653 research outputs found

    Multimethod optimization in the cloud: A case‐study in systems biology modelling

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    [Abstract] Optimization problems appear in many different applications in science and engineering. A large number of different algorithms have been proposed for solving them; however, there is no unique general optimization method that performs efficiently across a diverse set of problems. Thus, a multimethod optimization, in which different algorithms cooperate to outperform the results obtained by any of them in isolation, is a very appealing alternative. Besides, as real‐life optimization problems are becoming more and more challenging, the use of HPC techniques to implement these algorithms represents an effective strategy to speed up the time‐to‐solution. In addition, a parallel multimethod approach can benefit from the effortless access to q large number of distributed resources facilitated by cloud computing. In this paper, we propose a self‐adaptive cooperative parallel multimethod for global optimization. This proposal aims to perform a thorough exploration of the solution space by means of multiple concurrent executions of a broad range of search strategies. For its evaluation, we consider an extremely challenging case‐study from the field of computational systems biology. We also assess the performance of the proposal on a public cloud, demonstrating both the potential of the multimethod approach and the opportunity that the cloud provides for these problems.Gobierno de España; DPI2014‐55276‐C5‐2‐RGobierno de España; DPI2017‐82896‐C2‐2‐RGobierno de España; TIN2016‐75845‐PXunta de Galicia; R2016/045Xunta de Galicia; ED431C 2017/0

    Multimethod Optimization for Reverse Engineering of Complex Biological Networks

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    Publication :PBio 2018: Proceedings of the 6th International Workshop on Parallelism in Bioinformatics[Abstract] Optimization problems appears in different areas of science and engineering. This paper considers the general problem of reverse engineering in computational biology by means of mixed-integer nonlinear dynamic optimization (MIDO). Although this kind of problems are typically hard, solutions can be achieved for rather complex networks by applying global optimization metaheuristics. The main objective of this work is to handle them by means of multimethod optimization, in which different metaheuristics cooperate to outperform the results obtained by any of them isolated. For its preliminary evaluation we consider a synthetic signaling pathway case study and we assess the performance of the proposal on a public cloud. These results open up new possibilities for other MIDO-based large-scale applications in computational systems biology.Gobierno de España; DPI2017-82896-C2-2-RGobierno de España; TIN2016-75845-PXunta de Galicia; R2016/045Xunta de Galicia; ED431C 2017/0

    Using the Cloud for Parameter Estimation Problems: Comparing Spark vs MPI with a Case-Study

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    Date of Conference: 14-17 May 2017. Conference Location: Madrid[Abstract] Systems biology is an emerging approach focused in generating new knowledge about complex biological systems by combining experimental data with mathematical modeling and advanced computational techniques. Many problems in this field are extremely challenging and require substantial supercomputing resources to be solved. This is the case of parameter estimation in large-scale nonlinear dynamic systems biology models. Recently, Cloud Computing has emerged as a new paradigm for on-demand delivery of computing resources. However, scientific computing community has been quite hesitant in using the Cloud, simply because traditional programming models do not fit well with the new paradigm, and the earliest cloud programming models do not allow most scientific computations being efficiently run in the Cloud. In this paper we explore and compare two distributed computing models: the MPI (message-passing interface) model, that is high-performance oriented, and the Spark model, which is throughput oriented but outperforms other cloud programming solutions adding improved support for iterative algorithms through in-memory computing. The performance of a very well known metaheuristic, the Differential Evolution algorithm, has been thoroughly assessed using a challenging parameter estimation problem from the domain of computational systems biology. The experiments have been carried out both in a local cluster and in the Microsoft Azure public cloud, allowing performance and cost evaluation for both infrastructures.Gobierno de España; DPI2014-55276-C5-2-RFondos Feder; TIN2016-75845-PXunta de Galicia; R2016/045Xunta de Galicia; GRC2013/05

    Immediate effects of neurodynamic versus muscle stretching on hamstring flexibility in subjects with short hamstring syndrome

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    To compare the effectiveness of an isolated neurodynamic sciatic sliding technique (Neurodynamic group) versus static stretching (Stretching group) in comparison to a Control group receiving a placebo intervention

    Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology

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    [Abstract] This paper describes and assesses a parallel multimethod hyperheuristic for the solution of complex global optimization problems. In a multimethod hyperheuristic, different metaheuristics cooperate to outperform the results obtained by any of them isolated. The results obtained show that the cooperation of individual parallel searches modifies the systemic properties of the hyperheuristic, achieving significant performance improvements versus the sequential and the non-cooperative parallel solutions. Here we present and evaluate a hybrid parallel scheme of the multimethod, using both message-passing (MPI) and shared memory (OpenMP) models. The hybrid parallelization allows to achieve a better trade-off between performance and computational resources, through a compromise between diversity (number of islands) and intensity (number of threads per island). For the performance evaluation, we considered the general problem of reverse engineering nonlinear dynamic models in systems biology, which yields very large mixed-integer dynamic optimization problems. In particular, three very challenging problems from the domain of dynamic modeling of cell signaling were used as case studies. In addition, experiments have been carried out in a local cluster, a large supercomputer and a public cloud, to show the suitability of the proposed solution in different execution platforms.Gobierno de España; DPI2017-82896-C2-2-RGobierno de España; TIN2016-75845-PXunta de Galicia; R2016/045Xunta de Galicia; ED431C 2017/0

    Diversity of oat varieties in eliciting the early inflammatory events in celiac disease

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    Purpose Celiac disease (CD) is an autoimmune enteropathy, triggered by dietary gluten. The only treatment is a strict gluten-free diet. Oats are included in the list of gluten-free ingredients by European Regulation, but the safety of oats in CD is still a matter of debate. The present study examined the capability of different oat cultivars of activating the gliadin-induced transglutaminase-2 (TG2)-dependent events in some in vitro models of CD. In addition, we compared this capability with the electrophoresis pattern of peptic\u2013tryptic digests of the proteins of the oat cultivars. Methods K562(S) cells agglutination, transepithelial electrical resistance of T84-cell monolayers, intracellular levels of TG2 and phosphorylated form of protein 42\u201344 in T84 cells were the early gliadin-dependent events studied. Results The results showed that the Nave oat cultivar elicited these events, whereas Irina and Potenza varieties did not. The ability of a cultivar to activate the above-described events was associated with the electrophoretic pattern of oat proteins and their reactivity to anti-gliadin antibodies. Conclusion We found significant differences among oat cultivars in eliciting the TG2-mediated events of CD inflammation. Therefore, the safety of an oat cultivar in CD might be screened in vitro by means of biochemical and biological assays, before starting a clinical trial to definitely assess its safety

    Automatic Balancing Mechanisms for Mixed Pension Systems under Different Investment Strategies

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    State pension systems are usually pay-as-you-go financed, i.e. current contributions cover pension expenditure. However, some countries combine funding and pay-as-you-go (PAYG) elements within the first pillar. The aim of this paper is twofold. First, using nonlinear optimisation based on Godínez-Olivares, Boado-Penas, and Haberman (2016), it seeks to assess the impact of a compulsory funded defined contribution (DC) pension scheme that complements the traditional defined benefit (DB) PAYG on the level of pension benefits. Future expected returns for both the funded part and the buffer fund of the PAYG are simulated through the non-overlapping block bootstrap technique. Second, in the case of a partial financial sustainability, we design different optimal strategies, that involve variables such as the contribution rate, age of retirement and indexation of pensions, to restore the long-term financial equilibrium of the system. We show that the adjustments needed to ensure sustainability for the mixed pension systems are less severe that the pure DB PAYG but the total replacement rate for the former is lower in most of the cases studied. When calculating the return that the individuals would receive, we prove that some cohorts are better off under a mixed pension system

    Effectiveness of manual therapy compared to usual care by the general practitioner for chronic tension-type headache: design of a randomised clinical trial

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    <p>Abstract</p> <p>Background</p> <p>Patients with Chronic Tension Type Headache (CTTH) report functional and emotional impairments (loss of workdays, sleep disturbances, emotional well-being) and are at risk for overuse of medication. Manual therapy may improve symptoms through mobilisation of the spine, correction of posture, and training of cervical muscles.</p> <p>We present the design of a randomised clinical trial (RCT) evaluating the effectiveness of manual therapy (MT) compared to usual care by the general practitioner (GP) in patients with CTTH.</p> <p>Methods and design</p> <p>Patients are eligible for participation if they present in general practice with CTTH according to the classification of the International Headache Society (IHS).</p> <p>Participants are randomised to either usual GP care according to the national Dutch general practice guidelines for headache, or manual therapy, consisting of mobilisations (high- and low velocity techniques), exercise therapy for the cervical and thoracic spine and postural correction. The primary outcome measures are the number of headache days and use of medication. Secondary outcome measures are severity of headache, functional status, sickness absence, use of other healthcare resources, active cervical range of motion, algometry, endurance of the neckflexor muscles and head posture. Follow-up assessments are conducted after 8 and 26 weeks.</p> <p>Discussion</p> <p>This is a pragmatic trial in which interventions are offered as they are carried out in everyday practice. This increases generalisability of results, but blinding of patients, GPs and therapists is not possible.</p> <p>The results of this trial will contribute to clinical decision making of the GP regarding referral to manual therapy in patients with chronic tension headache.</p

    Lack of a synergistic effect of a non-viral ALS gene therapy based on BDNF and a TTC fusion molecule

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    Significant improvements in behavioral and electrophysiological results, motoneuron survival and anti-apoptotic/survival-activated pathways were observed with BDNF-TTC treatment. However, no synergistic effect was found for this fusion molecule. Although BDNF in the fusion molecule is capable of activating autocrine and neuroprotective pathways, TTC treatment alone yielded similar neuroprotection. Therefore, an accurate study of the neuroprotective effects of TTC fusion molecules should be performed to obtain a better understanding of its effect
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