Scalability analysis of Dalton,a molecular structure program

Dalton is a molecular electronic structure program featuring common methods of computational chemistry that are based on pure quantum mechanics (QM) as well as hybrid quantum mechanics/molecular mechanics (QM/MM). It is specialized and has a leading position in calculation of molecular properties with a large world-wide user community (over 2000 licenses issued). In this paper, we present a performance characterization and optimization of Dalton. We also propose a solution to avoid the master/worker design of Dalton to become a performance bottleneck for larger process numbers. With these improvements we obtain speedups of 4x, increasing the parallel efficiency of the code and being able to run in it in a much bigger number of cores.     

Overcoming organizational challenges to secure knowledge management

Incident management systems have the potential to improve security dramatically but often experience problems stemming from organizational, interpersonal and social constraints that limit their effectiveness. These limits may cause underreporting of incidents, leading to erroneous perceptions of the actual safety and security situation of the organization. The true security situation may be better understood and underreporting may be reduced if underlying systemic issues surrounding security incident management are taken into account. A dynamic simulation, based on the parallel experience of industrial incident management systems, illustrates the cumulative effects of rewards, learning, and retributions on the fate of a hypothetical knowledge management system designed to collect information about events and incidents. Simulation studies are part of an ongoing research project to develop sustainable knowledge and knowledge transfer tools that support the development of a security culture.

Parameter Learning in Object-Oriented Bayesian Networks

This paper describes a method for parameter learning in Object-Oriented Bayesian Networks (OOBNs). We propose a methodology for learning parameters in OOBNs, and prove that maintaining the object orientation imposed by the prior model will increase the learning speed in object-oriented domains. We also propose a method to efficiently estimate the probability parameters in domains that are not strictly object oriented. Finally, we attack type uncertainty, a special case of model uncertainty typical to object-oriented domains.     

An empirical study of variations in COTS-based software development processes in the Norwegian IT industry

More and more software projects use Commercial-Off-The-Shelf (COTS) components. Although previous studies have proposed specific COTS-based development processes, there are few empirical studies that investigate how to use and customize COTS-based development processes for different project contexts. This paper describes an exploratory study of state-of-the-practice of COTS-based development processes. Sixteen software projects in the Norwegian IT companies have been studied by structured interviews. The results are that COTS-specific activities can be successfully incorporated in most traditional development processes (such as waterfall or prototyping), given proper guidelines to reduce risks and provide specific assistance. We have identified four COTS-specific activities—the build vs. buy decision, COTS component selection, learning and understanding COTS components, and COTS component integration – and one new role, that of a knowledge keeper. We have also found a special COTS component selection activity for unfamiliar components, combining Internet searches with hands-on trials. The process guidelines are expressed as scenarios, problems encountered, and examples of good practice. They can be used to customize the actual development processes, such as in which lifecycle phase to put the new activities into. Such customization crucially depends on the project context, such as previous familiarity with possible COTS components and flexibility of requirements.

Circulatory Neutrophils Exhibit Enhanced Neutrophil Extracellular Trap Formation in Early Puerperium: NETs at the Nexus of Thrombosis and Immunity

Pregnancy is associated with elevated maternal levels of cell-free DNA of neutrophil extracellular trap (NET) origin, as circulatory neutrophils exhibit increased spontaneous NET formation, mainly driven by G-CSF and finely modulated by sex hormones. The postpartum period, on the other hand, involves physiological alterations consistent with the need for protection against infections and fatal haemorrhage. Our findings indicate that all relevant serum markers of neutrophil degranulation and NET release are substantially augmented postpartum. Neutrophil pro-NETotic activity in vitro is also upregulated particularly in post-delivery neutrophils. Moreover, maternal puerperal neutrophils exhibit a strong pro-NETotic phenotype, associated with increased levels of all key players in the generation of NETs, namely citH3, MPO, NE, and ROS, compared to non-pregnant and pregnant controls. Intriguingly, post-delivery NET formation is independent of G-CSF in contrast to late gestation and complemented by the presence of TF on the NETs, alterations in the platelet activity status, and activation of the coagulation cascade, triggered by circulating microparticles. Taken together, our results reveal the highly pro-NETotic and potentially procoagulant nature of postpartum neutrophils, bridging an overt immune activation with possible harmful thrombotic incidence.     

Effect of selenium on the growth of some selected green and blue-green algae

An algal assay procedure using microplate technique was carried out to assess the effect of selenium on the growth of some green and blue-green algae. Sodium selenite pentahydrate (Na₂SeO₃.5H₂O) and selendioxide (Se₂O₄) were tested as selenium. The test algae were Selenastrum capricornutum, Scenedesmus obliquus, Chlorella sp., Monoraphidium convolutum, Monoraphidium contortum, Monoraphidium griffithii, Anabaena flos-aquae, Micro-cystis aeruginosa, and Oscillatoria agardhii. The blue-green algae are toxin-producing strains. Cell number and in vivo chlorophyll fluorescence were the growth parameters of green and blue-green algae respectively. Dose-response curves quantify the selenium toxicity in terms of EC₅₀. The lowest selenium concentrations giving no detectable growth (EC₁₀₀) were visually inspected. The test algae showed distinctly different responses to various selenium treatments. Selenium at concentrations < 0.1 mg L⁻¹ stimulates, to varying degrees, the growth of all the green algae with one exception: S. capricornutum was dramatically inhibited at all treatments. O. agardhii, A. flos-aquae and M. aeruginosa showed marginal growth stimulation up to 0.1 mg Se L⁻¹, 1.0 mg Se L⁻¹ and 3.2 mg Se L⁻¹ respectively. In terms of EC₅₀, the compound selendioxide was more toxic to greens than sodium selenite. The reverse was indicated for the blue-greens. In general, the EC₅₀ presented a wide range (0.08–7.2 mg Se L⁻¹), with the lowest values reported for S. obliquus and the highest for M. aeruginosa. All the test algae, except S. obliquus, maintained observable growths at higher selenium levels (EC₁₀₀>1.0<100mg Se L⁻¹).     

Cell-membrane damage and element leaching in transplanted Parmelia sulcata lichen related to ambient SO2, temperature, and precipitation

Measurements were performed in lichen (Parmelia sulcata) transplants, to gain insight into the lichen vitality as possibly affected by both element deposition or lichen element content and further ambient atmospheric conditions (temperature, precipitation, SO2 levels). The electrical conductivity of rinsing solutions was used to assess cell-membrane damage in Parmelia sulcata in an experiment, which ran from August 2001 until August 2002. Element contents of the solutions and lichens were determined by inductively coupled plasma-optical emission spectrometry and by k0-instrumental neutron activation analysis, respectively. Factor analysis (MCATTFA) was used to determine grouping of elements of similar origin and/ or behavior. All in all, the data indicate that, apartfrom lichen Na and Cl levels, and for temperature and precipitation, no clear relationships with conductivity could be observed. Conductivity was mostly related to released Na, Cl, K, Mg, and Cs. On the basis of concentrations, Na, Cl, and K could be considered as largely determining the conductivity. The data suggest a different origin for K than that for Na and Cl: the latter two are most probably due to effects from sea salt sprays. Parmelia sulcata was sensitive enough to reflect appreciable ambient rises in air SO2 and resistant enough to recover afterward. MCATTFA on selected elements (K, Sc, Cu, V, As, and Sb) indicated the absence of any comparability between K and V, As and Sb, suggesting differences in origin and/or chemico-physical occurrence. Generally speaking, the present data suggest that the comparability of lichen vitality in large geographical areas may be limited and governed by the area's variability in temperature and precipitation rather than by variability in metal deposition rates. The leaching data on all elements and element groups, however, strongly suggest that wet deposition may also severely affect lichen elemental levels. This latter observation means that comparing outcomes for time or spatial series of lichen samples should be accompanied by a comparably careful monitoring of (preceding) ambient conditions.     

A new phase diagram for layered antiferromagnetic films

Magnetic multilayer films provide convenient model systems for studying the physics of antiferromagnetic films and surfaces. Here we report on the magnetic reversal and domain structure in antiferromagnetically coupled Co/Pt multilayers that are isomorphic to layered antiferromagnetic films with perpendicular magnetic anisotropy. We observe two distinct remanent states and reversal modes of the system. In mode 1 the magnetization in each layer reverses independently, producing an antiferromagnetic remanent state that shows full lateral correlation and vertical anticorrelation across the interlayers. In mode 2 the reversal in adjacent layers is locally synchronized with a remanent state that is vertically correlated but laterally anticorrelated in ferromagnetic stripe domains. Theoretical energy calculations of the two ground states identify a new phase boundary that is in good agreement with our experimental results.