Logistic regression on Markov chains for crop rotation modelling.

Often, in dynamical systems, such as farmer's crop choices, the dynamics is driven by external non-stationary factors, such as rainfall, temperature, and economy. Such dynamics can be modelled by a non-stationary Markov chain, where the transition probabilities are logistic functions of such external factors. We investigate the problem of estimating the parameters of the logistic model from data, using conjugate analysis with a fairly broad class of priors, to accommodate scarcity of data and lack of strong prior expert opinions. We show how maximum likelihood methods can be used to get bounds on the posterior mode of the parameters

A robust Bayesian analysis of the impact of policy decisions on crop rotations.

We analyse the impact of a policy decision on crop rotations, using the imprecise land use model that was developed by the authors in earlier work. A specific challenge in crop rotation models is that farmer’s crop choices are driven by both policy changes and external non-stationary factors, such as rainfall, temperature and agricultural input and output prices. Such dynamics can be modelled by a non-stationary stochastic process, where crop transition probabilities are multinomial logistic functions of such external factors. We use a robust Bayesian approach to estimate the parameters of our model, and validate it by comparing the model response with a non-parametric estimate, as well as by cross validation. Finally, we use the resulting predictions to solve a hypothetical yet realistic policy problem

Whole egg consumption and cortical bone in healthy children

Eggs contain bioactive compounds thought to benefit pediatric bone. This cross-sectional study shows a positive link between childhood egg intake and radius cortical bone. If randomized trials confirm our findings, incorporating eggs into children's diets could have a significant impact in preventing childhood fractures and reducing the risk of osteoporosis. INTRODUCTION: This study examined the relationships between egg consumption and cortical bone in children. METHODS: The cross-sectional study design included 294 9-13-year-old black and white males and females. Three-day diet records determined daily egg consumption. Peripheral quantitative computed tomography measured radius and tibia cortical bone. Body composition and biomarkers of bone turnover were assessed using dual-energy X-ray absorptiometry and ELISA, respectively. RESULTS: Egg intake was positively correlated with radius and tibia cortical bone mineral content (Ct.BMC), total bone area, cortical area, cortical thickness, periosteal circumference, and polar strength strain index in unadjusted models (r = 0.144-0.224, all P < 0.050). After adjusting for differences in race, sex, maturation, fat-free soft tissue mass (FFST), and protein intakes, tibia relationships were nullified; however, egg intake remained positively correlated with radius Ct.BMC (r = 0.138, P = 0.031). Egg intake positively correlated with total body bone mineral density, BMC, and bone area in the unadjusted models only (r = 0.119-0.224; all P < 0.050). After adjusting for covariates, egg intake was a positive predictor of radius FFST (β = 0.113, P < 0.050) and FFST was a positive predictor of Ct.BMC (β = 0.556, P < 0.050) in path analyses. There was a direct influence of egg on radius Ct.BMC (β = 0.099, P = 0.035), even after adjusting for the mediator, FFST (β = 0.137, P = 0.020). Egg intake was positively correlated with osteocalcin in both the unadjusted (P = 0.005) and adjusted (P = 0.049) models. CONCLUSION: If the positive influence of eggs on Ct.BMC observed in this study is confirmed through future randomized controlled trials, whole eggs may represent a viable strategy to promote pediatric bone development and prevent fractures

Gravitational lensing as a contaminant of the gravity wave signal in CMB

Gravity waves (GW) in the early universe generate B-type polarization in the cosmic microwave background (CMB), which can be used as a direct way to measure the energy scale of inflation. Gravitational lensing contaminates the GW signal by converting the dominant E polarization into B polarization. By reconstructing the lensing potential from CMB itself one can decontaminate the B mode induced by lensing. We present results of numerical simulations of B mode delensing using quadratic and iterative maximum-likelihood lensing reconstruction methods as a function of detector noise and beam. In our simulations we find the quadratic method can reduce the lensing B noise power by up to a factor of 7, close to the no noise limit. In contrast, the iterative method shows significant improvements even at the lowest noise levels we tested. We demonstrate explicitly that with this method at least a factor of 40 noise power reduction in lensing induced B power is possible, suggesting that T/S=10^-6 may be achievable in the absence of sky cuts, foregrounds, and instrumental systematics. While we do not find any fundamental lower limit due to lensing, we find that for high-sensitivity detectors residual lensing noise dominates over the detector noise.Comment: 6 pages, 2 figures, submitted to PR

Meta-Analysis of Genome-Wide Linkage Studies in Celiac Disease.

OBJECTIVE: A meta-analysis of genome-wide linkage studies allows us to summarize the extensive information available from family-based studies, as the field moves into genome-wide association studies. METHODS: Here we apply the genome scan meta-analysis (GSMA) method, a rank-based, model-free approach, to combine results across eight independent genome-wide linkages performed on celiac disease (CD), including 554 families with over 1,500 affected individuals. We also investigate the agreement between signals we identified from this meta-analysis of linkage studies and those identified from genome-wide association analysis using a hypergeometric distribution. RESULTS: Not surprisingly, the most significant result was obtained in the HLA region. Outside the HLA region, suggestive evidence for linkage was obtained at the telomeric region of chromosome 10 (10q26.12-qter; p = 0.00366), and on chromosome 8 (8q22.2-q24.21; p = 0.00491). Testing signals of association and linkage within bins showed no significant evidence for co-localization of results. CONCLUSION: This meta-analysis allowed us to pool the results from available genome-wide linkage studies and to identify novel regions potentially harboring predisposing genetic variation contributing to CD. This study also shows that linkage and association studies may identify different types of disease-predisposing variants

Antibody validation of immunohistochemistry for biomarker discovery: Recommendations of a consortium of academic and pharmaceutical based histopathology researchers

As biomarker discovery takes centre-stage, the role of immunohistochemistry within that process is increasing. At the same time, the number of antibodies being produced for ‘‘research use’’ continues to rise and it is important that antibodies to be used as biomarkers are validated for specificity and sensitivity before use. This guideline seeks to provide a stepwise approach for the validation of an antibody for immunohistochemical assays, reflecting the views of a consortium of academic and pharmaceutical based histopathology researchers. We propose that antibodies are placed into a tier system, level 1–3, based on evidence of their usage in immunohistochemistry, and that the degree of validation required is proportionate to their place on that tier

Facts, Values and Quanta

Quantum mechanics is a fundamentally probabilistic theory (at least so far as the empirical predictions are concerned). It follows that, if one wants to properly understand quantum mechanics, it is essential to clearly understand the meaning of probability statements. The interpretation of probability has excited nearly as much philosophical controversy as the interpretation of quantum mechanics. 20th century physicists have mostly adopted a frequentist conception. In this paper it is argued that we ought, instead, to adopt a logical or Bayesian conception. The paper includes a comparison of the orthodox and Bayesian theories of statistical inference. It concludes with a few remarks concerning the implications for the concept of physical reality.Comment: 30 pages, AMS Late

Near-Earth asteroid sample return missions

The rate of discovery of new NEAs and the success of D-S 1 and NEAR-Shoemaker, suggest that sample return from NEAs is now technically feasible. Here we present a summary of a recent workshop on the topic

Non-detection of a statistically anisotropic power spectrum in large-scale structure

We search a sample of photometric luminous red galaxies (LRGs) measured by the Sloan Digital Sky Survey (SDSS) for a quadrupolar anisotropy in the primordial power spectrum, in which P(\vec{k}) is an isotropic power spectrum P(k) multiplied by a quadrupolar modulation pattern. We first place limits on the 5 coefficients of a general quadrupole anisotropy. We also consider axisymmetric quadrupoles of the form P(\vec{k}) = P(k){1 + g_*[(\hat{k}\cdot\hat{n})^2-1/3]} where \hat{n} is the axis of the anisotropy. When we force the symmetry axis \hat{n} to be in the direction (l,b)=(94 degrees,26 degrees) identified in the recent Groeneboom et al. analysis of the cosmic microwave background, we find g_*=0.006+/-0.036 (1 sigma). With uniform priors on \hat{n} and g_* we find that -0.41<g_*<+0.38 with 95% probability, with the wide range due mainly to the large uncertainty of asymmetries aligned with the Galactic Plane. In none of these three analyses do we detect evidence for quadrupolar power anisotropy in large scale structure.Comment: 23 pages; 10 figures; 3 tables; replaced with version published in JCAP (added discussion of scale-varying quadrupolar anisotropy

Foreground removal from WMAP 7yr polarization maps using an MLP neural network

One of the fundamental problems in extracting the cosmic microwave background signal (CMB) from millimeter/submillimeter observations is the pollution by emission from the Milky Way: synchrotron, free-free, and thermal dust emission. To extract the fundamental cosmological parameters from CMB signal, it is mandatory to minimize this pollution since it will create systematic errors in the CMB power spectra. In previous investigations, it has been demonstrated that the neural network method provide high quality CMB maps from temperature data. Here the analysis is extended to polarization maps. As a concrete example, the WMAP 7-year polarization data, the most reliable determination of the polarization properties of the CMB, has been analysed. The analysis has adopted the frequency maps, noise models, window functions and the foreground models as provided by the WMAP Team, and no auxiliary data is included. Within this framework it is demonstrated that the network can extract the CMB polarization signal with no sign of pollution by the polarized foregrounds. The errors in the derived polarization power spectra are improved compared to the errors derived by the WMAP Team.Comment: Accepted for publication in Astrophysics & Space Scienc