Generic Subsequence Matching Framework: Modularity, Flexibility, Efficiency

Subsequence matching has appeared to be an ideal approach for solving many problems related to the fields of data mining and similarity retrieval. It has been shown that almost any data class (audio, image, biometrics, signals) is or can be represented by some kind of time series or string of symbols, which can be seen as an input for various subsequence matching approaches. The variety of data types, specific tasks and their partial or full solutions is so wide that the choice, implementation and parametrization of a suitable solution for a given task might be complicated and time-consuming; a possibly fruitful combination of fragments from different research areas may not be obvious nor easy to realize. The leading authors of this field also mention the implementation bias that makes difficult a proper comparison of competing approaches. Therefore we present a new generic Subsequence Matching Framework (SMF) that tries to overcome the aforementioned problems by a uniform frame that simplifies and speeds up the design, development and evaluation of subsequence matching related systems. We identify several relatively separate subtasks solved differently over the literature and SMF enables to combine them in straightforward manner achieving new quality and efficiency. This framework can be used in many application domains and its components can be reused effectively. Its strictly modular architecture and openness enables also involvement of efficient solutions from different fields, for instance efficient metric-based indexes. This is an extended version of a paper published on DEXA 2012.Comment: This is an extended version of a paper published on DEXA 201

Shigella flexneri utilize the spectrin cytoskeleton during invasion and comet tail generation

<p>Abstract</p> <p>Background</p> <p>The spectrin cytoskeleton is emerging as an important host cell target of enteric bacterial pathogens. Recent studies have identified a crucial role for spectrin and its associated proteins during key pathogenic processes of <it>Listeria monocytogenes </it>and <it>Salmonella </it>Typhimurium infections. Here we investigate the involvement of spectrin cytoskeletal components during the pathogenesis of the invasive pathogen <it>Shigella flexneri.</it></p> <p>Results</p> <p>Immunofluorescent microscopy reveals that protein 4.1 (p4.1), but not adducin or spectrin, is robustly recruited to sites of <it>S. flexneri </it>membrane ruffling during epithelial cell invasion. Through siRNA-mediated knockdowns, we identify an important role for spectrin and the associated proteins adducin and p4.1 during <it>S. flexneri </it>invasion. Following internalization, all three proteins are recruited to the internalized bacteria, however upon generation of actin-rich comet tails, we observed spectrin recruitment to those structures in the absence of adducin or p4.1.</p> <p>Conclusion</p> <p>These findings highlight the importance of the spectrin cytoskeletal network during <it>S. flexneri </it>pathogenesis and further demonstrate that pathogenic events that were once thought to exclusively recruit the actin cytoskeletal system require additional cytoskeletal networks.</p

A comparative study for the pair-creation contact process using series expansions

A comparative study between two distinct perturbative series expansions for the pair-creation contact process is presented. In contrast to the ordinary contact process, whose supercritical series expansions provide accurate estimates for its critical behavior, the supercritical approach does not work properly when applied to the pair-creation process. To circumvent this problem a procedure is introduced in which one-site creation is added to the pair-creation. An alternative method is the generation of subcritical series expansions which works even for the case of the pure pair-creation process. Differently from the supercritical case, the subcritical series yields estimates that are compatible with numerical simulations

Thermal Impact on Spiking Properties in Hodgkin-Huxley Neuron with Synaptic Stimulus

The effect of environmental temperature on neuronal spiking behaviors is investigated by numerically simulating the temperature dependence of spiking threshold of the Hodgkin-Huxley neuron subject to synaptic stimulus. We find that the spiking threshold exhibits a global minimum in a "comfortable temperature" range where spike initiation needs weakest synaptic strength, indicating the occurrence of optimal use of synaptic transmission in neural system. We further explore the biophysical origin of this phenomenon in ion channel gating kinetics and also discuss its possible biological relevance in information processing in neural systems.Comment: 10 pages, 4 figure

X-Ray Scattering at FeCo(001) Surfaces and the Crossover between Ordinary and Normal Transitions

In a recent experiment by Krimmel et al. [PRL 78, 3880 (1997)], the critical behavior of FeCo near a (001) surface was studied by x-ray scattering. Here the experimental data are reanalyzed, taking into account recent theoretical results on order-parameter profiles in the crossover regime between ordinary and normal transitions. Excellent agreement between theoretical expectations and the experimental results is found.Comment: 9 pages, Latex, 1 PostScript figure, to be published in Phys.Rev.

Psychosocial outcomes of an inclusive adapted sport and adventurous training course for military personnel.

PURPOSE: To explore the psychosocial outcomes of an inclusive adapted sport and adventurous training course that aims to support the rehabilitation and personal development of military personnel who have sustained physical and/or psychological disability. METHOD: Narrative life story interviews were conducted with 11 men aged 20-43 taking part in one of the 5-day courses. A thematic narrative analysis was conducted, focusing on accounts that provided insights into personally meaningful psychosocial outcomes of the course. FINDINGS: We identified six themes, falling into two distinct clusters. "Bringing me back to myself" was achieved through the themes of (1) returning to activity, (2) rediscovering a sense of purpose, and (3) reconnecting to others. "New rooms to explore" was realised through (4) experiencing new activities, (5) being valued/respected/cared for and (6) being inspired by other people. CONCLUSION: Involvement in the course stimulated a balance of present- and future-oriented psychosocial outcomes through which participants both recreated aspects of themselves that had been lost through injury/trauma and moved forward with their lives as a result of new horizons of possibility. IMPLICATIONS FOR REHABILITATION: This 5-day inclusive adapted sport and adventurous training course offered meaningful psychosocial outcomes among military personnel who had experienced physical and/or psychological disability. The course helped participants recover aspects of their previous life and self through becoming physically active again, rediscovering a sense of purpose and reconnecting to others. Participants describe a broadening of life horizons as a result of the course, through new activities, being valued/respected/cared for, and being inspired by other people

Four Kinds of Reproducibility in Scale Analysis

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/68060/2/10.1177_001316445501500416.pd

High-Throughput N-Glycan Analysis with Rapid Magnetic Bead-Based Sample Preparation

N-glycan profi ling of therapeutic glycoproteins is essential to ensure the activity and effi cacy of these promising new-generation drugs. The N-linked glycan moieties of these entities highly affect circulation half- life, immunogenicity and receptor-binding activity as well as physicochemical and thermal stability properties. In addition, more than half of the biopharmaceuticals are glycoproteins representing multibillion dollar worldwide business, further emphasizing the importance of their analysis. In the biomedical fi eld, on the other hand, revealing disease-related glycan structure alterations holds the promise of the discovery of new biomarkers for early diagnostics. Therefore, there is a great demand for widely applicable, high-throughput sample preparation and analysis methods for N-glycan profi ling of glycoproteins. One of the newest exciting developments of the fi eld is the magnetic bead based glycoprotein sample preparation technique. A detailed protocol of this method is given in this chapter in conjunction with rapid capillary electrophoresis analysis of the prepared samples by laser induced fl uorescence detection (CE-LIF). N-glycans are digested by the endoglycosidase PNGase F and the released carbohydrates are labeled with the charged fl uorophore dye of aminopyrenetrisulfonate (APTS). Effective glycan capture by magnetic microparticles enabled fast, easily automated sample preparation both in individual (single vial) and 96-well plate formats, including excess dye removal. Rapid separation of APTS labeled IgG glycans is also shown utilizing an optimized CE-LIF protocol

A grid-based infrastructure for distributed retrieval

In large-scale distributed retrieval, challenges of latency, heterogeneity, and dynamicity emphasise the importance of infrastructural support in reducing the development costs of state-of-the-art solutions. We present a service-based infrastructure for distributed retrieval which blends middleware facilities and a design framework to ‘lift’ the resource sharing approach and the computational services of a European Grid platform into the domain of e-Science applications. In this paper, we give an overview of the DILIGENT Search Framework and illustrate its exploitation in the field of Earth Science

Typing and Compositionality for Security Protocols::A Generalization to the Geometric Fragment

We integrate, and improve upon, prior relative soundness results of two kinds. The first kind are typing results showing that any security protocol that fulfils a number of sufficient conditions has an attack if it has a well-typed attack. The second kind considers the parallel composition of protocols, showing that when running two protocols in parallel allows for an attack, then at least one of the protocols has an attack in isolation. The most important generalization over previous work is the support for all security properties of the geometric fragment