Dynamic SLA Negotiation in Autonomic Federated Environments

Abstract. Federated computing environments offer requestors the ability to dynamically invoke services offered by collaborating providers in the virtual service network. Without an efficient resource management that includes Dynamic SLA Negotiation, however, the assignment of providers to customer’s requests cannot be optimized and cannot offer high reliability without relevant SLA guarantees. We propose a new SLA-based SERViceable Metacomputing Environment (SERVME) capable of matching providers based on QoS requirements and performing autonomic provisioning and deprovisioning of services according to dynamic requestor needs. This paper presents the SLA negotiation process that includes on-demand provisioning and uses an object-oriented SLA model for large-scale service-oriented systems supported by SERVME. An initial reference implementation in the SORCER environment is also described

Cloud condensation nuclei activity, droplet growth kinetics, and hygroscopicity of biogenic and anthropogenic secondary organic aerosol (SOA)

© 2016 Author(s).Interaction of biogenic volatile organic compounds (VOCs) with Anthropogenic VOC (AVOC) affects the physicochemical properties of secondary organic aerosol (SOA). We investigated cloud droplet activation (CCN activity), droplet growth kinetics, and hygroscopicity of mixed anthropogenic and biogenic SOA (ABSOA) compared to pure biogenic SOA (BSOA) and pure anthropogenic SOA (ASOA). Selected monoterpenes and aromatics were used as representative precursors of BSOA and ASOA, respectively. We found that BSOA, ASOA, and ABSOA had similar CCN activity despite the higher oxygen to carbon ratio (O/C) of ASOA compared to BSOA and ABSOA. For individual reaction systems, CCN activity increased with the degree of oxidation. Yet, when considering all different types of SOA together, the hygroscopicity parameter, κ$_CCN$, did not correlate with O/C. Droplet growth kinetics of BSOA, ASOA, and ABSOA were comparable to that of (NH$_4$)$_2$SO$_4$, which indicates that there was no delay in the water uptake for these SOA in supersaturated conditions. In contrast to CCN activity, the hygroscopicity parameter from a hygroscopic tandem differential mobility analyzer (HTDMA) measurement, κ$_HTDMA$, of ASOA was distinctively higher (0.09-0.10) than that of BSOA (0.03-0.06), which was attributed to the higher degree of oxidation of ASOA. The ASOA components in mixed ABSOA enhanced aerosol hygroscopicity. Changing the ASOA fraction by adding biogenic VOC (BVOC) to ASOA or vice versa (AVOC to BSOA) changed the hygroscopicity of aerosol, in line with the change in the degree of oxidation of aerosol. However, the hygroscopicity of ABSOA cannot be described by a simple linear combination of pure BSOA and ASOA systems. This indicates that additional processes, possibly oligomerization, affected the hygroscopicity. Closure analysis of CCN and HTDMA data showed κ$_HTDMA$ was lower than κ$_CCN$ by 30-70 %. Better closure was achieved for ASOA compared to BSOA. This discrepancy can be attributed to several reasons. ASOA seemed to have higher solubility in subsaturated conditions and/or higher surface tension at the activation point than that of BSOA.EUROCHAMP2 European Commission 7th framework, NordForsk, VILLUM Foundatio

Plasma Plasmodium falciparum Histidine-Rich Protein-2 Concentrations Are Associated with Malaria Severity and Mortality in Tanzanian Children

Plasma Plasmodium falciparum histidine-rich protein-2 (PfHRP-2) concentrations, a measure of parasite biomass, have been correlated with malaria severity in adults, but not yet in children. We measured plasma PfHRP-2 in Tanzanian children with uncomplicated (n = 61) and cerebral malaria (n = 45; 7 deaths). Median plasma PfHRP-2 concentrations were higher in cerebral malaria (1008 [IQR 342–2572] ng/mL) than in uncomplicated malaria (465 [IQR 36–1426] ng/mL; p = 0.017). In cerebral malaria, natural log plasma PfHRP-2 was associated with coma depth (r = −0.42; p = 0.006) and mortality (OR: 3.0 [95% CI 1.03–8.76]; p = 0.04). In this relatively small cohort study in a mesoendemic transmission area of Africa, plasma PfHRP-2 was associated with pediatric malaria severity and mortality. Further studies among children in areas of Africa with higher malaria transmission and among children with different clinical manifestations of severe malaria will help determine the wider utility of quantitative PfHRP-2 as a measure of parasite biomass and prognosis in sub-Saharan Africa

Variability in the Dynamics of Mortality and Immobility Responses of Freshwater Arthropods Exposed to Chlorpyrifos

The species sensitivity distribution (SSD) concept is an important probabilistic tool for environmental risk assessment (ERA) and accounts for differences in species sensitivity to different chemicals. The SSD model assumes that the sensitivity of the species included is randomly distributed. If this assumption is violated, indicator values, such as the 50% hazardous concentration, can potentially change dramatically. Fundamental research, however, has discovered and described specific mechanisms and factors influencing toxicity and sensitivity for several model species and chemical combinations. Further knowledge on how these mechanisms and factors relate to toxicologic standard end points would be beneficial for ERA. For instance, little is known about how the processes of toxicity relate to the dynamics of standard toxicity end points and how these may vary across species. In this article, we discuss the relevance of immobilization and mortality as end points for effects of the organophosphate insecticide chlorpyrifos on 14 freshwater arthropods in the context of ERA. For this, we compared the differences in response dynamics during 96 h of exposure with the two end points across species using dose response models and SSDs. The investigated freshwater arthropods vary less in their immobility than in their mortality response. However, differences in observed immobility and mortality were surprisingly large for some species even after 96 h of exposure. As expected immobility was consistently the more sensitive end point and less variable across the tested species and may therefore be considered as the relevant end point for population of SSDs and ERA, although an immobile animal may still potentially recover. This is even more relevant because an immobile animal is unlikely to survive for long periods under field conditions. This and other such considerations relevant to the decision-making process for a particular end point are discussed

A toxicokinetic model for thiamethoxam in rats: implications for higher-tier risk assessment

Risk assessment for mammals is currently based on external exposure measurements, but effects of toxicants are better correlated with the systemically available dose than with the external administered dose. So for risk assessment of pesticides, toxicokinetics should be interpreted in the context of potential exposure in the field taking account of the timescale of exposure and individual patterns of feeding. Internal concentration is the net result of absorption, distribution, metabolism and excretion (ADME). We present a case study for thiamethoxam to show how data from ADME study on rats can be used to parameterize a body burden model which predicts body residue levels after exposures to LD50 dose either as a bolus or eaten at different feeding rates. Kinetic parameters were determined in male and female rats after an intravenous and oral administration of 14C labelled by fitting one-compartment models to measured pesticide concentrations in blood for each individual separately. The concentration of thiamethoxam in blood over time correlated closely with concentrations in other tissues and so was considered representative of pesticide concentration in the whole body. Body burden model simulations showed that maximum body weight-normalized doses of thiamethoxam were lower if the same external dose was ingested normally than if it was force fed in a single bolus dose. This indicates lower risk to rats through dietary exposure than would be estimated from the bolus LD50. The importance of key questions that should be answered before using the body burden approach in risk assessment, data requirements and assumptions made in this study are discussed in detail

Phase partitioning and volatility of secondary organic aerosol components formed from alpha-pinene ozonolysis and OH oxidation : the importance of accretion products and other low volatility compounds

We measured a large suite of gas- and particle-phase multi-functional organic compounds with a Filter Inlet for Gases and AEROsols (FIGAERO) coupled to a high-resolution time-of-flight chemical ionization mass spectrometer (HR-ToF-CIMS) developed at the University of Washington. The instrument was deployed on environmental simulation chambers to study monoterpene oxidation as a secondary organic aerosol (SOA) source. We focus here on results from experiments utilizing an ionization method most selective towards acids (acetate negative ion proton transfer), but our conclusions are based on more general physical and chemical properties of the SOA. Hundreds of compounds were observed in both gas and particle phases, the latter being detected by temperature-programmed thermal desorption of collected particles. Particulate organic compounds detected by the FIGAERO-HR-ToF-CIMS are highly correlated with, and explain at least 25-50% of, the organic aerosol mass measured by an Aerodyne aerosol mass spectrometer (AMS). Reproducible multi-modal structures in the thermograms for individual compounds of a given elemental composition reveal a significant SOA mass contribution from high molecular weight organics and/or oligomers (i.e., multi-phase accretion reaction products). Approximately 50% of the HR-ToF-CIMS particle-phase mass is associated with compounds having effective vapor pressures 4 or more orders of magnitude lower than commonly measured monoterpene oxidation products. The relative importance of these accretion-type and other extremely low volatility products appears to vary with photochemical conditions. We present a desorption-temperature-based framework for apportionment of thermogram signals into volatility bins. The volatility-based apportionment greatly improves agreement between measured and modeled gas-particle partitioning for select major and minor components of the SOA, consistent with thermal decomposition during desorption causing the conversion of lower volatility components into the detected higher volatility compounds.Peer reviewe

PDBe-KB: collaboratively defining the biological context of structural data

The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive

Rapid, Specific Detection of Alphaviruses from Tissue Cultures Using a Replicon-Defective Reporter Gene Assay

We established a rapid, specific technique for detecting alphaviruses using a replicon-defective reporter gene assay derived from the Sindbis virus XJ-160. The pVaXJ expression vector containing the XJ-160 genome was engineered to form the expression vectors pVaXJ-EGFP expressing enhanced green fluorescence protein (EGFP) or pVaXJ-GLuc expressing Gaussia luciferase (GLuc). The replicon-defective reporter plasmids pVaXJ-EGFPΔnsp4 and pVaXJ-GLucΔnsp4 were constructed by deleting 1139 bp in the non-structural protein 4 (nsP4) gene. The deletion in the nsP4 gene prevented the defective replicons from replicating and expressing reporter genes in transfected BHK-21 cells. However, when these transfected cells were infected with an alphavirus, the non-structural proteins expressed by the alphavirus could act on the defective replicons in trans and induce the expression of the reporter genes. The replicon-defective plasmids were used to visualize the presence of alphavirus qualitatively or detect it quantitatively. Specificity tests showed that this assay could detect a variety of alphaviruses from tissue cultures, while other RNA viruses, such as Japanese encephalitis virus and Tahyna virus, gave negative results with this system. Sensitivity tests showed that the limit of detection (LOD) of this replicon-defective assay is between 1 and 10 PFU for Sindbis viruses. These results indicate that, with the help of the replicon-defective alphavirus detection technique, we can specifically, sensitively, and rapidly detect alphaviruses in tissue cultures. The detection technique constructed here may be well suited for use in clinical examination and epidemiological surveillance, as well as for rapid screening of potential viral biological warfare agents

A Cell-Free Microtiter Plate Screen for Improved [FeFe] Hydrogenases

, a potential renewable fuel. Attempts to exploit these catalysts in engineered systems have been hindered by the biotechnologically inconvenient properties of the natural enzymes, including their extreme oxygen sensitivity. Directed evolution has been used to improve the characteristics of a range of natural catalysts, but has been largely unsuccessful for [FeFe] hydrogenases because of a lack of convenient screening platforms. [FeFe] hydrogenase HydA1 with a specific activity ∼4 times that of the wild-type enzyme. cell extracts, which allows unhindered access to the protein maturation and assay environment