptychographic tomography. Ptychographic tomography relies on 2D ptychography to supply projections to conventional tomographic algorithms, whilst multi-slice ptychography uses the redundancy in ptychographic data to split the reconstruction into a series of axial slices. Whilst multi-slice ptychography can handle multiple-scattering thick specimens and has a much smaller data requirement than ptychographic tomography, its depth resolution is relatively poor. Here we propose an imaging modality that combines the benefits of the two approaches, enabling isotropic 3D resolution imaging of thick specimens with a small number of angular measurements. Optical experiments validate our proposed method

Immunological assays for chemokine detection in in-vitro culture of CNS cells

Herein we review the various methods currently in use for determining the expression of chemokines by CNS cells in vitro. Chemokine detection assays are used in conjuction with one another to provide a comprehensive, biologically relevant assessment of the chemokines which is necessary for correct data interpretation of a specific observed biological effect. The methods described include bioassays for soluble chemokine receptors, RNA extraction, RT-PCR, Real - time quantitative PCR, gene array analysis, northern blot analysis, Ribonuclease Protection assay, Flow cytometry, ELISPOT, western blot analysis, and ELISA. No single method of analysis meets the criteria for a comprehensive, biologically relevant assessment of the chemokines, therefore more than one assay might be necessary for correct data interpretation, a choice that is based on development of a scientific rationale for the method with emphasis on the reliability and relevance of the method