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

Hidden Conditional Random Fields for Visual Speech Recognition

In this paper we present the application of Hidden Conditional Random Fields (HCRFs) to modelling speech for visual speech recognition. HCRFs may be easily adapted to model long range dependencies across an observation sequence. As a result visual word recognition performance can be improved as the model is able to take more of a contextual approach to generating state sequences. Results are presented from a speaker-dependent, isolated digit, visual speech recognition task using comparisons with a baseline HMM system. We firstly illustrate that word recognition rates on clean video using HCRFs can be improved by increasing the number of past and future observations being taken into account by each state. Secondly we compare model performances using various levels of video compression on the test set. As far as we are aware this is the first attempted use of HCRFs for visual speech recognition.

The outflow ranking method for weighted directed graphs

A ranking method assigns to every weighted directed graph a (weak) ordering of the nodes. In this paper we axiomatize the ranking method that ranks the nodes according to their outflow using four independent axioms. Besides the well-known axioms of anonymity and positive responsiveness we introduce outflow monotonicity – meaning that in pairwise comparison between two nodes, a node is not doing worse in case its own outflow does not decrease and the other node’s outflow does not increase – and order preservation – meaning that adding two weighted digraphs such that the pairwise ranking between two nodes is the same in both weighted digraphs, then this is also their pairwise ranking in the ‘sum’ weighted digraph. The outflow ranking method generalizes the ranking by outdegree for directed graphs, and therefore also generalizes the ranking by Copeland score for tournaments.

Systematic random sampling of the comet assay

The comet assay is a technique used to quantify DNA damage and repair at a cellular level. In the assay, cells are embedded in agarose and the cellular content is stripped away leaving only the DNA trapped in an agarose cavity which can then be electrophoresed. The damaged DNA can enter the agarose and migrate while the undamaged DNA cannot and is retained. DNA damage is measured as the proportion of the migratory ‘tail’ DNA compared to the total DNA in the cell. The fundamental basis of these arbitrary values is obtained in the comet acquisition phase using fluorescence microscopy with a stoichiometric stain in tandem with image analysis software. Current methods deployed in such an acquisition are expected to be both objectively and randomly obtained. In this paper we examine the ‘randomness’ of the acquisition phase and suggest an alternative method that offers both objective and unbiased comet selection. In order to achieve this, we have adopted a survey sampling approach widely used in stereology, which offers a method of systematic random sampling (SRS). This is desirable as it offers an impartial and reproducible method of comet analysis that can be used both manually or automated. By making use of an unbiased sampling frame and using microscope verniers, we are able to increase the precision of estimates of DNA damage. Results obtained from a multiple-user pooled variation experiment showed that the SRS technique attained a lower variability than that of the traditional approach. The analysis of a single user with repetition experiment showed greater individual variances while not being detrimental to overall averages. This would suggest that the SRS method offers a better reflection of DNA damage for a given slide and also offers better user reproducibility.

Structural change in multipartite entanglement sharing: A random matrix approach

We study the typical entanglement properties of a system comprising two independent qubit environments interacting via a shuttling ancilla. The initial preparation of the environments is modeled using random matrix techniques. The entanglement measure used in our study is then averaged over many histories of randomly prepared environmental states. Under a Heisenberg interaction model, the average entanglement between the ancilla and one of the environments remains constant, regardless of the preparation of the latter and the details of the interaction. We also show that, upon suitable kinematic and dynamical changes in the ancillaenvironment subsystems, the entanglement-sharing structure undergoes abrupt modifications associated with a change in the multipartite entanglement class of the overall system's state. These results are invariant with respect to the randomized initial state of the environments.

Random walk simulations of fossil proxy data

A wealth of palaeoecological studies (e.g. pollen, diatoms, chironomids and macrofossils from deposits such as lakes or bogs) have revealed major as well as more subtle ecosystem changes over decadal to multimillennial timescales. Such ecosystem changes are usually assumed to have been forced by specific environmental changes. Here, we test if the observed changes in palaeoecological records may be reproduced by random simulations, and we find that simple procedures generate abrupt events, long-term trends, quasi-cyclic behaviour, extinctions and immigrations. Our results highlight the importance of replicated and multiproxy data for reliable reconstructions of past climate and environmental changes.