Reflections in a Polished Tube

When one of us (E.B.M.) dislodged a metal tube from an electric door chime recently, she inadvertently introduced her father to an attractive and instructive optical phenomenon. Looking down the highly polished inner surface of the cylinder we could see a spot surrounded by a series of bright concentric rings. The pattern looked much like the display of fringes produced by a Fabry-Perot or Michelson interferometer, except that the rings were more evenly spaced instead of crowding together strongly near the edge of the field of view. [excerpt

Connected speech processes as multitier/multiarticulator prosodic modulations

A model is proposed that interprets a variety of connected speech processes as resulting from prosodic modulations at different tiers of functional speech motor control along the hypo-hyper dimension [10]. The general background of the model is given by the trichotomy of A-, B- and C-prosodic phenomena [15] that together constitute the acoustic makeup of any speech utterance (with regard to their respective time domains at the uttarance/phrase level, the syllabic level and the segmental level)

Von Kempelen et al. : remarks on the history of articulatory-acoustic modelling

The contribution of von Kempelen’s “Mechanism of Speech” to the ‘phonetic sciences‘ will be analyzed with respect to his theoretical reasoning on speech and speech production on the one hand and on the other in connection with his practical insights during his struggle in constructing a speaking machine. Whereas in his theoretical considerations von Kempelen’s view is focussed on the natural functioning of the speech organs – cf. his membraneous glottis model – in constructing his speaking machine he clearly orientates himself towards the auditory result – cf. the bag pipe model for the sound generator used for the speaking machine instead. Concerning vowel production his theoretical description remains questionable, but his practical insight that vowels and speech sounds in general are only perceived correctly in connection with their surrounding sounds – i.e. the discovery of coarticulation – is clearly a milestone in the development of the phonetic sciences: He therefore dispenses with the Kratzenstein tubes, although they might have been based on more thorough acoustic modelling. Finally, von Kempelen’s model of speech production will be discussed in relation to the discussion of the acoustic nature of vowels afterwards [Willis and Wheatstone as well as von Helmholtz and Hermann in the 19th century and Stumpf, Chiba & Kajiyama as well as Fant and Ungeheuer in the 20th century]

Compression Driven Jamming of Athermal Frictionless Spherocylinders in Two Dimensions

We simulate numerically the compression driven jamming of athermal, frictionless, soft-core spherocylinders in two dimensions, for a range of particle aspect ratios $\alpha$. We find the critical packing fraction $\phi_J(\alpha)$ for the jamming transition, and the average number of contacts per particle $z_J(\alpha)$ at jamming. We find that both are nonmonotonic, with a peak at $\alpha\approx 1$. We find that configurations at the compression driven jamming point are always hypostatic for all $\alpha$, with $z_J<z_\mathrm{iso}=2d_f=6$ the isostatic value. We show that, for moderately elongated spherocylinders, there is no orientational ordering upon athermal compression through jamming. We analyze in detail the eigenmodes of the dynamical matrix close to the jamming point for a few different values of the aspect ratio, from nearly circular to moderately elongated. We find that there are low frequency bands containing $N(z_\mathrm{iso}-z_J)/2$ modes, such that the frequency of these modes vanish as $\phi\to\phi_J$. We consider the extended vs localized nature of these low frequency modes, and the extent to which they involve translational or rotational motion, and find many low frequency sliding modes where particles can move with little rotation. We highlight the importance of treating side-to-side contacts, along flat sides of the spherocylinder, properly for the correct determination of $z_J$. We note the singular nature of taking the $\alpha\to 0$ limit. We discuss the similarities and differences with previous work on jammed ellipses and ellipsoids, to illustrate the effects that different particle shape have on configurations at jamming.Comment: 19 pages, 21 figures, revised with published versio

Sensitive Long-Indel-Aware Alignment of Sequencing Reads

The tremdendous advances in high-throughput sequencing technologies have made population-scale sequencing as performed in the 1000 Genomes project and the Genome of the Netherlands project possible. Next-generation sequencing has allowed genom-wide discovery of variations beyond single-nucleotide polymorphisms (SNPs), in particular of structural variations (SVs) like deletions, insertions, duplications, translocations, inversions, and even more complex rearrangements. Here, we design a read aligner with special emphasis on the following properties: (1) high sensitivity, i.e. find all (reasonable) alignments; (2) ability to find (long) indels; (3) statistically sound alignment scores; and (4) runtime fast enough to be applied to whole genome data. We compare performance to BWA, bowtie2, stampy and find that our methods is especially advantageous on reads containing larger indels

Surface palatalization of polish bilabial stops : articulation and acoustics

Bilabial stops undergoing Surface Palatalization (SP) were analyzed in an EMMA/EPG study. Articulatorily, the point of maximal palatal contact and the labial opening movement were analyzed. The acoustic analysis pertained to stop related timing and the point of the highest F2-value. Results show (i) that SP yields a higher F2 at vowel onset and a lengthened opening gesture and (ii) that morphemeinduced palatalizations are distinguished from word initial ones and sandhi-palatalizations articulatorily and acoustically by a shorter delay of palatal target position with respect to stop production; (iii) no differences are found between ‘repalatalized’ and plain segments in case of sandhi palatalization

Construction of minimal DFAs from biological motifs

Deterministic finite automata (DFAs) are constructed for various purposes in computational biology. Little attention, however, has been given to the efficient construction of minimal DFAs. In this article, we define simple non-deterministic finite automata (NFAs) and prove that the standard subset construction transforms NFAs of this type into minimal DFAs. Furthermore, we show how simple NFAs can be constructed from two types of patterns popular in bioinformatics, namely (sets of) generalized strings and (generalized) strings with a Hamming neighborhood