Methods and algorithms for unsupervised learning of morphology

This is an accepted manuscript of a chapter published by Springer in Computational Linguistics and Intelligent Text Processing. CICLing 2014. Lecture Notes in Computer Science, vol 8403 in 2014 available online: https://doi.org/10.1007/978-3-642-54906-9_15 The accepted version of the publication may differ from the final published version.This paper is a survey of methods and algorithms for unsupervised learning of morphology. We provide a description of the methods and algorithms used for morphological segmentation from a computational linguistics point of view. We survey morphological segmentation methods covering methods based on MDL (minimum description length), MLE (maximum likelihood estimation), MAP (maximum a posteriori), parametric and non-parametric Bayesian approaches. A review of the evaluation schemes for unsupervised morphological segmentation is also provided along with a summary of evaluation results on the Morpho Challenge evaluations.Published versio

An Alternating GluN1-2-1-2 Subunit Arrangement in Mature NMDA Receptors

NMDA receptors (NMDARs) form glutamate-gated ion channels that play a critical role in CNS physiology and pathology. Together with AMPA and kainate receptors, NMDARs are known to operate as tetrameric complexes with four membrane-embedded subunits associating to form a single central ion-conducting pore. While AMPA and some kainate receptors can function as homomers, NMDARs are obligatory heteromers composed of homologous but distinct subunits, most usually of the GluN1 and GluN2 types. A fundamental structural feature of NMDARs, that of the subunit arrangement around the ion pore, is still controversial. Thus, in a typical NMDAR associating two GluN1 and two GluN2 subunits, there is evidence for both alternating 1/2/1/2 and non-alternating 1/1/2/2 arrangements. Here, using a combination of electrophysiological and cross-linking experiments, we provide evidence that functional GluN1/GluN2A receptors adopt the 1/2/1/2 arrangement in which like subunits are diagonal to one another. Moreover, based on the recent crystal structure of an AMPA receptor, we show that in the agonist-binding and pore regions, the GluN1 subunits occupy a “proximal” position, closer to the central axis of the channel pore than that of GluN2 subunits. Finally, results obtained with reducing agents that differ in their membrane permeability indicate that immature (intracellular) and functional (plasma-membrane inserted) pools of NMDARs can adopt different subunit arrangements, thus stressing the importance of discriminating between the two receptor pools in assembly studies. Elucidating the quaternary arrangement of NMDARs helps to define the interface between the subunits and to understand the mechanism and pharmacology of these key signaling receptors

Cardiac disease in patients with mucopolysaccharidosis: presentation, diagnosis and management

The mucopolysaccharidoses (MPSs) are inherited lysosomal storage disorders caused by the absence of functional enzymes that contribute to the degradation of glycosaminoglycans (GAGs). The progressive systemic deposition of GAGs results in multi-organ system dysfunction that varies with the particular GAG deposited and the specific enzyme mutation(s) present. Cardiac involvement has been reported in all MPS syndromes and is a common and early feature, particularly for those with MPS I, II, and VI. Cardiac valve thickening, dysfunction (more severe for left-sided than for right-sided valves), and hypertrophy are commonly present; conduction abnormalities, coronary artery and other vascular involvement may also occur. Cardiac disease emerges silently and contributes significantly to early mortality

Breaking Symmetric Cryptosystems Using Quantum Period Finding

Due to Shor's algorithm, quantum computers are a severe threat for public key cryptography. This motivated the cryptographic community to search for quantum-safe solutions. On the other hand, the impact of quantum computing on secret key cryptography is much less understood. In this paper, we consider attacks where an adversary can query an oracle implementing a cryptographic primitive in a quantum superposition of different states. This model gives a lot of power to the adversary, but recent results show that it is nonetheless possible to build secure cryptosystems in it. We study applications of a quantum procedure called Simon's algorithm (the simplest quantum period finding algorithm) in order to attack symmetric cryptosystems in this model. Following previous works in this direction, we show that several classical attacks based on finding collisions can be dramatically sped up using Simon's algorithm: finding a collision requires $\Omega(2^{n/2})$ queries in the classical setting, but when collisions happen with some hidden periodicity, they can be found with only $O(n)$ queries in the quantum model. We obtain attacks with very strong implications. First, we show that the most widely used modes of operation for authentication and authenticated encryption e.g. CBC-MAC, PMAC, GMAC, GCM, and OCB) are completely broken in this security model. Our attacks are also applicable to many CAESAR candidates: CLOC, AEZ, COPA, OTR, POET, OMD, and Minalpher. This is quite surprising compared to the situation with encryption modes: Anand et al. show that standard modes are secure with a quantum-secure PRF. Second, we show that Simon's algorithm can also be applied to slide attacks, leading to an exponential speed-up of a classical symmetric cryptanalysis technique in the quantum model.Comment: 31 pages, 14 figure

GYGD pore motifs in neighbouring potassium channel subunits interact to determine ion selectivity

Cells maintain a negative resting membrane potential through the constitutive activity of background K+ channels. A novel multigene family of such K+ channels has recently been identified. A unique characteristic of these K+ channels is the presence of two homologous, subunit-like domains, each containing a pore-forming region. Sequence co-variations in the GYGD signature motifs of the two pore regions suggested an interaction between neighbouring pore domains.Mutations of the GYGD motif in the rat drk1 (Kv2.1) K+ channel showed that the tyrosine (Y) position was important for K+ selectivity and single channel conductance, whereas the aspartate (D) position was a critical determinant of open state stability.Tandem constructs engineered to mimic the GYGx-GxGD pattern seen in two-domain K+ channels delineated a co-operative intersubunit interaction between the Y and D positions, which determined ion selectivity, conductance and gating.In the bacterial KcsA K+ channel crystal structure, the equivalent aspartate residue (D80) does not directly interact with permeating K+ ions. However, the data presented here show that the D position is able to fine-tune ion selectivity through a functional interaction with the Y position in the neighbouring subunit.These data indicate a physiological basis for the extensive sequence variation seen in the GYGD motifs of two-domain K+ channels. It is suggested that a cell can precisely regulate its resting membrane potential by selectively expressing a complement of two-domain K+ channels