Genetic variation of the razor clam Ensis siliqua (Jeffreys, 1875) along the European coast based on random amplified polymorphic DNA markers

Ensis siliqua is regarded as an increasingly valuable fishery resource with potential for commercial aquaculture in many European countries. The genetic variation of this razor clam was analysed by randomly amplified polymorphic DNA (RAPD) in six populations from Spain, Portugal and Ireland. Out of the 40 primers tested, five were chosen to assess genetic variation. A total of 61 RAPD loci were developed ranging in size from 400 to 2000 bp. The percentages of polymorphic loci, the allele effective number and the genetic diversity were comparable among populations, and demonstrated a high level of genetic variability. The values of Nei's genetic distance were small among the Spanish and Portuguese populations (0.051-0.065), and high between these and the Irish populations. Cluster and principal coordinate analyses supported these findings. A mantel test performed between geographic and genetic distance matrices showed a significant correlation (r=0.84, P

Asymmetric information without common priors: an indirect evolutionary analysis of quantity competition

The common prior assumption justifies private beliefs as posterior probabilities when updating a common prior based on individual information. We dispose of the common prior assumption for a homogeneous oligopoly market with uncertain costs and firms entertaining arbitrary priors about other firms' cost-type. We show that true prior beliefs can not be evolutionarily stable when truly expected profit measures (reproductive) success.

Commentary on Jeffreys v. Boosey (1854)

The second decision of the House of Lords to consider the nature of copyright law. As was the case in Donaldson v. Becket (1774) (uk_1774) the law lords were in disagreement with the majority of common law judges invited to speak to the issue for the consideration of the House. In the course of their opinions, two of the law lords (Lord Brougham and Lord St Leonards) explicitly reject the concept of copyright at common law. Rather than a natural authorial property right, they present copyright as a purely statutory phenomenon specifically grounded in public interest concerns. Ultimately, the Lords decided that a foreign national, resident abroad, but first publishing in Britain, enjoys no protection in his work under British copyright law.

Bridging Jeffrey's Rule, AGM Revision and Dempster Conditioning in the Theory of Evidence

Belief revision characterizes the process of revising an agent’s beliefs when receiving new evidence. In the field of artificial intelligence, revision strategies have been extensively studied in the context of logic-based formalisms and probability kinematics. However, so far there is not much literature on this topic in evidence theory. In contrast, combination rules proposed so far in the theory of evidence, especially Dempster rule, are symmetric. They rely on a basic assumption, that is, pieces of evidence being combined are considered to be on a par, i.e. play the same role. When one source of evidence is less reliable than another, it is possible to discount it and then a symmetric combination operation
is still used. In the case of revision, the idea is to let prior knowledge of an agent be altered by some input information. The change problem is thus intrinsically asymmetric. Assuming the input information is reliable, it should be retained whilst the prior information should be changed minimally to that effect. To deal with this issue, this paper defines the notion of revision for the theory of evidence in such a way as to bring together probabilistic and logical views. Several revision rules previously proposed are reviewed and we advocate one of them as better corresponding to the idea of revision. It is extended to cope with inconsistency between prior and input information. It reduces to Dempster
rule of combination, just like revision in the sense of Alchourron, Gardenfors, and Makinson (AGM) reduces to expansion, when the input is strongly consistent with the prior belief function. Properties of this revision rule are also investigated and it is shown to generalize Jeffrey’s rule of updating, Dempster rule of conditioning and a form of AGM revision.

Flexible paleoclimate age-depth models using an autoregressive gamma process

Radiocarbon dating is routinely used in paleoecology to build chronolo- gies of lake and peat sediments, aiming at inferring a model that would relate the sediment depth with its age. We present a new approach for chronology building (called “Bacon”) that has received enthusiastic attention by paleoecologists. Our methodology is based on controlling core accumulation rates using a gamma autoregressive semiparametric model with an arbitrary number of subdivisions along the sediment. Using prior knowledge about accumulation rates is crucial and informative priors are routinely used. Since many sediment cores are currently analyzed, using different data sets and prior distributions, a robust (adaptive) MCMC is very useful. We use the t-walk (Christen and Fox, 2010), a self adjusting, robust MCMC sampling algorithm, that works acceptably well in many situations. Outliers are also addressed using a recent approach that considers a Student-t model for radiocarbon data. Two examples are presented here, that of a peat core and a core from a lake, and our results are compared with other approaches.

WASP-23b: a transiting hot Jupiter around a K dwarf and its Rossiter-McLaughlin effect

We report the discovery of a new transiting planet in the southern hemisphere. It was found by the WASP-south transit survey and confirmed photometrically and spectroscopically by the 1.2 m Swiss Euler telescope, LCOGT 2m Faulkes South Telescope, the 60 cm TRAPPIST telescope, and the ESO 3.6 m telescope. The orbital period of the planet is 2.94 days. We find that it is a gas giant with a mass of 0.88 ± 0.10 MJ and an estimated radius of 0.96 ± 0.05 RJ. We obtained spectra during transit with the HARPS spectrograph and detect the Rossiter-McLaughlin effect despite its small amplitude. Because of the low signal-to-noise ratio of the effect and a small impact parameter, we cannot place a strong constraint on the projected spin-orbit angle. We find two conflicting values for the stellar rotation. We find, via spectral line broadening, that v sin I = 2.2 ± 0.3 km s-1, while applying another method, based on the activity level using the index log R'_HK, gives an equatorial rotation velocity of only v = 1.35 ± 0.20 km s-1. Using these as priors in our analysis, the planet might be either misaligned or aligned. This result raises doubts about the use of such priors. There is evidence of neither eccentricity nor any radial velocity drift with time. Using WASP-South photometric observations confirmed with LCOGT Faulkes South Telescope, the 60 cm TRAPPIST telescope, the CORALIE spectrograph and the camera from the Swiss 1.2 m Euler Telescope placed at La Silla, Chile, as well as with the HARPS spectrograph, mounted on the ESO 3.6 m, also at La Silla, under proposal 084.C-0185. The data is publicly available at the CDS Strasbourg and on demand to the main author.RV data is only available at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/531/A24Appendix is available in electronic form at http://www.aanda.org

Bagging statistical network inference from large-scale gene expression data.

Modern biology and medicine aim at hunting molecular and cellular causes of biological functions and diseases. Gene regulatory networks (GRN) inferred from gene expression data are considered an important aid for this research by providing a map of molecular interactions. Hence, GRNs have the potential enabling and enhancing basic as well as applied research in the life sciences. In this paper, we introduce a new method called BC3NET for inferring causal gene regulatory networks from large-scale gene expression data. BC3NET is an ensemble method that is based on bagging the C3NET algorithm, which means it corresponds to a Bayesian approach with noninformative priors. In this study we demonstrate for a variety of simulated and biological gene expression data from S. cerevisiae that BC3NET is an important enhancement over other inference methods that is capable of capturing biochemical interactions from transcription regulation and protein-protein interaction sensibly. An implementation of BC3NET is freely available as an R package from the CRAN repository. © 2012 de Matos Simoes, Emmert-Streib.

Type Ia supernova bolometric light curves and ejected mass estimates from the nearby supernova factory

We present a sample of normal Type Ia supernovae (SNe Ia) from the Nearby Supernova Factory data set with spectrophotometry at sufficiently late phases to estimate the ejected mass using the bolometric light curve.Wemeasure Ni masses from the peak bolometric luminosity, then compare the luminosity in the Co-decay tail to the expected rate of radioactive energy release from ejecta of a given mass. We infer the ejected mass in a Bayesian context using a semi-analytic model of the ejecta, incorporating constraints from contemporary numerical models as priors on the density structure and distribution of Ni throughout the ejecta. We find a strong correlation between ejected mass and light-curve decline rate, and consequently Ni mass, with ejected masses in our data ranging from 0.9 to 1.4 M. Most fast-declining (SALT2 x <-1) normal SNe Ia have significantly sub-Chandrasekhar ejected masses in our fiducial analysis.