Proximity Networks and Epidemics

Disease spread in most biological populations requires the proximity of agents. In populations where the individuals have spatial mobility, the contact graph is generated by the "collision dynamics" of the agents, and thus the evolution of epidemics couples directly to the spatial dynamics of the population. We first briefly review the properties and the methodology of an agent-based simulation (EPISIMS) to model disease spread in realistic urban dynamic contact networks. Using the data generated by this simulation, we introduce the notion of dynamic proximity networks which takes into account the relevant time scales for disease spread: contact duration, infectivity period and rate of contact creation. This approach promises to be a good candidate for a unified treatment of epidemic types that are driven by agent collision dynamics. In particular, using a simple model, we show that it can can account for the observed qualitative differences between the degree distributions of contact graphs of diseases with short infectivity period (such as air-transmitted diseases) or long infectivity periods (such as HIV)

Going through Rough Times: from Non-Equilibrium Surface Growth to Algorithmic Scalability

Efficient and faithful parallel simulation of large asynchronous systems is a challenging computational problem. It requires using the concept of local simulated times and a synchronization scheme. We study the scalability of massively parallel algorithms for discrete-event simulations which employ conservative synchronization to enforce causality. We do this by looking at the simulated time horizon as a complex evolving system, and we identify its universal characteristics. We find that the time horizon for the conservative parallel discrete-event simulation scheme exhibits Kardar-Parisi-Zhang-like kinetic roughening. This implies that the algorithm is asymptotically scalable in the sense that the average progress rate of the simulation approaches a non-zero constant. It also implies, however, that there are diverging memory requirements associated with such schemes.Comment: to appear in the Proceedings of the MRS, Fall 200

Suppressing Roughness of Virtual Times in Parallel Discrete-Event Simulations

In a parallel discrete-event simulation (PDES) scheme, tasks are distributed among processing elements (PEs), whose progress is controlled by a synchronization scheme. For lattice systems with short-range interactions, the progress of the conservative PDES scheme is governed by the Kardar-Parisi-Zhang equation from the theory of non-equilibrium surface growth. Although the simulated (virtual) times of the PEs progress at a nonzero rate, their standard deviation (spread) diverges with the number of PEs, hindering efficient data collection. We show that weak random interactions among the PEs can make this spread nondivergent. The PEs then progress at a nonzero, near-uniform rate without requiring global synchronizations

Composite sponges for in situ alveolar bone regeneration following tooth extraction

This research concerns the development of solvent-cast lyophilised composite sponges in the bioactive glass-alginate-chitosan system for alveolar bone tissue maintenance following tooth extraction. Hydroxyapatite formed on the surfaces of pure alginate, 50:50 alginate:chitosan blend and pure chitosan sponges blended with 10 wt.% bioactive glass within 7 days of exposure to simulated body fluid, indicating that they possess the potential to stimulate bone tissue formation. In the absence of bioactive glass, pure chitosan sponges also demonstrated in vitro bioactivity, to a lesser extent; unlike pure alginate and 50:50 alginate:chitosan blend, which did not. All samples formed macroporous sponges whose biocompatibility with human osteosarcoma cells increased as a function of chitosan-content. Polyelectrolyte complex formation between alginate and chitosan, and the incorporation of bioactive glass were found to increase the swelling capacity of the sponges in SBF. The findings of this study demonstrate that, bioactive glass-chitosan sponges are the favoured candidates for alveolar bone tissue augmentation as their rate of hydroxyapatite formation and biocompatibility are superior to those of the other samples

An in vitro comparison of the enamel remineralisation potential of bioactive glass, hydroxyapatite and CPP-ACP

The objective of this research was to investigate the comparative in vitro enamel remineralisation potential of commercial toothpastes containing bioactive glass (BG) particles, hydroxyapatite (HAP) particles or casein phosphopeptide – amorphous calcium phosphate (CPP-ACP) nanocomplexes. Eighteen extracted permanent teeth were coated with varnish leaving a window on the buccal surface and placed in demineralising solution for 24 h to create artificial caries-like white spot lesions (WSLs). The teeth were randomly assigned to six groups and sectioned longitudinally through the WSLs. The roots were removed and the teeth were re-varnished, leaving the WSLs exposed. Groups A, B and C were subjected to an optimum remineralisation protocol in which the “control” half of each tooth was incubated in artificial saliva for 24 h at 37 ◦C and the “treatment” half of each corresponding tooth was cyclically exposed to artificial saliva and to 1:2 toothpaste solution containing either BG, HAP or CPP-CAP, respectively. Groups D, E and F were subjected to an acid-challenge remineralisation protocol which was similar to that of Groups A, B and C but which also incorporated cyclic exposure to demineralising solution. Scanning electron microscopy and energy dispersive X-ray analysis were used to compare the remineralisation of the surface and depth of the control and treatment WSLs. Under optimum conditions BG and CPP-ACP provided sub-surface repair by diffusion of calcium and phosphate ions into the WSLs. HAP did not influence remineralisation under neutral pH conditions. Conversely, under acid-challenge conditions, HAP was able to dissolve to release calcium and phosphate ions which diffused in to the WSLs and also protected the enamel surface from further erosion. BG and CPP-ACP both coated the enamel surface under acidic conditions, although their ability to remineralise the body of the lesion was compromised at low pH

Synchronization Landscapes in Small-World-Connected Computer Networks

Motivated by a synchronization problem in distributed computing we studied a simple growth model on regular and small-world networks, embedded in one and two-dimensions. We find that the synchronization landscape (corresponding to the progress of the individual processors) exhibits Kardar-Parisi-Zhang-like kinetic roughening on regular networks with short-range communication links. Although the processors, on average, progress at a nonzero rate, their spread (the width of the synchronization landscape) diverges with the number of nodes (desynchronized state) hindering efficient data management. When random communication links are added on top of the one and two-dimensional regular networks (resulting in a small-world network), large fluctuations in the synchronization landscape are suppressed and the width approaches a finite value in the large system-size limit (synchronized state). In the resulting synchronization scheme, the processors make close-to-uniform progress with a nonzero rate without global intervention. We obtain our results by ``simulating the simulations", based on the exact algorithmic rules, supported by coarse-grained arguments.Comment: 20 pages, 22 figure

Extreme fluctuations in noisy task-completion landscapes on scale-free networks

We study the statistics and scaling of extreme fluctuations in noisy task-completion landscapes, such as those emerging in synchronized distributed-computing networks, or generic causally-constrained queuing networks, with scale-free topology. In these networks the average size of the fluctuations becomes finite (synchronized state) and the extreme fluctuations typically diverge only logarithmically in the large system-size limit ensuring synchronization in a practical sense. Provided that local fluctuations in the network are short-tailed, the statistics of the extremes are governed by the Gumbel distribution. We present large-scale simulation results using the exact algorithmic rules, supported by mean-field arguments based on a coarse-grained description.Comment: 16 pages, 6 figures, revte

The effects of grape seed on apoptosis-related gene expression and oxidative stress in streptozotocin-induced diabetic rats

WOS: 000350554300002PubMed ID: 25565258Background: Diabetic nephropathy is the most common cause of end-stage renal disease. Emerging evidences indicate that many mechanistic pathways including apoptosis play an important role in the pathogenesis and progression of macrovascular and microvascular complications of diabetes mellitus. The aim of the present study is to show the effects of grape seed extract (GSE) on oxidative stress and apoptosis in the kidney of streptozotocin-induced diabetic rats. Materials and methods: The study included control group, diabetic group without treatment and diabetic group treated with GSE (n = 7) group. GSE was given orally (100 mg/kg/day) for six weeks. Following parameters were evaluated; oxidative stress index, caspase 1, IL1-alpha, caspase 2, IL1-beta, BCL2-associated agonist of cell death (BAD), X-linked inhibitor of apoptosis (XIAP), DNA fragmentation factor, alpha subunit and beta bubunit (DFFA, DFFB), BH3 interacting domain death agonist (BID), caspase 6, Bcl2-like 1 (BCL-XL), caspase 8, tumor necrosis factor receptor superfamily, member 1 b (TNFRSF1B) and IAP-binding mitochondrial protein (DIABLO). Results: Oxidative stress index levels were significantly increased in the kidney of diabetic group without treatment compared to control group, and decreased in diabetic + GSE group compared to diabetic group without treatment. In the kidney of diabetic group without treatment, caspase 1, IL-1 alpha, BAD, DFFA, DFFB and caspase-6 gene expressions were significantly higher compared to control group. In diabetic + GSE group caspase 1, caspase 2, XIAP, DFFA, BID, BCL-XL and TNFRSF1B genes were significantly decreased compared to control group. Conclusions: Grape seed reduces oxidative stress and apoptosis gene expression suggesting the protective effect on diabetic nephropathy

Ecological Invasion, Roughened Fronts, and a Competitor's Extreme Advance: Integrating Stochastic Spatial-Growth Models

Both community ecology and conservation biology seek further understanding of factors governing the advance of an invasive species. We model biological invasion as an individual-based, stochastic process on a two-dimensional landscape. An ecologically superior invader and a resident species compete for space preemptively. Our general model includes the basic contact process and a variant of the Eden model as special cases. We employ the concept of a "roughened" front to quantify effects of discreteness and stochasticity on invasion; we emphasize the probability distribution of the front-runner's relative position. That is, we analyze the location of the most advanced invader as the extreme deviation about the front's mean position. We find that a class of models with different assumptions about neighborhood interactions exhibit universal characteristics. That is, key features of the invasion dynamics span a class of models, independently of locally detailed demographic rules. Our results integrate theories of invasive spatial growth and generate novel hypotheses linking habitat or landscape size (length of the invading front) to invasion velocity, and to the relative position of the most advanced invader.Comment: The original publication is available at www.springerlink.com/content/8528v8563r7u2742

Predicting reasoner performance on ABox intensive OWL 2 EL ontologies

In this article, the authors introduce the notion of ABox intensity in the context of predicting reasoner performance to improve the representativeness of ontology metrics, and they develop new metrics that focus on ABox features of OWL 2 EL ontologies. Their experiments show that taking into account the intensity through the proposed metrics contributes to overall prediction accuracy for ABox intensive ontologies