Publications

Abstract

Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity and unique immunity. High-quality genomes are crucial for understanding the molecular basis and evolution of these traits. Here we incorporated long-read sequencing and state-of-the-art scaffolding protocols1 to generate, to our knowledge, the first reference-quality genomes of six bat species (Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pipistrellus kuhlii and Molossus molossus). We integrated gene projections from our ‘Tool to infer Orthologs from Genome Alignments’ (TOGA) software with de novo and homology gene predictions as well as short- and long-read transcriptomics to generate highly complete gene annotations. To resolve the phylogenetic position of bats within Laurasiatheria, we applied several phylogenetic methods to comprehensive sets of orthologous protein-coding and noncoding regions of the genome, and identified a basal origin for bats within Scrotifera. Our genome-wide screens revealed positive selection on hearing-related genes in the ancestral branch of bats, which is indicative of laryngeal echolocation being an ancestral trait in this clade. We found selection and loss of immunity-related genes (including pro-inflammatory NF-κB regulators) and expansions of anti-viral APOBEC3 genes, which highlights molecular mechanisms that may contribute to the exceptional immunity of bats. Genomic integrations of diverse viruses provide a genomic record of historical tolerance to viral infection in bats. Finally, we found and experimentally validated bat-specific variation in microRNAs, which may regulate bat-specific gene-expression programs. Our reference-quality bat genomes provide the resources required to uncover and validate the genomic basis of adaptations of bats, and stimulate new avenues of research that are directly relevant to human health and disease

Abstract

In 7 experiments the authors investigated the locus of word frequency effects in speech production. Experiment 1 demonstrated a frequency effect in picture naming that was robust over repetitions. Experiments 2, 3, and 7 excluded contributions from object identification and initiation of articulation. Experiments 4 and 5 investigated whether the effect arises in accessing the syntactic word (lemma) by using a grammatical gender decision task. Although a frequency effect was found, it dissipated under repeated access to word's gender. Experiment 6 tested whether the robust frequency effect arises in accessing the phonological form (lexeme) by having Ss translate words that produced homophones. Low-frequent homophones behaved like high-frequent controls, inheriting the accessing speed of their high-frequent homophone twins. Because homophones share the lexeme, not the lemma, this suggests a lexeme-level origin of the robust effect.

Abstract

Thematic roles characterise the functions of participants in events, but there is no agreement on how these roles are identified in the real world. In three experiments, we examined how role identification in push events is supported by the visual object-tracking system. Participants saw one to three push events in visual scenes with nine identical randomly moving circles. After a period of random movement, two circles from one of the push events and a foil object were given different colours and the participants had to identify their roles in the push with an active sentence, such as red pushed blue. It was found that the participants could track the agent and patient targets and generate descriptions that identified their roles at above chance levels, even under difficult conditions, such as when tracking multiple push events (Experiments 1–3), fixating their gaze (Experiment 1), performing a concurrent speeded-response task (Experiment 2), and when tracking objects that were temporarily invisible (Experiment 3). The results were consistent with previous findings of an average tracking capacity limit of four objects, individual differences in this capacity, and the use of attentional strategies. The studies demonstrated that thematic role information can be maintained when tracking the identity of visually identical objects, then used to map role fillers (e.g., the agent of a push event) into their appropriate sentence positions. This suggests that thematic role features are stored temporarily in the visual object-tracking system.

Abstract

There is a range of variability in the speed with which a single speaker will produce the same word from one instance to another. Individual differences studies have shown that the speed of production and the ability to maintain attention are related. This study investigated whether fluctuations in production latencies can be explained by spontaneous fluctuations in speakers' attention just prior to initiating speech planning. A relationship between individuals' incidental attentional state and response performance is well attested in visual perception, with lower prestimulus alpha power associated with faster manual responses. Alpha is thought to have an inhibitory function: Low alpha power suggests less inhibition of a specific brain region, whereas high alpha power suggests more inhibition. Does the same relationship hold for cognitively demanding tasks such as word production? In this study, participants named pictures while EEG was recorded, with alpha power taken to index an individual's momentary attentional state. Participants' level of alpha power just prior to picture presentation and just prior to speech onset predicted subsequent naming latencies. Specifically, higher alpha power in the motor system resulted in faster speech initiation. Our results suggest that one index of a lapse of attention during speaking is reduced inhibition of motor-cortical regions: Decreased motor-cortical alpha power indicates reduced inhibition of this area while early stages of production planning unfold, which leads to increased interference from motor-cortical signals and longer naming latencies. This study shows that the language production system is not impermeable to the influence of attention.

Abstract

In conversation, speech planning can overlap with listening to the interlocutor. It has been
postulated that once there is enough information to formulate a response, planning is initiated
and the response is maintained in working memory. Concurrently, the auditory input is
monitored for the turn end such that responses can be launched promptly. In three EEG
experiments, we aimed to identify the neural signature of phonological planning and monitoring
by comparing delayed responding to not responding (reading aloud, repetition and lexical
decision). These comparisons consistently resulted in a sustained positivity and beta power
reduction over posterior regions. We argue that these effects reflect attention to the sequence
end. Phonological planning and maintenance were not detected in the neural signature even
though it is highly likely these were taking place. This suggests that EEG must be used cautiously
to identify response planning when the neural signal is overridden by attention effects

Abstract

Understanding spoken language requires the integration and weighting of multiple cues, and may call on cue integration mechanisms that have been studied in other areas of perception. In the current study, we used eye-tracking (visual-world paradigm) to examine how contextual speech rate (a lower-level, perceptual cue) and morphosyntactic knowledge (a higher-level, linguistic cue) are iteratively combined and integrated. Results indicate that participants used contextual rate information immediately, which we interpret as evidence of perceptual inference and the generation of predictions about upcoming morphosyntactic information. Additionally, we observed that early rate effects remained active in the presence of later conflicting lexical information. This result demonstrates that (1) contextual speech rate functions as a cue to morphosyntactic inferences, even in the presence of subsequent disambiguating information; and (2) listeners iteratively use multiple sources of information to draw inferences and generate predictions during speech comprehension. We discuss the implication of these demonstrations for theories of language processing

Abstract

During spoken language comprehension, listeners make use of both knowledge-based and signal-based sources of information, but little is known about how cues from these distinct levels of representational hierarchy are weighted and integrated online. In an eye-tracking experiment using the visual world paradigm, we investigated the flexible weighting and integration of morphosyntactic gender marking (a knowledge-based cue) and contextual speech rate (a signal-based cue). We observed that participants used the morphosyntactic cue immediately to make predictions about upcoming referents, even in the presence of uncertainty about the cue’s reliability. Moreover, we found speech rate normalization effects in participants’ gaze patterns even in the presence of preceding morphosyntactic information. These results demonstrate that cues are weighted and integrated flexibly online, rather than adhering to a strict hierarchy. We further found rate normalization effects in the looking behavior of participants who showed a strong behavioral preference for the morphosyntactic gender cue. This indicates that rate normalization effects are robust and potentially automatic. We discuss these results in light of theories of cue integration and the two-stage model of acoustic context effects

Abstract

Neural oscillations track linguistic information during speech comprehension (e.g., Ding et al., 2016; Keitel et al., 2018), and are known to be modulated by acoustic landmarks and speech intelligibility (e.g., Doelling et al., 2014; Zoefel & VanRullen, 2015). However, studies investigating linguistic tracking have either relied on non-naturalistic isochronous stimuli or failed to fully control for prosody. Therefore, it is still unclear whether low frequency activity tracks linguistic structure during natural speech, where linguistic structure does not follow such a palpable temporal pattern. Here, we measured electroencephalography (EEG) and manipulated the presence of semantic and syntactic information apart from the timescale of their occurrence, while carefully controlling for the acoustic-prosodic and lexical-semantic information in the signal. EEG was recorded while 29 adult native speakers (22 women, 7 men) listened to naturally-spoken Dutch sentences, jabberwocky controls with morphemes and sentential prosody, word lists with lexical content but no phrase structure, and backwards acoustically-matched controls. Mutual information (MI) analysis revealed sensitivity to linguistic content: MI was highest for sentences at the phrasal (0.8-1.1 Hz) and lexical timescale (1.9-2.8 Hz), suggesting that the delta-band is modulated by lexically-driven combinatorial processing beyond prosody, and that linguistic content (i.e., structure and meaning) organizes neural oscillations beyond the timescale and rhythmicity of the stimulus. This pattern is consistent with neurophysiologically inspired models of language comprehension (Martin, 2016, 2020; Martin & Doumas, 2017) where oscillations encode endogenously generated linguistic content over and above exogenous or stimulus-driven timing and rhythm information.

Abstract

Day-to-day interpretations of “space” are enmeshed in specific cultural and linguistic practices. For example, many cultures have an association between vertical height and social standing; more powerful people may be placed literally higher than others at social gatherings, and be spoken of as having higher status. This questionnaire is a guide for exploring relationships between space, language, and social structure. The goal is to better understand how space is organised in the focus community, and to investigate the extent to which space is used as a model for reproducing social forms.

Abstract

Human speakers often produce sentences incrementally. They can start speaking having in mind only a fragmentary idea of what they want to say, and while saying this they refine the contents underlying subsequent parts of the utterance. This capability imposes a number of constraints on the design of a syntactic processor. This paper explores these constraints and evaluates some recent computational sentence generators from the perspective of incremental production.

Abstract

Comments on a study by Frazier and others on Dutch-language lexical processing. Claims that the control condition in the experiment was inadequate and that an assumption made by Frazier about closed class verbal items is inaccurate, and proposes an alternative account of a subset of the data from the experiment

Abstract

Raises objections to L. Frazier et al's (see record 1994-32229-001) report of an experimental study intended to test Schreuder's (1990) Morphological Integration (MI) model concerning the processing of separable and inseparable verbs and shows that the logic of the experiment is flawed. The problem is rooted in the notion of a separable complex verb. The conclusion is drawn that Frazier et al's experimental data cannot be taken as evidence for the theoretical propositions they develop about the MI model.

Abstract

This article makes the case for the universality of the sequence organization observable in informal human conversational interaction. Using the descriptive schema developed by Schegloff (2007), we examine the major patterns of action-sequencing in a dozen nearly all unrelated languages. What we find is that these patterns are instantiated in very similar ways for the most part right down to the types of different action sequences. There are also some notably different cultural exploitations of the patterns, but the patterns themselves look strongly universal. Recent work in gestural communication in the great apes suggests that sequence organization may have been a crucial route into the development of language. Taken together with the fundamental role of this organization in language acquisition, sequential behavior of this kind seems to have both phylogenetic and ontogenetic priority, which probably puts substantial functional pressure on language form.

Abstract

Autosomal recessive Stargardt disease (STGD1) is associated with variants in the ABCA4 gene. The phenotypes range from early-onset STGD1, that clinically resembles severe cone-rod dystrophy, to intermediate STGD1 and late-onset STGD1. These different phenotypes can be correlated with different combinations of ABCA4 variants which can be classified according to their degree of severity. A significant fraction of STGD1 cases, particularly late-onset STGD1 cases, were shown to carry only a single ABCA4 variant. A frequent coding variant (p.Asn1868Ile) was recently identified which – in combination with a severe ABCA4 variant – is generally associated with late-onset STGD1. In addition, an increasing number of rare deep-intronic variants have been found and some of these are also associated with late-onset STGD1. The effect of these and other variants on ABCA4 RNA was tested using in vitro assays in human kidney cells using specially designed midigenes. With stem cells and photoreceptor progenitor cells derived from patient skin or blood cells, retina-specific splice defects can be assessed. With expert clinical examination to distinguish STGD1 cases from other maculopathies, as well as in-depth genomics and transcriptomics data, it is now possible to identify both mutant ABCA4 alleles in > 95% of cases.

Abstract

Noncanonical splice-site mutations are an important cause of inherited diseases. Based on in vitro and stem-cell-based studies, some splice-site variants show a stronger splice defect than expected based on their predicted effects, suggesting that other sequence motifs influence the outcome. We investigated whether splice defects due to human-inherited-disease-associated variants in noncanonical splice-site sequences in ABCA4, DMD, and TMC1 could be rescued by strengthening the splice site on the other side of the exon. Noncanonical 5′- and 3′-splice-site variants were selected. Rescue variants were introduced based on an increase in predicted splice-site strength, and the effects of these variants were analyzed using in vitro splice assays in HEK293T cells. Exon skipping due to five variants in noncanonical splice sites of exons in ABCA4, DMD, and TMC1 could be partially or completely rescued by increasing the predicted strengths of the other splice site of the same exon. We named this mechanism “splicing interdependency”, and it is likely based on exon recognition by splicing machinery. Awareness of this interdependency is of importance in the classification of noncanonical splice-site variants associated with disease and may open new opportunities for treatments

Abstract

A central question in the psycholinguistic study of multilingualism is how syntax is shared across languages. We implement a model to investigate whether error-based implicit learning can provide an account of cross-language structural priming. The model is based on the Dual-path model of
sentence-production (Chang, 2002). We implement our model using the Bilingual version of Dual-path (Tsoukala, Frank, & Broersma, 2017). We answer two main questions: (1) Can structural priming of active and passive constructions occur between English and Spanish in a bilingual version of the Dual-
path model? (2) Does cross-language priming differ quantitatively from within-language priming in this model? Our results show that cross-language priming does occur in the model. This finding adds to the viability of implicit learning as an account of structural priming in general and cross-language
structural priming specifically. Furthermore, we find that the within-language priming effect is somewhat stronger than the cross-language effect. In the context of mixed results from
behavioral studies, we interpret the latter finding as an indication that the difference between cross-language and within-
language priming is small and difficult to detect statistically.

Abstract

Humans vary in almost every dimension imaginable, and language is no
exception. In this article, we review the past research that has focused on
individual differences (IDs) in first language acquisition. We first consider
how different theoretical traditions in language acquisition treat IDs, and
we argue that a focus on IDs is important given its potential to reveal the
developmental dynamics and architectural constraints of the linguistic system.
We then review IDs research that has examined variation in children’s
linguistic input, early speech perception, and vocabulary and grammatical
development. In each case, we observe systematic and meaningful variation,
such that variation in one domain (e.g., early auditory and speech
processing) has meaningful developmental consequences for development
in higher-order domains (e.g., vocabulary). The research suggests a high
degree of integration across the linguistic system, in which development
across multiple linguistic domains is tightly coupled.

Abstract

Statistical learning (SL) has been a prominent focus of research in developmental and adult populations, guided by the assumption that it is a fundamental component of learning underlying higher-order cognition. In developmental populations, however, there have been recent concerns regarding the degree to which many current tasks reliably measure SL, particularly in younger children. In the current article, we present the results of two studies that measured auditory statistical learning (ASL) of linguistic stimuli in children aged 5–8 years. Children listened to 6 min of continuous syllables comprising four trisyllabic pseudowords. Following the familiarization phase, children completed (a) a two-alternative forced-choice task and (b) a serial recall task in which they repeated either target sequences embedded during familiarization or foils, manipulated for sequence length. Results showed that, although both measures consistently revealed learning at the group level, the recall task better captured learning across the full range of abilities and was more reliable at the individual level. We conclude that, as has also been demonstrated in adults, the method holds promise for future studies of individual differences in ASL of linguistic stimuli.

Abstract

Much of Lieven’s pioneering work has helped move the study of individual differences to the centre of child language research. The goal of the present chapter is to illustrate how the study of individual differences provides crucial insights into the language acquisition process. In part one, we summarise some of the evidence showing how pervasive individual differences are across the whole of the language system; from gestures to morphosyntax. In part two, we describe three causal factors implicated in explaining individual differences, which, we argue, must be built into any theory of language acquisition (intrinsic differences in the neurocognitive learning mechanisms, the child’s communicative environment, and developmental cascades in which each new linguistic skill that the child has to acquire depends critically on the prior acquisition of foundational abilities). In part three, we present an example study on the role of the speed of linguistic processing on vocabulary development, which illustrates our approach to individual differences. The results show evidence of a changing relationship between lexical processing speed and vocabulary over developmental time, perhaps as a result of the changing nature of the structure of the lexicon. The study thus highlights the benefits of an individual differences approach in building, testing, and constraining theories of language acquisition.

Abstract

This study attempts to reveal the mechanisms behind the online formation of Wh-Filler-Gap Dependencies (WhFGD). Specifically, we aim to uncover the way in which maintenance and retrieval work in WhFGD processing, by paying special attention to the information that is retrieved when the gap is recognized. We use the agreement attraction phenomenon (Wagers, M. W., Lau, E. F., & Phillips, C. (2009). Agreement attraction in comprehension: Representations and processes. Journal of Memory and Language, 61(2), 206-237) as a probe. The first and second experiments examined the type of information that is maintained and how maintenance is motivated, investigating the retrieved information at the gap for reactivated fillers and definite NPs. The third experiment examined the role of the retrieval, comparing reactivated and active fillers. We contend that the information being accessed reflects the extent to which the filler is maintained, where the reader is able to access fine-grained information including category information as well as a representation of both the head and the modifier at the verb.

Abstract

This task investigates the expression of “enter” and “exit” events, and is a supplement to the Motion Elicitation task (https://doi.org/10.17617/2.3003391). Consultants are asked to describe a series of animated clips where a man moves into or out of a house. The clips focus on contrasts to do with perspective (e.g., whether the man appears to move away or towards the viewer) and transitional movement (e.g., whether the man walks or “teleports” into his new location).

Abstract

Do our hands 'speak the same language' across cultures? Gesture is the silent partner of spoken languages in face-to-face interaction, but we still have a lot to learn about gesture practices in different speech communities. The primary purpose of this task is to collect data in naturalistic settings that can be used to investigate the linguistic and cultural relativity of gesture performance, especially spatially indicative gestures. It involves video-recording pairs of speakers in both free conversation and more structured communication tasks (e.g., describing film plots).

Please note: the stimuli mentioned in this entry are available elsewhere: 'The Pear Story', a short film made at the University of California at Berkeley; "Frog, where are you?" from the original Mayer (1969) book, as published in the Appendix of Berman & Slobin (1994).

Abstract

In the first, critical part of this study, a small sample of simple German sentences with their empirically determined pitch contours is used to demonstrate the incorrectness of numerous currently hold views of German sentence intonation. In the second, more constructive part, several interrogative sentence types are analysed and an attempt is made to show that intonation, besides other functions, indicates the permantently changing 'thematic score' in on-going discourse as well as certain validity claims.