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.

Intravitreal Injection of Normal Saline Induces Retinal Degeneration in the C57BL/6J Mouse

Purpose: To investigate the adverse effect of intravitreal injection of normal saline (NS) and phosphate buffered saline (PBS) in mouse eyes.

Methods: NS or PBS was injected intravitreally into C57BL/6J mouse eyes. Retinal lesions were monitored by fundus imaging, spectral-domain optical coherence tomography (SD-OCT), and histological investigations. Retinal immune gene expression was determined by real-time polymerase chain reaction (PCR). The toxic effect of NS and PBS or retinal protein from NS- or PBS-injected eyes on retinal pigment epithelium (RPE) was tested in B6-RPE-07 mouse RPE cell cultures.

Results: Intravitreal injection of NS dose-dependently induced localized retinal lesion in mice. Histological investigations revealed multiple vacuoles in photoreceptor outer segments and RPE cells. The lesions recovered over time and by 3 weeks post injection the majority of lesions vanished in eyes receiving 1 μl NS. Inflammatory genes, including TNF-α, IL-1β, IL-6, iNOS, and VEGF were upregulated in NS injected eyes. Intravitreal injection of PBS did not cause any pathology. The treatment of B6-RPE07 cells with 30% PBS or 30% NS did not affect RPE viability. However, incubation of 1-μg/ml retinal protein from NS-injected eyes, but not PBS-injected eyes induced RPE cell death.

Conclusion: NS is toxic to the C57BL/6J mouse retina and should not be used as a vehicle for intraocular injection. PBS is not toxic to the retina and is a preferred vehicle.

Translational Relevance: NS is not a physiological solution for intraocular injection in the C57BL/6J mice and questions its suitability for intraocular injection in other species, including human.

Improved diffusive gradients in thin films (DGT) measurement of total dissolved inorganic arsenic in waters and soils using a hydrous zirconium oxide binding layer

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A high-capacity diffusive gradients in thin films (DGT) technique has been developed for measurement of total dissolved inorganic arsenic (As) using a long shelf life binding gel layer containing hydrous zirconium oxide (Zr-oxide). Both As(III) and As(V) were rapidly accumulated in the Zr-oxide gel and could be quantitatively recovered by elution using 1.0 M NaOH for freshwater or a mixture of 1.0 M NaOH and 1.0 M H2O2 for seawater. DGT uptake of As(III) and As(V) increased linearly with deployment time and was independent of pH (2.0–9.1), ionic strength (0.01–750 mM), the coexistence of phosphate (0.25–10 mg P L–1), and the aging of the Zr-oxide gel up to 24 months after production. The capacities of the Zr-oxide DGT were 159 μg As(III) and 434 μg As(V) per device for freshwater and 94 μg As(III) and 152 μg As(V) per device for seawater. These values were 5–29 times and 3–19 times more than those reported for the commonly used ferrihydrite and Metsorb DGTs, respectively. Deployments of the Zr-oxide DGT in As-spiked synthetic seawater provided accurate measurements of total dissolved inorganic As over the 96 h deployment, whereas ferrihydrite and Metsorb DGTs only measured the concentrations accurately up to 24 and 48 h, respectively. Deployments in soils showed that the Zr-oxide DGT was a reliable and robust tool, even for soil samples heavily polluted with As. In contrast, As in these soils was underestimated by ferrihydrite and Metsorb DGTs due to insufficient effective capacities, which were likely suppressed by the competing effects of phosphate.

Rough Waters, Dark Shadows and Cross-Cutting Winds:the impact of European Union enlargement on Turkey’s EU accession negotiations

For a multiplicity of socio-economic, geo-political, strategic and identity-based reasons, Turkey’s progress towards EU membership is often treated as a sui generis case. Yet although Turkey’s accession negotiations with the European Union (EU) are essentially a bilateral – and often stormy – affair, they take place within a wider and dynamic process of enlargement in which not only can the gloomy – sometimes dark – shadows of past and prospective enlargements be clearly detected, but so too can the often chill winds from ongoing, parallel negotiations with other candidates. How the EU negotiates accession and what it expects from candidates has continued to evolve since the EU began drawing up its framework for negotiations with Turkey ten years ago. This paper charts this evolution by first identifying changes in the light of Croatia’s negotiating experience, the ‘lessons learnt’ by the EU in meeting the challenges of Bulgarian and Romanian accession, the EU’s handling of Iceland’s membership bid and accession negotiations, and the revised approach to negotiating accession evident in the more recent frameworks for accession negotiations with Montenegro and Serbia. The paper then explores the extent to which these changes have impacted on the approach the EU has adopted in framing and progressing accession negotiations with Turkey. In doing so, it questions both the consistency with which the EU’s negotiates accession and the extent to which Turkey’s progress towards EU membership is conditioned by the broader dynamics of EU enlargement as opposed to simply the dynamics within EU-Turkey relations and domestic Turkish reform efforts.

Dye adsorption onto mesoporous materials: PH influence, kinetics and equilibrium in buffered and saline media

Mesoporous materials were used as adsorbents for dye removal in different media: non-ionic, buffered and saline. The mesoporous materials used were commercial (silica gel) as well as as-synthesised materials (SBA-15 and a novel mesoporous carbon). Dye adsorption onto all the materials was very fast and the equilibrium was reached before 1h. The pH has a significant influence on the adsorption capacity for the siliceous materials since the electrostatic interactions are the driving forces. However, the influence of the pH on the adsorption capacity of the carbonaceous material was lower, since the van der Waals interactions are the driving forces. The ionic strength has a great impact on the siliceous materials adsorption capacity, being their adsorption capacity in a buffered medium six times higher than the corresponding to a non-ionic medium. Nevertheless, ionic strength does not influence on the dye adsorption on the mesoporous carbon. Overall, the as-synthesised carbon material presents a clear potential to treat dye effluents, showing high adsorption capacity (q_e≈200mg/g) in all the pH range studied (from 3 to 11); even at low concentrations (C_e≈10mg/L) and at short contact times (t_e<30min).

Air pollutant contamination and acidification of surface waters in the North York Moors, UK: Multi-proxy evidence from the sediments of a moorland pool

Despite the extensive geographical range of palaeolimnological studies designed to assess the extent of surface water acidification in the United Kingdom during the 1980s, little attention was paid to the status of surface waters in the North York Moors (NYM). In this paper, we present sediment core data from a moorland pool in the NYM that provide a record of air pollution contamination and surface water acidification. The 41-cm-long core was divided into three lithostratigraphic units. The lower two comprise peaty soils and peats, respectively, that date to between approximately 8080 and 6740 cal. BP. The uppermost unit comprises peaty lake muds dating from between approximately ad 1790 and the present day (ad 2006). The lower two units contain pollen dominated by forest taxa, whereas the uppermost unit contains pollen indicative of open landscape conditions similar to those of the present. Heavy metal, spheroidal carbonaceous particle, mineral magnetics and stable isotope analysis of the upper sediments show clear evidence of contamination by air pollutants derived from fossil-fuel combustion over the last c. 150years, and diatom analysis indicates that the naturally acidic pool became more acidic during the 20th century. We conclude that the exceptionally acidic surface waters of the pool at present (pH=c. 4.1) are the result of a long history of air pollution and not because of naturally acidic local conditions. We argue that the highly acidic surface waters elsewhere in the NYM are similarly acidified and that the lack of evidence of significant recovery from acidification, despite major reductions in the emissions of acidic gases that have taken place over the last c. 30years, indicates the continuing influence of pollutant sulphur stored in catchment peats, a legacy of over 150years of acid deposition.

Physico-chemical treatment methods for the removal of microcystins (cyanobacterial hepatotoxins) from potable waters

The incidence of cyanobacterial blooms in freshwaters, including drinking water reservoirs, has increased over the past few decades due to rising nutrient levels. Microcystins are hepatotoxins released from cyanobacteria and have been responsible for the death of humans as well as domestic and wild animals. Microcystins are chemically very stable and many processes have only limited efficacy in removing them. In this paper we review a range of water treatment methods which have been applied to removing microcystins from potable waters.

The Environmental Fate of polybrominated diphenyl ethers in western Taiwan and coastal waters: evaluation with a fugacity based model

The environmental fate of polybrominated diphenyl ethers (PBDEs), a group of flame retardants that are considered to be persistent organic pollutants (POPs), around the Zhuoshui River and Changhua County regions of Taiwan was assessed. An investigation into emissions, partitioning, and fate of selected PBDEs was conducted based on the equilibrium constant (EQC) fugacity model developed at Trent University, Canada. Emissions for congeners PBDE 47, PBDE 99, and PBDE 209 to air (4.9–92 × 10−3 kg/h), soil (0.91–17.4 × 10−3 kg/h), and water (0.21–4.04 × 10−3 kg/h), were estimated by modifying previous models on PBDE emission rates by considering both industrial and domestic rates. It was found that fugacity modeling can give a reasonable estimation of the behavior, partitioning, and concentrations of PBDE congeners in and around Taiwan. Results indicate that PBDE congeners have a high affinity for partitioning into sediments then soils. As congener number decreases, the PBDEs then partition more readily into air. As the degree of bromination increases, congeners more readily partition to sediments. Sediments may then act as a long-term source of PBDEs which can be released back into the water column due to resuspension during storm events.

Stock structure of Atlantic herring Clupea harengus in the Norwegian Sea and adjacent waters

The genetic structure of Atlantic herring Clupea harengus L. was investigated in its north-easterly distribution in the Norwegian Sea and adjacent waters, using 23 neutral and one non-neutral (Cpa111) microsatellite loci. Fish from the suspected 2 main populations - the Norwegian spring-spawning herring (NSSH) and the Icelandic summer-spawning herring (ISSH) - were collected at spawning locations in their respective spawning seasons from 2009 to 2012. Samples were also collected from Norwegian autumn spawning locations, from different local Norwegian fjords such as the inner part of Trondheimsfjorden, Lindås pollene, Landvikvannet and Lusterfjorden, as well as from suspected Faroese spawning components. The observed level of genetic differentiation was significant but low (F_ST = 0.007) and mostly attributable to the differentiation of the local Norwegian fjord populations. The locus Cpa111, which was detected to putatively be under positive selection, exhibited the highest FST value (0.044). The observed genetic patterns were robust to exclusion of this locus. Landvikvannet herring was also genetically distinguishable from the 3 other fjord populations. In addition, the present study does not support genetic structuring among the ISSH and the NSSH.

Life history of turbot in Icelandic waters: Intra- and inter-population genetic diversity and otolith tracking of environmental temperatures

The stock structure of turbot was investigated between samples from S-Norway, the Irish Sea and the Kattegat, using 12 microsatellite loci and compared to the turbot caught in Icelandic waters. Highly significant genetic differentiation was observed between samples from Kattegat and other areas. Significant genetic differentiation was also observed between the Irish Sea sample on one hand and Iceland and S-Norway on the other hand. No significant genetic differentiation was observed between Iceland and S-Norway. Otoliths of 25 turbot, age ranging from 3 to 19 years, were subjected to nearly 300 mass spectrometry determinations of stable oxygen and carbon isotopes. Oxygen isotope composition (δ¹⁸O) in the otolith samples was used to estimate ambient temperature at time of otolith accretion, and yielded estimated temperatures experienced by the turbot ranging from 3 to 15°C. Overall, the genetic analysis indicates panmixia between turbot in Icelandic and Norwegian waters. While the extensive migration of larvae between Norway and Iceland is unlikely, passive drift of turbot larva from other areas (e.g. Ireland) cannot be ruled out. 

Novel precipitated zirconia-based DGT technique for high-resolution imaging of oxyanions in waters and sediments

Water-sediment exchange is a fundamental component of oxyanion cycling in the environment. Yet, many of the (im)mobilization processes overlay complex spatial and temporal redox regimes that occur within millimeters of the interface. Only a few methods exist that can reliably capture these porewater fluxes, with the most popular being high-resolution diffusive gradients in thin films (HR-DGT). However, functionality of HR-DGT is restricted by the availability of suitable analyte binding agents within the sampler, which must be simple to cast and homogeneously distributed in the binding layer, exhibit adequate sorption capacities, be resistive to chemical change, and possess a very fine particle size (≤10 μm). A novel binding layer was synthesized to meet these requirements by in situ precipitation of zirconia into a precast hydrogel. The particle diameter ≤0.2 μm of zirconia in this precipitated gel was uniform and at least 50-times smaller than the conventional molding approach. Further, this gel had superior binding and stability characteristics compared with the commonly used ferrihydrite HR-DGT technique and could be easily fabricated as an ultrathin gel (60 μm) for simultaneous oxygen imaging in conjunction with planar-optodes. Chemical imaging of anion and oxygen fluxes using the new sampler were evaluated on Lake Taihu sediments.