Exploring and enriching a language resource archive via the web

The ”download first, then process paradigm” is still the predominant working method amongst the research community. The web-based paradigm, however, offers many advantages from a tool development and data management perspective as they allow a quick adaptation to changing research environments. Moreover, new ways of combining tools and data are increasingly becoming available and will eventually enable a true web-based workflow approach, thus challenging the ”download first, then process” paradigm. The necessary infrastructure for managing, exploring and enriching language resources via the Web will need to be delivered by projects like CLARIN and DARIA

Structural models of genome-wide covariance identify multiple common dimensions in autism

Common genetic variation has been associated with multiple symptoms in Autism Spectrum Disorder (ASD). However, our knowledge of shared genetic factor structures contributing to this highly heterogeneous neurodevelopmental condition is limited. Here, we developed a structural equation modelling framework to directly model genome-wide covariance across core and non-core ASD phenotypes, studying autistic individuals of European descent using a case-only design. We identified three independent genetic factors most strongly linked to language/cognition, behaviour and motor development, respectively, when studying a population-representative sample (N=5,331). These analyses revealed novel associations. For example, developmental delay in acquiring personal-social skills was inversely related to language, while developmental motor delay was linked to self-injurious behaviour. We largely confirmed the three-factorial structure in independent ASD-simplex families (N=1,946), but uncovered simplex-specific genetic overlap between behaviour and language phenotypes. Thus, the common genetic architecture in ASD is multi-dimensional and contributes, in combination with ascertainment-specific patterns, to phenotypic heterogeneity

The third moments of the site frequency spectrum

The analysis of patterns of segregating (i.e. polymorphic) sites in aligned sequences is routine in population genetics. Quantities of interest include the total number of segregating sites and the number of sites with mutations of different frequencies, the so-called site frequency spectrum. For neutrally evolving sequences, some classical results are available, including the expected value and variance of the spectrum in the Kingman coalescent model without recombination as calculated by Fu (1995). In this work, we use similar techniques to compute the third moments of the frequencies of three linked sites. Based on these results, we derive analytical results for the bias of Tajima's D and other neutrality tests. As a corollary, we obtain the second moments of the frequencies of two linked mutations conditional on the presence of a third mutation with a certain frequency. These moments can be used for the normalisation of new neutrality tests relying on these spectra. (C) 2017 The Authors. Published by Elsevier Inc

Demography-adjusted tests of neutrality based on genome-wide SNP data

Tests of the neutral evolution hypothesis are usually built on the standard null model which assumes that mutations are neutral and the population size remains constant over time. However, it is unclear how such tests are affected if the last assumption is dropped. Here, we extend the unifying framework for tests based on the site frequency spectrum, introduced by Achaz and Ferretti, to populations of varying size. Key ingredients are the first two moments of the site frequency spectrum. We show how these moments can be computed analytically if a population has experienced two instantaneous size changes in the past. We apply our method to data from ten human populations gathered in the 1000 genomes project, estimate their demographies and define demography-adjusted versions of Tajima's D, Fay & Wu's H, and Zeng's E. Our results show that demography-adjusted test statistics facilitate the direct comparison between populations and that most of the differences among populations seen in the original unadjusted tests can be explained by their underlying demographies. Upon carrying out whole-genome screens for deviations from neutrality, we identify candidate regions of recent positive selection. We provide track files with values of the adjusted and unadjusted tests for upload to the UCSC genome browser. (C) 2014 Elsevier Inc. All rights reserved

ELAN : a professional framework for multimodality research

Utilization of computer tools in linguistic research has gained importance with the maturation of media frameworks for the handling of digital audio and video. The increased use of these tools in gesture, sign language and multimodal interaction studies has led to stronger requirements on the flexibility, the efficiency and in particular the time accuracy of annotation tools. This paper describes the efforts made to make ELAN a tool that meets these requirements, with special attention to the developments in the area of time accuracy. In subsequent sections an overview will be given of other enhancements in the latest versions of ELAN, that make it a useful tool in multimodality research