A cascaded approach to normalising gene mentions in biomedical literature

Linking gene and protein names mentioned in the literature to unique identifiers in referent genomic databases is an essential step in accessing and integrating knowledge in the biomedical domain. However, it remains a challenging task due to lexical and terminological variation, and ambiguity of gene name mentions in documents. We present a generic and effective rule-based approach to link gene mentions in the literature to referent genomic databases, where pre-processing of both gene synonyms in the databases and gene mentions in text are first applied. The mapping method employs a cascaded approach, which combines exact, exact-like and token-based approximate matching by using flexible representations of a gene synonym dictionary and gene mentions generated during the pre-processing phase. We also consider multi-gene name mentions and permutation of components in gene names. A systematic evaluation of the suggested methods has identified steps that are beneficial for improving either precision or recall in gene name identification. The results of the experiments on the BioCreAtIvE2 data sets (identification of human gene names) demonstrated that our methods achieved highly encouraging results with F-measure of up to 81.20%

Localized modes in mini-gaps opened by periodically modulated intersite coupling in two-dimensional nonlinear lattices

Spatially periodic modulation of the intersite coupling in two-dimensional (2D) nonlinear lattices modifies the eigenvalue spectrum by opening mini-gaps in it. This work aims to build stable localized modes in the new bandgaps. Numerical analysis shows that single-peak and composite two- and four-peak discrete static solitons and breathers emerge as such modes in certain parameter areas inside the mini-gaps of the 2D superlattice induced by the periodic modulation of the intersite coupling along both directions.The single-peak solitons and four-peak discrete solitons are stable in a part of their existence domain, while unstable stationary states (in particular, two-soliton complexes) may readily transform into robust localized breathers.Comment: Chaos, in pres

Constrained Dynamics of Tachyon Field in FRWL Spacetime

In this paper we continue study of tachyon scalar field described by a Dirac-Born-Infeld (DBI) type action with constraints in the cosmological context. The proposed extension of the system introducing an auxiliary field in the minisuperspace framework is discussed. A new equivalent set of constraints is constructed, satisfying the usual regularity conditions.Comment: 10 pages, to be published in the Special Issue of the Facta Universitatis Series: Physics, Chemistry and Technology devoted to the SEENET-MTP Balkan Workshop BSW2019 (3-14 June 2018, Nis, Serbia

Soliton stability and collapse in the discrete nonpolynomial Schrodinger equation with dipole-dipole interactions

The stability and collapse of fundamental unstaggered bright solitons in the discrete Schrodinger equation with the nonpolynomial on-site nonlinearity, which models a nearly one-dimensional Bose-Einstein condensate trapped in a deep optical lattice, are studied in the presence of the long-range dipole-dipole (DD) interactions. The cases of both attractive and repulsive contact and DD interaction are considered. The results are summarized in the form of stability/collapse diagrams in the parametric space of the model, which demonstrate that the the attractive DD interactions stabilize the solitons and help to prevent the collapse. Mobility of the discrete solitons is briefly considered too.Comment: 6 figure

High- and low-frequency phonon modes in dipolar quantum gases trapped in deep lattices

We study normal modes propagating on top of the stable uniform background in arrays of dipolar Bose-Einstein condensate (BEC) droplets trapped in a deep optical lattice. Both the on-site mean-field dynamics of the droplets and their displacement due to the repulsive dipole-dipole interactions (DDIs) are taken into account. Dispersion relations for two modes, \textit{viz}., high- and low- frequency counterparts of optical and acoustic phonon modes in condensed matter, are derived analytically and verified by direct simulations, for both cases of the repulsive and attractive contact interactions. The (counterpart of the) optical-phonon branch does not exist without the DDIs. These results are relevant in the connection to emerging experimental techniques enabling real-time imaging of the condensate dynamics and direct experimental measurement of phonon dispersion relations in BECs.Comment: Physical Review A, in pres

Miller Fisher Syndrome: The Localisation of Pathology

The syndrome described by Miller Fisher (1956) comprises an acute ophthalmoplegia (or ophthalmoparesis) associated with severe ataxia, predominantly of gait and trunk, and a mild to moderate increase in the cerebrospinal fluid protein level unassociated with pleocytosis. As in the Guillain-Barre syndrome, there is usually an antecedent infection commonly of the upper respiratory tract. The illness has a benign course with rapid and usually complete recovery. The precise nature, aetiology and main site of pathological changes in the Miller Fisher syndrome are not well understood and have been the subject of some controversy. Since neuropathological evidence from typical cases of the syndrome is lacking, due to the benign nature of the illness, hypotheses have been based on clinical observations. Opinions have suggested either that the syndrome is related to acute inflammatory demyelinating polyradiculoneuropathy, or, that it is due to a brainstem inflammatory lesion, or, that both such types of component are present. This thesis is an attempt to address the question of identification of the main site of action of the pathological process in the Miller Fisher syndrome. Comprehensive multimodal and serial neurophysiological investigations, testing both the peripheral and central nervous system, have been applied to a group of seven typical patients with the syndrome at standardised intervals from onset of the illness up to and after full recovery. The results are compared with those from 20 patients with classical Guillain-Barre syndrome systematically investigated in a similar way, and with those previously reported in the literature. The findings are then discussed in the context of peripheral versus central nervous system dysfunction. In the first chapter, a review is presented of a small number of reports of similar cases described incompletely prior to Fisher's original 1956 account, followed by an analysis of 84 patients with the syndrome reported in the literature and by an outline of some of the controversies concerning the underlying pathology. Chapter 2 describes the clinical findings together with the course, laboratory investigations and case analysis of 7 patients with typical Miller Fisher syndrome. In chapter 3, the neurophysiological methods and the timing of their application are detailed, together with a critical appraisal of their reliability. The investigations used included: 1. electromyography. 2. nerve conduction studies. 3. late response (H-reflex and F-wave) studies. 4. estimation of motor unit numbers and motor unit potentials analysis. 5. peripheral facial nerve and blink reflex studies. 6. computerised quantitative sensory (thermal and vibration) threshold measurements. 7. muscle silent period studies. 8. multimodal evoked potentials (somatosensory, brainstem auditory and visual) studies. 9. electroencephalography. 10. Quantitative pupillometric and pharmacological observations on the pupils. The results of the neurophysiological investigations and their evolution with time are presented in chapter 4. The findings indicated the presence of a significant dysfunction in the peripheral nerves of the limbs, the facial nerves and in the postganglionic parasympathetic fibres subserving the pupils. They also provided support for a peripheral disturbance as the underlying mechanism for the ataxia observed in patients with the Miller Fisher syndrome. The results of comparably timed, similar comprehensive neurophysiological investigation in 20 patients with the Guillain-Barre syndrome for a total period of 18 months are described in chapter 5. The results are compared with those of other studies from the literature. In chapter 6, the lack of any significant neurophysiological or brain imaging evidence for central nervous system involvement in the group of patients with the Miller Fisher syndrome is outlined. In the main discussion in chapter 7, the neurophysiological findings in the patients with the Miller Fisher syndrome are critically assessed and compared with those from the patients with the Guillain-Barre syndrome in the present study and in reports from the literature. This discussion is set in the context of concepts of peripheral and of central nervous system involvement. Clinical similarities between the Miller Fisher and the Guillain-Barre syndromes are outlined and 20 patients who appear to have overlapping features which suggest a link or continuum between the two syndromes, are reviewed from the literature. (Abstract shortened by ProQuest.)

Discrete solitons in an array of quantum dots

We develop a theory for the interaction of classical light fields with an a chain of coupled quantum dots (QDs), in the strong-coupling regime, taking into account the local-field effects. The QD chain is modeled by a one-dimensional (1D) periodic array of two-level quantum particles with tunnel coupling between adjacent ones. The local-field effect is taken into regard as QD depolarization in the Hartree-Fock-Bogoliubov approximation. The dynamics of the chain is described by a system of two discrete nonlinear Schr\"{o}dinger (DNLS) equations for local amplitudes of the probabilities of the ground and first excited states. The two equations are coupled by a cross-phase-modulation cubic terms, produced by the local-field action, and by linear terms too. In comparison with previously studied DNLS systems, an essentially new feature is a phase shift between the intersite-hopping constants in the two equations. By means of numerical solutions, we demonstrate that, in this QD chain, Rabi oscillations (RO) self-trap into stable bright\textit{\ Rabi solitons} or \textit{Rabi breathers}. Mobility of the solitons is considered too. The related behavior of observable quantities, such as energy, inversion, and electric-current density, is given a physical interpretation. The results apply to a realistic region of physical parameters.Comment: 12 pages, 10 figures, Phys. Rev. B, in pres