Estimating the effect of joint interventions from observational data in sparse high-dimensional settings

We consider the estimation of joint causal effects from observational data. In particular, we propose new methods to estimate the effect of multiple simultaneous interventions (e.g., multiple gene knockouts), under the assumption that the observational data come from an unknown linear structural equation model with independent errors. We derive asymptotic variances of our estimators when the underlying causal structure is partly known, as well as high-dimensional consistency when the causal structure is fully unknown and the joint distribution is multivariate Gaussian. We also propose a generalization of our methodology to the class of nonparanormal distributions. We evaluate the estimators in simulation studies and also illustrate them on data from the DREAM4 challenge.Comment: 30 pages, 3 figures, 45 pages supplemen

Optical study of flow and combustion in an HCCI engine with negative valve overlap

One of the most widely used methods to enable Homogeneous Charge Compression Ignition (HCCI) combustion is using negative valve overlapping to trap a sufficient quantity of hot residual gas. The characteristics of air motion with specially designed valve events having reduced valve lift and durations associated with HCCI engines and their effect on subsequent combustion are not yet fully understood. In addition, the ignition process and combustion development in such engines are very different from those in conventional spark-ignition or diesel compression ignition engines. Very little data has been reported concerning optical diagnostics of the flow and combustion in the engine using negative valve overlapping. This paper presents an experimental investigation into the in-cylinder flow characteristics and combustion development in an optical engine operating in HCCI combustion mode. PIV measurements have been taken under motored engine conditions to provide a quantitative flow characterisation of negative valve overlap in-cylinder flows. The ignition and combustion process was imaged using a high resolution charge coupled device (CCD) camera and the combustion imaging data was supplemented by simultaneously recorded in-cylinder pressure data which assisted the analysis of the images. It is found that the flow characteristics with negative valve overlapping are less stable and more valve event driven than typical spark ignition in-cylinder flows, while the combustion initiation locations are not uniformly distributed. © 2006 IOP Publishing Ltd

Learning high-dimensional directed acyclic graphs with latent and selection variables

We consider the problem of learning causal information between random variables in directed acyclic graphs (DAGs) when allowing arbitrarily many latent and selection variables. The FCI (Fast Causal Inference) algorithm has been explicitly designed to infer conditional independence and causal information in such settings. However, FCI is computationally infeasible for large graphs. We therefore propose the new RFCI algorithm, which is much faster than FCI. In some situations the output of RFCI is slightly less informative, in particular with respect to conditional independence information. However, we prove that any causal information in the output of RFCI is correct in the asymptotic limit. We also define a class of graphs on which the outputs of FCI and RFCI are identical. We prove consistency of FCI and RFCI in sparse high-dimensional settings, and demonstrate in simulations that the estimation performances of the algorithms are very similar. All software is implemented in the R-package pcalg.Comment: Published in at http://dx.doi.org/10.1214/11-AOS940 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Sunward-propagating Alfv\'enic fluctuations observed in the heliosphere

The mixture/interaction of anti-sunward-propagating Alfv\'enic fluctuations (AFs) and sunward-propagating Alfv\'enic fluctuations (SAFs) is believed to result in the decrease of the Alfv\'enicity of solar wind fluctuations with increasing heliocentric distance. However, SAFs are rarely observed at 1 au and solar wind AFs are found to be generally outward. Using the measurements from Voyager 2 and Wind, we perform a statistical survey of SAFs in the heliosphere inside 6 au. We first report two SAF events observed by Voyager 2. One is in the anti-sunward magnetic sector with a strong positive correlation between the fluctuations of magnetic field and solar wind velocity. The other one is in the sunward magnetic sector with a strong negative magnetic field-velocity correlation. Statistically, the percentage of SAFs increases gradually with heliocentric distance, from about 2.7% at 1.0 au to about 8.7% at 5.5 au. These results provide new clues for understanding the generation mechanism of SAFs

Green cities and health: a question of scale?

<p><b>Background:</b> Cities are expanding and accommodating an increasing proportion of the world's population. It is important to identify features of urban form that promote the health of city dwellers. Access to green space has been associated with health benefits at both individual and neighbourhood level. We investigated whether a relationship between green space coverage and selected mortality rates exists at the city level in the USA.</p> <p><b>Methods:</b> An ecological cross-sectional study. A detailed land use data set was used to quantify green space for the largest US cities (n=49, combined population of 43 million). Linear regression models were used to examine the association between city-level ‘greenness’ and city-level standardised rates of mortality from heart disease, diabetes, lung cancer, motor vehicle fatalities and all causes, after adjustment for confounders.</p> <p><b>Results:</b> There was no association between greenness and mortality from heart disease, diabetes, lung cancer or automobile accidents. Mortality from all causes was significantly higher in greener cities.</p> <p><b>Conclusions:</b> While considerable evidence suggests that access to green space yields health benefits, we found no such evidence at the scale of the American city. In the USA, greener cities tend also to be more sprawling and have higher levels of car dependency. Any benefits that the green space might offer seem easily eclipsed by these other conditions and the lifestyles that accompany them. The result merits further investigation as it has important implications for how we increase green space access in our cities.</p&gt

Genetic and phenotypic divergence in an island bird: isolation by distance, by colonization or by adaptation?

Discerning the relative roles of adaptive and nonadaptive processes in generating differences among populations and species, as well as how these processes interact, is a fundamental aim in biology. Both genetic and phenotypic divergence across populations can be the product of limited dispersal and gradual genetic drift across populations (isolation by distance), of colonization history and founder effects (isolation by colonization) or of adaptation to different environments preventing migration between populations (isolation by adaptation). Here, we attempt to differentiate between these processes using island populations of Berthelot's pipit (Anthus berthelotii), a passerine bird endemic to three Atlantic archipelagos. Using microsatellite markers and approximate Bayesian computation, we reveal that the northward colonization of this species ca. 8500years ago resulted in genetic bottlenecks in the colonized archipelagos. We then show that high levels of genetic structure exist across archipelagos and that these are consistent with a pattern of isolation by colonization, but not with isolation by distance or adaptation. Finally, we show that substantial morphological divergence also exists and that this is strongly concordant with patterns of genetic structure and bottleneck history, but not with environmental differences or geographic distance. Overall, our data suggest that founder effects are responsible for both genetic and phenotypic changes across archipelagos. Our findings provide a rare example of how founder effects can persist over evolutionary timescales and suggest that they may play an important role in the early stages of speciation

Dispersion Relations for Thermally Excited Waves in Plasma Crystals

Thermally excited waves in a Plasma crystal were numerically simulated using a Box_Tree code. The code is a Barnes_Hut tree code proven effective in modeling systems composed of large numbers of particles. Interaction between individual particles was assumed to conform to a Yukawa potential. Particle charge, mass, density, Debye length and output data intervals are all adjustable parameters in the code. Employing a Fourier transform on the output data, dispersion relations for both longitudinal and transverse wave modes were determined. These were compared with the dispersion relations obtained from experiment as well as a theory based on a harmonic approximation to the potential. They were found to agree over a range of 0.9<k<5, where k is the shielding parameter, defined by the ratio between interparticle distance a and dust Debye length lD. This is an improvement over experimental data as current experiments can only verify the theory up to k = 1.5.Comment: 8 pages, Presented at COSPAR '0

Optical parameters of leaves of seven weed species

The absorption coefficient (k), infinite reflectance (R), and scattering coefficient (s) were tabulated for five wavelengths and analyzed for statistical differences for seven weed species. The wavelengths were: 0.55-micrometer, 0.65-micrometers, 0.85-micrometer, 1.65-micrometers, and 2.20-micrometer. The R of common lambsquarters (Chenopodium album L.), Johnsongrass (Sorghum halepense (L.) Pers.), and annual sowthistle (Sonchus oleraceus L.) leaves at the 0.85-micrometer wavelength were significantly (p=0.05) higher than for sunflower (Heliantus annus L.), ragweed parthenium (Parthenium hysterophorus L.), or London rocket (Sisymbrium irio L.). Annual sowthistle had the largest k value, and Plamer amaranth (Amaranthus palmer S. Wats.) had the smallest k value at the 0.65 approximately chlorophyll absorption wavelength. In general, john-songress, ragweed parthenium, or London rocket had the largest s values among the five wavelengths, wereas annual sowthistle and plamar amaranth were usually lowest

Cost of inpatient rehabilitation care in the Department of Veterans Affairs

Abstract—We investigated the determinants of inpatient rehabilitation costs in the Department of Veterans Affairs (VA) and examined the relationship between length of stay (LOS) and discharge costs using data from VA and community rehabilitation hospitals. We estimated regression models to identify patient characteristics associated with specialized inpatient rehabilitation costs. VA data included 3,535 patients discharged from 63 facilities in fiscal year 2001. We compared VA costs to community rehabilitation hospitals using a sample from the Uniform Data System for Medical Rehabilitation of 190,112 patients discharged in 1999 from 697 facilities. LOS was a strong predictor of cost for VA and non-VA hospitals. Functional status, measured by Functional Independence Measure (FIM) scores at admission, was statistically significant but added little explanatory value after controlling for LOS. Although FIM scores were associated with LOS, FIM scores accounted for little variance in cost after controlling for LOS. These results are most applicable to researchers conducting cost-effectiveness analyses.average costs, billing, charges, cost, health economics, micro-cost methods, reimbursement, rehabilitation, VA, veterans