Exchangeability of mammalian DNA ligases between base excision repair pathways

In mammalian cells, DNA ligase IIIalpha and DNA ligase I participate in the short- and long-patch base excision repair pathways, respectively. Using an in vitro repair assay employing DNA ligase-depleted cell extracts and DNA substrates containing a single lesion repaired either through short-patch (regular abasic site) or long-patch (reduced abasic site) base excision repair pathways, we addressed the question whether DNA ligases are specific to each pathway or if they are exchangeable. We find that immunodepletion of DNA ligase I did not affect the short-patch repair pathway but blocked long-patch repair, suggesting that DNA ligase IIIa is not able to substitute DNA ligase I during long-patch repair. In contrast, immunodepletion of DNA ligase IIIa did not significantly affect either pathway. Moreover, repair of normal abasic sites in wild-type and X-ray cross-complementing gene 1 (XRCC1)-DNA ligase IIIalpha-immunodepleted cell extracts involved similar proportions of short- and long-patch repair events. This suggests that DNA ligase I was able to efficiently substitute the XRCC1-DNA ligase IIIa complex during short-patch repair.

The concept of exchangeability in ensemble forecasting

A set of random variables is exchangeable if its joint distribution function is invariant under permutation of the arguments. The concept of exchangeability is discussed, with a view towards potential application in evaluating ensemble forecasts. It is argued that the paradigm of ensembles being an independent draw from an underlying distribution function is probably too narrow; allowing ensemble members to be merely exchangeable might be a more versatile model. The question is discussed whether established methods of ensemble evaluation need alteration under this model, with reliability being given particular attention. It turns out that the standard methodology of rank histograms can still be applied. As a first application of the exchangeability concept, it is shown that the method of minimum spanning trees to evaluate the reliability of high dimensional ensembles is mathematically sound.

Structural Interactions in Spatial Panels

Until recently, much effort has been devoted to the estimation of panel data regression models without adequate attention being paid to the drivers of diffusion and interaction across cross section and spatial units. We discuss some new methodologies in this emerging area and demonstrate their use in measurement and inferences on cross section and spatial interactions. Specifically, we highlight the important distinction between spatial dependence driven by unobserved common factors and those based on a spatial weights matrix. We argue that, purely factor driven models of spatial dependence may be somewhat inadequate because of their connection with the exchangeability assumption. Limitations and potential enhancements of the existing methods are discussed, and several directions for new research are highlighted.

Characterization of lead-recycling facility emissions at various workplaces : major insights for sanitary risks assessment

Most available studies on lead smelter emissions deal with the environmental impact of outdoor particles, but only a few focus on air quality at workplaces. The objective of this study is to physically and chemically characterize the Pb-rich particles emitted at different workplaces in a lead recycling plant. A multi-scale characterization was conducted from bulk analysis to the level of individual particles, to assess the particles properties in relation with Pb speciation and availability. Process PM from various origins were sampled and then compared; namely Furnace and Refining PM respectively present in the smelter and at refinery workplaces, Emissions PM present in channeled emissions.These particles first differed by their morphology and size distribution, with finer particles found in emissions. Differences observed in chemical composition could be explained by the industrial processes. All PM contained the same major phases (Pb, PbS, PbO, PbSO4 and PbO·PbSO4) but differed on the nature and amount of minor phases. Due to high content in PM, Pb concentrations in the CaCl2 extractant reached relatively high values (40 mg.L-1). However, the ratios (soluble/total) of CaCl2 exchangeable Pb were relatively low (< 0.02%) in comparison with Cd (up to 18%). These results highlight the interest to assess the soluble fractions of all metals (minor and major) and discuss both total metal concentrations and ratios for risk evaluations. In most cases metal extractability increased with decreasing size of particles, in particular, lead exchangeability was highest for channeled emissions. Such type of study could help in the choice of targeted sanitary protection procedures and for further toxicological investigations. In the present context, particular attention is given to Emissions and Furnace PM. Moreover, exposure to other metals than Pb should be considered. [Authors]

A generalized mechanistic codon model.

Models of codon evolution have attracted particular interest because of their unique capabilities to detect selection forces and their high fit when applied to sequence evolution. We described here a novel approach for modeling codon evolution, which is based on Kronecker product of matrices. The 61 × 61 codon substitution rate matrix is created using Kronecker product of three 4 × 4 nucleotide substitution matrices, the equilibrium frequency of codons, and the selection rate parameter. The entities of the nucleotide substitution matrices and selection rate are considered as parameters of the model, which are optimized by maximum likelihood. Our fully mechanistic model allows the instantaneous substitution matrix between codons to be fully estimated with only 19 parameters instead of 3,721, by using the biological interdependence existing between positions within codons. We illustrate the properties of our models using computer simulations and assessed its relevance by comparing the AICc measures of our model and other models of codon evolution on simulations and a large range of empirical data sets. We show that our model fits most biological data better compared with the current codon models. Furthermore, the parameters in our model can be interpreted in a similar way as the exchangeability rates found in empirical codon models.

Random assignment of intervention points in two phase single-case designs: data-division-specific distributions

The present study explores the statistical properties of a randomization test based on the random assignment of the intervention point in a two-phase (AB) single-case design. The focus is on randomization distributions constructed with the values of the test statistic for all possible random assignments and used to obtain p-values. The shape of those distributions is investigated for each specific data division defined by the moment in which the intervention is introduced. Another aim of the study consisted in testing the detection of inexistent effects (i.e., production of false alarms) in autocorrelated data series, in which the assumption of exchangeability between observations may be untenable. In this way, it was possible to compare nominal and empirical Type I error rates in order to obtain evidence on the statistical validity of the randomization test for each individual data division. The results suggest that when either of the two phases has considerably less measurement times, Type I errors may be too probable and, hence, the decision making process to be carried out by applied researchers may be jeopardized.

Practical Data Collection: Establishing Methods and Procedures for Measuring Water Clarity and Turbidity of Storm Water Run-Off from Active Major Highway Construction Sites, 2014

In anticipation of regulation involving numeric turbidity limit at highway construction sites, research was done into the most appropriate, affordable methods for surface water monitoring. Measuring sediment concentration in streams may be conducted a number of ways. As part of a project funded by the Iowa Department of Transportation, several testing methods were explored to determine the most affordable, appropriate methods for data collection both in the field and in the lab. The primary purpose of the research was to determine the exchangeability of the acrylic transparency tube for water clarity analysis as compared to the turbidimeter.

Random sums of exchangeable variables and actuarial applications

In this paper we study the accumulated claim in some fixed time period, skipping the classical assumption of mutual independence between the variables involved. Two basic models are considered: Model I assumes that any pair of claims are equally correlated which means that the corresponding square-integrable sequence is exchangeable one. Model 2 states that the correlations between the adjacent claims are the same. Recurrence and explicit expressions for the joint probability generating function are derived and the impact of the dependence parameter (correlation coefficient) in both models is examined. The Markov binomial distribution is obtained as a particular case under assumptions of Model 2. (C) 2007 Elsevier B.V. All rights reserved.

Sets of probability distributions, independence, and convexity

This paper analyzes concepts of independence and assumptions of convexity in the theory of sets of probability distributions. The starting point is Kyburg and Pittarelli's discussion of "convex Bayesianism" (in particular their proposals concerning E-admissibility, independence, and convexity). The paper offers an organized review of the literature on independence for sets of probability distributions; new results on graphoid properties and on the justification of "strong independence" (using exchangeability) are presented. Finally, the connection between Kyburg and Pittarelli's results and recent developments on the axiomatization of non-binary preferences, and its impact on "complete" independence, are described.

Detection of one slowly exchanging substrate water molecule in the S3 state of photosystem II.

The exchangeability of the substrate water molecules at the catalytic site of water oxidation in photosystem II has been probed by isotope-exchange measurements using mass spectrometric detection of flash-induced oxygen evolution. A stirred sample chamber was constructed to reduce the lag time between injection of H2(18)O and the detecting flash by a factor of more than 1000 compared to the original experiments by R. Radmer and O. Ollinger [(1986) FEBS Lett. 195, 285-289]. Our data show that there is a slow (t1/2 approximately 500 ms, 10 degrees C) and a fast (t1/2 <25 ms, 10 degrees C) exchanging substrate water molecule in the S3 state of photosystem II. The slow exchange is coupled with an activation energy of about 75 kJ/mol and is discussed in terms of a terminal manganese oxo ligand, while the faster exchanging substrate molecule may represent a water molecule not directly bound to the manganese center.

On The Dirichlet Distribution

The Dirichlet distribution is a multivariate generalization of the Beta distribution. It is an important multivariate continuous distribution in probability and statistics. In this report, we review the Dirichlet distribution and study its properties, including statistical and information-theoretic quantities involving this distribution. Also, relationships between the Dirichlet distribution and other distributions are discussed. There are some different ways to think about generating random variables with a Dirichlet distribution. The stick-breaking approach and the Pólya urn method are discussed. In Bayesian statistics, the Dirichlet distribution and the generalized Dirichlet distribution can both be a conjugate prior for the Multinomial distribution. The Dirichlet distribution has many applications in different fields. We focus on the unsupervised learning of a finite mixture model based on the Dirichlet distribution. The Initialization Algorithm and Dirichlet Mixture Estimation Algorithm are both reviewed for estimating the parameters of a Dirichlet mixture. Three experimental results are shown for the estimation of artificial histograms, summarization of image databases and human skin detection.

Shifting Processes with Cyclically Exchangeable Increments at Random

International audience

Evidence that risk adjustment is unnecessary in estimates of the User cost of money

Investors value the special attributes of monetary assets (e.g., exchangeability, liquidity, and safety) and pay a premium for holding them in the form of a lower return rate -- The user cost of holding monetary assets can be measured approximately by the difference between the returns on illiquid risky assets and those of safer liquid assets -- A more appropriate measure should adjust this difference by the differential risk of the assets in question -- We investigate the impact that time non-separable preferences has on the estimation of the risk-adjusted user cost of money -- Using U.K. data from 1965Q1 to 2011Q1, we estimate a habit-based asset pricing model with money in the utility function and find that the risk adjustment for risky monetary assets is negligible -- Thus, researchers can dispense with risk adjusting the user cost of money in constructing monetary aggregate indexes