Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs

We present kleuren, a novel assembly-free method to reconstruct phylogenetic trees using the Colored de Bruijn Graph. kleuren works by constructing the Colored de Bruijn Graph and then traversing it, finding bubble structures in the graph that provide phylogenetic signal. The bubbles are then aligned and concatenated to form a supermatrix, from which a phylogenetic tree is inferred. We introduce the algorithms that kleuren uses to accomplish this task, and show its performance on reconstructing the phylogenetic tree of 12 Drosophila species. kleuren reconstructed the established phylogenetic tree accurately, and is a viable tool for phylogenetic tree reconstruction using whole genome sequences. Software package available at: https://github.com/Colelyman/kleurenComment: 6 pages, 3 figures, accepted at BIBE 2017. Minor modifications to the text due to reviewer feedback and fixed typo

Morphological variation and sensitivity to frequency of forms among native speakers of Czech

This article looks at inter-speaker variation in two environments: the genitive and locative singular cases of masculine ‘hard inanimate’ nouns in Czech, using a large-scale survey of native speakers that used two tasks to test their preferences for certain forms (acceptability) and their choices (gap filling). Our hypothesis that such variation exists was upheld, but only within limited parameters. Most biographical data (age, gender, education) played no role in respondents’ choices or preferences. Their region of origin played a small but significant role, although not the one expected. Relating the two types of tasks to each other, we found that respondents’ use of the ratings scale did not correlate to their choice of forms, but their overall strength of preference for one form over another did correlate with their choices. Inter-speaker variation does thus go some way to explaining the persistent diversity in this paradigm and arguably may contribute to its maintenance

Utterance Selection Model of Language Change

We present a mathematical formulation of a theory of language change. The theory is evolutionary in nature and has close analogies with theories of population genetics. The mathematical structure we construct similarly has correspondences with the Fisher-Wright model of population genetics, but there are significant differences. The continuous time formulation of the model is expressed in terms of a Fokker-Planck equation. This equation is exactly soluble in the case of a single speaker and can be investigated analytically in the case of multiple speakers who communicate equally with all other speakers and give their utterances equal weight. Whilst the stationary properties of this system have much in common with the single-speaker case, time-dependent properties are richer. In the particular case where linguistic forms can become extinct, we find that the presence of many speakers causes a two-stage relaxation, the first being a common marginal distribution that persists for a long time as a consequence of ultimate extinction being due to rare fluctuations.Comment: 21 pages, 17 figure

The source ambiguity problem: Distinguishing the effects of grammar and processing on acceptability judgments

Judgments of linguistic unacceptability may theoretically arise from either grammatical deviance or significant processing difficulty. Acceptability data are thus naturally ambiguous in theories that explicitly distinguish formal and functional constraints. Here, we consider this source ambiguity problem in the context of Superiority effects: the dispreference for ordering a wh-phrase in front of a syntactically “superior” wh-phrase in multiple wh-questions, e.g., What did who buy? More specifically, we consider the acceptability contrast between such examples and so-called D-linked examples, e.g., Which toys did which parents buy? Evidence from acceptability and self-paced reading experiments demonstrates that (i) judgments and processing times for Superiority violations vary in parallel, as determined by the kind of wh-phrases they contain, (ii) judgments increase with exposure, while processing times decrease, (iii) reading times are highly predictive of acceptability judgments for the same items, and (iv) the effects of the complexity of the wh-phrases combine in both acceptability judgments and reading times. This evidence supports the conclusion that D-linking effects are likely reducible to independently motivated cognitive mechanisms whose effects emerge in a wide range of sentence contexts. This in turn suggests that Superiority effects, in general, may owe their character to differential processing difficulty

The impact of sound field systems on learning and attention in elementary school classrooms

Purpose: An evaluation of the installation and use of sound field systems (SFS) was carried out to investigate their impact on teaching and learning in elementary school classrooms. Methods: The evaluation included acoustic surveys of classrooms, questionnaire surveys of students and teachers and experimental testing of students with and without the use of SFS. Students ’ perceptions of classroom environments and objective data evaluating change in performance on cognitive and academic assessments with amplification over a six month period are reported. Results: Teachers were positive about the use of SFS in improving children’s listening and attention to verbal instructions. Over time students in amplified classrooms did not differ from those in nonamplified classrooms in their reports of listening conditions, nor did their performance differ in measures of numeracy, reading or spelling. Use of SFS in the classrooms resulted in significantly larger gains in performance in the number of correct items on the nonverbal measure of speed of processing and the measure of listening comprehension. Analysis controlling for classroom acoustics indicated that students ’ listening comprehension score

Predicting the Position of Attributive Adjectives in the French NP

Cet article est une version révisée de l'article paru dans Student session of the European Summer School for Logic, Language and Information, Copenhague : Danemark (2010)International audienceThis article proposes a quantitative study of the placement alternation for the adjective within the noun phrase in French. Taking the hypothesis that position constraints are mostly preferential as a starting point, we develop a methodology based on statistical inference in order to provide a formal account of the relative importance of different groups of constraints. Results show the relative importance of lexical constraints and that frequency-based and length constraints are the best predictors. This suggests that the placement of adjectives not only depends on our knowledge of lexical items but also on the knowledge of the way in which we use them in discourse, i.e. on usage

Genetic association of CDC2 with cerebrospinal fluid tau in Alzheimer's disease

We have recently reported that a polymorphism in the cell division cycle (CDC2) gene, designated Ex6 + 7I/D, is associated with Alzheimer's disease (AD). The CDC2 gene is located on chromosome 10q21.1 close to the marker D10S1225 linked to AD. Active cdc2 accumulates in neurons containing neurofibrillary tangles (NFT), a process that can precede the formation of NFT. Therefore, CDC2 is a promising candidate susceptibility gene for AD. We investigated the possible effects of the CDC2 polymorphism on cerebrospinal fluid (CSF) biomarkers in AD patients. CDC2 genotypes were evaluated in relation to CSF protein levels of total tau, phospho-tau and beta-amyloid (1-42) in AD patients and control individuals, and in relation to the amount of senile plaques and NFT in the frontal cortex and in the hippocampus in patients with autopsy-proven AD and controls. The CDC2 Ex6 + 7I allele was associated with a gene dose-dependent increase of CSF total tau levels (F-2,F- 626 = 7.0, p = 0.001) and the homozygous CDC2Ex6 +7II genotype was significantly more frequent among AD patients compared to controls (p = 0.006, OR = 1.57, 95% CI 1.13-2.17). Our results provide further evidence for an involvement of cdc2 in the pathogenesis of AD. Copyright (C) 2005 S. Karger AG, Basel

Preverbs: an introduction

The notion ‘preverb’ is a traditional descriptive notion in Indo-European linguistics. It refers to morphemes that appear in front of a verb, and which form a close semantic unit with that verb. In many cases, the morpheme that functions as a preverb can also function without a preverbal context, often as an adverb or an adposition. Most linguists use the notion ‘preverb’ as a cover term for preverbal words and preverbal prefixes. The preverb may be separated from the verb whilst retaining its close cohesion with the verb, which is called ‘tmesis’. It may also develop into a bound morpheme, that is, a prefix inseparable from the verb, with concomitant reduction of phonological form in some cases. If the preverb has become a real prefix, we may use the more specific notion of ‘complex verb’, whereas we take the notion ‘complex predicate’ to refer generally to multi-morphemic expressions with verbal valency. That is, we make a terminological distinction between complex predicates and complex verbs. The latter are multi-morphemic, but behave as single grammatical words