Theoretical analysis of NO formation near the primary reaction zone in methane combustion

The complete kinetics of the CH4-air reaction are to study the details of NO formation near the primary reaction zone. The species and energy conservation equations are used in the analysis, however, diffusion and heat conduction within the reaction zone are neglected. The overshoot of the concentrations of the radicals O, OH, and H over their post flame equilibrium values appears to explain the phenomenon of "prompt NO" due to the very high NO formation rate near the flame for values of the equivalence ratio [phi] 2 rections, which may influence NO production through their effect on radical recombination, were compared.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/21826/1/0000227.pd

Galilean quantum gravity with cosmological constant and the extended q-Heisenberg algebra

We define a theory of Galilean gravity in 2+1 dimensions with cosmological constant as a Chern-Simons gauge theory of the doubly-extended Newton-Hooke group, extending our previous study of classical and quantum gravity in 2+1 dimensions in the Galilean limit. We exhibit an r-matrix which is compatible with our Chern-Simons action (in a sense to be defined) and show that the associated bi-algebra structure of the Newton-Hooke Lie algebra is that of the classical double of the extended Heisenberg algebra. We deduce that, in the quantisation of the theory according to the combinatorial quantisation programme, much of the quantum theory is determined by the quantum double of the extended q-deformed Heisenberg algebra.Comment: 22 page

Reaching within a dynamic virtual environment

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

The urologic epithelial stem cell database (UESC) – a web tool for cell type-specific gene expression and immunohistochemistry images of the prostate and bladder

Background: Public databases are crucial for analysis of high-dimensional gene and protein expression data. The Urologic Epithelial Stem Cells (UESC) database http://scgap.systemsbiology.net/ is a public database that contains gene and protein information for the major cell types of the prostate, prostate cancer cell lines, and a cancer cell type isolated from a primary tumor. Similarly, such information is available for urinary bladder cell types. Description: Two major data types were archived in the database, protein abundance localization data from immunohistochemistry images, and transcript abundance data principally from DNA microarray analysis. Data results were organized in modules that were made to operate independently but built upon a core functionality. Gene array data and immunostaining images for human and mouse prostate and bladder were made available for interrogation. Data analysis capabilities include: (1) CD (cluster designation) cell surface protein data. For each cluster designation molecule, a data summary allows easy retrieval of images (at multiple magnifications). (2) Microarray data. Single gene or batch search can be initiated with Affymetrix Probeset ID, Gene Name, or Accession Number together with options of coalescing probesets and/or replicates. Conclusion: Databases are invaluable for biomedical research, and their utility depends on data quality and user friendliness. UESC provides for database queries and tools to examine cell typespecific gene expression (normal vs. cancer), whereas most other databases contain only whole tissue expression datasets. The UESC database provides a valuable tool in the analysis of differential gene expression in prostate cancer genes in cancer progression.This work was supported by grant 1U01 DK63630 from NIDDK. Additional funding came from grants CA85859, CA98699 and CA111244 from NCI

Seasonal winter forecasts and the stratosphere

Published© 2016 Royal Meteorological Society. We investigate seasonal forecasts of the winter North Atlantic Oscillation (NAO) and their relationship with the stratosphere. Climatological frequencies of sudden stratospheric warming (SSW) and strong polar vortex (SPV) events are well represented and the predicted risk of events varies between 25 and 90% from winter to winter, indicating predictability beyond the deterministic range. The risk of SSW and SPV events relates to predicted NAO as expected, with NAO shifts of -6.5 and +4.8hPa in forecast members containing SSW and SPV events. Most striking of all is that forecast skill of the surface winter NAO vanishes from these hindcasts if members containing SSW events are excluded.This work was supported by the Joint DECC/Defra Met Office Hadley Centre Climate Programme (GA01101), the UK Public Weather Service research program and the European Union Framework 7 SPECS project. The contribution of AYK is funded by FMI’s tenure track program and the Academy of Finland under grant 286298

Genotoxic mixtures and dissimilar action: Concepts for prediction and assessment

This article has been made available through the Brunel Open Access Publishing Fund. This article is distributed under the terms of the creative commons Attribution license which permits any use, distribution, and reproduction in any medium, provided the original author(s)and the source are credited.Combinations of genotoxic agents have frequently been assessed without clear assumptions regarding their expected (additive) mixture effects, often leading to claims of synergisms that might in fact be compatible with additivity. We have shown earlier that the combined effects of chemicals, which induce micronuclei (MN) in the cytokinesis-block micronucleus assay in Chinese hamster ovary-K1 cells by a similar mechanism, were additive according to the concept of concentration addition (CA). Here, we extended these studies and investigated for the first time whether valid additivity expectations can be formulated for MN-inducing chemicals that operate through a variety of mechanisms, including aneugens and clastogens (DNA cross-linkers, topoisomerase II inhibitors, minor groove binders). We expected that their effects should follow the additivity principles of independent action (IA). With two mixtures, one composed of various aneugens (colchicine, flubendazole, vinblastine sulphate, griseofulvin, paclitaxel), and another composed of aneugens and clastogens (flubendazole, doxorubicin, etoposide, melphalan and mitomycin C), we observed mixture effects that fell between the additivity predictions derived from CA and IA. We achieved better agreement between observation and prediction by grouping the chemicals into common assessment groups and using hybrid CA/IA prediction models. The combined effects of four dissimilarly acting compounds (flubendazole, paclitaxel, doxorubicin and melphalan) also fell within CA and IA. Two binary mixtures (flubendazole/paclitaxel and flubendazole/doxorubicin) showed effects in reasonable agreement with IA additivity. Our studies provide a systematic basis for the investigation of mixtures that affect endpoints of relevance to genotoxicity and show that their effects are largely additive.UK Food Standards Agenc

Message-Passing Methods for Complex Contagions

Message-passing methods provide a powerful approach for calculating the expected size of cascades either on random networks (e.g., drawn from a configuration-model ensemble or its generalizations) asymptotically as the number $N$ of nodes becomes infinite or on specific finite-size networks. We review the message-passing approach and show how to derive it for configuration-model networks using the methods of (Dhar et al., 1997) and (Gleeson, 2008). Using this approach, we explain for such networks how to determine an analytical expression for a "cascade condition", which determines whether a global cascade will occur. We extend this approach to the message-passing methods for specific finite-size networks (Shrestha and Moore, 2014; Lokhov et al., 2015), and we derive a generalized cascade condition. Throughout this chapter, we illustrate these ideas using the Watts threshold model.Comment: 14 pages, 3 figure

Gravitino Dark Matter in Tree Level Gauge Mediation with and without R-parity

We investigate the cosmological aspects of Tree Level Gauge Mediation, a recently proposed mechanism in which the breaking of supersymmetry is communicated to the soft scalar masses by extra gauge interactions at the tree level. Embedding the mechanism in a Grand Unified Theory and requiring the observability of sfermion masses at the Large Hadron Collider, it follows that the Lightest Supersymmetric Particle is a gravitino with a mass of the order of 10 GeV. The analysis in the presence of R-parity shows that a typical Tree Level Gauge Mediation spectrum leads to an overabundance of the Dark Matter relic density and a tension with the constraints from Big Bang Nucleosynthesis. This suggests to relax the exact conservation of the R-parity. The underlying SO(10) Grand Unified Theory together with the bounds from proton decay provide a rationale for considering only bilinear R-parity violating operators. We finally analyze the cosmological implications of this setup by identifying the phenomenologically viable regions of the parameter space.Comment: 28 pages, 5 figures. References added. To appear in JHE

Spatial and topological organization of DNA chains induced by gene co-localization

Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into discrete spatial foci called transcription factories. However, the mechanisms underlying the formation of these foci and the resulting topological order of the chromosome remain to be elucidated. Here we consider a thermodynamic framework based on a worm-like chain model of chromosomes where sparse designated sites along the DNA are able to interact whenever they are spatially close-by. This is motivated by recurrent evidence that there exists physical interactions between genes that operate together. Three important results come out of this simple framework. First, the resulting formation of transcription foci can be viewed as a micro-phase separation of the interacting sites from the rest of the DNA. In this respect, a thermodynamic analysis suggests transcription factors to be appropriate candidates for mediating the physical interactions between genes. Next, numerical simulations of the polymer reveal a rich variety of phases that are associated with different topological orderings, each providing a way to increase the local concentrations of the interacting sites. Finally, the numerical results show that both one-dimensional clustering and periodic location of the binding sites along the DNA, which have been observed in several organisms, make the spatial co-localization of multiple families of genes particularly efficient.Comment: Figures and Supplementary Material freely available on http://dx.doi.org/10.1371/journal.pcbi.100067