Code Verification Results of an LLNL ASC Code on Some Tri-Lab Verification Test Suite Problems

As scientific codes become more complex and involve larger numbers of developers and algorithms, chances for algorithmic implementation mistakes increase. In this environment, code verification becomes essential to building confidence in the code implementation. This paper will present first results of a new code verification effort within LLNL's B Division. In particular, we will show results of code verification of the LLNL ASC ARES code on the test problems: Su Olson non-equilibrium radiation diffusion, Sod shock tube, Sedov point blast modeled with shock hydrodynamics, and Noh implosion

In vivo imaging and quantitative analysis of leukocyte directional migration and polarization in inflamed tissue

Directional migration of transmigrated leukocytes to the site of injury is a central event in the inflammatory response. Here, we present an in vivo chemotaxis assay enabling the visualization and quantitative analysis of subtype-specific directional motility and polarization of leukocytes in their natural 3D microenvironment. Our technique comprises the combination of i) semi-automated in situ microinjection of chemoattractants or bacteria as local chemotactic stimulus, ii) in vivo near-infrared reflected-light oblique transillumination (RLOT) microscopy for the visualization of leukocyte motility and morphology, and iii) in vivo fluorescence microscopy for the visualization of different leukocyte subpopulations or fluorescence-labeled bacteria. Leukocyte motility parameters are quantified off-line in digitized video sequences using computer-assisted single cell tracking. Here, we show that perivenular microinjection of chemoattractants [macrophage inflammatory protein-1alpha (MIP-1alpha/Ccl3), platelet-activating factor (PAF)] or E. coli into the murine cremaster muscle induces target-oriented intravascular adhesion and transmigration as well as polarization and directional interstitial migration of leukocytes towards the locally administered stimuli. Moreover, we describe a crucial role of Rho kinase for the regulation of directional motility and polarization of transmigrated leukocytes in vivo. Finally, combining in vivo RLOT and fluorescence microscopy in Cx3CR1(gfp/gfp) mice (mice exhibiting green fluorescent protein-labeled monocytes), we are able to demonstrate differences in the migratory behavior of monocytes and neutrophils.Taken together, we propose a novel approach for investigating the mechanisms and spatiotemporal dynamics of subtype-specific motility and polarization of leukocytes during their directional interstitial migration in vivo

Circulating extracellular vesicles induce monocyte dysfunction and are associated with sepsis and high mortality in cirrhosis

BACKGROUND: Sepsis is common in cirrhosis and is often a result of immune dysregulation. Specific stimuli and pathways of inter-cellular communications between immune cells in cirrhosis and sepsis are incompletely understood. Immune cell-derived Extracellular Vesicles (EV) were studied to understand mechanisms of sepsis in cirrhosis. METHODS: Immune-cell derived EV were measured in cirrhosis patients [Child-Turcotte-Pugh (Child) score A, n=15; B n=16; C n=43 and Child-C with sepsis (n=38)], and healthy controls (HC, n=11). In-vitro and in-vivo functional relevance of EV in cirrhosis and associated sepsis was investigated. RESULTS: Monocyte, neutrophil and hematopoietic stem cells associated EV progressively increased with higher Child score (p0.3, p<0.001), which further increased in Child C sepsis than without sepsis(p<0.001); monocyte EV showing the highest association with disease stage [p=0.013; Odds ratio-4.14(1.34-12.42)]. A threshold level of monocyte EV of 53/µl predicted mortality in patients of Child C with sepsis [Odds ratio-6.2 (2.4-15.9), AUROC=0.76, p<0.01]. In vitro EV from cirrhotic with sepsis compared without sepsis, induced mobilization arrest in healthy monocytes within 4 hours (p=0.004), reduced basal oxygen consumption rate (p<0.001) and induced pro-inflammatory genes (p<0.05). The septic-EV on adoptive transfer to C57/BL6J mice, induced sepsis like condition within 24h with leukocytopenia (p=0.005), intrahepatic inflammation with increased CD11b+ cells (p=0.03) and bone marrow hyperplasia (p<0.01). CONCLUSION: Extracellular vesicles induce functional impairment in circulating monocytes and contribute to the development and perpetuation of sepsis. High levels of monocyte EV correlate with mortality and can help early stratification of sicker patients

Scaling Reliably: Improving the Scalability of the Erlang Distributed Actor Platform

Distributed actor languages are an effective means of constructing scalable reliable systems, and the Erlang programming language has a well-established and influential model. While the Erlang model conceptually provides reliable scalability, it has some inherent scalability limits and these force developers to depart from the model at scale. This article establishes the scalability limits of Erlang systems and reports the work of the EU RELEASE project to improve the scalability and understandability of the Erlang reliable distributed actor model. We systematically study the scalability limits of Erlang and then address the issues at the virtual machine, language, and tool levels. More specifically: (1) We have evolved the Erlang virtual machine so that it can work effectively in large-scale single-host multicore and NUMA architectures. We have made important changes and architectural improvements to the widely used Erlang/OTP release. (2) We have designed and implemented Scalable Distributed (SD) Erlang libraries to address language-level scalability issues and provided and validated a set of semantics for the new language constructs. (3) To make large Erlang systems easier to deploy, monitor, and debug, we have developed and made open source releases of five complementary tools, some specific to SD Erlang. Throughout the article we use two case studies to investigate the capabilities of our new technologies and tools: a distributed hash table based Orbit calculation and Ant Colony Optimisation (ACO). Chaos Monkey experiments show that two versions of ACO survive random process failure and hence that SD Erlang preserves the Erlang reliability model. While we report measurements on a range of NUMA and cluster architectures, the key scalability experiments are conducted on the Athos cluster with 256 hosts (6,144 cores). Even for programs with no global recovery data to maintain, SD Erlang partitions the network to reduce network traffic and hence improves performance of the Orbit and ACO benchmarks above 80 hosts. ACO measurements show that maintaining global recovery data dramatically limits scalability; however, scalability is recovered by partitioning the recovery data. We exceed the established scalability limits of distributed Erlang, and do not reach the limits of SD Erlang for these benchmarks at this scal

Fully adaptive multiresolution schemes for strongly degenerate parabolic equations with discontinuous flux

A fully adaptive finite volume multiresolution scheme for one-dimensional strongly degenerate parabolic equations with discontinuous flux is presented. The numerical scheme is based on a finite volume discretization using the Engquist--Osher approximation for the flux and explicit time--stepping. An adaptivemultiresolution scheme with cell averages is then used to speed up CPU time and meet memory requirements. A particular feature of our scheme is the storage of the multiresolution representation of the solution in a dynamic graded tree, for the sake of data compression and to facilitate navigation. Applications to traffic flow with driver reaction and a clarifier--thickener model illustrate the efficiency of this method

The factors associated to psychosocial stress among general practitioners in Lithuania. Cross-sectional study

BACKGROUND: There are number of studies showing that general practice is one of the most stressful workplace among health care workers. Since Baltic States regained independence in 1990, the reform of the health care system took place in which new role and more responsibilities were allocated to general practitioners' in Lithuania. This study aimed to explore the psychosocial stress level among Lithuanian general practitioner's and examine the relationship between psychosocial stress and work characteristics. METHODS: The cross-sectional study of 300 Lithuanian General practitioners. Psychosocial stress was investigated with a questionnaire based on the Reeder scale. Job demands were investigated with the R. Karasek scale. The analysis included descriptive statistics; interrelationship analysis between characteristics and multivariate logistic regression to estimate odds ratios for each of the independent variables in the model. RESULTS: Response rate 66% (N = 197). Our study highlighted highest prevalence of psychosocial stress among widowed, single and female general practitioners. Lowest prevalence of psychosocial stress was among males and older age general practitioners. Psychosocial stress occurs when job demands are high and job decision latitude is low (χ(2 )= 18,9; p < 0,01). The multivariate analysis shows that high job demands (OR 4,128; CI 2,102–8,104; p < 0,001), patient load more than 18 patients per day (OR 5,863; CI 1,549–22,188; p < 0,01) and young age of GP's (OR 6,874; CI 1,292–36,582; p < 0,05) can be assigned as significant predictors for psychosocial stress. CONCLUSION: One half of respondents suffering from work related psychosocial stress. High psychological workload demands combined with low decision latitude has the greatest impact to stress caseness among GP's. High job demands, high patient load and young age of GP's can be assigned as significant predictors of psychosocial stress among GP's

Interaction among general practitioners age and patient load in the prediction of job strain, decision latitude and perception of job demands. A Cross-sectional study

BACKGROUND: It is widely recognized and accepted that job strain adversely impacts the workforce. Individual responses to stressful situations can vary greatly and it has been shown that certain people are more likely to experience high levels of stress in their job than others. Studies highlighted that there can be age differences in job strain perception. METHODS: Cross-sectional postal survey of 300 Lithuanian general practitioners. Psychosocial stress was investigated with a questionnaire based on the Reeder scale. Job demands were investigated with the Karasek scale. The analysis included descriptive statistics; logistic regression beta coefficients to find out predictors and interactions between characteristics and predictors. RESULTS: Response rate was 66% (N = 197). Logistic regression as significant predictors for job strain assigned – duration of work in primary care; for job demands- age and duration of working in primary care; for decision latitude- age and patient load. The interactions with regard to job strain showed that GP's age and job strain are negatively associated to a low patient load. Lower decision latitude for older GP age is strongly related to higher patient load. Job demands and GP age are slightly positively related at low patient load. CONCLUSIONS: Lithuanian GP's have high patient load and are at risk of stress, they have high job demands and low decision latitude. Older GP's perceive less strain, lower job demands and higher decision latitude in case of low patient load. Young GP's decision latitude has week association to patient load. Regarding to the changes in patient load younger GP's perceive it more sensitively as changes in job demands

Social Participation and Disaster Risk Reduction Behaviors in Tsunami Prone Areas

This paper examines the relationships between social participation and disaster risk reduction actions. A survey of 557 households in tsunami prone areas in Phang Nga, Thailand was conducted following the 2012 Indian Ocean earthquakes. We use a multivariate probit model to jointly estimate the likelihood of undertaking three responses to earthquake and tsunami hazards (namely, (1) following disaster-related news closely, (2) preparing emergency kits and/or having a family emergency plan, and (3) having an intention to migrate) and community participation.We find that those who experienced losses from the 2004 tsunami are more likely to participate in community activities and respond to earthquake hazards. Compared to men, women are more likely to prepare emergency kits and/or have an emergency plan and have a greater intention to migrate. Living in a community with a higher proportion of women with tertiary education increases the probability of engaging in community activities and carrying out disaster risk reduction measures. Individuals who participate in village-based activities are 5.2% more likely to undertake all three risk reduction actions compared to those not engaging in community activities. This implies that encouraging participation in community activities can have positive externalities in disaster mitigation

Insight from the draft genome of Dietzia cinnamea P4 reveals mechanisms of survival in complex tropical soil habitats and biotechnology potential

The draft genome of Dietzia cinnamea strain P4 was determined using pyrosequencing. In total, 428 supercontigs were obtained and analyzed. We here describe and interpret the main features of the draft genome. The genome contained a total of 3,555,295 bp, arranged in a single replicon with an average G+C percentage of 70.9%. It revealed the presence of complete pathways for basically all central metabolic routes. Also present were complete sets of genes for the glyoxalate and reductive carboxylate cycles. Autotrophic growth was suggested to occur by the presence of genes for aerobic CO oxidation, formate/formaldehyde oxidation, the reverse tricarboxylic acid cycle and the 3-hydropropionate cycle for CO2 fixation. Secondary metabolism was evidenced by the presence of genes for the biosynthesis of terpene compounds, frenolicin, nanaomycin and avilamycin A antibiotics. Furthermore, a probable role in azinomycin B synthesis, an important product with antitumor activity, was indicated. The complete alk operon for the degradation of n-alkanes was found to be present, as were clusters of genes for biphenyl ring dihydroxylation. This study brings new insights in the genetics and physiology of D. cinnamea P4, which is useful in biotechnology and bioremediation

Procalcitonin for diagnosis of infection and guide to antibiotic decisions: past, present and future

There are a number of limitations to using conventional diagnostic markers for patients with clinical suspicion of infection. As a consequence, unnecessary and prolonged exposure to antimicrobial agents adversely affect patient outcomes, while inappropriate antibiotic therapy increases antibiotic resistance. A growing body of evidence supports the use of procalcitonin (PCT) to improve diagnosis of bacterial infections and to guide antibiotic therapy. For patients with upper and lower respiratory tract infection, post-operative infections and for severe sepsis patients in the intensive care unit, randomized-controlled trials have shown a benefit of using PCT algorithms to guide decisions about initiation and/or discontinuation of antibiotic therapy. For some other types of infections, observational studies have shown promising first results, but further intervention studies are needed before use of PCT in clinical routine can be recommended. The aim of this review is to summarize the current evidence for PCT in different infections and clinical settings, and discuss the reliability of this marker when used with validated diagnostic algorithms