Minimal inference from incomplete 2x2-tables

Estimates based on 2x2 tables of frequencies are widely used in statistical applications. However, in many cases these tables are incomplete in the sense that the data required to compute the frequencies for a subset of the cells defining the table are unavailable. Minimal inference addresses those situations where this incompleteness leads to target parameters for these tables that are interval, rather than point, identifiable. In particular, we develop the concept of corroboration as a measure of the statistical evidence in the observed data that is not based on likelihoods. The corroboration function identifies the parameter values that are the hardest to refute, i.e., those values which, under repeated sampling, remain interval identified. This enables us to develop a general approach to inference from incomplete 2x2 tables when the additional assumptions required to support a likelihood-based approach cannot be sustained based on the data available. This minimal inference approach then provides a foundation for further analysis that aims at making sharper inference supported by plausible external beliefs

Adaptive Calibration for Prediction of Finite Population Totals

Sample weights can be calibrated to reflect the known population totals of a set of auxiliary variables. Predictors of finite population totals calculated using these weights have low bias if these variables are related to the variable of interest, but can have high variance if too many auxiliary variables are used. This article develops an adaptive calibration approach, where the auxiliary variables to be used in weighting are selected using sample data. Adaptively calibrated estimators are shown to have lower mean squared error and better coverage properties than non-adaptive estimators in many cases

An analysis of the transit times of CoRoT-1b

I report the results from a study of the transit times for CoRoT-1b, which was one of the first planets discovered by CoRoT. Analysis of the pipeline reduced CoRoT light curve yields a new determination of the physical and orbital parameters of planet and star, along with 35 individual transit times at a typical precision of 36 s. I estimate a planet-to-star radii ratio of 0.1433 +/- 0.0010, a ratio of the planet's orbital semimajor axis to the host star radius of 4.751 +/- 0.045, and an orbital inclination for the planet of 83.88 +/- 0.29 deg. The observed transit times are consistent with CoRoT-1b having a constant period and there is no evidence of an additional planet in the system. I use the observed constancy of the transit times to set limits on the mass of a hypothetical additional planet in a nearby, stable orbit. I ascertain that the most stringent limits (4 M_earth at 3 sigma confidence) can be placed on planets residing in a 1:2 mean motion resonance with the transiting planet. In contrast, the data yield less stringent limits on planets near a 1:3 mean motion resonance (5 M_jup at 3 sigma confidence) than in the surrounding parameter space. In addition, I use a simulation to investigate what sensitivity to additional planets could be obtained from the analysis of data measured for a similar system during a CoRoT long run (100 sequential transit times). I find that for such a scenario, planets with masses greater than twice that of Mars (0.2 M_earth) in the 1:2 mean motion resonance would cause high-significance transit time deviations. Therefore, such planets could be detected or ruled out using CoRoT long run data. I conclude that CoRoT data will indeed be very useful for searching for planets with the transit timing method.Comment: accepted for publication in A&A; v2 replaces with accepted versio

Bone Is Not Essential for Osteoclast Activation

Background: The mechanism whereby bone activates resorptive behavior in osteoclasts, the cells that resorb bone, is unknown. It is known that avb3 ligands are important, because blockade of avb3 receptor signaling inhibits bone resorption, but this might be through inhibition of adhesion or migration rather than resorption itself. Nor is it known whether avb3 ligands are sufficient for resorption the consensus is that bone mineral is essential for the recognition of bone as the substrate appropriate for resorption. Methodology/Principal Findings: Vitronectin- but not fibronectin-coated coverslips induced murine osteoclasts to secrete tartrate-resistant acid phosphatase, as they do on bone. Osteoclasts incubated on vitronectin, unlike fibronectin, formed podosome belts on glass coverslips, and these were modulated by resorption-regulating cytokines. Podosome belts formed on vitronectin-coated surfaces whether the substrates were rough or smooth, rigid or flexible. We developed a novel approach whereby the substrate-apposed surface of cells can be visualized in the scanning electron microscope. With this approach, supported by transmission electron microscopy, we found that osteoclasts on vitronectin-coated surfaces show ruffled borders and clear zones characteristic of resorbing osteoclasts. Ruffles were obscured by a film if cells were incubated in the cathepsin inhibitor E64, suggesting that removal of the film represents substrate-degrading behavior. Analogously, osteoclasts formed resorption-like trails on vitronectin-coated substrates. Like bone resorption, these trails were dependent upon resorbogenic cytokines and were inhibited by E64. Bone mineral induced actin rings and surface excavation only if first coated with vitronectin. Fibronectin could not substitute in any of these activities, despite enabling adhesion and cell spreading. Conclusions/Significance: Our results show that ligands avb3 are not only necessary but sufficient for the induction of resorptive behavior in osteoclasts; and suggest that bone is recognized through its affinity for these ligands, rather than by its mechanical or topographical attributes, or through a putative ‘mineral receptor’

The Gaia-ESO Survey::chemical signatures of rocky accretion in a young solar-type star

It is well known that newly formed planetary systems undergo processes of orbital reconfiguration and planetary migration. As a result, planets or protoplanetary objects may accrete onto the central star, being fused and mixed into its external layers. If the accreted mass is sufficiently high and the star has a sufficiently thin convective envelope, such events may result in a modification of the chemical composition of the stellar photosphere in an observable way, enhancing it with elements that were abundant in the accreted mass. The recent Gaia-ESO Survey observations of the 10-20 Myr old Gamma Velorum cluster have enabled identifying a star that is significantly enriched in iron with respect to other cluster members. In this Letter we further investigate the abundance pattern of this star, showing that its abundance anomaly is not limited to iron, but is also present in the refractory elements, whose overabundances are correlated with the condensation temperature. This finding strongly supports the hypothesis of a recent accretion of rocky material.Comment: Accepted for publicatio

Genetic parameters for growth, wood density and pulp yield in Eucalyptus globulus

Genetic variation and co-variation among the key pulpwood selection traits for Eucalyptus globulus were estimated for a range of sites in Portugal, with the aim of improving genetic parameters used to predict breeding values and correlated response to selection. The trials comprised clonally replicated full-sib families (eight trials) and unrelated clones (17 trials), and exhibited varying levels of pedigree connectivity. The traits studied were stem diameter at breast height, Pilodyn penetration (an indirect measure of wood basic density) and near infrared reflectance predicted pulp yield. Univariate and multivariate linear mixed models were fitted within and across sites, and estimates of additive genetic, total genetic, environmental and phenotypic variances and covariances were obtained. All traits studied exhibited significant levels of additive genetic variation. The average estimated within-site narrowsense heritability was 0.19±0.03 for diameter and 0.29± 0.03 for Pilodyn penetration, and the pooled estimate for predicted pulp yield was 0.42±0.14. When they could be tested, dominance and epistatic effects were generally not statistically significant, although broad-sense heritability estimates were slightly higher than narrow-sense heritability estimates. Averaged across trials, positive additive (0.64±0.08), total genetic (0.58±0.04), environmental (0.38±0.03) and phenotypic (0.43±0.02) correlation estimates were consistently obtained between diameter and Pilodyn penetration. This data argues for at least some form of pleiotropic relationship between these two traits and that selection for fast growth will adversely affect wood density in this population. Estimates of the across-site genetic correlations for diameter and Pilodyn penetration were high, indicating that the genotype by environment interaction is low across the range of sites tested. This result supports the use of single aggregated selection criteria for growth and wood density across planting environments in Portugal, as opposed to having to select for performance in different environment

Planet Populations as a Function of Stellar Properties

Exoplanets around different types of stars provide a window into the diverse environments in which planets form. This chapter describes the observed relations between exoplanet populations and stellar properties and how they connect to planet formation in protoplanetary disks. Giant planets occur more frequently around more metal-rich and more massive stars. These findings support the core accretion theory of planet formation, in which the cores of giant planets form more rapidly in more metal-rich and more massive protoplanetary disks. Smaller planets, those with sizes roughly between Earth and Neptune, exhibit different scaling relations with stellar properties. These planets are found around stars with a wide range of metallicities and occur more frequently around lower mass stars. This indicates that planet formation takes place in a wide range of environments, yet it is not clear why planets form more efficiently around low mass stars. Going forward, exoplanet surveys targeting M dwarfs will characterize the exoplanet population around the lowest mass stars. In combination with ongoing stellar characterization, this will help us understand the formation of planets in a large range of environments.Comment: Accepted for Publication in the Handbook of Exoplanet

Evidence for carbon sequestration by agricultural liming

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95356/1/gbc1382.pd

Habitable Zones in the Universe

Habitability varies dramatically with location and time in the universe. This was recognized centuries ago, but it was only in the last few decades that astronomers began to systematize the study of habitability. The introduction of the concept of the habitable zone was key to progress in this area. The habitable zone concept was first applied to the space around a star, now called the Circumstellar Habitable Zone. Recently, other, vastly broader, habitable zones have been proposed. We review the historical development of the concept of habitable zones and the present state of the research. We also suggest ways to make progress on each of the habitable zones and to unify them into a single concept encompassing the entire universe.Comment: 71 pages, 3 figures, 1 table; to be published in Origins of Life and Evolution of Biospheres; table slightly revise