Overcoming the Scalability Challenges of Epidemic Simulations on Blue Waters

Modeling dynamical systems represents an important application class covering a wide range of disciplines including but not limited to biology, chemistry, finance, national security, and health care. Such applications typically involve large-scale, irregular graph processing, which makes them difficult to scale due to the evolutionary nature of their workload, irregular communication and load imbalance. EpiSimdemics is such an application simulating epidemic diffusion in extremely large and realistic social contact networks. It implements a graph-based system that captures dynamics among co-evolving entities. This paper presents an implementation of EpiSimdemics in Charm++ that enables future research by social, biological and computational scientists at unprecedented data and system scales. We present new methods for application-specific processing of graph data and demonstrate the effectiveness of these methods on a Cray XE6, specifically NCSA's Blue Waters system.

Preliminary investigation of mixed adsorbents for the removal of copper and methylene blue from aqueous solutions

With most recent studies being focused on the development of
advanced chemical adsorbents, this paper investigates the possibility of
using two natural low-cost materials for selective adsorption. Multiadsorbent
systems containing tea waste and dolomite have been tested for
their effectiveness in the removal of copper and methylene blue from
aqueous solutions. The effects of contact time, solution pH and
adsorption isotherms on the sorption behaviour were investigated. The
Langmuir and Freundlich isotherms adequately described the adsorption of
copper ions and methylene blue by both materials in different systems.
The highest adsorption capacities for Cu and MB were calculated as 237.7
at pH 4.5 and 150.44 mg.g‒1 at pH 7 for DO and TW+DO respectively. Tea
waste (TW) and dolomite (DO) were characterized by Fourier transform
infrared spectroscopy, scanning electron microscopy and Energy dispersive
X-ray analysis. The removal of Cu and MB by dolomite was mainly via
surface complexation while physisorption was responsible for most of the
Cu and MB adsorption onto tea waste. Identifying the fundamental mechanisms and behaviour is key to the development of practical multi-adsorbent packed columns.

Interference Investigation for Cognitive Spectrum Sharing Networks with Reactive DF Relay Selection

Cognitive radio (CR) with spectrum-sharing has been envisioned as emerging technology for the next generation of mobile and wireless networks by allowing the unlicensed customers simultaneously utilize the licensed radio frequency spectrums. However, the CR has faced some practical challenges due to its deduced system performance as compared to non spectrum-sharing counterpart. In this paper, we therefore consider the potential of incorporating the cooperative communications into CR by introducing the concept of reactive multiple decode-and-forward (DF) relays. In particular, we derive new results for exact and asymptotic expressions for the performance of cognitive relay networks with K-th best relay selection. Our novel results have exhibited the significance of using relay networks to enhance the system performance of CR.

Serum amyloid A-related inflammation is lowered by increased fruit and vegetable intake, while high-sensitive C-reactive protein, IL-6 and E-selectin remain unresponsive

The present study assessed whether increased fruit and vegetable (F&V) intake reduced the concentrations of the inflammatory marker serum amyloid A (SAA) in serum, HDL2 and HDL3 and whether the latter reduction influenced any of the functional properties of these HDL subfractions. The present study utilised samples from two previous studies: (1) the FAVRIT (Fruit and Vegetable Randomised Intervention Trial) study - hypertensive subjects (systolic blood pressure (BP) range 140-190 mmHg; diastolic BP range 90-110 mmHg) were randomised to receive a 1-, 3- or 6-portion F&V/d intervention for 8 weeks, and (2) the ADIT (Ageing and Dietary Intervention Trial) study - older subjects (65-85 years) were randomised to receive a 2- or 5-portion F&V/d intervention for 16 weeks. HDL2 and HDL3 were isolated by rapid ultracentrifugation. Measurements included the following: serum high-sensitive C-reactive protein (hsCRP) by an immunoturbidimetric assay; serum IL-6 and E-selectin and serum-, HDL2- and HDL3-SAA by ELISA procedures; serum-, HDL2- and HDL3-cholesterol ester transfer protein (CETP) activity by a fluorometric assay. Although the concentrations of hsCRP, IL-6 and E-selectin were unaffected by increasing F&V intake in both studies (P>0·05 for all comparisons), those of SAA in HDL3 decreased in the FAVRIT cohort (P= 0·049) and those in HDL2 and HDL3 decreased in the ADIT cohort (P= 0·035 and 0·032), which was accompanied by a decrease in the activity of CETP in HDL3 in the FAVRIT cohort (P= 0·010) and in HDL2 in the ADIT cohort (P= 0·030). These results indicate that SAA responds to increased F&V intake, while other inflammatory markers remain unresponsive, and this leads to changes in HDL2 and HDL3, which may influence their antiatherogenic potential. Overall, the present study provides tangible evidence of the effectiveness of increased F&V intake, which may be of use to health policy makers and the general public.

Photosensitisers - the progression from photodynamic therapy to anti-infective surfaces

Introduction: The application of light as a stimulus in pharmaceutical systems and the associated ability to provide precise spatiotemporal control over location, wavelength and intensity, allowing ease of external control independent of environmental conditionals, has led to its increased use. Of particular note is the use of light with photosensitisers.

Areas covered: Photosensitisers are widely used in photodynamic therapy to cause a cidal effect towards cells on irradiation due to the generation of reactive oxygen species. These cidal effects have also been used to treat infectious diseases. The effects and benefits of photosensitisers in the treatment of such conditions are still being developed and further realised, with the design of novel delivery strategies. This review provides an overview of the realisation of the pharmaceutically relevant uses of photosensitisers, both in the context of current research and in terms of current clinical application, and looks to the future direction of research.

Expert opinion: Substantial advances have been and are being made in the use of photosensitisers. Of particular note are their antimicrobial applications, due to absence of resistance that is so frequently associated with conventional treatments. Their potency of action and the ability to immobilise to polymeric supports is opening a wide range of possibilities with great potential for use in healthcare infection prevention strategies.

Mineralogical Characteristics and Transformations during Long-Term Operation of a Zerovalent Iron Reactive Barrier

Design and operation of Fe⁰ permeable reactive barriers (PRBs) can be improved by understanding the long-term mineralogical transformations that occur within PRBs. Changes in mineral precipitates, cementation, and corrosion of Fe⁰ filings within an in situ pilot-scale PRB were examined after the first 30 months of operation and compared with results of a previous study of the PRB conducted 15 months earlier using X-ray diffraction and scanning electron microscopy employing energy dispersive X-ray and backscatter electron analyses. Iron (oxy)hydroxides, aragonite, and maghemite and/or magnetite occurred throughout the cores collected 30 mo after installation. Goethite, lepidocrocite, mackinawite, aragonite, calcite, and siderite were associated with oxidized and cemented areas, while green rusts were detected in more reduced zones. Basic differences from our last detailed investigation include (i) mackinawite crystallized from amorphous FeS, (ii) aragonite transformed into calcite, (iii) akaganeite transformed to goethite and lepidocrocite, (iv) iron (oxy)hydroxides and calcium and iron carbonate minerals increased, (v) cementation was greater in the more recent study, and (vi) oxidation, corrosion, and disintegration of Fe⁰ filings were greater, especially in cemented areas, in the more recent study. If the degree of corrosion and cementation that was observed from 15 to 30 mo after installation continues, certain portions of the PRB (i.e., up-gradient entrance of the ground water to the Fe⁰ section of the PRB) may last less than five more years, thus reducing the effectiveness of the PRB to mitigate contaminants.

Impact of sample preparation on mineralogical analysis of zero-valent iron reactive barrier materials

Permeable reactive barriers (PRBs) of zero-valent iron (Fe⁰) are increasingly being used to remediate contaminated ground water. Corrosion of Fe⁰ filings and tbe formation of precipitates can occur when the PRB material comes in contact with ground water and may reduce the lifespan and effectiveness of the barrier. At present, there are no routine procedures for preparing and analyzing the mineral precipitates from Fe⁰ PRB material. These procedures are needed because mineralogical composition of corrosion products used to interpret the barrier processes can change with iron oxidation and sample preparation. The objectives of this study were (i) to investigate a method of preparing Fe⁰ reactive barrier material for mineralogical analysis by X-ray diffraction (XRD), and (ii) to identify Fe mineral phases and rates of transformations induced by different mineralogical preparation techniques. Materials from an in situ Fe⁰ PRB were collected by undisturbed coring and processed for XRD analysis after different times since sampling for three size fractions and by various drying treatments. We found that whole-sample preparation for analysis was necessary because mineral precipitates occurred within the PRB material in different size fractions of the samples. Green rusts quickly disappeared from acetone-dried samples and were not present in air-dried and oven-dried samples Maghemite/magnetite content increased over time and in oven-dried samples, especially after heating to 105°C. We conclude that care must be taken during sample preparation of Fe⁰ PRB material, especially for detection of green rusts, to ensure accurate identification of minerals present within the barrier system.

Repeated measures of body mass index and C-reactive protein in relation to all-cause mortality and cardiovascular disease: Results from the consortium on health and ageing network of cohorts in Europe and the United States (CHANCES)

Obesity has been linked with elevated levels of C-reactive protein (CRP), and both have been associated with increased risk of mortality and cardiovascular disease (CVD). Previous studies have used a single ‘baseline’ measurement and such analyses cannot account for possible changes in these which may lead to a biased estimation of risk. Using four cohorts from CHANCES which had repeated measures in participants 50 years and older, multivariate time-dependent Cox proportional hazards was used to estimate hazard ratios (HR) and 95 % confidence intervals (CI) to examine the relationship between body mass index (BMI) and CRP with all-cause mortality and CVD. Being overweight (≥25–<30 kg/m2) or moderately obese (≥30–<35) tended to be associated with a lower risk of mortality compared to normal (≥18.5–<25): ESTHER, HR (95 % CI) 0.69 (0.58–0.82) and 0.78 (0.63–0.97); Rotterdam, 0.86 (0.79–0.94) and 0.80 (0.72–0.89). A similar relationship was found, but only for overweight in Glostrup, HR (95 % CI) 0.88 (0.76–1.02); and moderately obese in Tromsø, HR (95 % CI) 0.79 (0.62–1.01). Associations were not evident between repeated measures of BMI and CVD. Conversely, increasing CRP concentrations, measured on more than one occasion, were associated with an increasing risk of mortality and CVD. Being overweight or moderately obese is associated with a lower risk of mortality, while CRP, independent of BMI, is positively associated with mortality and CVD risk. If inflammation links CRP and BMI, they may participate in distinct/independent pathways. Accounting for independent changes in risk factors over time may be crucial for unveiling their effects on mortality and disease morbidity.

Cytokine and C-reactive protein profiles induced by porcine circovirus type 2 experimental infection in 3-week-old piglets

The purpose of this study was to determine serum profiles of cytokines at a protein level and Creactive protein (CRP) during the development of postweaning multisystemic wasting syndrome (PMWS) in experimentally inoculated pigs. Levels of serum IFN-alpha, IL-6, IL-10, and CRP were examined for a 35-day period in 10 piglets experimentally infected with PCV2 at 3 weeks of age. Four of the infected piglets developed severe PMWS at 14 to 21 days post-infection (d.p.i.) and died prior to termination of the experiment. The remaining six PCV2-infected piglets experienced transient fever, but did not display overt clinical signs of PMWS and were considered as subclinically infected. A bioassay was used to detect IL-6 and ELISAs were used to detect IFN-alpha, IL-10, and CRP. There were no significant differences in cytokine or CRP expression from 0 to 7 d.p.i. between the PMWS-affected and the subclinically infected piglets. Levels of IL-10 and CRP were elevated from 10 and 14 d.p.i. respectively in the PMWS-affected piglets compared to the subclinically infected piglets. There were no significant differences in IFN-alpha and IL-6 expression between the PMWS-affected piglets and the subclinically infected piglets. The present study shows that elevated levels of serum CRP and IL-10 were associated with PCV2-infected piglets that subsequently developed severe PMWS. This may help to provide further insight into the immunoaetiogenesis of this syndrome.

Chemistry and Mechanism of Alizarin Red S and Methylene Blue Biosorption onto Olive Stone: Equilibrium and Kinetic

The biosorption process of anionic dye Alizarin Red S (ARS) and cationic dye methylene blue (MB) as a function of solution pH, initial concentration and contact time onto olive stone (OS) biomass has been investigated. The main objectives of the current study are to: (i) study the chemistry and the mechanism of ARS and MB biosorption onto olive stone and the type of OS–ARS, MB interactions occurring, (ii) study the biosorption equilibrium and kinetic experimental data required for the design and operation of column reactors. Equilibrium biosorption isotherms and kinetics were also examined. Experimental equilibrium data were fitted to four different isotherms by non-linear regression method, however, the biosorption experimental data for ARS and MB dyes were well interpreted by the Temkin and Langmuir isotherms, respectively. The maximum monolayer adsorption capacity for ARS and MB dyes were 109.0 and 102.6 mg/g, respectively. The kinetic data of the two dyes could be better described by the pseudo second-order model. The data showed that olive stone can be effectively used for removing dyes from wastewater.

The use of a novel compact fluorosensor for in situ monitoring of the photocatalytic destruction of methylene blue dye effluents

The use of TiO 2 photocatalysis for the destruction of dyes such as methylene blue has been extensively reported. One of the challenges faced in both the laboratory and large scale water treatment plants is the fact that the samples have to be removed from the reactor vessel and the catalyst separated prior to analysis being undertaken. In this paper we report the development of a simple fluorimeter instrument and its use in monitoring the photocatalytic destruction of methylene blue dyes in the presence of catalyst suspensions. The results reported show that the instrument provides an effective method for in situ monitoring of the photocatalytic destruction of fluorescent dyes hence allowing more accurate measurement due to the minimisation of sample loss and cross contamination. Furthermore it also provides a method for real time monitoring of the dye pollutant destruction in large scale photocatalytic reactors.