Van Berkum Research Articles

APOLO lncRNA, a self-calibrating switch of root development

APOLO lncRNA, a self-calibrating switch of root development

The processing signature of anticipatory reading: an eye-tracking study on lexical predictions

Abstract Current approaches to the human language faculty emphasize that during real-time processing anticipatory mechanisms play a vital role for people to parse and comprehend linguistic input at a sufficient pace. Consistent with this view, several Event-Related Potential (ERP) and behavioral self-paced reading (SPR) studies revealed a processing disadvantage for pre-nominal linguistic elements that (grammatically) mismatched with an expected upcoming noun. More recently, however, these findings have been challenged because the results are difficult to replicate. In the current study, I continue this line of replication research with a complementary method: eye tracking. I conducted two experiments aimed at reproducing prior findings of a SPR study of van Berkum, Jos J. A., Colin M. Brown, Pienie Zwitserlood, Valesca Kooijman & Hagoort Peter. 2005. Anticipating upcoming words in discourse: Evidence from ERPs and reading times. Journal of Experimental Psychology: Learning, Memory, and Cognition 31(3). 443–467. The participants read two-sentence stories constructed to elicit a strong lexical prediction about an upcoming noun. To assess whether readers were activating the lexical prediction, the noun was preceded by two gender-inflected adjectives carrying an inflectional suffix that either matched or mismatched with the syntactic gender of the predicted noun. Overall, I did not obtain evidence for strong lexical prediction as the eye-tracking metrics revealed no processing disadvantage for mismatching adjectives (i.e., contrary to the findings of van Berkum et al.). In fact, in some cases readers allocated more processing resources to pre-nominal adjectives that morphologically matched with the gender of the predicted noun. These intriguing findings will be discussed in the context of the time course, the processing costs, and the validation processes of lexical predictions.

When Couches Have Eyes: The Effect of Visual Context on Children's Reference Processing

We examined the effects of semantic and visual cues of animacy on children’s and adults’ interpretation of ambiguous pronouns, using the visual world paradigm. Participants listened to sentences with object relative clauses that varied the animacy of potential referents, followed by test sentences beginning with a referentially ambiguous subject pronoun he. Participants viewed images of the referents, with semantically inanimate objects (e.g., a TV) shown with or without added facial features. Results from offline verbal report and online gaze data revealed consistent effects of both semantic animacy and visual context on pronoun resolution in both groups: There was a preference for semantically animate referents as antecedent, but this preference decreased or disappeared when semantically inanimate referents had facial features. The results indicate that the use of animacy as a linguistic cue is flexible and responsive to the visual context. They further suggest that like adults (Nieuwland & Van Berkum, 2006), 4-year-olds already use fictional, here visual, context to adjust their online and offline language comprehension preferences.

Anticipating words during spoken discourse comprehension: A large-scale, pre-registered replication study using brain potentials

Numerous studies report brain potential evidence for the anticipation of specific words during language comprehension. In the most convincing demonstrations, highly predictable nouns exert an influence on processing even before they appear to a reader or listener, as indicated by the brain's neural response to a prenominal adjective or article when it mismatches the expectations about the upcoming noun. However, recent studies suggest that some well-known demonstrations of prediction may be hard to replicate. This could signal the use of data-contingent analysis, but might also mean that readers and listeners do not always use prediction-relevant information in the way that psycholinguistic theories typically suggest. To shed light on this issue, we performed a close replication of one of the best-cited ERP studies on word anticipation (Van Berkum, Brown, Zwitserlood, Kooijman & Hagoort, 2005; Experiment 1), in which participants listened to Dutch spoken mini-stories. In the original study, the marking of grammatical gender on pre-nominal adjectives (‘groot/grote’) elicited an early positivity when mismatching the gender of an unheard, highly predictable noun, compared to matching gender. The current pre-registered study involved that same manipulation, but used a novel set of materials twice the size of the original set, an increased sample size (N = 187), and Bayesian mixed-effects model analyses that better accounted for known sources of variance than the original. In our study, mismatching gender elicited more negative voltage than matching gender at posterior electrodes. However, this N400-like effect was small in size and lacked support from Bayes Factors. In contrast, we successfully replicated the original's noun effects. While our results yielded some support for prediction, they do not support the Van Berkum et al. effect and highlight the risks associated with commonly employed data-contingent analyses and small sample sizes. Our results also raise the question whether Dutch listeners reliably or consistently use adjectival inflection information to inform their noun predictions.

Male fashionistas and female football fans: Gender stereotypes affect neurophysiological correlates of semantic processing during speech comprehension

Abstract Recent studies have shown that pre-existing contextual information, such as gender stereotypes, is incorporated online during comprehension (e.g., Van Berkum, van den Brink, Tesink, Kos, & Hagoort, 2008). Stereotypes, however, are not static entities, and social role theory suggests that they may be influenced by the behavior of members of the group (Eagly, 1987). Consequently, our study examines how gender stereotypes affect the semantic processing of statements from both a male and a female speaker, as well as investigating how the influence of stereotypes may change as listeners gain experience with individual speakers. Participants listened to male and female speakers produce sentences about stereotypically feminine (fashion) and stereotypically masculine (sports) topics. Half of the participants heard a stereotype congruent pattern of sentences (e.g., for the male speaker, semantic errors about fashion but no semantic errors on sports sentences) and the other half heard a stereotype incongruent pattern. We found that the N400 effect of semantic correctness is larger in stereotype incongruent conditions. Furthermore, in stereotype congruent conditions, only stimuli presented in the male voice show an N400 effect in the expected direction (larger N400s to semantic violations). Additionally, when we examined ERP changes over the course of the experiment, we found that the degree of change in amplitude was predicted by individual differences in ambivalent sexism. These results suggest that not only are speaker characteristics incorporated during online language processing, but also that social knowledge influences language processing in a manner congruent with social role theory.

Adaptation to Animacy Violations during Listening Comprehension.

The goal of this study was to examine adaptation to various types of animacy violations in cartoon-like stories. We measured the event-related potentials (ERPs) elicited by words at the beginning, middle, and end of four-sentence stories in order to examine adaptation over time to conflicts between stored word knowledge and context-derived meaning (specifically, to inanimate objects serving as main characters, as they might in a cartoon). The fourth and final sentence of each story contained a predicate that required either an animate or an inanimate subject. The results showed that listeners quickly adapted to stories in the Inanimate Noun conditions, consistent with previous research (Filik & Leuthold, 2008; Nieuwland & Van Berkum, 2006). They showed evidence of processing difficulty for animacy-requiring predicates in the Inanimate Noun conditions in Sentence 1, but the effect dissipated in Sentences 2 and 3. In Sentences 2 and 4, we measured ERPs at three critical points where it was possible to observe the influence of both context-based expectations and expectations from prior knowledge on processing. Overall, the pattern of results demonstrates how listeners flexibly adapt to unusual, conflict-ridden input, using previous context to generate expectations about upcoming input, but that current context is weighted appropriately in combination with expectations from background knowledge and prior language experience.

Lexical prediction in language comprehension: a replication study of grammatical gender effects in Dutch

ABSTRACTAn important question in predictive language processing is the extent to which prediction effects can reliably be measured on pre-nominal material (e.g. articles before nouns). Here, we present a large sample (N = 58) close replication of a study by Otten and van Berkum (2009). They report ERP modulations in relation to the predictability of nouns in sentences, measured on gender-marked Dutch articles. We used nearly identical materials, procedures, and data analysis steps. We fail to replicate the original effect, but do observe a pattern consistent with the original data. Methodological differences between our replication and the original study that could potentially have contributed to the diverging results are discussed. In addition, we discuss the suitability of Dutch gender-marked determiners as a test-case for future studies of pre-activation of lexical items.

GRHL2-Dependent Enhancer Switching Maintains a Pluripotent Stem Cell Transcriptional Subnetwork after Exit from Naive Pluripotency

The enhancer landscape of pluripotent stem cells undergoes extensive reorganization during early mammalian development. The functions and mechanisms behind such reorganization, however, are unclear. Here, we show that the transcription factor GRHL2 is necessary and sufficient to activate an epithelial subset of enhancers as naive embryonic stem cells (ESCs) transition into formative epiblast-like cells (EpiLCs). Surprisingly, many GRHL2 target genes do not change in expression during the ESC-EpiLC transition. Instead, enhancers regulating these genes in ESCs diminish in activity in EpiLCs while GRHL2-dependent alternative enhancers become activated to maintain transcription. GRHL2 therefore assumes control over a subset of the naive network via enhancer switching to maintain expression of epithelial genes upon exit from naive pluripotency. These data evoke a model where the naive pluripotency network becomes partitioned into smaller, independent networks regulated by EpiLC-specific transcription factors, thereby priming cells for lineage specification.

Predicting semantic features in Chinese: Evidence from ERPs

This article reports two ERP studies that exploited the classifier system of Mandarin Chinese to investigate semantic prediction. In Mandarin, in certain contexts, a noun has to be preceded by a classifier, which has to match the noun in semantically-defined features. In both experiments, an N400 effect was elicited in response to a classifier that mismatched an up-coming predictable noun, relative to a matching classifier. Among the mismatching classifiers, the N400 effect was graded, being smaller for classifiers that were semantically related to the predicted word, relative to classifiers that were semantically unrelated to the predicted word. Given that the classifier occurred before the predicted word, this result shows that fine-grained semantic features of nouns can be pre-activated in advance of bottom-up input. The studies thus extend previous findings based on a more restricted range of highly grammaticalized features such as gender or animacy in Indo-European languages (Szewczyk & Schriefers, 2013; Van Berkum, Brown, Zwitserlood, Kooijman, & Hagoort, 2005; Wicha, Bates, Moreno, & Kutas, 2003).

An evaluation of diffraction peak profile analysis (DPPA) methods to study plastically deformed metals

A range of diffraction peak profile analysis (DPPA) techniques were used to determine details of the microstructure of plastically deformed alloys. Four different alloys were deformed by uniaxial tension and compression to a range of strains. The methods we have considered include, the full-width, Williamson-Hall methods, Warren-Averbach methods, and van Berkum's alternative method. Different metals were chosen to understand the effect of the deformation microstructure and crystal structure, a nickel alloy, two stainless steel alloys and two titanium alloys.The dislocation density values found by Williamson-Hall and Warren-Averbach methods were found to be close to those expected from TEM results of similar metals. When using the Warren-Averbach methods the results suggest that systematic errors in the dislocation density are introduced by three main factors: (1) separation of instrumental broadening, (2) separation of size and strain broadening, and (3) separation of dislocation density and arrangement. Which suggests in many cases the simpler Williamson-Hall method may be preferable.The other main parameters that can be determined by DPPA are the crystal size and the dislocation arrangement. The work suggests that further investigation is needed to understand what use if any these parameters have for quantifying the deformed microstructure of plastically deformed metals.

The IA|BE 2015 Mortality Projection for the Belgian Population

Life insurers, pension funds, health care providers and social security institutions face increasing expenses due to continuing improvements of mortality rates. The quantification of longevity risk in a systematic way requires stochastic mortality projection models, as Barrieu et al. (2012) indicate. The development of such models receives wide coverage in the actuarial, demographic and statistical literature, starting from the seminal work by Lee & Carter ([LC]) (Lee and Carter (1992)). As a follow-up to the 2002 mortality study of the former KVBA-ARAB (now: Institute of Actuaries in Belgium [IA|BE]) (see Lambrechts (2001), Brouhns et al. (2002a), Delfosse and Boelen (2002)), this report presents the set-up and technical specifications of the 2015 mortality projection model of the Institute of Actuaries in Belgium. The report also documents the resulting projections and the use of this model in actuarial applications. The IA|BE 2015 mortality projection model is a fully stochastic projection model of Li & Lee ([LL]) type, see Li and Lee (2005). The model is an application of the AG 2014 projection methodology of the Dutch Koninklijk Actuarieel Genootschap (see Koninklijk Actuarieel Genootschap (2014)) to the Belgian setting. This multi-population model projects Belgian mortality rates using Belgian mortality data together with observed mortality statistics for a collection of European countries with similar socioeconomic characteristics. A Lee & Carter model is imposed for the European mortality trend as well as for the Belgian deviation from this common trend. We have chosen this model as the preferred model from a comparative analysis of stochastic projection models proposed in recent scientific literature. As part of this comparative exercise we studied the single population mortality models from the papers by Cairns et al. (2009), Haberman and Renshaw (2011), Borger et al. (2014), Van Berkum et al. (2014), and the multi-population mortality models of Li and Lee (2005) and Koninklijk Actuarieel Genootschap (2014). The Cairns et al. (2006) stochastic two factor mortality model, and its generalizations proposed in Cairns et al. (2009), have not been investigated, since these Cairns, Blake & Dowd ([CBD]) mortality models are designed for pensioner age mortality only, whereas the IA|BE study puts focus on a projection model for the full age range (starting from age 0). For each model in the study we carefully examined its calibration, the modelling and projection of time dependent parameters and the produced forecasts. We evaluated the collection of mortality models using the criteria proposed in Cairns et al. (2009), supplemented with our own points of attention regarding biological reasonableness, statistical performance and transparency. The preferred model, and its calibration methodology, follows the AG2014 projection methodology as described in Koninklijk Actuarieel Genootschap (2014). Readers may want to consult the Koninklijk Actuarieel Genootschap (2014) documentation as additional reading material.This report is organized as follows. A technical description of the model is in Section 2. The subsections 2.1, 2.3 and 2.4 follow to a large extent Appendix A in Koninklijk Actuarieel Genootschap (2014). The use of the model and its applications are documented in Section 3. Section 4 concludes. Parameter estimates and the resulting IA|BE 2015 mortality projection for Belgium are available in an online appendix.

Characterization of the efficiency of soybean inoculation

The total demand for soybean in Hungary is 900 000 t·year -1 . 90–100 000 t·year -1 soybean is produced locally and approximately 800 000 t·year -1 is imported from South America. Soybean production in Hungary reached its lowest level in 1994, when the total sowing area was 9 197 ha, with a yield of 16 665 t·year -1 . From 1994 to 2011 the sowing area rose to 41 458 ha, with a total yield of 94 955 t·year -1 . In the same period the average yields rose from 1.84 t·ha -1 to 2.32 t·ha -1 (HUNGARIAN CENTRAL STATISTICAL OFFICE, 2014). The potential sowing area for soybean in Hungary is approximately 300 000 hectares. The results of modern genetic analyses have proved that soybean can be infected by six rhizobia belonging to three different genera, namely Bradyrhizobium, Mesorhizobium and Sinorhizobium (VAN BERKUM & EARDLY, 1998). The choice of microsymbiont species for soybean inoculation is greatly dependent on soil properties (SZEGI, 1967). While the efficiency of Sinorhizobium strains is higher in alkaline soils, Bradyrhizobium strains are more successful under neutral or slightly acidic pH conditions (ALBAREDA et al., 2009). In order to achieve optimal soybean yields via rhizobial inoculation, various conditions need to be considered. The average yield of soybean is in the range of 0.58–5.89 t·ha -1 , while its average nitrogen uptake is 219 kg·ha -1 . The yield and total nitrogen uptake are directly proportional, so 1 kg nitrogen is needed for the development of 12.7 kg soybean yield (SALVAGIOTTI et al., 2008). Some 36–69% of the total nitrogen utilised by soybean comes from biological nitrogen fixation (BNF). Even higher values were measured on subequatorial production areas, where the plants are able to use solar energy more efficiently (HUNGRIA et al., 2005). The efficiency of BNF may be influenced by various ecological soil factors,

The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer.

Mating-type switching in yeast occurs through gene conversion between the MAT locus and one of two silent loci (HML or HMR) on opposite ends of the chromosome. MATa cells choose HML as template, whereas MATα cells use HMR. The recombination enhancer (RE) located on the left arm regulates this process. One long-standing hypothesis is that switching is guided by mating-type-specific and possibly RE-dependent chromosome folding. Here, we use Hi-C, 5C, and live-cell imaging to characterize the conformation of chromosome III in both mating types. We discovered a mating-type-specific conformational difference in the left arm. Deletion of a 1-kb subregion within the RE, which is not necessary during switching, abolished mating-type-dependent chromosome folding. The RE is therefore a composite element with one subregion essential for donor selection during switching and a separate region involved in modulating chromosome conformation.

Structural Studies Reveal the Functional Modularity of the Scc2-Scc4 Cohesin Loader.

The remarkable accuracy of eukaryotic cell division is partly maintained by the cohesin complex acting as a molecular glue to prevent premature sister chromatid separation. The loading of cohesin onto chromosomes is catalyzed by the Scc2-Scc4 loader complex. Here, we report the crystal structure of Scc4 bound to the N terminus of Scc2 and show that Scc4 is a tetratricopeptide repeat (TPR) superhelix. The Scc2 N terminus adopts an extended conformation and is entrapped by the core of the Scc4 superhelix. Electron microscopy (EM) analysis reveals that the Scc2-Scc4 loader complex comprises three domains: a head, body, and hook. Deletion studies unambiguously assign the Scc2N-Scc4 as the globular head domain, whereas in vitro cohesin loading assays show that the central body and the hook domains are sufficient to catalyze cohesin loading onto circular DNA, but not chromatinized DNA in vivo, suggesting a possible role for Scc4 as a chromatin adaptor.

Does the speaker matter? Online processing of semantic and pragmatic information in L2 speech comprehension

The present study investigated how pragmatic information is integrated during L2 sentence comprehension. We put forward that the differences often observed between L1 and L2 sentence processing may reflect differences on how various types of information are used to process a sentence, and not necessarily differences between native and non-native linguistic systems. Based on the idea that when a cue is missing or distorted, one relies more on other cues available, we hypothesised that late bilinguals favour the cues that they master during sentence processing. To verify this hypothesis we investigated whether late bilinguals take the speaker's identity (inferred by the voice) into account when incrementally processing speech and whether this affects their online interpretation of the sentence. To do so, we adapted Van Berkum, J.J.A., Van den Brink, D., Tesink, C.M.J.Y., Kos, M., Hagoort, P., 2008. J. Cogn. Neurosci. 20(4), 580–591, study in which sentences with either semantic violations or pragmatic inconsistencies were presented. While both the native and the non-native groups showed a similar response to semantic violations (N400), their response to speakers’ inconsistencies slightly diverged; late bilinguals showed a positivity much earlier than native speakers (LPP). These results suggest that, like native speakers, late bilinguals process semantic and pragmatic information incrementally; however, what seems to differ between L1 and L2 processing is the time-course of the different processes. We propose that this difference may originate from late bilinguals’ sensitivity to pragmatic information and/or their ability to efficiently make use of the information provided by the sentence context to generate expectations in relation to pragmatic information during L2 sentence comprehension. In other words, late bilinguals may rely more on speaker identity than native speakers when they face semantic integration difficulties.

Electronic health records: We need to find needles, not stack more hay

<h3>Background</h3> CAR-T cell-based therapies hold great promise for neuroblastoma, because of its potential for targeted effects and already promising results in adult solid cancers. However, neuroblastoma tumour cells can escape T cell mediated killing by inhibition of T cells through secretion of immunosuppressive factors. Here, we have identified Macrophage Migration Inhibitory Factor (MIF) and Midkine (MDK) by scRNA-seq analysis to have a negative effect on the cytotoxicity of T cells. Next to that, we have found both MIF and MDK in high abundance in the secretome of neuroblastoma patient derived organoids. These factors have a suppressive effect on T cells and blocking their function might increase the efficacy of T cell based therapies for neuroblastoma. <h3>Materials and Methods</h3> To study immunoregulatory interactions in neuroblastoma, single-cell RNA-sequencing of 25 tumours were analysed using the CEL-seq2 platform. Interactions between tumour and immune cells were predicted using an unbiased ligand-receptor interaction analysis. Proteins secreted by tumour cells were analysed by performing mass spectrometry on conditioned medium from patient derived organoid cultures. The conditioned medium was concentrated using a 3kDa Millipore filter and prepared for LC-MS. Mass spectrometry data were acquired in data-dependent acquisition mode. For determining suppression, healthy donor PBMCs were stimulated with anti-CD28/anti-CD3 Dynabeads in the presence of recombinant proteins or concentrated conditioned medium from neuroblastoma organoids. In vitro killing assays were performed with GFP and luciferase transduced organoids and healthy donor PBMCs. <h3>Results</h3> Analysis of scRNA-seq of 25 neuroblastoma tumours showed a negative correlation between MIF and MDK expression and the cytotoxicity of NK cells, CD8 and γδ-T cells within the tumour. These findings could be confirmed with a previously published SEQC bulk-RNAseq dataset containing 498 patients. Next to that, a higher expression of MIF and MDK correlated with poor survival in the same dataset. In the secretome from cultured neuroblastoma organoids, we have used mass spectrometry to identify MIF and MDK amongst the top 100 most abundant proteins from a total of ~1200 proteins. In vitro, we showed that rMIF and rMDK have a suppressive effect on the activation of T cells and the amount of cytotoxic factors such as granzyme B and Perforin are produced by the T cells. This confirms our hypothesis that MIF and MDK negatively influence the cytotoxicity of T cells. <h3>Conclusions</h3> Using two different unbiased analyses -scRNA-seq analysis of tumours and mass spectrometry of neuroblastoma organoid secretome-, we have identified MIF and MDK as immunosuppressive factor in neuroblastoma. Currently, we are testing several MIF and MDK inhibitors to test if T cell mediated killing of neuroblastoma can be increased if the immunosuppressive MIF and MDK are blocked. <h3>Disclosure Information</h3> <b>J.G.M. Strijker:</b> None. <b>R.E. van Berkum:</b> None. <b>M. Damen:</b> None. <b>W. Wu:</b> None. <b>J.J. Molenaar:</b> None. <b>J. Wienke:</b> None.

What belongs together goes together: the speaker-hearer perspective. A commentary on MacDonald's PDC account

What belongs together goes together: the speaker-hearer perspective. A commentary on MacDonald's PDC account

How tightly are production and comprehension interwoven?

How tightly are production and comprehension interwoven?

Human mitotic chromosome structure: what happened to the 30-nm fibre?

EMBO J 31 7, 1644–1653 February172012 The long-standing view of chromosome packaging is that 10-nm beads-on-a string chromatin fibres fold into higher-order 30-nm fibres, which further twist and coil to form highly condensed chromosomes. After four decades of intense pursuit of the structure and properties of 30-nm chromatin fibres, work of Nishino et al (2012) in this issue of The EMBO Journal demonstrates that regular 30-nm fibres are absent from human mitotic chromosomes. The emerging view is that chromosome-level condensation can be achieved through packaging of 10-nm fibres in a fractal manner.

Meaningful physical changes mediate lexical–semantic integration: Top-down and form-based bottom-up information sources interact in the N400

Models of how the human brain reconstructs an intended meaning from a linguistic input often draw upon the N400 event-related potential (ERP) component as evidence. Current accounts of the N400 emphasise either the role of contextually induced lexical preactivation of a critical word (Lau, Phillips, & Poeppel, 2008) or the ease of integration into the overall discourse context including a wide variety of influencing factors (Hagoort & van Berkum, 2007). The present ERP study challenges both types of accounts by demonstrating a contextually independent and purely form-based bottom-up influence on the N400: the N400 effect for implausible sentence-endings was attenuated when the critical sentence-final word was capitalised (following a lowercase sentence context). By contrast, no N400 modulation occurred when the critical word involved a change from uppercase (sentence context) to lowercase. Thus, the N400 was only affected by a change to uppercase letters, as is often employed in computer-mediated communication as a sign of emphasis. This result indicates that N400 amplitude is reduced for unexpected words when a bottom-up (orthographic) cue signals that the word is likely to be highly informative. The lexical–semantic N400 thereby reflects the degree to which the semantic informativity of a critical word matches expectations, as determined by an interplay between top-down and bottom-up information sources, including purely form-based bottom-up information.