Publications

Abstract

Over recent years small submicroscopic DNA copy-number variants (CNVs) have been highlighted as an important source of variation in the human genome, human phenotypic diversity and disease susceptibility. Consequently, there is a pressing need for the development of methods that allow the efficient, accurate and cheap measurement of genomic copy number polymorphisms in clinical cohorts. We have developed a simple competitive PCR based method to determine DNA copy number which uses the entire genome of a single chimpanzee as a competitor thus eliminating the requirement for competitive sequences to be synthesized for each assay. This results in the requirement for only a single reference sample for all assays and dramatically increases the potential for large numbers of loci to be analysed in multiplex. In this study we establish proof of concept by accurately detecting previously characterized mutations at the PARK2 locus and then demonstrating the potential of quantitative interspecies competitive PCR (qicPCR) to accurately genotype CNVs in association studies by analysing chromosome 22q11 deletions in a sample of previously characterized patients and normal controls.

Abstract

We investigated how the strength of a foreign accent and varying types of experience with foreign-accented speech influence the recognition of accented words. In Experiment 1, native Dutch listeners with limited or extensive prior experience with German-accented Dutch completed a cross-modal priming experiment with strongly, medium, and weakly accented words. Participants with limited experience were primed by the medium and weakly accented words, but not by the strongly accented words. Participants with extensive experience were primed by all accent types. In Experiments 2 and 3, Dutch listeners with limited experience listened to a short story before doing the cross-modal priming task. In Experiment 2, the story was spoken by the priming task speaker and either contained strongly accented words or did not. Strongly accented exposure led to immediate priming by novel strongly accented words, while exposure to the speaker without strongly accented tokens led to priming only in the experiment’s second half. In Experiment 3, listeners listened to the story with strongly accented words spoken by a different German-accented speaker. Listeners were primed by the strongly accented words, but again only in the experiment’s second half. Together, these results show that adaptation to foreign-accented speech is rapid but depends on accent strength and on listener familiarity with those strongly accented words.

Abstract

The modality learning effect, according to Mayer (2001), proposes that learning is enhanced when information is presented in both the visual and auditory domain (e.g., pictures and spoken information), compared to presenting information solely in the visual channel (e.g., pictures and written text). Most of the evidence for this effect comes from adults in a laboratory setting. Therefore, we tested the modality effect with 80 children in the highest grade of elementary school, in a naturalistic setting. In a between-subjects design children either saw representational pictures with speech or representational pictures with text. Retention and transfer knowledge was tested at three moments: immediately after the intervention, one day after, and after one week. The present study did not find any evidence for a modality effect in children when the lesson is learner-paced. Instead, we found a reversed modality effect directly after the intervention for retention. A reversed modality effect was also found for the transfer questions one day later. This effect was robust, even when controlling for individual differences.

Abstract

Languages are among the most complex systems that evolution has created. With an unforeseen speed many of these unique results of evolution are currently disappearing: every two weeks one of the 6500 still spoken languages is dying and many are subject to extreme changes due to globalization. Experts understood the need to document the languages and preserve the cultural and linguistic treasures embedded in them for future generations. Also linguistic theory will need to consider the variation of the linguistic systems encoded in languages to improve our understanding of how human minds process language material, thus accessibility to all types of resources is increasingly crucial. Deeper insights into human language processing and a higher degree of integration and interoperability between resources will also improve our language processing technology. The DOBES programme is focussing on the documentation and preservation of language material. The Max Planck Institute developed the Language Archiving Technology to help researchers when creating, archiving and accessing language resources. The recently started CLARIN research infrastructure has as main goals to achieve a broad visibility and an easy
accessibility of language resources.

Abstract

Brain processing depends on the interactions between neuronal groups. Those interactions are governed by the pattern of anatomical connections and by yet unknown mechanisms that modulate the effective strength of a given connection. We found that the mutual influence among neuronal groups depends on the phase relation between rhythmic activities within the groups. Phase relations supporting interactions between the groups preceded those interactions by a few milliseconds, consistent with a mechanistic role. These effects were specific in time, frequency, and space, and we therefore propose that the pattern of synchronization flexibly determines the pattern of neuronal interactions.

Abstract

The ISOcat Data Category Registry provides a community computing environment for creating, storing, retrieving, harmonizing and standardizing data category specifications (DCs), used to register linguistic terms used in various fields. This chapter recounts the history of DC documentation in TC 37, beginning from paper-based lists created for lexicographers and terminologists and progressing to the development of a web-based resource for a much broader range of users. While describing the considerable strides that have been made to collect a very large comprehensive collection of DCs, it also outlines difficulties that have arisen in developing a fully operative web-based computing environment for achieving consensus on data category names, definitions, and selections and describes efforts to overcome some of the present shortcomings and to establish positive working procedures designed to engage a wide range of people involved in the creation of language resources.

Abstract

Im ISOcat-Datenkategorie-Register (Data Category Registry, www.isocat.org) des Technischen Komitees ISO/TC 37 (Terminology and other language and content resources) werden Feldnamen und Werte für Sprachressourcen beschrieben. Empfohlene Feldnamen und zuverlässige Definitionen sollen dazu beitragen, dass Sprachdaten unabhängig von Anwendungen, Plattformen und Communities of Practice (CoP) wiederverwendet werden können. Datenkategorie-Gruppen (Data Category Selections) können eingesehen, ausgedruckt, exportiert und nach kostenloser Registrierung auch neu erstellt werden.

Abstract

This auditory lexical decision study shows that cohort entropies, conditional root uniqueness points, and morphological family size all contribute to the dynamics of the auditory comprehension of prefixed words. Three entropy measures calculated for different positions in the stem of Dutch prefixed words revealed facilitation for higher entropies, except at the point of disambiguation, where we observed inhibition. Morphological family size was also facilitatory, but only for prefixed words in which the conditional root uniqueness point coincided with the conventional uniqueness point. For words with early conditional disambiguation, in contrast, only the morphologically related words that were onset-aligned with the target word facilitated lexical decision.

Abstract

We performed a resting-state functional connectivity study to investigate directly the functional correlations within the perisylvian language networks by seeding from 3 subregions of Broca's complex (pars opercularis, pars triangularis, and pars orbitalis) and their right hemisphere homologues. A clear topographical functional connectivity pattern in the left middle frontal, parietal, and temporal areas was revealed for the 3 left seeds. This is the first demonstration that a functional connectivity topology can be observed in the perisylvian language networks. The results support the assumption of the functional division for phonology, syntax, and semantics of Broca's complex as proposed by the memory, unification, and control (MUC) model and indicated a topographical functional organization in the perisylvian language networks, which suggests a possible division of labor for phonological, syntactic, and semantic function in the left frontal, parietal, and temporal areas.

Abstract

In the present study, event-related brain potentials (ERP) were recorded to investigate the role of pitch accent and lexical tone in spoken discourse comprehension. Chinese was used as material to explore the potential difference in the nature and time course of brain responses to sentence meaning as indicated by pitch accent and to lexical meaning as indicated by tone. In both cases, the pitch contour of critical words was varied. The results showed that both inconsistent pitch accent and inconsistent lexical tone yielded N400 effects, and there was no interaction between them. The negativity evoked by inconsistent pitch accent had the some topography as that evoked by inconsistent lexical tone violation, with a maximum over central–parietal electrodes. Furthermore, the effect for the combined violations was the sum of effects for pure pitch accent and pure lexical tone violation. However, the effect for the lexical tone violation appeared approximately 90 ms earlier than the effect of the pitch accent violation. It is suggested that there might be a correspondence between the neural mechanism underlying pitch accent and lexical meaning processing in context. They both reflect the integration of the current information into a discourse context, independent of whether the current information was sentence meaning indicated by accentuation, or lexical meaning indicated by tone. In addition, lexical meaning was processed earlier than sentence meaning conveyed by pitch accent during spoken language processing.

Abstract

Although sign language-using communities exist in all areas of the world, few sign languages have been documented in detail. Sign languages occur in a variety of sociocultural contexts, ranging from sign languages used in closed village communities to officially recognized national sign languages. They may be grouped into language families on historical grounds or may participate in various language contact situations. Systematic cross-linguistic comparison reveals both significant structural similarities and important typological differences between sign languages. Focusing on information from non-Western countries, this article provides an overview of the sign languages of the world.

Abstract

This article presents data on cardinal numerals in three sign languages from small-scale communities with hereditary deafness. The unusual features found in these data considerably extend the known range of typological variety across sign languages. Some features, such as non-decimal numeral bases, are unattested in sign languages, but familiar from spoken languages, while others, such as subtractive sub-systems, are rare in sign and speech. We conclude that for a complete typological appraisal of a domain, an approach to cross-modal typology, which includes a typologically diverse range of sign languages in addition to spoken languages, is both instructive and feasible.

Abstract

Celiac disease (CD) is an intolerance to dietary proteins of wheat, barley, and rye. CD may have substantial morbidity, yet it is quite common with a prevalence of 1%-2% in Western populations. It is not clear why the CD phenotype is so prevalent despite its negative effects on human health, especially because appropriate treatment in the form of a gluten-free diet has only been available since the 1950s, when dietary gluten was discovered to be the triggering factor. The high prevalence of CD might suggest that genes underlying this disease may have been favored by the process of natural selection. We assessed signatures of selection for ten confirmed CD-associated loci in several genome-wide data sets, comprising 8154 controls from four European populations and 195 individuals from a North African population, by studying haplotype lengths via the integrated haplotype score (iHS) method. Consistent signs of positive selection for CD-associated derived alleles were observed in three loci: IL12A, IL18RAP, and SH2B3. For the SH2B3 risk allele, we also show a difference in allele frequency distribution (F(st)) between HapMap phase II populations. Functional investigation of the effect of the SH2B3 genotype in response to lipopolysaccharide and muramyl dipeptide revealed that carriers of the SH2B3 rs3184504*A risk allele showed stronger activation of the NOD2 recognition pathway. This suggests that SH2B3 plays a role in protection against bacteria infection, and it provides a possible explanation for the selective sweep on SH2B3, which occurred sometime between 1200 and 1700 years ago.

Abstract

Genome-wide association studies using thousands to hundreds of thousands of single nucleotide polymorphism (SNP) markers and region-wide association studies using a dense panel of SNPs are already in use to identify disease susceptibility genes and to predict disease risk in individuals. Because these tasks become increasingly important, three different data sets were provided for the Genetic Analysis Workshop 15, thus allowing examination of various novel and existing data mining methods for both classification and identification of disease susceptibility genes, gene by gene or gene by environment interaction. The approach most often applied in this presentation group was random forests because of its simplicity, elegance, and robustness. It was used for prediction and for screening for interesting SNPs in a first step. The logistic tree with unbiased selection approach appeared to be an interesting alternative to efficiently select interesting SNPs. Machine learning, specifically ensemble methods, might be useful as pre-screening tools for large-scale association studies because they can be less prone to overfitting, can be less computer processor time intensive, can easily include pair-wise and higher-order interactions compared with standard statistical approaches and can also have a high capability for classification. However, improved implementations that are able to deal with hundreds of thousands of SNPs at a time are required.

Abstract

The lexicons of many sign languages hold large proportions of “frozen” forms, viz. signs that are generally considered to have been formed productively (as classifier predicates), but that have diachronically undergone processes of lexicalisation. Nederlandse Gebarentaal (Sign Language of the Netherlands; henceforth: NGT) also has many of these signs (Van der Kooij 2002, Zwitserlood 2003). In contrast to the general view on “frozen” forms, a few researchers claim that these signs may be formed according to productive sign formation rules, notably Brennan (1990) for BSL, and Meir (2001, 2002) for ISL. Following these claims, I suggest an analysis of “frozen” NGT signs as morphologically complex, using the framework of Distributed Morphology. The signs in question are derived in a similar way as classifier predicates; hence their similar form (but diverging characteristics). I will indicate how and why the structure and use of classifier predicates and “frozen” forms differ. Although my analysis focuses on NGT, it may also be applicable to other sign languages.

Abstract

This paper reports on an exploration of the ways in which multiple entities are expressed in Turkish Sign Language (TİD). The (descriptive and quantitative) analyses provided are based on a corpus of both spontaneous data and specifically elicited data, in order to provide as comprehensive an account as possible. We have found several devices in TİD for expression of multiple entities, in particular localization, spatial plural predicate inflection, and a specific form used to express multiple entities that are side by side in the same configuration (not reported for any other sign language to date), as well as numerals and quantifiers. In contrast to some other signed languages, TİD does not appear to have a productive system of plural reduplication. We argue that none of the devices encountered in the TİD data is a genuine plural marking device and that the plural interpretation of multiple entity localizations and plural predicate inflections is a by-product of the use of space to indicate the existence or the involvement in an event of multiple entities.

Abstract

Sign language lexicography has thus far been a relatively obscure area in the world of lexicography. Therefore, this article will contain background information on signed languages and the communities in which they are used, on the lexicography of sign languages, the situation in the Netherlands as well as a review of a sign language dictionary that has recently been published in the Netherlands.