Toward a first-principles integrated simulation of tokamak edge plasmas

Performance of the ITER is anticipated to be highly sensitive to the edge plasma condition. The edge pedestal in ITER needs to be predicted from an integrated simulation of the necessary first-principles, multi-scale physics codes. The mission of the SciDAC Fusion Simulation Project (FSP) Prototype Center for Plasma Edge Simulation (CPES) is to deliver such a code integration framework by (1) building new kinetic codes XGC0 and XGC1, which can simulate the edge pedestal buildup; (2) using and improving the existing MHD codes ELITE, M3D-OMP, M3D-MPP and NIMROD, for study of large-scale edge instabilities called Edge Localized Modes (ELMs); and (3) integrating the codes into a framework using cutting-edge computer science technology. Collaborative effort among physics, computer science, and applied mathematics within CPES has created the first working version of the End-to-end Framework for Fusion Integrated Simulation (EFFIS), which can be used to study the pedestal-ELM cycles

Finding regions of interest on toroidal meshes

Fusion promises to provide clean and safe energy, and a considerable amount of research effort is underway to turn this aspiration intoreality. This work focuses on a building block for analyzing data produced from the simulation of microturbulence in magnetic confinementfusion devices: the task of efficiently extracting regions of interest. Like many other simulations where a large amount of data are produced,the careful study of ``interesting'' parts of the data is critical to gain understanding. In this paper, we present an efficient approach forfinding these regions of interest. Our approach takes full advantage of the underlying mesh structure in magnetic coordinates to produce acompact representation of the mesh points inside the regions and an efficient connected component labeling algorithm for constructingregions from points. This approach scales linearly with the surface area of the regions of interest instead of the volume as shown with bothcomputational complexity analysis and experimental measurements. Furthermore, this new approach is 100s of times faster than a recentlypublished method based on Cartesian coordinates

Evaluation of SOVAT: An OLAP-GIS decision support system for community health assessment data analysis

Background. Data analysis in community health assessment (CHA) involves the collection, integration, and analysis of large numerical and spatial data sets in order to identify health priorities. Geographic Information Systems (GIS) enable for management and analysis using spatial data, but have limitations in performing analysis of numerical data because of its traditional database architecture. On-Line Analytical Processing (OLAP) is a multidimensional datawarehouse designed to facilitate querying of large numerical data. Coupling the spatial capabilities of GIS with the numerical analysis of OLAP, might enhance CHA data analysis. OLAP-GIS systems have been developed by university researchers and corporations, yet their potential for CHA data analysis is not well understood. To evaluate the potential of an OLAP-GIS decision support system for CHA problem solving, we compared OLAP-GIS to the standard information technology (IT) currently used by many public health professionals. Methods. SOVAT, an OLAP-GIS decision support system developed at the University of Pittsburgh, was compared against current IT for data analysis for CHA. For this study, current IT was considered the combined use of SPSS and GIS ("SPSS-GIS"). Graduate students, researchers, and faculty in the health sciences at the University of Pittsburgh were recruited. Each round consisted of: an instructional video of the system being evaluated, two practice tasks, five assessment tasks, and one post-study questionnaire. Objective and subjective measurement included: task completion time, success in answering the tasks, and system satisfaction. Results. Thirteen individuals participated. Inferential statistics were analyzed using linear mixed model analysis. SOVAT was statistically significant (α = .01) from SPSS-GIS for satisfaction and time (p < .002). Descriptive results indicated that participants had greater success in answering the tasks when using SOVAT as compared to SPSS-GIS. Conclusion. Using SOVAT, tasks were completed more efficiently, with a higher rate of success, and with greater satisfaction, than the combined use of SPSS and GIS. The results from this study indicate a potential for OLAP-GIS decision support systems as a valuable tool for CHA data analysis. © 2008 Scotch et al; licensee BioMed Central Ltd

Systematic analysis of the ability of Nitric Oxide donors to dislodge biofilms formed by Salmonella enterica and Escherichia coli O157:H7

Biofilms in the industrial environment could be problematic. Encased in extracellular polymeric substances, pathogens within biofilms are significantly more resistant to chlorine and other disinfectants. Recent studies suggest that compounds capable of manipulating nitric oxide-mediated signaling in bacteria could induce dispersal of sessile bacteria and provide a foundation for novel approaches to controlling biofilms formed by some microorganisms. In this work, we compared the ability of five nitric oxide donors (molsidomine, MAHMA NONOate, diethylamine NONOate, diethylamine NONOate diethylammonium salt, spermine NONOate) to dislodge biofilms formed by non-typhoidal Salmonella enterica and pathogenic E. coli on plastic and stainless steel surfaces at different temperatures. All five nitric oxide donors induced significant (35-80%) dispersal of biofilms, however, the degree of dispersal and the optimal dispersal conditions varied. MAHMA NONOate and molsidomine were strong dispersants of the Salmonella biofilms formed on polystyrene. Importantly, molsidomine induced dispersal of up to 50% of the pre-formed Salmonella biofilm at 4 degrees C, suggesting that it could be effective even under refrigerated conditions. Biofilms formed by E. coli O157:H7 were also significantly dispersed. Nitric oxide donor molecules were highly active within 6 hours of application. To better understand mode of action of these compounds, we identified Salmonella genomic region recA-hydN, deletion of which led to an insensitivity to the nitric oxide donors

An Inverse Method to Obtain Porosity, Fibre Diameterand Density of Fibrous Sound Absorbing Materials

Characterization of sound absorbing materials is essential to predict its acoustic behaviour. The most commonly used models to do so consider the flow resistivity, porosity, and average fibre diameter as parameters to determine the acoustic impedance and sound absorbing coefficient. Besides direct experimental techniques, numerical approaches appear to be an alternative to estimate the material's parameters. In this work an inverse numerical method to obtain some parameters of a fibrous material is presented. Using measurements of the normal incidence sound absorption coefficient and then using the model proposed by Voronina, subsequent application of basic minimization techniques allows one to obtain the porosity, average fibre diameter and density of a sound absorbing material. The numerical results agree fairly well with the experimental data.This work has been supported by the Ministerio de Educacion y Ciencia-D.G. Investigacion (BIA2007-68098-C02-01 and BIA2007-68098-C02-02) and also from the Spanish Ministry of Foreign Affairs and Cooperation through the Inter-University and Scientific Research Cooperation Program (A/023748/09).Alba Fernández, J.; Rey Tormos, RMD.; Ramis Soriano, J.; Arenas, JP. (2011). An Inverse Method to Obtain Porosity, Fibre Diameterand Density of Fibrous Sound Absorbing Materials. Archives of Acoustics. 36(3):561-574. https://doi.org/10.2478/v10168-011-0040-xS561574363Allard, J., & Champoux, Y. (1992). New empirical equations for sound propagation in rigid frame fibrous materials. The Journal of the Acoustical Society of America, 91(6), 3346-3353. doi:10.1121/1.402824Attenborough, K. (1983). Acoustical characteristics of rigid fibrous absorbents and granular materials. The Journal of the Acoustical Society of America, 73(3), 785-799. doi:10.1121/1.389045Bies, D. A., & Hansen, C. H. (1980). Flow resistance information for acoustical design. Applied Acoustics, 13(5), 357-391. doi:10.1016/0003-682x(80)90002-xChampoux, Y., Stinson, M. R., & Daigle, G. A. (1991). Air‐based system for the measurement of porosity. The Journal of the Acoustical Society of America, 89(2), 910-916. doi:10.1121/1.1894653Crocker, M. J., & Arenas, J. P. (s. f.). Use of Sound-Absorbing Materials. Handbook of Noise and Vibration Control, 696-713. doi:10.1002/9780470209707.ch57Delany, M. E., & Bazley, E. N. (1970). Acoustical properties of fibrous absorbent materials. Applied Acoustics, 3(2), 105-116. doi:10.1016/0003-682x(70)90031-9Dunn, I. P., & Davern, W. A. (1986). Calculation of acoustic impedance of multi-layer absorbers. Applied Acoustics, 19(5), 321-334. doi:10.1016/0003-682x(86)90044-7Fellah, Z. E. A., Berger, S., Lauriks, W., Depollier, C., Aristégui, C., & Chapelon, J.-Y. (2003). Measuring the porosity and the tortuosity of porous materials via reflected waves at oblique incidence. The Journal of the Acoustical Society of America, 113(5), 2424-2433. doi:10.1121/1.1567275Fellah, Z. E. A., Berger, S., Lauriks, W., Depollier, C., & Fellah, M. (2003). Measuring the porosity of porous materials having a rigid frame via reflected waves: A time domain analysis with fractional derivatives. Journal of Applied Physics, 93(1), 296-303. doi:10.1063/1.1524025Fellah, Z. E. A., Berger, S., Lauriks, W., Depollier, C., Trompette, P., & Chapelon, J. Y. (2003). Ultrasonic measurement of the porosity and tortuosity of air-saturated random packings of beads. Journal of Applied Physics, 93(11), 9352-9359. doi:10.1063/1.1572191Fellah, Z. E. A., Mitri, F. G., Fellah, M., Ogam, E., & Depollier, C. (2007). Ultrasonic characterization of porous absorbing materials: Inverse problem. Journal of Sound and Vibration, 302(4-5), 746-759. doi:10.1016/j.jsv.2006.12.007Garai, M., & Pompoli, F. (2005). A simple empirical model of polyester fibre materials for acoustical applications. Applied Acoustics, 66(12), 1383-1398. doi:10.1016/j.apacoust.2005.04.008ISO (1998), 10534-2:1998. Acoustics - determination of sound absorption coefficient and impedance in impedance tubes - Part 2: transfer-function method, International Organization for Standardization, Geneva.Miki, Y. (1990). Acoustical properties of porous materials. Modifications of Delany-Bazley models. Journal of the Acoustical Society of Japan (E), 11(1), 19-24. doi:10.1250/ast.11.19Miki, Y. (1990). Acoustical properties of porous materials. Generalizations of empirical models. Journal of the Acoustical Society of Japan (E), 11(1), 25-28. doi:10.1250/ast.11.25Ramis, J., Alba, J., Del Rey, R., Escuder, E., & Sanchís, V. J. (2010). Nuevos materiales absorbentes acústicos basados en fibra de kenaf. Materiales de Construcción, 60(299), 133-143. doi:10.3989/mc.2010.50809Shoshani, Y., & Yakubov, Y. (2000). Numerical assessment of maximal absorption coefficients for nonwoven fiberwebs. Applied Acoustics, 59(1), 77-87. doi:10.1016/s0003-682x(99)00015-8Umnova, O., Attenborough, K., Shin, H.-C., & Cummings, A. (2005). Deduction of tortuosity and porosity from acoustic reflection and transmission measurements on thick samples of rigid-porous materials. Applied Acoustics, 66(6), 607-624. doi:10.1016/j.apacoust.2004.02.005Voronina, N. (1994). Acoustic properties of fibrous materials. Applied Acoustics, 42(2), 165-174. doi:10.1016/0003-682x(94)90005-1Voronina, N. (1996). Improved empirical model of sound propagation through a fibrous material. Applied Acoustics, 48(2), 121-132. doi:10.1016/0003-682x(95)00055-eVoronina, N. (1998). An empirical model for elastic porous materials. Applied Acoustics, 55(1), 67-83. doi:10.1016/s0003-682x(97)00098-4Voronina, N. (1999). An empirical model for rigid-frame porous materials with low porosity. Applied Acoustics, 58(3), 295-304. doi:10.1016/s0003-682x(98)00076-0Voronina, N. ., & Horoshenkov, K. . (2003). A new empirical model for the acoustic properties of loose granular media. Applied Acoustics, 64(4), 415-432. doi:10.1016/s0003-682x(02)00105-6Wang, X., Eisenbrey, J., Zeitz, M., & Sun, J. Q. (2004). Multi-stage regression analysis of acoustical properties of polyurethane foams. Journal of Sound and Vibration, 273(4-5), 1109-1117. doi:10.1016/j.jsv.2003.09.039Wilson, D. K. (1997). Simple, relaxational models for the acoustical properties of porous media. Applied Acoustics, 50(3), 171-188. doi:10.1016/s0003-682x(96)00048-

Salmonella enterica biofilm-mediated dispersal by nitric oxide donors in association with cellulose nanocrystal hydrogels

Protected by extracellular polymers, microbes within biofilms are significantly more resistant to disinfectants. Current research has been instrumental in identifying nitric oxide donors and hydrogels as potential disinfectant additives. Nitric oxide (NO) donors are considered a very promising molecule as biofilm dispersal agents and hydrogels have recently attracted a lot of interest due to their biocompatible properties and ability to form stable thin films. When the NO donor MAHMA NONOate was dissolved in phosphate saline buffer, it was able to reduce the biomass of well-established biofilms up to 15% for at least 24 h of contact time. Encapsulation of MAHMA NONOate and molsidomine within a hydrogel composed of cellulose nanocrystals (CNC) has shown a synergistic effect in dispersing well-established biofilms: after 2 h of exposure, moderate but significant dispersion was measured. After 6 h of exposure, the number of cells transitioning from the biofilm to the planktonic state was up to 0.6 log higher when compared with non-treated biofilms. To further explore the transport processes of NO donors within hydrogels, we measured the nitric oxide flux from gels, at 25°C for a composite of 0.1 µM MAHMA NONOate–CNC. Nitric oxide diffuses up to 500 µm from the hydrogel surface, with flux decreasing according to Fick’s law. 60% of NO was released from the hydrogel composite during the first 23 min. These data suggest that the combined treatments with nitric oxide donor and hydrogels may allow for new sustainable cleaning strategies

Erythropoietin Improves the Survival of Fat Tissue after Its Transplantation in Nude Mice

Background: Autologous transplanted fat has a high resorption rate, providing a clinical challenge for the means to reduce it. Erythropoietin (EPO) has non-hematopoietic targets, and we hypothesized that EPO may improve long-term fat graft survival because it has both pro-angiogenic and anti-apoptotic properties. We aimed to determine the effect of EPO on the survival of human fat tissue after its transplantation in nude mice. Methodology/Principal Findings: Human fat tissue was injected subcutaneously into immunologically-compromised nude mice, and the grafts were then treated with either 20 IU or 100 IU EPO. At the end of the 15-week study period, the extent of angiogenesis, apoptosis, and histology were assessed in the fat grafts. The results were compared to vascular endothelial growth factor (VEGF)-treated and phosphate-buffered saline (PBS)-treated fat grafts. The weight and volume of the EPOtreated grafts were higher than those of the PBS-treated grafts, whose weights and volumes were not different from those of the VEGF-treated grafts. EPO treatment also increased the expression of angiogenic factors and microvascular density, and reduced inflammation and apoptosis in a dose-dependent manner in the fat grafts. Conclusions/Significance: Our data suggest that stimulation of angiogenesis by a cluster of angiogenic factors and decreased fat cell apoptosis account for potential mechanisms that underlie the improved long-term survival of fa

REDD1 Protects Osteoblast Cells from Gamma Radiation-Induced Premature Senescence

Radiotherapy is commonly used for cancer treatment. However, it often results in side effects due to radiation damage in normal tissue, such as bone marrow (BM) failure. Adult hematopoietic stem and progenitor cells (HSPC) reside in BM next to the endosteal bone surface, which is lined primarily by hematopoietic niche osteoblastic cells. Osteoblasts are relatively more radiation-resistant than HSPCs, but the mechanisms are not well understood. In the present study, we demonstrated that the stress response gene REDD1 (regulated in development and DNA damage responses 1) was highly expressed in human osteoblast cell line (hFOB) cells after γ irradiation. Knockdown of REDD1 with siRNA resulted in a decrease in hFOB cell numbers, whereas transfection of PCMV6-AC-GFP-REDD1 plasmid DNA into hFOB cells inhibited mammalian target of rapamycin (mTOR) and p21 expression and protected these cells from radiation-induced premature senescence (PS). The PS in irradiated hFOB cells were characterized by significant inhibition of clonogenicity, activation of senescence biomarker SA-β-gal, and the senescence-associated cytokine secretory phenotype (SASP) after 4 or 8 Gy irradiation. Immunoprecipitation assays demonstrated that the stress response proteins p53 and nuclear factor κ B (NFkB) interacted with REDD1 in hFOB cells. Knockdown of NFkB or p53 gene dramatically suppressed REDD1 protein expression in these cells, indicating that REDD1 was regulated by both factors. Our data demonstrated that REDD1 is a protective factor in radiation-induced osteoblast cell premature senescence

SSeCKS/Gravin/AKAP12 attenuates expression of proliferative and angiogenic genes during suppression of v-Src-induced oncogenesis

BACKGROUND: SSeCKS is a major protein kinase C substrate with kinase scaffolding and metastasis-suppressor activity whose expression is severely downregulated in Src- and Ras-transformed fibroblast and epithelial cells and in human prostate, breast, and gastric cancers. We previously used NIH3T3 cells with tetracycline-regulated SSeCKS expression plus a temperature-sensitive v-Src allele to show that SSeCKS re-expression inhibited parameters of v-Src-induced oncogenic growth without attenuating in vivo Src kinase activity. METHODS: We use cDNA microarrays and semi-quantitative RT-PCR analysis to identify changes in gene expression correlating with i) SSeCKS expression in the absence of v-Src activity, ii) activation of v-Src activity alone, and iii) SSeCKS re-expression in the presence of active v-Src. RESULTS: SSeCKS re-expression resulted in the attenuation of critical Src-induced proliferative and pro-angiogenic gene expression including Afp, Hif-1α, Cdc20a and Pdgfr-β, and conversely, SSeCKS induced several cell cycle regulatory genes such as Ptpn11, Gadd45a, Ptplad1, Cdkn2d (p19), and Rbbp7. CONCLUSION: Our data provide further evidence that SSeCKS can suppress Src-induced oncogenesis by modulating gene expression downstream of Src kinase activity