Efficient motif finding algorithms for large-alphabet inputs

<p>Abstract</p> <p>Background</p> <p>We consider the problem of identifying motifs, recurring or conserved patterns, in the biological sequence data sets. To solve this task, we present a new deterministic algorithm for finding patterns that are embedded as exact or inexact instances in all or most of the input strings.</p> <p>Results</p> <p>The proposed algorithm (1) improves search efficiency compared to existing algorithms, and (2) scales well with the size of alphabet. On a synthetic planted DNA motif finding problem our algorithm is over 10× more efficient than MITRA, PMSPrune, and RISOTTO for long motifs. Improvements are orders of magnitude higher in the same setting with large alphabets. On benchmark TF-binding site problems (FNP, CRP, LexA) we observed reduction in running time of over 12×, with high detection accuracy. The algorithm was also successful in rapidly identifying protein motifs in Lipocalin, Zinc metallopeptidase, and supersecondary structure motifs for Cadherin and Immunoglobin families.</p> <p>Conclusions</p> <p>Our algorithm reduces computational complexity of the current motif finding algorithms and demonstrate strong running time improvements over existing exact algorithms, especially in important and difficult cases of large-alphabet sequences.</p

Correlating matched-filter model for analysis and optimisation of neural networks

A new formalism is described for modelling neural networks by means of which a clear physical understanding of the network behaviour can be gained. In essence, the neural net is represented by an equivalent network of matched filters which is then analysed by standard correlation techniques. The procedure is demonstrated on the synchronous Little-Hopfield network. It is shown how the ability of this network to discriminate between stored binary, bipolar codes is optimised if the stored codes are chosen to be orthogonal. However, such a choice will not often be possible and so a new neural network architecture is proposed which enables the same discrimination to be obtained for arbitrary stored codes. The most efficient convergence of the synchronous Little-Hopfield net is obtained when the neurons are connected to themselves with a weight equal to the number of stored codes. The processing gain is presented for this case. The paper goes on to show how this modelling technique can be extended to analyse the behaviour of both hard and soft neural threshold responses and a novel time-dependent threshold response is described

Patent arterial duct, bottle-meal, and fatal myocardial ischaemia

A patent arterial duct in pre-term neonates is frequent. Systemic complications consecutive to left-to-right shunting are well known but fatal myocardial ischaemia has not been described till now. The presented premature baby died from catecholamine refractory cardiogenic shock. Autoptic examination revealed acute ischaemic changes predominantly in the inner third of myocardium, speaking of coronary hypoperfusion due to a steal phenomenon secondary to the patent arterial duc

Dispersion and polarization conversion of whispering gallery modes in arbitrary cross-section nanowires

We investigate theoretically the optical properties of Nano-Wires (NWs) with cross sections having either discrete or cylindrical symmetry. The material forming the wire is birefringent, showing a different dielectric response in the plane and along the axis of the wire, which is typically the case for wires made of wurtzite materials, such as ZnO or GaN. We look for solutions of Maxwell`s equations having the proper symmetry. The dispersions and the linewidths versus angle of incident light for the modes having high momentum in the cross-section plane, so called whispering gallery modes, are calculated. We put a special emphasis on the case of hexagonal cross sections. The energy positions of the modes for a set of azimuthal quantum numbers are shown. We demonstrate the dependence of the energy splitting between TE and TM modes versus birefringence. The polarization conversion from TE to TM with increase of the axial wave vectoris discussed for both cylindrical and discrete symmetry.Comment: 9 pages, 10 figure

TRANSFORMERS: Robust spatial joins on non-uniform data distributions

Spatial joins are becoming increasingly ubiquitous in many applications, particularly in the scientific domain. While several approaches have been proposed for joining spatial datasets, each of them has a strength for a particular type of density ratio among the joined datasets. More generally, no single proposed method can efficiently join two spatial datasets in a robust manner with respect to their data distributions. Some approaches do well for datasets with contrasting densities while others do better with similar densities. None of them does well when the datasets have locally divergent data distributions. In this paper we develop TRANSFORMERS, an efficient and robust spatial join approach that is indifferent to such variations of distribution among the joined data. TRANSFORMERS achieves this feat by departing from the state-of-the-art through adapting the join strategy and data layout to local density variations among the joined data. It employs a join method based on data-oriented partitioning when joining areas of substantially different local densities, whereas it uses big partitions (as in space-oriented partitioning) when the densities are similar, while seamlessly switching among these two strategies at runtime. We experimentally demonstrate that TRANSFORMERS outperforms state-of-the-art approaches by a factor of between 2 and 8

Gene expression profiles among murine strains segregate with distinct differences in the progression of radiation-induced lung disease.

Molecular mechanisms underlying development of acute pneumonitis and/or late fibrosis following thoracic irradiation remain poorly understood. Here, we hypothesize that heterogeneity in disease progression and phenotypic expression of radiation-induced lung disease (RILD) across murine strains presents an opportunity to better elucidate mechanisms driving tissue response toward pneumonitis and/or fibrosis. Distinct differences in disease progression were observed in age- and sex-matched CBA/J, C57L/J and C57BL/6J mice over 1 year after graded doses of whole-thorax lung irradiation (WTLI). Separately, comparison of gene expression profiles in lung tissue 24 h post-exposure demonstrated \u3e5000 genes to be differentially expressed (P\u3c0.01; \u3etwofold change) between strains with early versus late onset of disease. An immediate divergence in early tissue response between radiation-sensitive and -resistant strains was observed. In pneumonitis-prone C57L/J mice, differentially expressed genes were enriched in proinflammatory pathways, whereas in fibrosis-prone C57BL/6J mice, genes were enriched in pathways involved in purine and pyrimidine synthesis, DNA replication and cell division. At 24 h post-WTLI, different patterns of cellular damage were observed at the ultrastructural level among strains but microscopic damage was not yet evident under light microscopy. These data point toward a fundamental difference in patterns of early pulmonary tissue response to WTLI, consistent with the macroscopic expression of injury manifesting weeks to months after exposure. Understanding the mechanisms underlying development of RILD might lead to more rational selection of therapeutic interventions to mitigate healthy tissue damage

Electric generation of vortices in an exciton-polariton superfluid

We have theoretically demonstrated the on demand electric generation of vortices in an exciton-polariton superfluid. Electric pulses applied to a horseshoe-shaped metallic mesa, deposited on top of the microcavity, generate a non-cylindrically symmetric solitonic wave in the system. Breakdown of its wavefront at focal points leads to the formation of vortex-antivortex pairs which subsequently propagate in the superfluid. The trajectory of these vortex dipoles can be controlled by applying a voltage to additional electrodes. They can be confined within channels formed by metallic stripes and unbound by a wedged mesa giving birth to grey solitons. Finally single static vortices can be generated using a single metallic plate configuration.Comment: 7 pages and 7 figure

GeV-scale neutrinos: interactions with mesons and DUNE sensitivity

The simplest extension of the SM to account for the observed neutrino masses and mixings is the addition of at least two singlet fermions (or right-handed neutrinos). If their masses lie at or below the GeV scale, such new fermions would be produced in meson decays. Similarly, provided they are sufficiently heavy, their decay channels may involve mesons in the final state. Although the couplings between mesons and heavy neutrinos have been computed previously, significant discrepancies can be found in the literature. The aim of this paper is to clarify such discrepancies and provide consistent expressions for all relevant effective operators involving mesons with masses up to 2 GeV. Moreover, the effective Lagrangians obtained for both the Dirac and Majorana scenarios are made publicly available as FeynRules models so that fully differential event distributions can be easily simulated. As an application of our setup, we numerically compute the expected sensitivity of the DUNE near detector to these heavy neutral leptons.Comment: v4: Minor updates and text modifications. Published in EPJC. FeynRules models performance improved, B mesons include

Eye movement analysis and cognitive assessment: the use of comparative visual search tasks in a non-immersive vr application

Background: An adequate behavioral response depends on attentional and mnesic processes. When these basic cognitive functions are impaired, the use of non-immersive Virtual Reality Applications (VRAs) can be a reliable technique for assessing the level of impairment. However, most non-immersive VRAs use indirect measures to make inferences about visual attention and mnesic processes (e.g., time to task completion, error rate). Objectives: To examine whether the eye movement analysis through eye tracking (ET) can be a reliable method to probe more effectively where and how attention is deployed and how it is linked with visual working memory during comparative visual search tasks (CVSTs) in non-immersive VRAs. Methods: The eye movements of 50 healthy participants were continuously recorded while CVSTs, selected from a set of cognitive tasks in the Systemic Lisbon Battery (SLB). Then a VRA designed to assess of cognitive impairments were randomly presented. Results: The total fixation duration, the number of visits in the areas of interest and in the interstimulus space, along with the total execution time was significantly different as a function of the Mini Mental State Examination (MMSE) scores. Conclusions: The present study demonstrates that CVSTs in SLB, when combined with ET, can be a reliable and unobtrusive method for assessing cognitive abilities in healthy individuals, opening it to potential use in clinical samples.info:eu-repo/semantics/submittedVersio

Formal Derivation of Concurrent Garbage Collectors

Concurrent garbage collectors are notoriously difficult to implement correctly. Previous approaches to the issue of producing correct collectors have mainly been based on posit-and-prove verification or on the application of domain-specific templates and transformations. We show how to derive the upper reaches of a family of concurrent garbage collectors by refinement from a formal specification, emphasizing the application of domain-independent design theories and transformations. A key contribution is an extension to the classical lattice-theoretic fixpoint theorems to account for the dynamics of concurrent mutation and collection.Comment: 38 pages, 21 figures. The short version of this paper appeared in the Proceedings of MPC 201