An approximate Bayesian computation approach to overcome biases that arise when using amplified fragment length polymorphism markers to study population structure

There is great interest in using amplified fragment length polymorphism (AFLP) markers because they are inexpensive and easy to produce. It is, therefore, possible to generate a large number of markers that have a wide coverage of species genotnes. Several statistical methods have been proposed to study the genetic structure using AFLP's but they assume Hardy-Weinberg equilibrium and do not estimate the inbreeding coefficient, F-IS. A Bayesian method has been proposed by Holsinger and colleagues that relaxes these simplifying assumptions but we have identified two sources of bias that can influence estimates based on these markers: (i) the use of a uniform prior on ancestral allele frequencies and (ii) the ascertainment bias of AFLP markers. We present a new Bayesian method that avoids these biases by using an implementation based on the approximate Bayesian computation (ABC) algorithm. This new method estimates population-specific F-IS and F-ST values and offers users the possibility of taking into account the criteria for selecting the markers that are used in the analyses. The software is available at our web site (http://www-leca.uif-grenoble.fi-/logiciels.htm). Finally, we provide advice on how to avoid the effects of ascertainment bias.

The APE atlas

This Atlas presents statistical analyses of the simulations submitted to the Aqua-Planet Experiment (APE) data archive. The simulations are from global Atmospheric General Circulation Models (AGCM) applied to a water-covered earth. The AGCMs include ones actively used or being developed for numerical weather prediction or climate research. Some are mature, application models and others are more novel and thus less well tested in Earth-like applications. The experiment applies AGCMs with their complete parameterization package to an idealization of the planet Earth which has a greatly simplified lower boundary that consists of an ocean only. It has no land and its associated orography, and no sea ice. The ocean is represented by Sea Surface Temperatures (SST) which are specified everywhere with simple, idealized distributions. Thus in the hierarchy of tests available for AGCMs, APE falls between tests with simplified forcings such as those proposed by Held and Suarez (1994) and Boer and Denis (1997) and Earth-like simulations of the Atmospheric Modeling Intercomparison Project (AMIP, Gates et al., 1999). Blackburn and Hoskins (2013) summarize the APE and its aims. They discuss where the APE fits within a modeling hierarchy which has evolved to evaluate complete models and which provides a link between realistic simulation and conceptual models of atmospheric phenomena. The APE bridges a gap in the existing hierarchy. The goals of APE are to provide a benchmark of current model behaviors and to stimulate research to understand the cause of inter-model differences., APE is sponsored by the World Meteorological Organization (WMO) joint Commission on Atmospheric Science (CAS), World Climate Research Program (WCRP) Working Group on Numerical Experimentation (WGNE). Chapter 2 of this Atlas provides an overview of the specification of the eight APE experiments and of the data collected. Chapter 3 lists the participating models and includes brief descriptions of each. Chapters 4 through 7 present a wide variety of statistics from the 14 participating models for the eight different experiments. Additional intercomparison figures created by Dr. Yukiko Yamada in AGU group are available at http://www.gfd-dennou.org/library/ape/comparison/. This Atlas is intended to present and compare the statistics of the APE simulations but does not contain a discussion of interpretive analyses. Such analyses are left for journal papers such as those included in the Special Issue of the Journal of the Meteorological Society of Japan (2013, Vol. 91A) devoted to the APE. Two papers in that collection provide an overview of the simulations. One (Blackburn et al., 2013) concentrates on the CONTROL simulation and the other (Williamson et al., 2013) on the response to changes in the meridional SST profile. Additional papers provide more detailed analysis of the basic simulations, while others describe various sensitivities and applications. The APE experiment data base holds a wealth of data that is now publicly available from the APE web site: http://climate.ncas.ac.uk/ape/. We hope that this Atlas will stimulate future analyses and investigations to understand the large variation seen in the model behaviors.

Taking the shopping centre online: new models in e-commerce

Purpose – This paper aims to provide a brief re´sume´ of previous research which has analysed the impact of e-commerce on retail real estate in the UK, and to examine the important marketing role of the internet for shopping centre managers, and retail landlords. Design/methodology/approach – Based on the results from a wider study carried out in 2003, the paper uses case studies from two different shopping centres in the UK, and documents the innovative uses of both web-based marketing and online retailing by organisations that historically have not directly been involved in the retailing process. Findings – The paper highlights the importance of considering online sales within a multi-channel approach to retailing. The two types of emerging shopping centre model which are identified are characterised by their ultimate relationship with the physical shopping centre on whose web site they reside. These can be summarised as: the “centre-led” approach, and the “brand-led” or “marketing-led” approach. Research limitations/implications – The research is based on a limited number of in-depth case studies and secondary data. Further research is needed to monitor the continuing impact of e-commerce on retail property and the marketing strategies of shopping centre managers and owners. Practical implications – Internet-based sales provide an important adjunct to conventional retail sales and an important source of potential risk for landlords and tenants in the real estate investment market. Regardless of whether retailers use the internet as a sales channel, as a product-sourcing tool, or merely to provide information to the consumer, the internet has become a keystone within the greater retail marketing mix. The findings have ramifications for understanding the way in which landlords are structuring their retail property to defray potential risks. Originality/value – The paper examines shopping centre online marketing models for the first time in detail, and will be of value to retail occupiers, owners and other stakeholders of shopping centres.

A framework for the forensic analysis of user interaction with social media

The increasing use of social media, applications or platforms that allow users to interact online, ensures that this environment will provide a useful source of evidence for the forensics examiner. Current tools for the examination of digital evidence find this data problematic as they are not designed for the collection and analysis of online data. Therefore, this paper presents a framework for the forensic analysis of user interaction with social media. In particular, it presents an inter-disciplinary approach for the quantitative analysis of user engagement to identify relational and temporal dimensions of evidence relevant to an investigation. This framework enables the analysis of large data sets from which a (much smaller) group of individuals of interest can be identified. In this way, it may be used to support the identification of individuals who might be ‘instigators’ of a criminal event orchestrated via social media, or a means of potentially identifying those who might be involved in the ‘peaks’ of activity. In order to demonstrate the applicability of the framework, this paper applies it to a case study of actors posting to a social media Web site.

The FunFOLD2 server for the prediction of protein-ligand interactions

The FunFOLD2 server is a new independent server that integrates our novel protein–ligand binding site and quality assessment protocols for the prediction of protein function (FN) from sequence via structure. Our guiding principles were, first, to provide a simple unified resource to make our function prediction software easily accessible to all via a simple web interface and, second, to produce integrated output for predictions that can be easily interpreted. The server provides a clean web interface so that results can be viewed on a single page and interpreted by non-experts at a glance. The output for the prediction is an image of the top predicted tertiary structure annotated to indicate putative ligand-binding site residues. The results page also includes a list of the most likely binding site residues and the types of predicted ligands and their frequencies in similar structures. The protein–ligand interactions can also be interactively visualized in 3D using the Jmol plug-in. The raw machine readable data are provided for developers, which comply with the Critical Assessment of Techniques for Protein Structure Prediction data standards for FN predictions. The FunFOLD2 webserver is freely available to all at the following web site: http://www.reading.ac.uk/bioinf/FunFOLD/FunFOLD_form_2_0.html.