Weighted decomposition in high-performance lattice-Boltzmann simulations: Are some lattice sites more equal than others?

Obtaining a good load balance is a significant challenge in scaling up lattice-Boltzmann simulations of realistic sparse problems to the exascale. Here we analyze the effect of weighted decomposition on the performance of the HemeLB lattice-Boltzmann simulation environment, when applied to sparse domains. Prior to domain decomposition, we assign wall and in/outlet sites with increased weights which reflect their increased computational cost. We combine our weighted decomposition with a second optimization, which is to sort the lattice sites according to a space filling curve. We tested these strategies on a sparse bifurcation and very sparse aneurysm geometry, and find that using weights reduces calculation load imbalance by up to 85 %, although the overall communication overhead is higher than some of our runs.This work has received funding from the CRESTA and MAPPER projects within the EC-FP7 (ICT-2011.9.13) under Grant Agreements nos. 287703 and 261507, and from EPSRC Grants EP/I017909/1 (www.2020science.net) and EP/I034602/1

Systemic tuberculosis presenting with acute transient myopia: a case report

<p>Abstract</p> <p>Introduction</p> <p>Transient myopia has been reported to occur in a number of conditions, either ocular in origin or associated with an underlying systemic cause. We present a rare case of this abnormality occurring in the setting of systemic tuberculosis.</p> <p>Case presentation</p> <p>A 29-year-old Indian woman presented with sudden onset blurred distance vision and fever. Examination revealed visual acuity of counting fingers in both eyes improving to 6/9 with pinhole with N5 reading acuity. Anterior segment examination revealed narrow angles on gonioscopy. Posterior segments were normal. Systemic examination revealed a fluctuant mass in her left loin, aspiration of which yielded pus which was culture-positive for <it>Mycobacterium tuberculosis</it>. The Mantoux test elicited a strongly positive reaction. Chest X-ray and magnetic resonance imaging of the brain were unremarkable. Computed tomography scan and magnetic resonance imaging of the spine and abdomen revealed a large psoas abscess communicating with the loin mass. Two vertebrae were involved but not the spinal cord or canal.</p> <p>Conclusion</p> <p>Transient myopia is a rare presenting feature of systemic tuberculosis. A postulated mechanism in this patient is that development of a uveal effusion related to systemic tuberculosis caused anterior rotation of the iris-lens diaphragm, thereby inducing narrowing of the angle and acute myopia.</p

Point-of-care screening for a current Hepatitis C virus infection: influence on uptake of a concomitant offer of HIV screening

Eliminating hepatitis C as a public health threat requires an improved understanding of how to increase testing uptake. We piloted point-of-care testing (POCT) for a current HCV infection in an inner-city Emergency Department (ED) and assessed the influence on uptake of offering concomitant screening for HIV. Over four months, all adults attending ED with minor injuries were first invited to complete an anonymous questionnaire then invited to test in alternating cycles offering HCV POCT or HCV+HIV POCT. Viral RNA was detected in finger-prick blood by GeneXpert. 814/859 (94.8%) questionnaires were returned and 324/814 (39.8%) tests were accepted, comprising 211 HCV tests and 113 HCV+HIV tests. Offering concomitant HIV screening reduced uptake after adjusting for age and previous HCV testing (odds ratio 0.51; 95% confidence interval [CI] 0.38–0.68; p < 0.001). HCV prevalence was 1/324 (0.31%; 95% CI 0.05–1.73); no participant tested positive for HIV. 167/297 (56.2%) POCT participants lived in the most deprived neighbourhoods in England. HCV RNA testing using finger-prick blood was technically feasible. Uptake was moderate and the offer of concomitant HIV screening showed a detrimental impact on acceptability in this low prevalence population. The findings should be confirmed in a variety of other community settings

Analyzing and Modeling the Performance of the HemeLB Lattice-Boltzmann Simulation Environment

We investigate the performance of the HemeLB lattice-Boltzmann simulator for cerebrovascular blood flow, aimed at providing timely and clinically relevant assistance to neurosurgeons. HemeLB is optimised for sparse geometries, supports interactive use, and scales well to 32,768 cores for problems with ∼81 million lattice sites. We obtain a maximum performance of 29.5 billion site updates per second, with only an 11% slowdown for highly sparse problems (5% fluid fraction). We present steering and visualisation performance measurements and provide a model which allows users to predict the performance, thereby determining how to run simulations with maximum accuracy within time constraints

Coalesced communication: a design pattern for complex parallel scientific software

We present a new design pattern for high-performance parallel scientific software, named coalesced communication. This pattern allows for a structured way to improve the communication performance through coalescence of multiple communication needs using two communication management components. We apply the design pattern to several simulations of a lattice-Boltzmann blood flow solver with streaming visualisation which engenders a reduction in the communication overhead of approximately 40%

Spasticity of the gastrosoleus muscle is related to the development of reduced passive dorsiflexion of the ankle in children with cerebral palsy: A registry analysis of 2,796 examinations in 355 children

Background and purpose Spasticity and muscle contracture are two common manifestations of cerebral palsy (CP). A spastic muscle may inhibit growth in length of the muscle, but the importance of this relationship is not known. In 1994, a register and a healthcare program for children with CP in southern Sweden were initiated. The child's muscle tone according to the Ashworth scale and the ankle range of motion (ROM) is measured annually during the entire growth period. We have used these data to analyze the relationship between spasticity and ROM of the gastrosoleus muscle. Patients and methods All measurements in the total population of children with CP aged 0-18 years during the period January 1995 through June 2008 were analyzed. The study was based on 2,796 examinations in 355 children. In the statistical analysis, the effect of muscle tone on ROM was estimated using a random effects model. Results The range of dorsiflexion of the ankle joint decreased in the total material by mean 19 (95% CI: 14-24) degrees during the first 18 years of life. There was a statistically significant association between the ROM and the child's level of spasticity during the year preceding the ROM measurement. Interpretation Spasticity is related to the development of muscle contracture. In the treatment of children with CP, the spasticity, contracture, and strength of the gastrosoleus muscle must be considered together

Oscillatory surface rheotaxis of swimming E. coli bacteria

Bacterial contamination of biological conducts, catheters or water resources is a major threat to public health and can be amplified by the ability of bacteria to swim upstream. The mechanisms of this rheotaxis, the reorientation with respect to flow gradients, often in complex and confined environments, are still poorly understood. Here, we follow individual E. coli bacteria swimming at surfaces under shear flow with two complementary experimental assays, based on 3D Lagrangian tracking and fluorescent flagellar labelling and we develop a theoretical model for their rheotactic motion. Three transitions are identified with increasing shear rate: Above a first critical shear rate, bacteria shift to swimming upstream. After a second threshold, we report the discovery of an oscillatory rheotaxis. Beyond a third transition, we further observe coexistence of rheotaxis along the positive and negative vorticity directions. A full theoretical analysis explains these regimes and predicts the corresponding critical shear rates. The predicted transitions as well as the oscillation dynamics are in good agreement with experimental observations. Our results shed new light on bacterial transport and reveal new strategies for contamination prevention.Comment: 12 pages, 5 figure

Cellular Automata Applications in Shortest Path Problem

Cellular Automata (CAs) are computational models that can capture the essential features of systems in which global behavior emerges from the collective effect of simple components, which interact locally. During the last decades, CAs have been extensively used for mimicking several natural processes and systems to find fine solutions in many complex hard to solve computer science and engineering problems. Among them, the shortest path problem is one of the most pronounced and highly studied problems that scientists have been trying to tackle by using a plethora of methodologies and even unconventional approaches. The proposed solutions are mainly justified by their ability to provide a correct solution in a better time complexity than the renowned Dijkstra's algorithm. Although there is a wide variety regarding the algorithmic complexity of the algorithms suggested, spanning from simplistic graph traversal algorithms to complex nature inspired and bio-mimicking algorithms, in this chapter we focus on the successful application of CAs to shortest path problem as found in various diverse disciplines like computer science, swarm robotics, computer networks, decision science and biomimicking of biological organisms' behaviour. In particular, an introduction on the first CA-based algorithm tackling the shortest path problem is provided in detail. After the short presentation of shortest path algorithms arriving from the relaxization of the CAs principles, the application of the CA-based shortest path definition on the coordinated motion of swarm robotics is also introduced. Moreover, the CA based application of shortest path finding in computer networks is presented in brief. Finally, a CA that models exactly the behavior of a biological organism, namely the Physarum's behavior, finding the minimum-length path between two points in a labyrinth is given.Comment: To appear in the book: Adamatzky, A (Ed.) Shortest path solvers. From software to wetware. Springer, 201

Próteses parciais fixas reforçadas por fibras: um estudo clínico retrospectivo preliminar

The aim of this study was to evaluate the clinical performance (retention rate) of fiber-reinforced composite fixed partial dentures (FPDs). Polyethylene fiber (Ribbond®) was used combined with restorative composite during FPDs fabrication. FPDs were placed in thirteen patients in a private clinic. Nineteen FPDs were evaluated. The prosthetic space was filled with only one pontic using extracted teeth (2 cases), acrylic resin teeth (11 cases), or with composite resin (6 cases), combined with Polyethylene fiber. The clinical criterion used was based on retention rate of FPDs. If FPDs were in function in the mouth at the time of examination without previous repair they were classified as Complete Survival (CS) restorations. A classification of Survival with Rebonding (SR) was assigned in the event of an adhesive failure, but after rebonding the FPD still remained under evaluation. Treatment was classified as a Failure (F) if the FPD restoration was lost. The time of evaluation was 41.15 months (±15.13). The FPDs evaluated were retained (CS=94.75%), and no failure was found except for in one situation which required rebonding (SR=5.25%). According to the survival estimation method of Kaplan-Meyer the mean survival time was 42.3 months. At the time of evaluation investigated, polyethylene-reinforced FPDs showed a favorable retention rate in preliminary data.O objetivo deste estudo foi avaliar a performance clínica (percentagem de retenção) de próteses parciais fixas reforçadas por fibras. Fibras de polietileno (Ribbond®) foram usadas em combinação com resina composta durante a confecção das próteses. Os tratamentos foram realizadas em 13 pacientes, em uma clínica privada., sendo que 19 próteses foram reavaliadas. O espaço protético era preenchido com um pôntico usando o próprio dente extraído (2 casos), dentes de acrílico (11 casos) ou confeccionados com resina composta (6 casos), em todas as situações eram empregadas fibras de polietileno. Os critérios clínicos usados foram baseados na percentagem de retenção das próteses parciais fixas. As próteses que estavam em função no momento da avaliação, sem nunca necessitar de qualquer reparo prévio, foram classificadas como sobrevivência completa (SC). A classificação de sobrevivência com nova colagem (SR) foi utilizada para os casos de falha adesiva, com posterior cimentação da peça, a qual permanecia em função. O tratamento era classificado como falha (F) quando a restauração era perdida. O tempo médio de avaliação foi de 41,15 meses (±15,13). Nenhum caso de falha foi detectado, em apenas um caso houve falha adesiva com posterior colagem da peça (SR=5,25%) e em 94.75% dos casos as próteses permaneciam em função.. De acordo com o método de sobrevida de Kaplan-Meyer o tempo médio de sobrevida foi de 42,3 meses. As próteses parciais fixas reforçadas por fibras mostraram uma percentagem de retenção favorável neste estudo preliminar

Flexible composition and execution of high performance, high fidelity multiscale biomedical simulations

Multiscale simulations are essential in the biomedical domain to accurately model human physiology. We present a modular approach for designing, constructing and executing multiscale simulations on a wide range of resources, from laptops to petascale supercomputers, including combinations of these. Our work features two multiscale applications, in-stent restenosis and cerebrovascular bloodflow, which combine multiple existing single-scale applications to create a multiscale simulation. These applications can be efficiently coupled, deployed and executed on computers up to the largest (peta) scale, incurring a coupling overhead of 1–10% of the total execution time