The Locus Algorithm III: A Grid Computing system to generate catalogues of optimised pointings for Differential Photometry

This paper discusses the hardware and software components of the Grid Computing system used to implement the Locus Algorithm to identify optimum pointings for differential photometry of 61,662,376 stars and 23,799 quasars. The scale of the data, together with initial operational assessments demanded a High Performance Computing (HPC) system to complete the data analysis. Grid computing was chosen as the HPC solution as the optimum choice available within this project. The physical and logical structure of the National Grid computing Infrastructure informed the approach that was taken. That approach was one of layered separation of the different project components to enable maximum flexibility and extensibility

An Introduction to the 'Special Volume Spectroscopy and Chemometrics in R'

This special volume collates ten issues under the rubric "Spectroscopy and Chemometrics in R". In so doing, it provides an overview of the breadth, depth and state of the art of R-based software projects for spectroscopy and chemometrics applications. Just as the authors have contributed to R their documentation and source code, so has R contributed to the quality, standardization and dissemination of their software, as this volume attests. We hope that the volume is inspiring to both computational statisticians interested in applications of their methodologies and to spectroscopists or chemometricians in need of solutions to their data analysis problems.

Interdependent binary choices under social influence: phase diagram for homogeneous unbiased populations

Coupled Ising models are studied in a discrete choice theory framework, where they can be understood to represent interdependent choice making processes for homogeneous populations under social influence. Two different coupling schemes are considered. The nonlocal or group interdependence model is used to study two interrelated groups making the same binary choice. The local or individual interdependence model represents a single group where agents make two binary choices which depend on each other. For both models, phase diagrams, and their implications in socioeconomic contexts, are described and compared in the absence of private deterministic utilities (zero opinion fields).Comment: 17 pages, 3 figures. This is the pre-peer reviewed version of the following article: Ana Fern\'andez del R\'io, Elka Korutcheva and Javier de la Rubia, Interdependent binary choices under social influence, Wiley's Complexity, 2012; which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1002/cplx.21397/abstrac

Econometrics in R: Past, Present, and Future

Recently, computational methods and software have been receiving more attention in the econometrics literature, emphasizing that they are integral components of modern econometric research. This has also promoted the development of many new econometrics software packages written in R and made available on the Comprehensive R Archive Network. This special volume on "Econometrics in R" features a selection of these recent activities that includes packages for econometric analysis of cross-section, time series and panel data. This introduction to the special volume highlights the contents of the contributions and embeds them into a brief overview of other past, present, and future projects for econometrics in R.

An Evaluation of The Host Response to An Interspinous Process Device Based on A Series of Spine Explants: Device for Intervertebral Assisted Motion (DIAM®)

Background: The objective of this study was to evaluate the host response to an interspinous process device [Device for Intervertebral Assisted Motion (DIAM®)] based on a series of nine spine explants with a mean post-operative explant time of 35 months. Methods: Explanted periprosthetic tissues were processed for histology and stained with H&E, Wright-Giemsa stain, and Oil Red O. Brightfield and polarized light microscopy were used to evaluate the host response to the device and the resultant particulate debris. The host response was graded per ASTM F981-04. Quantitative histomorphometry was used to characterize particle size, shape, and area per ASTM F1877-05. The presence or absence of bone resorption was also evaluated when bony tissue samples were provided. Results: Periprosthetic tissues demonstrated a non-specific foreign body response composed of macrophages and foreign body giant cells to the DIAM® device in most of the accessions. The foreign body reaction was not the stated reason for explantation in any of the accessions. Per ASTM F981-04, a “very slight” to “mild” to “moderate” chronic inflammatory response was observed to the biomaterials and particulate, and this varied by tissue sample and accession. Particle sizes were consistent amongst the explant patients with mean particle size on the order of several microns. Osteolysis, signs of toxicity, necrosis, an immune response, and/or device related infection were not observed. Conclusions: Cyclic loading of the spine can cause wear in dynamic stabilization systems such as DIAM®. The fabric nature of the DIAM® device’s polyethylene terephthalate jacket coupled with the generation of polymeric particulate debris predisposes the device to a foreign body reaction consisting of macrophages and foreign body giant cells. Although not all patients are aware of symptoms associated with a foreign body reaction to a deeply implanted device, surgeons should be aware of the host response to this device

Kinetic multi-layer model of gas-particle interactions in aerosols and clouds (KM-GAP): linking condensation, evaporation and chemical reactions of organics, oxidants and water

We present a novel kinetic multi-layer model for gas-particle interactions in aerosols and clouds (KM-GAP) that treats explicitly all steps of mass transport and chemical reaction of semi-volatile species partitioning between gas phase, particle surface and particle bulk. KM-GAP is based on the PRA model framework (Pöschl-Rudich-Ammann, 2007), and it includes gas phase diffusion, reversible adsorption, surface reactions, bulk diffusion and reaction, as well as condensation, evaporation and heat transfer. The size change of atmospheric particles and the temporal evolution and spatial profile of the concentration of individual chemical species can be modelled along with gas uptake and accommodation coefficients. Depending on the complexity of the investigated system, unlimited numbers of semi-volatile species, chemical reactions, and physical processes can be treated, and the model shall help to bridge gaps in the understanding and quantification of multiphase chemistry and microphysics in atmo- spheric aerosols and clouds. In this study we demonstrate how KM-GAP can be used to analyze, interpret and design experimental investigations of changes in particle size and chemical composition in response to condensation, evaporation, and chemical reaction. For the condensational growth of water droplets, our kinetic model results provide a direct link between laboratory observations and molecular dynamic simulations, confirming that the accommodation coefficient of water at 270 K is close to unity. Literature data on the evaporation of dioctyl phthalate as a function of particle size and time can be reproduced, and the model results suggest that changes in the experimental conditions like aerosol particle concentration and chamber geometry may influence the evaporation kinetics and can be optimized for eðcient probing of specific physical effects and parameters. With regard to oxidative aging of organic aerosol particles, we illustrate how the formation and evaporation of volatile reaction products like nonanal can cause a decrease in the size of oleic acid particles exposed to ozone

topicmodels: An R Package for Fitting Topic Models

Topic models allow the probabilistic modeling of term frequency occurrences in documents. The fitted model can be used to estimate the similarity between documents as well as between a set of specified keywords using an additional layer of latent variables which are referred to as topics. The R package topicmodels provides basic infrastructure for fitting topic models based on data structures from the text mining package tm. The package includes interfaces to two algorithms for fitting topic models: the variational expectation-maximization algorithm provided by David M. Blei and co-authors and an algorithm using Gibbs sampling by Xuan-Hieu Phan and co-authors.