Publications

Displaying 701 - 765 of 765
  • Tendolkar, I., Arnold, J., Petersson, K. M., Weis, S., Brockhaus-Dumke, A., Van Eijndhoven, P., Buitelaar, J., & Fernández, G. (2007). Probing the neural correlates of associative memory formation: A parametrically analyzed event-related functional MRI study. Brain Research, 1142, 159-168. doi:10.1016/j.brainres.2007.01.040.

    Abstract

    The medial temporal lobe (MTL) is crucial for declarative memory formation, but the function of its subcomponents in associative memory formation remains controversial. Most functional imaging studies on this topic are based on a stepwise approach comparing a condition with and one without associative encoding. Extending this approach we applied additionally a parametric analysis by varying the amount of associative memory formation. We found a hippocampal subsequent memory effect of almost similar magnitude regardless of the amount of associations formed. By contrast, subsequent memory effects in rhinal and parahippocampal cortices were parametrically and positively modulated by the amount of associations formed. Our results indicate that the parahippocampal region supports associative memory formation as tested here and the hippocampus adds a general mnemonic operation. This pattern of results might suggest a new interpretation. Instead of having either a fixed division of labor between the hippocampus (associative memory formation) and the rhinal cortex (non-associative memory formation) or a functionally unitary MTL system, in which all substructures are contributing to memory formation in a similar way, we propose that the location where associations are formed within the MTL depends on the kind of associations bound: If visual single-dimension associations, as used here, can already be integrated within the parahippocampal region, the hippocampus might add a general purpose mnemonic operation only. In contrast, if associations have to be formed across widely distributed neocortical representations, the hippocampus may provide a binding operation in order to establish a coherent memory.
  • Terrill, A. (1998). Biri. München: Lincom Europa.

    Abstract

    This work presents a salvage grammar of the Biri language of Eastern Central Queensland, a Pama-Nyungan language belonging to the large Maric subgroup. As the language is no longer used, the grammatical description is based on old written sources and on recordings made by linguists in the 1960s and 1970s. Biri is in many ways typical of the Pama-Nyungan languages of Southern Queensland. It has split case marking systems, marking nouns according to an ergative/absolutive system and pronouns according to a nominative/accusative system. Unusually for its area, Biri also has bound pronouns on its verb, cross-referencing the person, number and case of core participants. As far as it is possible, the grammatical discussion is ‘theory neutral’. The first four chapters deal with the phonology, morphology, and syntax of the language. The last two chapters contain a substantial discussion of Biri’s place in the Pama-Nyungan family. In chapter 6 the numerous dialects of the Biri language are discussed. In chapter 7 the close linguistic relationship between Biri and the surrounding languages is examined.
  • Terrill, A. (2007). [Review of ‘Andrew Pawley, Robert Attenborough, Jack Golson, and Robin Hide, eds. 2005. Papuan pasts: Cultural, linguistic and biological histories of Papuan-speaking people]. Oceanic Linguistics, 46(1), 313-321. doi:10.1353/ol.2007.0025.
  • Theakston, A. L., Lieven, E. V., Pine, J. M., & Rowland, C. F. (2005). The acquisition of auxiliary syntax: BE and HAVE. Cognitive Linguistics, 16(1), 247-277. doi:10.1515/cogl.2005.16.1.247.

    Abstract

    This study examined patterns of auxiliary provision and omission for the auxiliaries BE and HAVE in a longitudinal data set from 11 children between the ages of two and three years. Four possible explanations for auxiliary omission—a lack of lexical knowledge, performance limitations in production, the Optional Infinitive hypothesis, and patterns of auxiliary use in the input—were examined. The data suggest that although none of these accounts provides a full explanation for the pattern of auxiliary use and nonuse observed in children's early speech, integrating input-based and lexical learning-based accounts of early language acquisition within a constructivist approach appears to provide a possible framework in which to understand the patterns of auxiliary use found in the children's speech. The implications of these findings for models of children's early language acquisition are discussed.
  • Tomasello, M., Carpenter, M., & Liszkowski, U. (2007). A new look at infant pointing. Child Development, 78, 705-722. doi:10.1111/j.1467-8624.2007.01025.x.

    Abstract

    The current article proposes a new theory of infant pointing involving multiple layers of intentionality and shared intentionality. In the context of this theory, evidence is presented for a rich interpretation of prelinguistic communication, that is, one that posits that when 12-month-old infants point for an adult they are in some sense trying to influence her mental states. Moreover, evidence is also presented for a deeply social view in which infant pointing is best understood—on many levels and in many ways—as depending on uniquely human skills and motivations for cooperation and shared intentionality (e.g., joint intentions and attention with others). Children's early linguistic skills are built on this already existing platform of prelinguistic communication.
  • Trilsbeek, P., & Wittenburg, P. (2005). Archiving challenges. In J. Gippert, N. Himmelmann, & U. Mosel (Eds.), Essentials of language documentation (pp. 311-335). Berlin: Mouton de Gruyter.
  • Trilsbeek, P., & Wittenburg, P. (2007). "Los acervos lingüísticos digitales y sus desafíos". In J. Haviland, & F. Farfán (Eds.), Bases de la documentacíon lingüística (pp. 359-385). Mexico: Instituto Nacional de Lenguas Indígenas.

    Abstract

    This chapter describes the challenges that modern digital language archives are faced with. One essential aspect of such an archive is to have a rich metadata catalog such that the archived resources can be easily discovered. The challenge of the archive is to obtain these rich metadata descriptions from the depositors without creating too much overhead for them. The rapid changes in storage technology, file formats and encoding standards make it difficult to build a long-lasting repository, therefore archives need to be set up in such a way that a straightforward and automated migration process to newer technology is possible whenever certain technology becomes obsolete. Other problems arise from the fact that there are many different groups of users of the archive, each of them with their own specific expectations and demands. Often conflicts exist between the requirements for different purposes of the archive, e.g. between long-term preservation of the data versus direct access to the resources via the web. The task of the archive is to come up with a technical solution that works well for most usage scenarios.
  • Tufvesson, S. (2007). Expressives. In A. Majid (Ed.), Field Manual Volume 10 (pp. 53-58). Nijmegen: Max Planck Institute for Psycholinguistics. doi:10.17617/2.492919.
  • Tuinman, A., Mitterer, H., & Cutler, A. (2007). Speakers differentiate English intrusive and onset /r/, but L2 listeners do not. In J. Trouvain, & W. J. Barry (Eds.), Proceedings of the 16th International Congress of Phonetic Sciences (ICPhS 2007) (pp. 1905-1908). Dudweiler: Pirrot.

    Abstract

    We investigated whether non-native listeners can exploit phonetic detail in recognizing potentially ambiguous utterances, as native listeners can [6, 7, 8, 9, 10]. Due to the phenomenon of intrusive /r/, the English phrase extra ice may sound like extra rice. A production study indicates that the intrusive /r/ can be distinguished from the onset /r/ in rice, as it is phonetically weaker. In two cross-modal identity priming studies, however, we found no conclusive evidence that Dutch learners of English are able to make use of this difference. Instead, auditory primes such as extra rice and extra ice with onset and intrusive /r/s activate both types of targets such as ice and rice. This supports the notion of spurious lexical activation in L2 perception.
  • Van Alphen, P. M. (2007). Prevoicing in Dutch initial plosives: Production, perception, and word recognition. In J. van de Weijer, & E. van der Torre (Eds.), Voicing in Dutch (pp. 99-124). Amsterdam: Benjamins.

    Abstract

    Prevoicing is the presence of vocal fold vibration during the closure of initial voiced plosives (negative VOT). The presence or absence of prevoicing is generally used to describe the voicing distinction in Dutch initial plosives. However, a phonetic study showed that prevoicing is frequently absent in Dutch. This article discusses the role of prevoicing in the production and perception of Dutch plosives. Furthermore, two cross-modal priming experiments are presented that examined the effect of prevoicing variation on word recognition. Both experiments showed no difference between primes with 12, 6 or 0 periods of prevoicing, even though a third experiment indicated that listeners could discriminate these words. These results are discussed in light of another priming experiment that did show an effect of the absence of prevoicing, but only when primes had a voiceless word competitor. Phonetic detail appears to influence lexical access only when it helps to distinguish between lexical candidates.
  • Van Alphen, P. M., De Bree, E., Fikkert, P., & Wijnen, F. (2007). The role of metrical stress in comprehension and production of Dutch children at risk of dyslexia. In Proceedings of Interspeech 2007 (pp. 2313-2316). Adelaide: Causal Productions.

    Abstract

    The present study compared the role of metrical stress in comprehension and production of three-year-old children with a familial risk of dyslexia with that of normally developing children. A visual fixation task with stress (mis-)matches in bisyllabic words, as well as a non-word repetition task with bisyllabic targets were presented to the control and at-risk children. Results show that the at-risk group is less sensitive to stress mismatches in word recognition than the control group. Correct production of metrical stress patterns did not differ significantly between the groups, but the percentages of phonemes produced correctly were lower for the at-risk than the control group. The findings indicate that processing of metrical stress patterns is not impaired in at-risk children, but that the at-risk group cannot exploit metrical stress in word recognition
  • Van Turennout, M., Hagoort, P., & Brown, C. M. (1998). Brain activitity during speaking: From syntax to phonology in 40 milliseconds. Science, 280, 572-574.

    Abstract

    In normal conversation, speakers translate thoughts into words at high speed. To enable this speed, the retrieval of distinct types of linguistic knowledge has to be orchestrated with millisecond precision. The nature of this orchestration is still largely unknown. This report presents dynamic measures of the real-time activation of two basic types of linguistic knowledge, syntax and phonology. Electrophysiological data demonstrate that during noun-phrase production speakers retrieve the syntactic gender of a noun before its abstract phonological properties. This two-step process operates at high speed: the data show that phonological information is already available 40 milliseconds after syntactic properties have been retrieved.
  • Van Turennout, M., Hagoort, P., & Brown, C. M. (1998). Brain activity during speaking: From syntax to phonology in 40 milliseconds. Science, 280(5363), 572-574. doi:10.1126/science.280.5363.572.
  • Van Berkum, J. J. A., Hijne, H., De Jong, T., Van Joolingen, W. R., & Njoo, M. (1995). Characterizing the application of computer simulations in education: Instructional criteria. In A. Ram, & D. B. Leake (Eds.), Goal-driven learning (pp. 381-392). Cambridge, M: MIT Press.
  • Van de Geer, J. P., & Levelt, W. J. M. (1963). Detection of visual patterns disturbed by noise: An exploratory study. Quarterly Journal of Experimental Psychology, 15, 192-204. doi:10.1080/17470216308416324.

    Abstract

    An introductory study of the perception of stochastically specified events is reported. The initial problem was to determine whether the perceiver can split visual input data of this kind into random and determined components. The inability of subjects to do so with the stimulus material used (a filmlike sequence of dot patterns), led to the more general question of how subjects code this kind of visual material. To meet the difficulty of defining the subjects' responses, two experiments were designed. In both, patterns were presented as a rapid sequence of dots on a screen. The patterns were more or less disturbed by “noise,” i.e. the dots did not appear exactly at their proper places. In the first experiment the response was a rating on a semantic scale, in the second an identification from among a set of alternative patterns. The results of these experiments give some insight in the coding systems adopted by the subjects. First, noise appears to be detrimental to pattern recognition, especially to patterns with little spread. Second, this shows connections with the factors obtained from analysis of the semantic ratings, e.g. easily disturbed patterns show a large drop in the semantic regularity factor, when only a little noise is added.
  • Van Ooijen, B., Cutler, A., & Berinetto, P. M. (1993). Click detection in Italian and English. In Eurospeech 93: Vol. 1 (pp. 681-684). Berlin: ESCA.

    Abstract

    We report four experiments in which English and Italian monolinguals detected clicks in continous speech in their native language. Two of the experiments used an off-line location task, and two used an on-line reaction time task. Despite there being large differences between English and Italian with respect to rhythmic characteristics, very similar response patterns were found for the two language groups. It is concluded that the process of click detection operates independently from language-specific differences in perceptual processing at the sublexical level.
  • Van Donselaar, W., Koster, M., & Cutler, A. (2005). Exploring the role of lexical stress in lexical recognition. Quarterly Journal of Experimental Psychology, 58A(2), 251-273. doi:10.1080/02724980343000927.

    Abstract

    Three cross-modal priming experiments examined the role of suprasegmental information in the processing of spoken words. All primes consisted of truncated spoken Dutch words. Recognition of visually presented word targets was facilitated by prior auditory presentation of the first two syllables of the same words as primes, but only if they were appropriately stressed (e.g., OKTOBER preceded by okTO-); inappropriate stress, compatible with another word (e.g., OKTOBER preceded by OCto-, the beginning of octopus), produced inhibition. Monosyllabic fragments (e.g., OC-) also produced facilitation when appropriately stressed; if inappropriately stressed, they produced neither facilitation nor inhibition. The bisyllabic fragments that were compatible with only one word produced facilitation to semantically associated words, but inappropriate stress caused no inhibition of associates. The results are explained within a model of spoken-word recognition involving competition between simultaneously activated phonological representations followed by activation of separate conceptual representations for strongly supported lexical candidates; at the level of the phonological representations, activation is modulated by both segmental and suprasegmental information.
  • Van Berkum, J. J. A., Koornneef, A. W., Otten, M., & Nieuwland, M. S. (2007). Establishing reference in language comprehension: An electrophysiological perspective. Brain Research, 1146, 158-171. doi:10.1016/j.brainres.2006.06.091.

    Abstract

    The electrophysiology of language comprehension has long been dominated by research on syntactic and semantic integration. However, to understand expressions like "he did it" or "the little girl", combining word meanings in accordance with semantic and syntactic constraints is not enough--readers and listeners also need to work out what or who is being referred to. We review our event-related brain potential research on the processes involved in establishing reference, and present a new experiment in which we examine when and how the implicit causality associated with specific interpersonal verbs affects the interpretation of a referentially ambiguous pronoun. The evidence suggests that upon encountering a singular noun or pronoun, readers and listeners immediately inspect their situation model for a suitable discourse entity, such that they can discriminate between having too many, too few, or exactly the right number of referents within at most half a second. Furthermore, our implicit causality findings indicate that a fragment like "David praised Linda because..." can immediately foreground a particular referent, to the extent that a subsequent "he" is at least initially construed as a syntactic error. In all, our brain potential findings suggest that referential processing is highly incremental, and not necessarily contingent upon the syntax. In addition, they demonstrate that we can use ERPs to relatively selectively keep track of how readers and listeners establish reference.
  • Van Berkum, J. J. A., Brown, C. M., Zwitserlood, P., Kooijman, V., & Hagoort, P. (2005). Anticipating upcoming words in discourse: Evidence from ERPs and reading times. Journal of Experimental Psychology: Learning, Memory, and Cognition, 31(3), 443-467. doi:10.1037/0278-7393.31.3.443.

    Abstract

    The authors examined whether people can use their knowledge of the wider discourse rapidly enough to anticipate specific upcoming words as a sentence is unfolding. In an event-related brain potential (ERP) experiment, subjects heard Dutch stories that supported the prediction of a specific noun. To probe whether this noun was anticipated at a preceding indefinite article, stories were continued with a gender-marked adjective whose suffix mismatched the upcoming noun's syntactic gender. Prediction-inconsistent adjectives elicited a differential ERP effect, which disappeared in a no-discourse control experiment. Furthermore, in self-paced reading, prediction-inconsistent adjectives slowed readers down before the noun. These findings suggest that people can indeed predict upcoming words in fluent discourse and, moreover, that these predicted words can immediately begin to participate in incremental parsing operations.
  • Van Halteren, H., Baayen, R. H., Tweedie, F., Haverkort, M., & Neijt, A. (2005). New machine learning methods demonstrate the existence of a human stylome. Journal of Quantitative Linguistics, 12(1), 65-77. doi:10.1080/09296170500055350.

    Abstract

    Earlier research has shown that established authors can be distinguished by measuring specific properties of their writings, their stylome as it were. Here, we examine writings of less experienced authors. We succeed in distinguishing between these authors with a very high probability, which implies that a stylome exists even in the general population. However, the number of traits needed for so successful a distinction is an order of magnitude larger than assumed so far. Furthermore, traits referring to syntactic patterns prove less distinctive than traits referring to vocabulary, but much more distinctive than expected on the basis of current generativist theories of language learning.
  • Van Wingen, G., Van Broekhoven, F., Verkes, R. J., Petersson, K. M., Bäckström, T., Buitelaar, J., & Fernández, G. (2007). How progesterone impairs memory for biologically salient stimuli in healthy young women. Journal of Neuroscience, 27(42), 11416-11423. doi:10.1523/JNEUROSCI.1715-07.2007.

    Abstract

    Progesterone, or rather its neuroactive metabolite allopregnanolone, modulates amygdala activity and thereby influences anxiety. Cognition and, in particular, memory are also altered by allopregnanolone. In the present study, we investigated whether allopregnanolone modulates memory for biologically salient stimuli by influencing amygdala activity, which in turn may affect neural processes in other brain regions. A single progesterone dose was administered orally to healthy young women in a double-blind, placebo-controlled, crossover design, and participants were asked to memorize and recognize faces while undergoing functional magnetic resonance imaging. Progesterone decreased recognition accuracy without affecting reaction times. The imaging results show that the amygdala, hippocampus, and fusiform gyrus supported memory formation. Importantly, progesterone decreased responses to faces in the amygdala and fusiform gyrus duringmemoryencoding, whereas it increased hippocampal responses. The progesterone-induced decrease in neural activity in the amygdala and fusiform gyrus predicted the decrease in memory performance across subjects. However, progesterone did not modulate the differential activation between subsequently remembered and subsequently forgotten faces in these areas. A similar pattern of results was observed in the fusiform gyrus and prefrontal cortex during memory retrieval. These results suggest that allopregnanolone impairs memory by reducing the recruitment of those brain regions that support memory formation and retrieval. Given the important role of the amygdala in the modulation of memory, these results suggest that allopregnanolone alters memory by influencing amygdala activity, which in turn may affect memory processes in other brain regions
  • Van Valin Jr., R. D. (2005). Exploring the syntax-semantics interface. Cambridge University Press.

    Abstract

    Language is a system of communication in which grammatical structures function to express meaning in context. While all languages can achieve the same basic communicative ends, they each use different means to achieve them, particularly in the divergent ways that syntax, semantics and pragmatics interact across languages. This book looks in detail at how structure, meaning, and communicative function interact in human languages. Working within the framework of Role and Reference Grammar (RRG), Van Valin proposes a set of rules, called the ‘linking algorithm’, which relates syntactic and semantic representations to each other, with discourse-pragmatics playing a role in the linking. Using this model, he discusses the full range of grammatical phenomena, including the structures of simple and complex sentences, verb and argument structure, voice, reflexivization and extraction restrictions. Clearly written and comprehensive, this book will be welcomed by all those working on the interface between syntax, semantics and pragmatics.
  • Van Geenhoven, V. (1998). On the Argument Structure of some Noun Incorporating Verbs in West Greenlandic. In M. Butt, & W. Geuder (Eds.), The Projection of Arguments - Lexical and Compositional Factors (pp. 225-263). Stanford, CA, USA: CSLI Publications.
  • Van Valin Jr., R. D. (1998). The acquisition of WH-questions and the mechanisms of language acquisition. In M. Tomasello (Ed.), The new psychology of language: Cognitive and functional approaches to language structure (pp. 221-249). Mahwah, New Jersey: Erlbaum.
  • Van de Geer, J. P., Levelt, W. J. M., & Plomp, R. (1962). The connotation of musical consonance. Acta Psychologica, 20, 308-319.

    Abstract

    As a preliminary to further research on musical consonance an explanatory investigation was made on the different modes of judgment of musical intervals. This was done by way of a semantic differential. Subjects rated 23 intervals against 10 scales. In a factor analysis three factors appeared: pitch, evaluation and fusion. The relation between these factors and some physical characteristics has been investigated. The scale consonant-dissonant showed to be purely evaluative (in opposition to Stumpf's theory). This evaluative connotation is not in accordance with the musicological meaning of consonance. Suggestions to account for this difference have been given.
  • Van Valin Jr., R. D. (2007). Some thoughts on the reason for the lesser status of typology in the USA as opposed to Europe. Linguistic Typology, 11(1), 253-257. doi:10.1515/LINGTY.2007.019.

    Abstract

    This article addresses the issue of the different status that typology has in American linguistics as opposed to European linguistics. The historical roots of the difference lie in both structural and generative linguistics, in the contrasts between post-Bloomfieldian structuralism in the US vs. Praguean structuralism in Europe, and in the extent of the influence of generative grammar on the two continents.
  • Van Valin Jr., R. D. (1995). Toward a functionalist account of so-called ‘extraction constraints’. In B. Devriendt (Ed.), Complex structures: A functionalist perspective (pp. 29-60). Berlin: Mouton de Gruyter.
  • Van Uytvanck, D., Dukers, A., Ringersma, J., & Wittenburg, P. (2007). Using Google Earth to access language resources. Language Archive Newsletter, (9), 4-7.

    Abstract

    Over the past ten years Geographic Information Systems (GIS) have evolved from a highly specialised niche technology to one that is used daily by a wide range of people. This article describes geographic browsing of language archives, which provides intuitive exploration of resources and permits integration and correlation of information from different archives, even across different research disciplines. In order to facilitate both exploration and management of resources, digital language archives are organised according to criteria such as language name, research topic, project information, researchers, countries, or genres. A set of such criteria can form a tree-like classification scheme, such as in the MPI-IMDI archive, which in turn forms the main method of searching and querying the archive resources. Searching for information can be difficult for occasional users because effective use of these search-fields typically requires specialised knowledge. We assume that many non-specialist users of language resources will search by language name, language family, or geographic area, so that geographic navigation would offer a very powerful search method. We also assume that such users are familiar with maps, and that geographic browsing is more intuitive than browsing classification trees, so these users would prefer to start with a large scale map and then zoom in to find the data that interests them. Therefore, classification trees and geographic maps provide complementary methods for accessing language resources to meet the needs of different user groups. We selected Google Earth (GE) as a geographic browsing system and overlaid it with linguistic information. GE was chosen because it is available via the web, it has good navigation controls, it is familiar to many web users, and because the overlaid linguistic information can be formulated in XML, making it comparatively easy to interchange with other geographic systems.
  • Verhagen, J. (2005). The role of the nonmodal auxiliary 'hebben' in Dutch as a second language. Zeitschrift für Literaturwissenschaft und Linguistik, 140, 109-127.

    Abstract

    The acquisition of non-modal auxiliaries has been assumed to constitute an important step in the acquisition of finiteness in Germanic languages (cf. Jordens/Dimroth 2005, Jordens 2004, Becker 2005). This paper focuses onthe role of the auxiliary hebben (>to have<) in the acquisition of Dutch as a second language. More specifically, it investigates whether learners' production of hebben is related to their acquisition of two phenomena commonly associated with finiteness, i.e., topicalization and negation. Data are presented from 16 Turkish and 36 Moroccan learners of Dutch who participated in an experiment involving production and imitation tasks. The production data suggest that learners use topicalization and post-verbal negation only after they have learned to produce the auxiliary hebben. The results from the imitation task indicate, that learners are more sensitive to topicalization and post-verbal negation in sentences with hebben than in sentences with lexical verbs. Interestingly this holds also for learners that did not show productive command of hebben in the production tasks. Thus, in general, the results of the experiment provide support for the idea that non-modal auxiliaries are crucial in the acquisition of (certain properties of) finiteness.
  • Verhagen, J. (2005). The role of the nonmodal auxiliary 'hebben' in Dutch as a second language. Toegepaste Taalwetenschap in Artikelen, 73, 41-52.
  • Vernes, S. C., Spiteri, E., Nicod, J., Groszer, M., Taylor, J. M., Davies, K. E., Geschwind, D., & Fisher, S. E. (2007). High-throughput analysis of promoter occupancy reveals direct neural targets of FOXP2, a gene mutated in speech and language disorders. American Journal of Human Genetics, 81(6), 1232-1250. doi:10.1086/522238.

    Abstract

    We previously discovered that mutations of the human FOXP2 gene cause a monogenic communication disorder, primarily characterized by difficulties in learning to make coordinated sequences of articulatory gestures that underlie speech. Affected people have deficits in expressive and receptive linguistic processing and display structural and/or functional abnormalities in cortical and subcortical brain regions. FOXP2 provides a unique window into neural processes involved in speech and language. In particular, its role as a transcription factor gene offers powerful functional genomic routes for dissecting critical neurogenetic mechanisms. Here, we employ chromatin immunoprecipitation coupled with promoter microarrays (ChIP-chip) to successfully identify genomic sites that are directly bound by FOXP2 protein in native chromatin of human neuron-like cells. We focus on a subset of downstream targets identified by this approach, showing that altered FOXP2 levels yield significant changes in expression in our cell-based models and that FOXP2 binds in a specific manner to consensus sites within the relevant promoters. Moreover, we demonstrate significant quantitative differences in target expression in embryonic brains of mutant mice, mediated by specific in vivo Foxp2-chromatin interactions. This work represents the first identification and in vivo verification of neural targets regulated by FOXP2. Our data indicate that FOXP2 has dual functionality, acting to either repress or activate gene expression at occupied promoters. The identified targets suggest roles in modulating synaptic plasticity, neurodevelopment, neurotransmission, and axon guidance and represent novel entry points into in vivo pathways that may be disturbed in speech and language disorders.
  • Vonk, W., & Cozijn, R. (2007). Psycholinguïstiek: Een kwantitatieve wetenschap. Tijdschrift voor Nederlandse Taal- en Letterkunde, 123, 55-69.
  • De Vos, C. (2005). Cataphoric pronoun resolution (Unpublished bachelor thesis). Nijmegen: Department of Linguistics, Radboud University.

    Abstract

    Processing of cataphoric coreferential relationships.
  • Warner, N., Smits, R., McQueen, J. M., & Cutler, A. (2005). Phonological and statistical effects on timing of speech perception: Insights from a database of Dutch diphone perception. Speech Communication, 46(1), 53-72. doi:10.1016/j.specom.2005.01.003.

    Abstract

    We report detailed analyses of a very large database on timing of speech perception collected by Smits et al. (Smits, R., Warner, N., McQueen, J.M., Cutler, A., 2003. Unfolding of phonetic information over time: A database of Dutch diphone perception. J. Acoust. Soc. Am. 113, 563–574). Eighteen listeners heard all possible diphones of Dutch, gated in portions of varying size and presented without background noise. The present report analyzes listeners’ responses across gates in terms of phonological features (voicing, place, and manner for consonants; height, backness, and length for vowels). The resulting patterns for feature perception differ from patterns reported when speech is presented in noise. The data are also analyzed for effects of stress and of phonological context (neighboring vowel vs. consonant); effects of these factors are observed to be surprisingly limited. Finally, statistical effects, such as overall phoneme frequency and transitional probabilities, along with response biases, are examined; these too exercise only limited effects on response patterns. The results suggest highly accurate speech perception on the basis of acoustic information alone.
  • Warner, N., Kim, J., Davis, C., & Cutler, A. (2005). Use of complex phonological patterns in speech processing: Evidence from Korean. Journal of Linguistics, 41(2), 353-387. doi:10.1017/S0022226705003294.

    Abstract

    Korean has a very complex phonology, with many interacting alternations. In a coronal-/i/ sequence, depending on the type of phonological boundary present, alternations such as palatalization, nasal insertion, nasal assimilation, coda neutralization, and intervocalic voicing can apply. This paper investigates how the phonological patterns of Korean affect processing of morphemes and words. Past research on languages such as English, German, Dutch, and Finnish has shown that listeners exploit syllable structure constraints in processing speech and segmenting it into words. The current study shows that in parsing speech, listeners also use much more complex patterns that relate the surface phonological string to various boundaries.
  • Wassenaar, M., & Hagoort, P. (2007). Thematic role assignment in patients with Broca's aphasia: Sentence-picture matching electrified. Neuropsychologia, 45(4), 716-740. doi:10.1016/j.neuropsychologia.2006.08.016.

    Abstract

    An event-related brain potential experiment was carried out to investigate on-line thematic role assignment during sentence–picture matching in patients with Broca's aphasia. Subjects were presented with a picture that was followed by an auditory sentence. The sentence either matched the picture or mismatched the visual information depicted. Sentences differed in complexity, and ranged from simple active semantically irreversible sentences to passive semantically reversible sentences. ERPs were recorded while subjects were engaged in sentence–picture matching. In addition, reaction time and accuracy were measured. Three groups of subjects were tested: Broca patients (N = 10), non-aphasic patients with a right hemisphere (RH) lesion (N = 8), and healthy aged-matched controls (N = 15). The results of this study showed that, in neurologically unimpaired individuals, thematic role assignment in the context of visual information was an immediate process. This in contrast to patients with Broca's aphasia who demonstrated no signs of on-line sensitivity to the picture–sentence mismatches. The syntactic contribution to the thematic role assignment process seemed to be diminished given the reduction and even absence of P600 effects. Nevertheless, Broca patients showed some off-line behavioral sensitivity to the sentence–picture mismatches. The long response latencies of Broca's aphasics make it likely that off-line response strategies were used.
  • Wassenaar, M., & Hagoort, P. (2005). Word-category violations in patients with Broca's aphasia: An ERP study. Brain and Language, 92, 117-137. doi:10.1016/j.bandl.2004.05.011.

    Abstract

    An event-related brain potential experiment was carried out to investigate on-line syntactic processing in patients with Broca’s aphasia. Subjects were visually presented with sentences that were either syntactically correct or contained violations of word-category. Three groups of subjects were tested: Broca patients (N=11), non-aphasic patients with a right hemisphere (RH) lesion (N=9), and healthy aged-matched controls (N=15). Both control groups appeared sensitive to the violations of word-category as shown by clear P600/SPS effects. The Broca patients displayed only a very reduced and delayed P600/SPS effect. The results are discussed in the context of a lexicalist parsing model. It is concluded that Broca patients are hindered to detect on-line violations of word-category, if word class information is incomplete or delayed available.
  • Wassenaar, M. (2005). Agrammatic comprehension: An electrophysiological approach. PhD Thesis, Radboud University Nijmegen, Nijmegen. doi:10.17617/2.60340.

    Abstract

    This dissertation focuses on syntactic comprehension problems in patients with Broca's aphasia from an electrophysiological perspective. The central objective of this dissertation was to further explore what syntax-related event-related brain potential (ERP) effects can reveal about the nature of the deficit that underlies syntactic comprehension problems in patients with Broca's aphasia. Chapter two to four describe experiments in which event-related brain potentials were recorded while subjects (Broca patients, non-aphasic patients with a right-hemisphere lesion, and healthy elderly controls) were presented with sentences that contained either violations of syntactic constraints or were syntactically correct. Chapter two investigates ERP effects of subject-verb agreement violations in the different subject groups, and seeks to answer the following questions: Do agrammatic comprehenders show sensitivity to subject-verb agreement violations as indicated by a syntax-related ERP effect? In addition, does the severity of the syntactic comprehension impairment in the Broca patients affect the ERP responses? Chapter three describes an investigation of whether Broca patients show sensitivity to violations of word order as indicated by a syntax-related ERP effect, and whether the ERP responses in the Broca patients are affected by the severity of their syntactic comprehension impairment. Chapter four reports on ERP effects of violations of word-category. In addition, also a semantic violation condition was added to track possible dissociations in the sensitivity to semantic and syntactic information in the Broca patients. Chapter five describes the development of a paradigm in which the electrophysiological approach and the classical sentence-picture matching approach are combined. In this chapter, the ERP method is applied to study on-line thematic role assignment in Broca patients during sentence-picture matching. Also the relation between ERP effects and behavioral responses is pursued. Finally, Chapter 6 provides a summary of the main findings of the experiments and a general discussion.

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  • Weber, A. (1998). Listening to nonnative language which violates native assimilation rules. In D. Duez (Ed.), Proceedings of the European Scientific Communication Association workshop: Sound patterns of Spontaneous Speech (pp. 101-104).

    Abstract

    Recent studies using phoneme detection tasks have shown that spoken-language processing is neither facilitated nor interfered with by optional assimilation, but is inhibited by violation of obligatory assimilation. Interpretation of these results depends on an assessment of their generality, specifically, whether they also obtain when listeners are processing nonnative language. Two separate experiments are presented in which native listeners of German and native listeners of Dutch had to detect a target fricative in legal monosyllabic Dutch nonwords. All of the nonwords were correct realisations in standard Dutch. For German listeners, however, half of the nonwords contained phoneme strings which violate the German fricative assimilation rule. Whereas the Dutch listeners showed no significant effects, German listeners detected the target fricative faster when the German fricative assimilation was violated than when no violation occurred. The results might suggest that violation of assimilation rules does not have to make processing more difficult per se.
  • Weber, A., Melinger, A., & Lara Tapia, L. (2007). The mapping of phonetic information to lexical presentations in Spanish: Evidence from eye movements. In J. Trouvain, & W. J. Barry (Eds.), Proceedings of the 16th International Congress of Phonetic Sciences (ICPhS 2007) (pp. 1941-1944). Dudweiler: Pirrot.

    Abstract

    In a visual-world study, we examined spoken-wordrecognition in Spanish. Spanish listeners followed spoken instructions to click on pictures while their eye movements were monitored. When instructed to click on the picture of a door (puerta), they experienced interference from the picture of a pig (p u e r c o ). The same interference from phonologically related items was observed when the displays contained printed names or a combination of pictures with their names printed underneath, although the effect was strongest for displays with printed names. Implications of the finding that the interference effect can be induced with standard pictorial displays as well as with orthographic displays are discussed.
  • Wegener, C. (2005). Major word classes in Savosavo. Grazer Linguistische Studien, 64, 29-52.
  • Wheeldon, L. R., & Levelt, W. J. M. (1995). Monitoring the time course of phonological encoding. Journal of Memory and Language, 34(3), 311-334. doi:10.1006/jmla.1995.1014.

    Abstract

    Three experiments examined the time course of phonological encoding in speech production. A new methodology is introduced in which subjects are required to monitor their internal speech production for prespecified target segments and syllables. Experiment 1 demonstrated that word initial target segments are monitored significantly faster than second syllable initial target segments. The addition of a concurrent articulation task (Experiment 1b) had a limited effect on performance, excluding the possibility that subjects are monitoring a subvocal articulation of the carrier word. Moreover, no relationship was observed between the pattern of monitoring latencies and the timing of the targets in subjects′ overt speech. Subjects are not, therefore, monitoring an internal phonetic representation of the carrier word. Experiment 2 used the production monitoring task to replicate the syllable monitoring effect observed in speech perception experiments: responses to targets were faster when they corresponded to the initial syllable of the carrier word than when they did not. We conclude that subjects are monitoring their internal generation of a syllabified phonological representation. Experiment 3 provides more detailed evidence concerning the time course of the generation of this representation by comparing monitoring latencies to targets within, as well as between, syllables. Some amendments to current models of phonological encoding are suggested in light of these results.
  • Wilkins, D. (1993). Route Description Elicitation. In S. C. Levinson (Ed.), Cognition and space kit 1.0 (pp. 15-28). Nijmegen: Max Planck Institute for Psycholinguistics. doi:10.17617/2.3513141.

    Abstract

    When we want to describe a path through space, but do not share a common perceptual field with a conversation partner, language has to work doubly hard. This task investigates how people communicate the navigation of space in the absence of shared visual cues, as well as collecting data on motion verbs and the roles of symmetry and landmarks in route description. Two speakers (separated by a curtain or other barrier) are each given a model of a landscape, and one participant describes standard routes through this landscape for the other to match.
  • Wilkins, D., & Hill, D. (1993). Preliminary 'Come' and 'Go' Questionnaire. In S. C. Levinson (Ed.), Cognition and space kit 1.0 (pp. 29-46). Nijmegen: Max Planck Institute for Psycholinguistics. doi:10.17617/2.3513125.

    Abstract

    The encoding of apparently ‘simple’ movement concepts such as ‘COME’ and ‘GO’ can differ widely across languages (e.g., in regard to specifying direction of motion relative to the speaker). This questionnaire is used to identify the range of use of basic motion verbs in a language, and investigate semantic parameters that are involved in high frequency ‘COME’ and ‘GO’-like terms.
  • Wilkins, D. (1995). Towards a Socio-Cultural Profile of the Communities We Work With. In D. Wilkins (Ed.), Extensions of space and beyond: manual for field elicitation for the 1995 field season (pp. 70-79). Nijmegen: Max Planck Institute for Psycholinguistics. doi:10.17617/2.3513481.

    Abstract

    Field data are drawn from a particular speech community at a certain place and time. The intent of this survey is to enrich understanding of the various socio-cultural contexts in which linguistic and “cognitive” data may have been collected, so that we can explore the role which societal, cultural and contextual factors may play in this material. The questionnaire gives guidelines concerning types of ethnographic information that are important to cross-cultural and cross-linguistic enquiry, and will be especially useful to researchers who do not have specialised training in anthropology.
  • Wilkins, D., Pederson, E., & Levinson, S. C. (1995). Background questions for the "enter"/"exit" research. In D. Wilkins (Ed.), Extensions of space and beyond: manual for field elicitation for the 1995 field season (pp. 14-16). Nijmegen: Max Planck Institute for Psycholinguistics. doi:10.17617/2.3003935.

    Abstract

    How do languages encode different kinds of movement, and what features do people pay attention to when describing motion events? This document outlines topics concerning the investigation of “enter” and “exit” events. It helps contextualise research tasks that examine this domain (see 'Motion Elicitation' and 'Enter/Exit animation') and gives some pointers about what other questions can be explored.
  • Wilkins, D., Kita, S., & Enfield, N. J. (2007). 'Ethnography of pointing' - field worker's guide. In A. Majid (Ed.), Field Manual Volume 10 (pp. 89-95). Nijmegen: Max Planck Institute for Psycholinguistics. doi:10.17617/2.492922.

    Abstract

    Pointing gestures are recognised to be a primary manifestation of human social cognition and communicative capacity. The goal of this task is to collect empirical descriptions of pointing practices in different cultural settings.
  • Wilkins, D. (1995). Motion elicitation: "moving 'in(to)'" and "moving 'out (of)'". In D. Wilkins (Ed.), Extensions of space and beyond: manual for field elicitation for the 1995 field season (pp. 4-12). Nijmegen: Max Planck Institute for Psycholinguistics. doi:10.17617/2.3003391.

    Abstract

    How do languages encode different kinds of movement, and what features do people pay attention to when describing motion events? This task investigates the expression of “enter” and “exit” activities, that is, events involving motion in(to) and motion out (of) container-like items. The researcher first uses particular stimuli (a ball, a cup, rice, etc.) to elicit descriptions of enter/exit events from one consultant, and then asks another consultant to demonstrate the event based on these descriptions. See also the related entries Enter/Exit Animation and Background Questions for Enter/Exit Research.
  • Wilkins, D. P., & Hill, D. (1995). When "go" means "come": Questioning the basicness of basic motion verbs. Cognitive Linguistics, 6, 209-260. doi:10.1515/cogl.1995.6.2-3.209.

    Abstract

    The purpose of this paper is to question some of the basic assumpiions concerning motion verbs. In particular, it examines the assumption that "come" and "go" are lexical universals which manifest a universal deictic Opposition. Against the background offive working hypotheses about the nature of'come" and ''go", this study presents a comparative investigation of t wo unrelated languages—Mparntwe Arrernte (Pama-Nyungan, Australian) and Longgu (Oceanic, Austronesian). Although the pragmatic and deictic "suppositional" complexity of"come" and "go" expressions has long been recognized, we argue that in any given language the analysis of these expressions is much more semantically and systemically complex than has been assumed in the literature. Languages vary at the lexical semantic level äs t o what is entailed by these expressions, äs well äs differing äs t o what constitutes the prototype and categorial structure for such expressions. The data also strongly suggest that, ifthere is a lexical universal "go", then this cannof be an inherently deictic expression. However, due to systemic Opposition with "come", non-deictic "go" expressions often take on a deictic Interpretation through pragmatic attribution. Thus, this crosslinguistic investigation of "come" and "go" highlights the need to consider semantics and pragmatics äs modularly separate.
  • Willems, R. M., Ozyurek, A., & Hagoort, P. (2007). When language meets action: The neural integration of gesture and speech. Cerebral Cortex, 17(10), 2322-2333. doi:10.1093/cercor/bhl141.

    Abstract

    Although generally studied in isolation, language and action often co-occur in everyday life. Here we investigated one particular form of simultaneous language and action, namely speech and gestures that speakers use in everyday communication. In a functional magnetic resonance imaging study, we identified the neural networks involved in the integration of semantic information from speech and gestures. Verbal and/or gestural content could be integrated easily or less easily with the content of the preceding part of speech. Premotor areas involved in action observation (Brodmann area [BA] 6) were found to be specifically modulated by action information "mismatching" to a language context. Importantly, an increase in integration load of both verbal and gestural information into prior speech context activated Broca's area and adjacent cortex (BA 45/47). A classical language area, Broca's area, is not only recruited for language-internal processing but also when action observation is integrated with speech. These findings provide direct evidence that action and language processing share a high-level neural integration system.
  • Willems, R. M., & Hagoort, P. (2007). Neural evidence for the interplay between language, gesture, and action: A review. Brain and Language, 101(3), 278-289. doi:10.1016/j.bandl.2007.03.004.

    Abstract

    Co-speech gestures embody a form of manual action that is tightly coupled to the language system. As such, the co-occurrence of speech and co-speech gestures is an excellent example of the interplay between language and action. There are, however, other ways in which language and action can be thought of as closely related. In this paper we will give an overview of studies in cognitive neuroscience that examine the neural underpinnings of links between language and action. Topics include neurocognitive studies of motor representations of speech sounds, action-related language, sign language and co-speech gestures. It will be concluded that there is strong evidence on the interaction between speech and gestures in the brain. This interaction however shares general properties with other domains in which there is interplay between language and action.
  • Willems, R. M. (2007). The neural construction of a Tinkertoy [‘Journal club’ review]. The Journal of Neuroscience, 27, 1509-1510. doi:10.1523/JNEUROSCI.0005-07.2007.
  • Wittek, A. (1998). Learning verb meaning via adverbial modification: Change-of-state verbs in German and the adverb "wieder" again. In A. Greenhill, M. Hughes, H. Littlefield, & H. Walsh (Eds.), Proceedings of the 22nd Annual Boston University Conference on Language Development (pp. 779-790). Somerville, MA: Cascadilla Press.
  • Wittenburg, P., Skiba, R., & Trilsbeek, P. (2005). The language archive at the MPI: Contents, tools, and technologies. Language Archives Newsletter, 5, 7-9.
  • Wohlgemuth, J., & Dirksmeyer, T. (Eds.). (2005). Bedrohte Vielfalt. Aspekte des Sprach(en)tods – Aspects of language death. Berlin: Weißensee.

    Abstract

    About 5,000 languages are spoken in the world today. More than half of them have less than 10,000 speakers, a quarter of them even fewer than 1,000. The majority of these “small” languages will not live to see the end of this century; some estimates predict that no more than a dozen languages will still be spoken by the turn of the next millennium. This collection of papers approaches the subject of language extinction through five major topics: general aspects of language death, case studies, endangered subsystems, language protection and revitalization, language ecology. In 24 articles, the authors address the causes, manifestations, and consequences of language endangerment and extinction as well as the linguistic and social changes associated with it, drawing examples from a large number of languages.
  • Womelsdorf, T., Schoffelen, J.-M., Oostenveld, R., Singer, W., Desimone, R., Engel, A. K., & Fries, P. (2007). Modulation of neuronal interactions through neuronal synchronization. Science, 316, 1609-1612. doi:10.1126/science.1139597.

    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.
  • Young, D., Altmann, G. T., Cutler, A., & Norris, D. (1993). Metrical structure and the perception of time-compressed speech. In Eurospeech 93: Vol. 2 (pp. 771-774).

    Abstract

    In the absence of explicitly marked cues to word boundaries, listeners tend to segment spoken English at the onset of strong syllables. This may suggest that under difficult listening conditions, speech should be easier to recognize where strong syllables are word-initial. We report two experiments in which listeners were presented with sentences which had been time-compressed to make listening difficult. The first study contrasted sentences in which all content words began with strong syllables with sentences in which all content words began with weak syllables. The intelligibility of the two groups of sentences did not differ significantly. Apparent rhythmic effects in the results prompted a second experiment; however, no significant effects of systematic rhythmic manipulation were observed. In both experiments, the strongest predictor of intelligibility was the rated plausibility of the sentences. We conclude that listeners' recognition responses to time-compressed speech may be strongly subject to experiential bias; effects of rhythmic structure are most likely to show up also as bias effects.
  • Zeshan, U. (2005). Sign languages. In M. Haspelmath, M. S. Dryer, D. Gil, & B. Comrie (Eds.), The world atlas of language structures (pp. 558-559). Oxford: Oxford University Press.
  • Zeshan, U. (2005). Question particles in sign languages. In M. Haspelmath, M. S. Dryer, D. Gil, & B. Comrie (Eds.), The world atlas of language structures (pp. 564-567). Oxford: Oxford University Press.
  • Zeshan, U., & Panda, S. (2005). Professional course in Indian sign language. Mumbai: Ali Yavar Jung National Institute for the Hearing Handicapped.
  • Zeshan, U., Pfau, R., & Aboh, E. (2005). When a wh-word is not a wh-word: the case of Indian sign language. In B. Tanmoy (Ed.), Yearbook of South Asian languages and linguistics 2005 (pp. 11-43). Berlin: Mouton de Gruyter.
  • Zeshan, U., Vasishta, M. N., & Sethna, M. (2005). Implementation of Indian Sign Language in educational settings. Asia Pacific Disability Rehabilitation Journal, 16(1), 16-40.

    Abstract

    This article reports on several sub-projects of research and development related to the use of Indian Sign Language in educational settings. In many countries around the world, sign languages are now recognised as the legitimate, full-fledged languages of the deaf communities that use them. In India, the development of sign language resources and their application in educational contexts, is still in its initial stages. The work reported on here, is the first principled and comprehensive effort of establishing educational programmes in Indian Sign Language at a national level. Programmes are of several types: a) Indian Sign Language instruction for hearing people; b) sign language teacher training programmes for deaf people; and c) educational materials for use in schools for the Deaf. The conceptual approach used in the programmes for deaf students is known as bilingual education, which emphasises the acquisition of a first language, Indian Sign Language, alongside the acquisition of spoken languages, primarily in their written form.
  • Zeshan, U. (2005). Irregular negatives in sign languages. In M. Haspelmath, M. S. Dryer, D. Gil, & B. Comrie (Eds.), The world atlas of language structures (pp. 560-563). Oxford: Oxford University Press.
  • Zhang, J., Bao, S., Furumai, R., Kucera, K. S., Ali, A., Dean, N. M., & Wang, X.-F. (2005). Protein phosphatase 5 is required for ATR-mediated checkpoint activation. Molecular and Cellular Biology, 25, 9910-9919. doi:10.1128/​MCB.25.22.9910-9919.2005.

    Abstract

    In response to DNA damage or replication stress, the protein kinase ATR is activated and subsequently transduces genotoxic signals to cell cycle control and DNA repair machinery through phosphorylation of a number of downstream substrates. Very little is known about the molecular mechanism by which ATR is activated in response to genotoxic insults. In this report, we demonstrate that protein phosphatase 5 (PP5) is required for the ATR-mediated checkpoint activation. PP5 forms a complex with ATR in a genotoxic stress-inducible manner. Interference with the expression or the activity of PP5 leads to impairment of the ATR-mediated phosphorylation of hRad17 and Chk1 after UV or hydroxyurea treatment. Similar results are obtained in ATM-deficient cells, suggesting that the observed defect in checkpoint signaling is the consequence of impaired functional interaction between ATR and PP5. In cells exposed to UV irradiation, PP5 is required to elicit an appropriate S-phase checkpoint response. In addition, loss of PP5 leads to premature mitosis after hydroxyurea treatment. Interestingly, reduced PP5 activity exerts differential effects on the formation of intranuclear foci by ATR and replication protein A, implicating a functional role for PP5 in a specific stage of the checkpoint signaling pathway. Taken together, our results suggest that PP5 plays a critical role in the ATR-mediated checkpoint activation.
  • Ziegler, A., DeStefano, A. L., König, I. R., Bardel, C., Brinza, D., Bull, S., Cai, Z., Glaser, B., Jiang, W., Lee, K. E., Li, C. X., Li, J., Li, X., Majoram, P., Meng, Y., Nicodemus, K. K., Platt, A., Schwarz, D. F., Shi, W., Shugart, Y. Y. and 7 moreZiegler, A., DeStefano, A. L., König, I. R., Bardel, C., Brinza, D., Bull, S., Cai, Z., Glaser, B., Jiang, W., Lee, K. E., Li, C. X., Li, J., Li, X., Majoram, P., Meng, Y., Nicodemus, K. K., Platt, A., Schwarz, D. F., Shi, W., Shugart, Y. Y., Stassen, H. H., Sun, Y. V., Won, S., Wang, W., Wahba, G., Zagaar, U. A., & Zhao, Z. (2007). Data mining, neural nets, trees–problems 2 and 3 of Genetic Analysis Workshop 15. Genetic Epidemiology, 31(Suppl 1), S51-S60. doi:10.1002/gepi.20280.

    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.

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