1,515 research outputs found

    Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis

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    BACKGROUND: Chaos Game Representation (CGR) is an iterated function that bijectively maps discrete sequences into a continuous domain. As a result, discrete sequences can be object of statistical and topological analyses otherwise reserved to numerical systems. Characteristically, CGR coordinates of substrings sharing an L-long suffix will be located within 2(-L )distance of each other. In the two decades since its original proposal, CGR has been generalized beyond its original focus on genomic sequences and has been successfully applied to a wide range of problems in bioinformatics. This report explores the possibility that it can be further extended to approach algorithms that rely on discrete, graph-based representations. RESULTS: The exploratory analysis described here consisted of selecting foundational string problems and refactoring them using CGR-based algorithms. We found that CGR can take the role of suffix trees and emulate sophisticated string algorithms, efficiently solving exact and approximate string matching problems such as finding all palindromes and tandem repeats, and matching with mismatches. The common feature of these problems is that they use longest common extension (LCE) queries as subtasks of their procedures, which we show to have a constant time solution with CGR. Additionally, we show that CGR can be used as a rolling hash function within the Rabin-Karp algorithm. CONCLUSIONS: The analysis of biological sequences relies on algorithmic foundations facing mounting challenges, both logistic (performance) and analytical (lack of unifying mathematical framework). CGR is found to provide the latter and to promise the former: graph-based data structures for sequence analysis operations are entailed by numerical-based data structures produced by CGR maps, providing a unifying analytical framework for a diversity of pattern matching problems

    Drug-cured experimental Trypanosoma cruzi infections confer long-lasting and cross-strain protection.

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    BACKGROUND: The long term and complex nature of Chagas disease in humans has restricted studies on vaccine feasibility. Animal models also have limitations due to technical difficulties in monitoring the extremely low parasite burden that is characteristic of chronic stage infections. Advances in imaging technology offer alternative approaches that circumvent these problems. Here, we describe the use of highly sensitive whole body in vivo imaging to assess the efficacy of recombinant viral vector vaccines and benznidazole-cured infections to protect mice from challenge with Trypanosoma cruzi. METHODOLOGY/PRINCIPAL FINDINGS: Mice were infected with T. cruzi strains modified to express a red-shifted luciferase reporter. Using bioluminescence imaging, we assessed the degree of immunity to re-infection conferred after benznidazole-cure. Those infected for 14 days or more, prior to the onset of benznidazole treatment, were highly protected from challenge with both homologous and heterologous strains. There was a >99% reduction in parasite burden, with parasites frequently undetectable after homologous challenge. This level of protection was considerably greater than that achieved with recombinant vaccines. It was also independent of the route of infection or size of the challenge inoculum, and was long-lasting, with no significant diminution in immunity after almost a year. When the primary infection was benznidazole-treated after 4 days (before completion of the first cycle of intracellular infection), the degree of protection was much reduced, an outcome associated with a minimal T. cruzi-specific IFN-?+ T cell response. CONCLUSIONS/SIGNIFICANCE: Our findings suggest that a protective Chagas disease vaccine must have the ability to eliminate parasites before they reach organs/tissues, such as the GI tract, where once established, they become largely refractory to the induced immune response

    Bullying girls - Changes after brief strategic family therapy: A randomized, prospective, controlled trial with one-year follow-up

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    Background: Many girls bully others. They are conspicuous because of their risk-taking behavior, increased anger, problematic interpersonal relationships and poor quality of life. Our aim was to determine the efficacy of brief strategic family therapy (BSFT) for bullying-related behavior, anger reduction, improvement of interpersonal relationships, and improvement of health-related quality of life in girls who bully, and to find out whether their expressive aggression correlates with their distinctive psychological features. Methods: 40 bullying girls were recruited from the general population: 20 were randomly selected for 3 months of BSFT. Follow-up took place 12 months after the therapy had ended. The results of treatment were examined using the Adolescents' Risk-taking Behavior Scale (ARBS), the State-Trait Anger Expression Inventory (STAXI), the Inventory of Interpersonal Problems (IIP-D), and the SF-36 Health Survey (SF-36). Results: In comparison with the control group (CG) (according to the intent-to-treat principle), bullying behavior in the BSFT group was reduced (BSFT-G from n = 20 to n = 6; CG from n = 20 to n = 18, p = 0.05) and statistically significant changes in all risk-taking behaviors (ARBS), on most STAXI, IIP-D, and SF-36 scales were observed after BSFT. The reduction in expressive aggression (Anger-Out scale of the STAXI) correlated with the reduction on several scales of the ARBS, IIP-D, and SF-36. Follow-up a year later showed relatively stable events. Conclusions: Our findings suggest that bullying girls suffer from psychological and social problems which may be reduced by the use of BSFT. Expressive aggression in girls appears to correlate with several types of risk-taking behavior and interpersonal problems, as well as with health-related quality of life. Copyright (c) 2006 S. Karger AG, Basel

    Silent progression in disease activity-free relapsing multiple sclerosis.

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    ObjectiveRates of worsening and evolution to secondary progressive multiple sclerosis (MS) may be substantially lower in actively treated patients compared to natural history studies from the pretreatment era. Nonetheless, in our recently reported prospective cohort, more than half of patients with relapsing MS accumulated significant new disability by the 10th year of follow-up. Notably, "no evidence of disease activity" at 2 years did not predict long-term stability. Here, we determined to what extent clinical relapses and radiographic evidence of disease activity contribute to long-term disability accumulation.MethodsDisability progression was defined as an increase in Expanded Disability Status Scale (EDSS) of 1.5, 1.0, or 0.5 (or greater) from baseline EDSS = 0, 1.0-5.0, and 5.5 or higher, respectively, assessed from baseline to year 5 (±1 year) and sustained to year 10 (±1 year). Longitudinal analysis of relative brain volume loss used a linear mixed model with sex, age, disease duration, and HLA-DRB1*15:01 as covariates.ResultsRelapses were associated with a transient increase in disability over 1-year intervals (p = 0.012) but not with confirmed disability progression (p = 0.551). Relative brain volume declined at a greater rate among individuals with disability progression compared to those who remained stable (p < 0.05).InterpretationLong-term worsening is common in relapsing MS patients, is largely independent of relapse activity, and is associated with accelerated brain atrophy. We propose the term silent progression to describe the insidious disability that accrues in many patients who satisfy traditional criteria for relapsing-remitting MS. Ann Neurol 2019;85:653-666

    Larvicidal activity of Ramalina usnea lichen against Aedes aegypti

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    AbstractThe larvicidal activity of the methanol extract, fractions and compounds 2-hydroxy-4-methoxy-6-propyl-methyl benzoate and (+)-usnic acid identified from the lichen Ramalina usnea (L.) R. Howe, Ramalinaceae, was tested against the third instar larvae of the Aedes aegypti mosquito. The methanol extract and three fractions showed activity, killing 100% and 96.6% of the larvae at a concentration of 150μg/ml at 24h. The isolated compounds, 2-hydroxy-4-methoxy-6-propyl-methyl benzoate and the (+)-usnic acid showed larvicidal activity, presenting LC50 values of 4.85 and 4.48μg/ml, respectively. This is the first study of its kind reporting the larvicidal activity against the A. aegypti mosquito with compound (1)

    Experimental validation of a one-dimensional twin-entry radial turbine model under non-linear pulse conditions

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    This is the author¿s version of a work that was accepted for publication in International Journal of Engine Research. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published as https://doi.org/10.1177/1468087419869157[EN] This article presents the experimental validation of a complete integrated one-dimensional twin-scroll turbine model able to be used in reciprocating internal combustion engine unsteady simulations. A passenger car with a twin-entry-type turbine has been tested under engine-like pulse conditions by means of a specifically built gas stand. To obtain high-resolution quality data, the turbine and turbine line pipes have been instrumented with mean and instantaneous pressure sensors as well as temperature and mass flow sensors, employing a uniquely designed rotating valve for the pulse generation. This experimental configuration enables to obtain the pressure decomposition in both inlets and outlets of the turbine. Using the experimental data obtained, the model is fully validated, with special focus on the reflected and transmitted components for analysing the performance of the model and its non-linear acoustics prediction capabilities. The model presents a very high degree of correlation with the experimental results, providing a range of errors similar to the uncertainty of the measurements, even in the medium- and high-frequency spectra.The author(s) disclosed receipt of the following financial support for the research, authorship and/or publication of this article: This work was supported by the 'Ayuda a Primeros Proyectos de Investigacion' (PAID-06-18), Vicerrectorado de Investigacion, Innovacion y Transferencia de la Universitat Politecnica de Valencia (UPV), Valencia, Spain. P.S. was partially supported through contract FPI-2017-S2-1428 of Programa de Apoyo para la Investigacion y Desarrollo (PAID) of Universitat Politecnica de Valencia.Serrano, J.; Arnau Martínez, FJ.; García-Cuevas González, LM.; Soler-Blanco, P.; Cheung, R. (2021). Experimental validation of a one-dimensional twin-entry radial turbine model under non-linear pulse conditions. 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