Time Parallel Gravitational Collapse Simulation

This article demonstrates the applicability of the parallel-in-time method Parareal to the numerical solution of the Einstein gravity equations for the spherical collapse of a massless scalar eld. To account for the shrinking of the spatial domain in time, a tailored load balancing scheme is proposed and compared to load balancing based on number of time steps alone. The performance of Parareal is studied for both the sub-critical and black hole case; our experiments show that Parareal generates substantial speedup and, in the super-critical regime, can reproduce Choptuik's black hole mass scaling law

The social organization of fish shoals: a test of the predictive power of laboratory experiments for the field

By contrast with a multitude of laboratory studies on the social organization of fish, relatively little is known about the size, composition and dynamics of free-ranging fish shoals. We give an overview of the available information on fish shoals and assess to what degree the predictions made from laboratory studies are consistent with field data. The section on shoal choice behaviour in the laboratory is structured so that the evidence fur different shoaling preferences is discussed in the context of their mechanisms and functions. Predictions based on experiments in captivity regarding preferences for conspecifics, individuals of similar body length and unparasitized fish were highly consistent with field observations on free-ranging shoals whereas preferences for familiar conspecifics and kin remain to be conclusively demonstrated in the field. In general, there is a shortage of studies in which shoaling preferences have been investigated both in the laboratory) and the field, and field studies have so far been largely descriptive revealing little about the underlying mechanisms of observed patterns. Given their great importance of fish shoals both in fundamental and applied research, an advancement of our knowledge of their social organization should significantly contribute to a better understanding of a whole range of topics including reciprocal altruism, group-living and self-organization

Shoal choice in zebrafish, Danio rerio: the influence of shoal size and activity

Shoaling fish are expected, in many cases, to gain fitness benefits from being in a larger shoal and previous experiments have shown that fish are indeed capable of choosing between shoals of different sizes. We investigated the influence of shoal activity on shoal size preference in the zebrafish. We gave test fish the choice between shoals of one to four stimulus fish, presented at two different water temperatures, and so differing in their activity levels. Where all stimulus fish were in water of the same temperature, test fish generally preferred the larger shoal. However, this preference could be reduced by presenting the larger shoal in colder water and so reducing its activity. We discuss these findings with reference to the factors that may influence shoal activity, the effect of temperature on shoaling behaviour and the mechanisms that may be used by fish to discriminate shoal size. (C) 2001 The Association for the Study of Animal Behaviour

Preparation, structural characterisation and antibacterial properties of Ga-doped sol-gel phosphate-based glass

A sol-gel preparation of Ga-doped phosphate-based glass with potential application in antimicrobial devices has been developed. Samples of composition (CaO)(0.30)(Na2O)(0.20-x) (Ga2O3) (x) (P2O5)(0.50) where x = 0 and 0.03 were prepared, and the structure and properties of the gallium-doped sample compared with those of the sample containing no gallium. Analysis of the P-31 MAS NMR data demonstrated that addition of gallium to the sol-gel reaction increases the connectivity of the phosphate network at the expense of hydroxyl groups. This premise is supported by the results of the elemental analysis, which showed that the gallium-free sample contains significantly more hydrogen and by FTIR spectroscopy, which revealed a higher concentration of -OH groups in that sample. Ga K-edge extended X-ray absorption fine structure and X-ray absorption near-edge structure data revealed that the gallium ions are coordinated by six oxygen atoms. In agreement with the X-ray absorption data, the high-energy XRD results also suggest that the Ga3+ ions are octahedrally coordinated with respect to oxygen. Antimicrobial studies demonstrated that the sample containing Ga3+ ions had significant activity against Staphylococcus aureus compared to the control

Mesoscopic organization reveals the constraints governing C. elegans nervous system

One of the biggest challenges in biology is to understand how activity at the cellular level of neurons, as a result of their mutual interactions, leads to the observed behavior of an organism responding to a variety of environmental stimuli. Investigating the intermediate or mesoscopic level of organization in the nervous system is a vital step towards understanding how the integration of micro-level dynamics results in macro-level functioning. In this paper, we have considered the somatic nervous system of the nematode Caenorhabditis elegans, for which the entire neuronal connectivity diagram is known. We focus on the organization of the system into modules, i.e., neuronal groups having relatively higher connection density compared to that of the overall network. We show that this mesoscopic feature cannot be explained exclusively in terms of considerations, such as optimizing for resource constraints (viz., total wiring cost) and communication efficiency (i.e., network path length). Comparison with other complex networks designed for efficient transport (of signals or resources) implies that neuronal networks form a distinct class. This suggests that the principal function of the network, viz., processing of sensory information resulting in appropriate motor response, may be playing a vital role in determining the connection topology. Using modular spectral analysis, we make explicit the intimate relation between function and structure in the nervous system. This is further brought out by identifying functionally critical neurons purely on the basis of patterns of intra- and inter-modular connections. Our study reveals how the design of the nervous system reflects several constraints, including its key functional role as a processor of information.Comment: Published version, Minor modifications, 16 pages, 9 figure

Massive stars as thermonuclear reactors and their explosions following core collapse

Nuclear reactions transform atomic nuclei inside stars. This is the process of stellar nucleosynthesis. The basic concepts of determining nuclear reaction rates inside stars are reviewed. How stars manage to burn their fuel so slowly most of the time are also considered. Stellar thermonuclear reactions involving protons in hydrostatic burning are discussed first. Then I discuss triple alpha reactions in the helium burning stage. Carbon and oxygen survive in red giant stars because of the nuclear structure of oxygen and neon. Further nuclear burning of carbon, neon, oxygen and silicon in quiescent conditions are discussed next. In the subsequent core-collapse phase, neutronization due to electron capture from the top of the Fermi sea in a degenerate core takes place. The expected signal of neutrinos from a nearby supernova is calculated. The supernova often explodes inside a dense circumstellar medium, which is established due to the progenitor star losing its outermost envelope in a stellar wind or mass transfer in a binary system. The nature of the circumstellar medium and the ejecta of the supernova and their dynamics are revealed by observations in the optical, IR, radio, and X-ray bands, and I discuss some of these observations and their interpretations.Comment: To be published in " Principles and Perspectives in Cosmochemistry" Lecture Notes on Kodai School on Synthesis of Elements in Stars; ed. by Aruna Goswami & Eswar Reddy, Springer Verlag, 2009. Contains 21 figure

Glucose challenge increases circulating progenitor cells in Asian Indian male subjects with normal glucose tolerance which is compromised in subjects with pre-diabetes: A pilot study

<p>Abstract</p> <p>Background</p> <p>Haematopoietic stem cells undergo mobilization from bone marrow to blood in response to physiological stimuli such as ischemia and tissue injury. The aim of study was to determine the kinetics of circulating CD34⁺and CD133⁺CD34⁺progenitor cells in response to 75 g glucose load in subjects with normal and impaired glucose metabolism.</p> <p>Methods</p> <p>Asian Indian male subjects (n = 50) with no prior history of glucose imbalance were subjected to 2 hour oral glucose tolerance test (OGTT). 24 subjects had normal glucose tolerance (NGT), 17 subjects had impaired glucose tolerance (IGT) and 9 had impaired fasting glucose (IFG). The IGT and IFG subjects were grouped together as pre-diabetes group (n = 26). Progenitor cell counts in peripheral circulation at fasting and 2 hour post glucose challenge were measured using direct two-color flow cytometry.</p> <p>Results</p> <p>The pre-diabetes group was more insulin resistant (p < 0.0001) as measured by homeostasis assessment model (HOMA-IR) compared to NGT group. A 2.5-fold increase in CD34⁺cells (p = 0.003) and CD133⁺CD34⁺(p = 0.019) cells was seen 2 hours post glucose challenge in the NGT group. This increase for both the cell types was attenuated in subjects with IGT. CD34⁺cell counts in response to glucose challenge inversely correlated with neutrophil counts (ρ = -0.330, p = 0.019), while post load counts of CD133⁺CD34⁺cells inversely correlated with serum creatinine (ρ = -0.312, p = 0.023).</p> <p>Conclusion</p> <p>There is a 2.5-fold increase in the circulating levels of haematopoietic stem cells in response to glucose challenge in healthy Asian Indian male subjects which is attenuated in subjects with pre-diabetes.</p

Analysis and comparison of very large metagenomes with fast clustering and functional annotation

<p>Abstract</p> <p>Background</p> <p>The remarkable advance of metagenomics presents significant new challenges in data analysis. Metagenomic datasets (metagenomes) are large collections of sequencing reads from anonymous species within particular environments. Computational analyses for very large metagenomes are extremely time-consuming, and there are often many novel sequences in these metagenomes that are not fully utilized. The number of available metagenomes is rapidly increasing, so fast and efficient metagenome comparison methods are in great demand.</p> <p>Results</p> <p>The new metagenomic data analysis method Rapid Analysis of Multiple Metagenomes with a Clustering and Annotation Pipeline (<b>RAMMCAP</b>) was developed using an ultra-fast sequence clustering algorithm, fast protein family annotation tools, and a novel statistical metagenome comparison method that employs a unique graphic interface. RAMMCAP processes extremely large datasets with only moderate computational effort. It identifies raw read clusters and protein clusters that may include novel gene families, and compares metagenomes using clusters or functional annotations calculated by RAMMCAP. In this study, RAMMCAP was applied to the two largest available metagenomic collections, the "Global Ocean Sampling" and the "Metagenomic Profiling of Nine Biomes".</p> <p>Conclusion</p> <p>RAMMCAP is a very fast method that can cluster and annotate one million metagenomic reads in only hundreds of CPU hours. It is available from <url>http://tools.camera.calit2.net/camera/rammcap/</url>.</p