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

Vocal learning is a behavioral trait in which the social and acoustic environment shapes the vocal repertoire of individuals. Over the past century, the study of vocal learning has progressed at the intersection of ecology, physiology, neuroscience, molecular biology, genomics, and evolution. Yet, despite the complexity of this trait, vocal learning is frequently described as a binary trait, with species being classified as either vocal learners or vocal non-learners. As a result, studies have largely focused on a handful of species for which strong evidence for vocal learning exists. Recent studies, however, suggest a continuum in vocal learning capacity across taxa. Here, we further suggest that vocal learning is a multi-component behavioral phenotype comprised of distinct yet interconnected modules. Discretizing the vocal learning phenotype into its constituent modules would facilitate integration of findings across a wider diversity of species, taking advantage of the ways in which each excels in a particular module, or in a specific combination of features. Such comparative studies can improve understanding of the mechanisms and evolutionary origins of vocal learning. We propose an initial set of vocal learning modules supported by behavioral and neurobiological data and highlight the need for diversifying the field in order to disentangle the complexity of the vocal learning phenotype.

Abstract

It is unknown whether modality affects the efficiency with which humans learn novel word forms and their meanings, with previous studies reporting both written and auditory advantages. The current study implements controls whose absence in previous work likely offers explanation for such contradictory findings. In two novel word learning experiments, participants were trained and tested on pseudoword - novel object pairs, with controls on: modality of test, modality of meaning, duration of exposure and transparency of word form. In both experiments word forms were presented in either their written or spoken form, each paired with a pictorial meaning (novel object). Following a 20-minute filler task, participants were tested on their ability to identify the picture-word form pairs on which they were trained. A between subjects design generated four participant groups per experiment 1) written training, written test; 2) written training, spoken test; 3) spoken training, written test; 4) spoken training, spoken test. In Experiment 1 the written stimulus was presented for a time period equal to the duration of the spoken form. Results showed that when the duration of exposure was equal, participants displayed a written training benefit. Given words can be read faster than the time taken for the spoken form to unfold, in Experiment 2 the written form was presented for 300 ms, sufficient time to read the word yet 65% shorter than the duration of the spoken form. No modality effect was observed under these conditions, when exposure to the word form was equivalent. These results demonstrate, at least for proficient readers, that when exposure to the word form is controlled across modalities the efficiency with which word form-meaning associations are learnt does not differ. Our results therefore suggest that, although we typically begin as aural-only word learners, we ultimately converge on developing learning mechanisms that learn equally efficiently from both written and spoken materials.

Abstract

This study aimed to increase our understanding on the relationship between reading and listening comprehension. Both in comprehension theory and in educational practice, reading and listening comprehension are often seen as interchangeable, overlooking modality-specific aspects of them separately. Three questions were addressed. First, it was examined to what extent reading and listening comprehension comprise modality-specific, distinct skills or an overlapping, domain-general skill in terms of the amount of explained variance in one comprehension type by the opposite comprehension type. Second, general and modality-unique subskills of reading and listening comprehension were sought by assessing the contributions of the foundational skills word reading fluency, vocabulary, memory, attention, and inhibition to both comprehension types. Lastly, the practice of using either listening comprehension or vocabulary as a proxy of general comprehension was investigated. Reading and listening comprehension tasks with the same format were assessed in 85 second and third grade children. Analyses revealed that reading comprehension explained 34% of the variance in listening comprehension, and listening comprehension 40% of reading comprehension. Vocabulary and word reading fluency were found to be shared contributors to both reading and listening comprehension. None of the other cognitive skills contributed significantly to reading or listening comprehension. These results indicate that only part of the comprehension process is indeed domain-general and not influenced by the modality in which the information is provided. Especially vocabulary seems to play a large role in this domain-general part. The findings warrant a more prominent focus of modality-specific aspects of both reading and listening comprehension in research and education.

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

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

This article reports on results from a broad crosslinguistic study based on data from thirty-five signed languages around the world. The study is the first of its kind, and the typological generalizations presented here cover the domain of interrogative structures as they appear across a wide range of geographically and genetically distinct signed languages. Manual and nonmanual ways of marking basic types of questions in signed languages are investigated. As a result, it becomes clear that the range of crosslinguistic variation is extensive for some subparameters, such as the structure of question-word paradigms, while other parameters, such as the use of nonmanual expressions in questions, show more similarities across signed languages. Finally, it is instructive to compare the findings from signed language typology to relevant data from spoken languages at a more abstract, crossmodality level.

Abstract

This article presents a typology of negative constructions across a substantial number of sign languages from around the globe. After situating the topic within the wider context of linguistic typology, the main negation strategies found across sign languages are described. Nonmanual negation includes the use of head movements and facial expressions for negation and is of great importance in sign languages as well as particularly interesting from a typological point of view. As far as manual signs are concerned, independent negative particles represent the dominant strategy, but there are also instances of irregular negation in most sign languages. Irregular negatives may take the form of suppletion, cliticisation, affixing, or internal modification of a sign. The results of the study lead to interesting generalisations about similarities and differences between negatives in signed and spoken languages.

Abstract

Word learning happens in everyday contexts with many words and many potential referents for those words in view at the same time. It is challenging for young learners to find the correct referent upon hearing an unknown word at the moment. This problem of referential uncertainty has been deemed as the crux of early word learning (Quine, 1960). Recent empirical and computational studies have found support for a statistical solution to the problem termed cross-situational learning. Cross-situational learning allows learners to acquire word meanings across multiple exposures, despite each individual exposure is referentially uncertain. Recent empirical research shows that infants, children and adults rely on cross-situational learning to learn new words (Smith & Yu, 2008; Suanda, Mugwanya, & Namy, 2014; Yu & Smith, 2007). However, researchers have found evidence supporting two very different theoretical accounts of learning mechanisms: Hypothesis Testing (Gleitman, Cassidy, Nappa, Papafragou, & Trueswell, 2005; Markman, 1992) and Associative Learning (Frank, Goodman, & Tenenbaum, 2009; Yu & Smith, 2007). Hypothesis Testing is generally characterized as a form of learning in which a coherent hypothesis regarding a specific word-object mapping is formed often in conceptually constrained ways. The hypothesis will then be either accepted or rejected with additional evidence. However, proponents of the Associative Learning framework often characterize learning as aggregating information over time through implicit associative mechanisms. A learner acquires the meaning of a word when the association between the word and the referent becomes relatively strong. In this chapter, we consider these two psychological theories in the context of cross-situational word-referent learning. By reviewing recent empirical and cognitive modeling studies, our goal is to deepen our understanding of the underlying word learning mechanisms by examining and comparing the two theoretical learning accounts.

Abstract

In sentences like “the mouse that chased the cat was hungry”, the syntactically correct interpretation (the mouse chases the cat) is contradicted by semantic and pragmatic knowledge. Previous research has shown that L1 speakers sometimes base sentence interpretation on this type of knowledge (so-called “shallow” or “good-enough” processing). We made use of both behavioural and ERP measurements to investigate whether L2 learners differ from native speakers in the extent to which they engage in “shallow” syntactic processing. German learners of Dutch as well as Dutch native speakers read sentences containing relative clauses (as in the example above) for which the plausible thematic roles were or were not reversed, and made plausibility judgments. The results show that behaviourally, L2 learners had more difficulties than native speakers to discriminate plausible from implausible sentences. In the ERPs, we replicated the previously reported finding of a “semantic P600” for semantic reversal anomalies in native speakers, probably reflecting the effort to resolve the syntax-semantics conflict. In L2 learners, though, this P600 was largely attenuated and surfaced only in those trials that were judged correctly for plausibility. These results generally point at a more prevalent, but not exclusive occurrence of shallow syntactic processing in L2 learners.

Abstract

Semantic unification during sentence comprehension has been associated with amplitude change of the N400 in event-related potential (ERP) studies, and activation in the left inferior frontal gyrus (IFG) in functional magnetic resonance imaging (fMRI) studies. However, the specificity of this activation to semantic unification remains unknown. To more closely examine the brain processes involved in semantic unification, we employed simultaneous EEG-fMRI to time-lock the semantic unification related N400 change, and integrated trial-by-trial variation in both N400 and BOLD change beyond the condition-level BOLD change difference measured in traditional fMRI analyses. Participants read sentences in which semantic unification load was parametrically manipulated by varying cloze probability. Separately, ERP and fMRI results replicated previous findings, in that semantic unification load parametrically modulated the amplitude of N400 and cortical activation. Integrated EEG-fMRI analyses revealed a different pattern in which functional activity in the left IFG and bilateral supramarginal gyrus (SMG) was associated with N400 amplitude, with the left IFG activation and bilateral SMG activation being selective to the condition-level and trial-level of semantic unification load, respectively. By employing the EEG-fMRI integrated analyses, this study among the first sheds light on how to integrate trial-level variation in language comprehension.

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

We describe ViCoS, a tool for constructing and visualising conceptual spaces in the area of language documentation. ViCoS allows users to enrich existing lexical information about the words of a language with conceptual knowledge. Their work towards language-based, informal ontology building must be supported by easy-to-use workflows and supporting software, which we will demonstrate.

Abstract

Swedish morphemes are classified as prosodically specified or prosodically unspecified, depending on lexical or phonological stress, respectively. Here, we investigate the allomorphy of the suffix -(i)sk, which indicates the distinction between lexical and phonological stress; if attached to a lexically stressed morpheme, it takes a non-syllabic form (-sk), whereas if attached to a phonologically stressed morpheme, an epenthetic vowel is inserted (-isk). Using mismatch negativity (MMN), we explored the neural processing of this allomorphy across lexically stressed and phonologically stressed morphemes. In an oddball paradigm, participants were occasionally presented with congruent and incongruent derivations, created by the suffix -(i)sk, within the repetitive presentation of their monomorphemic stems. The results indicated that the congruent derivation of the lexically stressed stem elicited a larger MMN than the incongruent sequences of the same stem and the derivational suffix, whereas after the phonologically stressed stem a non-significant tendency towards an opposite pattern was observed. We argue that the significant MMN response to the congruent derivation in the lexical stress condition is in line with lexical MMN, indicating a holistic processing of the sequence of lexically stressed stem and derivational suffix. The enhanced MMN response to the incongruent derivation in the phonological stress condition, on the other hand, is suggested to reflect combinatorial processing of the sequence of phonologically stressed stem and derivational suffix. These findings bring a new aspect to the dual-system approach to neural processing of morphologically complex words, namely the specification of word stress.

Abstract

Speakers remember their own utterances better than those of their interlocutors, suggesting that language production is beneficial to memory. This may be partly explained by a generation effect: The act of generating a word is known to lead to a memory advantage (Slamecka & Graf, 1978). In earlier work, we showed a generation effect for recognition of images (Zormpa, Brehm, Hoedemaker, & Meyer, 2019). Here, we tested whether the recognition of their names would also benefit from name generation. Testing whether picture naming improves memory for words was our primary aim, as it serves to clarify whether the representations affected by generation are visual or conceptual/lexical. A secondary aim was to assess the influence of processing time on memory. Fifty-one participants named pictures in three conditions: after hearing the picture name (identity condition), backward speech, or an unrelated word. A day later, recognition memory was tested in a yes/no task. Memory in the backward speech and unrelated conditions, which required generation, was superior to memory in the identity condition, which did not require generation. The time taken by participants for naming was a good predictor of memory, such that words that took longer to be retrieved were remembered better. Importantly, that was the case only when generation was required: In the no-generation (identity) condition, processing time was not related to recognition memory performance. This work has shown that generation affects conceptual/lexical representations, making an important contribution to the understanding of the relationship between memory and language.

Abstract

The production effect (better memory for words read aloud than words read silently) and the picture superiority effect (better memory for pictures than words) both improve item memory in a picture naming task (Fawcett, J. M., Quinlan, C. K., & Taylor, T. L. (2012). Interplay of the production and picture superiority effects: A signal detection analysis. Memory (Hove, England), 20(7), 655–666. doi:10.1080/09658211.2012.693510). Because picture naming requires coming up with an appropriate label, the generation effect (better memory for generated than read words) may contribute to the latter effect. In two forced-choice memory experiments, we tested the role of generation in a picture naming task on later recognition memory. In Experiment 1, participants named pictures silently or aloud with the correct name or an unreadable label superimposed. We observed a generation effect, a production effect, and an interaction between the two. In Experiment 2, unreliable labels were included to ensure full picture processing in all conditions. In this experiment, we observed a production and a generation effect but no interaction, implying the effects are dissociable. This research demonstrates the separable roles of generation and production in picture naming and their impact on memory. As such, it informs the link between memory and language production and has implications for memory asymmetries between language production and comprehension.

Abstract

This paper discusses the construction of a cross-linguistic, bimodal corpus containing three modes of expression: expressions from two sign languages, speech and gestural expressions in two spoken languages and pantomimic expressions by users of two spoken languages who are requested to convey information without speaking. We discuss some problems and tentative solutions for the annotation of utterances expressing spatial information about referents in these three modes, suggesting a set of comparable codes for the description of both sign and gesture. Furthermore, we discuss the processing of entered annotations in ELAN, e.g. relating descriptive annotations to analytic annotations in all three modes and performing relational searches across annotations on different tiers.

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.