Introducing spatial information into predictive NF-kappa B modelling - an agent-based approach

Nature is governed by local interactions among lower-level sub-units, whether at the cell, organ, organism, or colony level. Adaptive system behaviour emerges via these interactions, which integrate the activity of the sub-units. To understand the system level it is necessary to understand the underlying local interactions. Successful models of local interactions at different levels of biological organisation, including epithelial tissue and ant colonies, have demonstrated the benefits of such 'agent-based' modelling [1-4]. Here we present an agent-based approach to modelling a crucial biological system the intracellular NF-kappa B signalling pathway. The pathway is vital to immune response regulation, and is fundamental to basic survival in a range of species [5-7]. Alterations in pathway regulation underlie a variety of diseases, including atherosclerosis and arthritis. Our modelling of individual molecules, receptors and genes provides a more comprehensive outline of regulatory network mechanisms than previously possible with equation-based approaches [8]. The method also permits consideration of structural parameters in pathway regulation; here we predict that inhibition of NF-kappa B is directly affected by actin filaments of the cytoskeleton sequestering excess inhibitors, therefore regulating steady-state and feedback behaviour

A Modified Magnitude System that Produces Well-Behaved Magnitudes, Colors, and Errors Even for Low Signal-to-Noise Ratio Measurements

We describe a modification of the usual definition of astronomical magnitudes, replacing the usual logarithm with an inverse hyperbolic sine function; we call these modified magnitudes `asinh magnitudes'. For objects detected at signal-to-noise ratios of greater than about five, our modified definition is essentially identical to the traditional one; for fainter objects (including those with a formally negative flux) our definition is well behaved, tending to a definite value with finite errors as the flux goes to zero. This new definition is especially useful when considering the colors of faint objects, as the difference of two `asinh' magnitudes measures the usual flux ratio for bright objects, while avoiding the problems caused by dividing two very uncertain values for faint objects. The Sloan Digital Sky Survey (SDSS) data products will use this scheme to express all magnitudes in their catalogs.Comment: 11 pages, including 3 postscript figures. Submitted to A

Type Ia Supernovae, Evolution, and the Cosmological Constant

We explore the possible role of evolution in the analysis of data on SNe Ia at cosmological distances. First, using a variety of simple sleuthing techniques, we find evidence that the properties of the high and low redshift SNe Ia observed so far differ from one another. Next, we examine the effects of including simple phenomenological models for evolution in the analysis. The result is that cosmological models and evolution are highly degenerate with one another, so that the incorporation of even very simple models for evolution makes it virtually impossible to pin down the values of $\Omega_M$ and $\Omega_\Lambda$, the density parameters for nonrelativistic matter and for the cosmological constant, respectively. Moreover, we show that if SNe Ia evolve with time, but evolution is neglected in analyzing data, then, given enough SNe Ia, the analysis hones in on values of $\Omega_M$ and $\Omega_\Lambda$ which are incorrect. Using Bayesian methods, we show that the probability that the cosmological constant is nonzero (rather than zero) is unchanged by the SNe Ia data when one accounts for the possibility of evolution, provided that we do not discriminate among open, closed and flat cosmologies a priori. The case for nonzero cosmological constant is stronger if the Universe is presumed to be flat, but still depends sensitively on the degree to which the peak luminosities of SNe Ia evolve as a function of redshift. The estimated value of $H_0$, however, is only negligibly affected by accounting for possible evolution.Comment: 45 pages, 15 figures; accepted for publication in The Astrophysical Journal. Minor revisions and clarifications made including addition of recent reference

A rapid, non-invasive procedure for quantitative assessment of drought survival using chlorophyll fluorescence

<p>Abstract</p> <p>Background</p> <p>Analysis of survival is commonly used as a means of comparing the performance of plant lines under drought. However, the assessment of plant water status during such studies typically involves detachment to estimate water shock, imprecise methods of estimation or invasive measurements such as osmotic adjustment that influence or annul further evaluation of a specimen's response to drought.</p> <p>Results</p> <p>This article presents a procedure for rapid, inexpensive and non-invasive assessment of the survival of soil-grown plants during drought treatment. The changes in major photosynthetic parameters during increasing water deficit were monitored via chlorophyll fluorescence imaging and the selection of the maximum efficiency of photosystem II (F_v/F_m) parameter as the most straightforward and practical means of monitoring survival is described. The veracity of this technique is validated through application to a variety of <it>Arabidopsis thaliana </it>ecotypes and mutant lines with altered tolerance to drought or reduced photosynthetic efficiencies.</p> <p>Conclusion</p> <p>The method presented here allows the acquisition of quantitative numerical estimates of <it>Arabidopsis </it>drought survival times that are amenable to statistical analysis. Furthermore, the required measurements can be obtained quickly and non-invasively using inexpensive equipment and with minimal expertise in chlorophyll fluorometry. This technique enables the rapid assessment and comparison of the relative viability of germplasm during drought, and may complement detailed physiological and water relations studies.</p

Sulfate and Phosphate Speleothems at Jenolan Caves, New South Wales, Australia

Sulfate and phosphate deposits at Jenolan Caves occur in a variety of forms and compositions including crusts, ‘flowers’ and fibrous masses of gypsum (selenite), and clusters of boss-like speleothems (potatoes) of ardealite (calcium sulphate, phosphate hydrate) with associated gypsum. This boss-like morphology of ardealite does not appear to have been previously described in the literature and this is the first report of ardealite in New South Wales. Gypsum var. selenite occurs in close association with pyrite-bearing palaeokarst, while the ardealite gypsum association appears to relate to deposits of mineralised bat guano. Isotope studies confirm that the two gypsum suites have separate sources of sulfur, one from the weathering of pyrite (-1.4 to +4.9 δ34S) for gypsum (selenite) and the other from alteration of bat guano (+11.4 to +12.9 δ34S) for the ardealite and gypsum crusts

Sulfate and Phosphate Speleothems at Jenolan Caves, New South Wales, Australia

Sulfate and phosphate deposits at Jenolan Caves occur in a variety of forms and compositions including crusts, ‘flowers’ and fibrous masses of gypsum (selenite), and clusters of boss-like speleothems (potatoes) of ardealite (calcium sulphate, phosphate hydrate) with associated gypsum. This boss-like morphology of ardealite does not appear to have been previously described in the literature and this is the first report of ardealite in New South Wales. Gypsum var. selenite occurs in close association with pyrite-bearing palaeokarst, while the ardealite gypsum association appears to relate to deposits of mineralised bat guano. Isotope studies confirm that the two gypsum suites have separate sources of sulfur, one from the weathering of pyrite (-1.4 to +4.9 δ34S) for gypsum (selenite) and the other from alteration of bat guano (+11.4 to +12.9 δ34S) for the ardealite and gypsum crusts

A Mathematical Framework for Agent Based Models of Complex Biological Networks

Agent-based modeling and simulation is a useful method to study biological phenomena in a wide range of fields, from molecular biology to ecology. Since there is currently no agreed-upon standard way to specify such models it is not always easy to use published models. Also, since model descriptions are not usually given in mathematical terms, it is difficult to bring mathematical analysis tools to bear, so that models are typically studied through simulation. In order to address this issue, Grimm et al. proposed a protocol for model specification, the so-called ODD protocol, which provides a standard way to describe models. This paper proposes an addition to the ODD protocol which allows the description of an agent-based model as a dynamical system, which provides access to computational and theoretical tools for its analysis. The mathematical framework is that of algebraic models, that is, time-discrete dynamical systems with algebraic structure. It is shown by way of several examples how this mathematical specification can help with model analysis.Comment: To appear in Bulletin of Mathematical Biolog

Minerals of Jenolan Caves, New South Wales, Australia: Geological and Biological Interactions

Geological and biological processes in the Jenolan Caves have formed a range of mineral species spanning several chemical groups. So far 25 mineral species have been either confirmed, or identified for the first time at Jenolan. Their chemical groups include carbonates: (calcite, aragonite, hydromagnesite, huntite, dolomite, ankerite); silicates: (kaolinite, K-deficient muscovite (‘illite’), montmorillonite clays); phosphates, (ardealite, hydroxylapatite, taranakite, leucophosphite, variscite, crandallite, montgomeryite, kingsmountite); sulfate: (gypsum); oxides: (quartz, cristobalite, amorphous silica, hematite, romanèchite); hydroxide: (goethite); nitrate: (niter); and chloride: (sylvite). Dolomitised limestone bedrock and ankerite veins can be recognised as a magnesium source of some magnesium carbonate minerals, as well as supplying a calcite inhibitor favouring aragonite formation. The cave clays have diverse origins. Some are recent sedimentary detritus. Older clays of Carboniferous age contain components of reworked altered volcaniclastics washed or blown into the caves, so these clays may represent argillic alteration of volcanic products. Some of the clays may have formed as alteration products of ascending hydrothermal fluids. The phosphates and some gypsum formed when bat guano reacted chemically with limestone and cave clays. Gypsum has also been formed from the breakdown of pyrite in altered bedrock or dolomitic palaeokarst. The niter and sylvite have crystalized from breakdown products of mainly wallaby guano

Caves and karst-like features in Proterozoic gneiss and Cambrian granite, southern and central Sri Lanka: An introduction

There has been little study of the geology and geomorphologyof the caves and karst-like features developed in the Proterozoicgneiss and Cambrian granite of Sri Lanka. This lack of studyis surprising given that caves and rockshelters in these rockscontain significant archaeological and cultural sites. Caves andkarren, both mimicking those developed in carbonate rocks,have formed both in gneiss, which is the dominant rock type ofthe Proterozoic crust of the island and in granite. In addition tooverhangs, boulder caves, soil pipes and tectonic caves, tunnelcaves, arch caves and block breakdown caves of significant sizeare developed in siliceous rocks in Sri Lanka. While metamorphoseddolomites are interfoliated within the gneissic suite,simple removal of carbonate by solution from within the surroundingrock cannot account for all or most of the speleogenesisobserved. While spalling and breakdown are responsiblefor cave enlargement cave initiation is probably due to eitherphreatic solution of silicates and/or phantom rock processes.Speleothems and cave minerals including silicates, phosphates,gypsum, carbonates and niter are found in the caves. Activesilicate speleothems are not restricted to joints and fissures andsuggest that solution of silicates is currently occurring withinthe body of the rock in the vadose zone. While guano is thelikely source of the phosphate, sulfate and nitrate, the sourceof the calcium in the carbonates remains unclear. Caves in theintrusive and metamorphic rocks of Sri Lanka are enigmatic.They are unexpectedly similar in appearance to their carbonatekarst counterparts. Continuing research will allow them tohold a mirror to our understanding of speleogenesis, mineralizationand sedimentation in carbonate karst caves

A Far-UV Variability Survey of the Globular Cluster M80

We have searched for variable sources in the core region of M80, using far ultra-violet data taken with the Advanced Camera for Surveys on board the Hubble Space Telescope. We found three sources that exhibit strong signs of variability in our data. Among these is source TDK1, which we believe to be an RR Lyrae star that reached maximum brightness during our observations. The light curve shows a >3 mag FUV brightening over the course of ~5 hours, with an estimated peak brightness of ~16.7 mag, followed by a decrease to ~20 mag. Archival optical data obtained with WFPC2 confirm that TDK1 is variable in all wavebands. TDK1's SED is reasonably fit by a star with temperature T(eff)=6700K and radius R=4.2R(sun), consistent with the suggestion that it is an RR Lyrae. Based on the photometric and variability characteristics of the other two variables, we suggest that TDK2 is likely to be an SX Phoenicis star with ~55 minutes period, and TDK3 is likely another RR Lyrae. Finally, we briefly discuss the FUV counterparts to two previously known variables in M80, the classical nova T Sco and the dwarf nova DN1.Comment: 12 pages, 9 figures and 3 tables. Accepted for publication in MNRAS