Oscillations and temporal signalling in cells

The development of new techniques to quantitatively measure gene expression in cells has shed light on a number of systems that display oscillations in protein concentration. Here we review the different mechanisms which can produce oscillations in gene expression or protein concentration, using a framework of simple mathematical models. We focus on three eukaryotic genetic regulatory networks which show "ultradian" oscillations, with time period of the order of hours, and involve, respectively, proteins important for development (Hes1), apoptosis (p53) and immune response (NFkB). We argue that underlying all three is a common design consisting of a negative feedback loop with time delay which is responsible for the oscillatory behaviour

Highly Accurate Multi-layer Perceptron Neural Network for Air Data System

The error backpropagation multi-layer perceptron algorithm is revisited. This algorithm is used to train and validate two models of three-layer neural networks that can be used to calibrate a 5-hole pressure probe. This paper addresses Occam's Razor problem as it describes the adhoc training methodology applied to improve accuracy and sensitivity. The trained outputs from 5-4-3 feed-forward network architecture with jump connection are comparable to second decimal digit (~0.05) accuracy, hitherto unreported in literature.Defence Science Journal, 2009, 59(6), pp.670-674, DOI:http://dx.doi.org/10.14429/dsj.59.157

Do the mildly superluminal VLBI knots exclude ultrarelativistic blazar jets?

We compute the effective values of apparent transverse velocity and flux boosting factors for the VLBI radio knots of blazar jets, by integrating over the angular distributions of these quantities across the widths of jets with finite opening angles but constant velocities. For high bulk Lorentz factors (Gamma > 10) variations across the jet can be quite large if the opening angle, omega, is even a few degrees on sub-parsec scales. The resulting apparent speeds are often much lower than those obtained from the usual analyses that ignore the finite jet opening angles. We can thus reconcile the usually observed subluminal or mildly superluminal speeds with the very high (>~ 20) Gamma factors, required by the inverse Compton origin and rapid variability of TeV fluxes, as well as by intraday radio variability. Thus it is possible to associate the VLBI radio knots directly with shocks in the ultra-relativistic main jet flow, without invoking very rapid jet deceleration on parsec scales, or extremely unlikely viewing angles.Comment: 10 pages, 1 figure, to appear in ApJ Letters, Nov. 10 2004 issu

Multi-epoch intra-night optical monitoring of 8 radio-quiet BL Lac candidates

For a new sample of 8 weak-line-quasars (WLQs) we report a sensitive search in 20 intranight monitoring sessions, for blazar-like optical flux variations on hour-like and longer time scale (day/month/year$-$like). The sample consists exclusively of the WLQs that are not radio$-$loud and have either been classified as `radio-weak probable BL Lac candidates' and/or are known to have exhibited at least one episode of large, blazar$-$like optical variability. Whereas only a hint of intra$-$night variability is seen for two of these WLQs, J104833.5$+$620305.0(z = 0.219) and J133219.6$+$622715.9 (z = 3.15), statistically significant inter$-$night variability at a few per cent level is detected for three of the sources, including the radio-intermediate WLQ J133219.6$+$622715.9 (z = 3.15) and the well known bona$-$fide radio$-$quiet WLQs J121221.5$+$534128.0 (z = 3.10) and WLQ J153259.9$-$003944.1 (z = 4.62). In the rest$-$frame, this variability is intra-day and in the far$-$UV band. On the time scale of a decade, we find for three of the WLQs large brightness changes, amounting to 1.655$\pm$0.009, 0.163$\pm$0.010 and 0.144$\pm$0.018 mag, for J104833.5$+$620305.0, J123743.1$+$630144.9 and J232428.4$+$144324.4, respectively. Whereas the latter two are confirmed radio-quiet WLQs, the extragalactic nature of J104833.5$+$620305.0 remains to be well established, thanks to the absence of any feature(s) in its available optical spectra. The present study forms a part of our ongoing campaign of intranight optical monitoring of radio quiet weak-line quasars, in order to improve the understanding of this enigmatic class of Active Galactic Nuclei and to look among them for a possible tiny, elusive population of radio-quiet BL Lacs.Comment: Accepted to MNRAS. 12 pages, 1 figure, 4 Tabl

Velvet bean roots stimulates humoral and cell mediated immunity and offers protection against Cyclophosphamide induced myelosuppression.

The objective of the study was to investigate the immunomodulatory activity of roots of Mucuna pruriens on cellular and humoral immunity.  Extraction and phytochemical screening of the roots were performed using standard methods, HPTLC fingerprinting profiles of the methanol extract were developed on CAMAG system, to resolve components, Quantification of β-Sitosterol  was done by validated HPTLC method. Immunomodulatory activity of the extract was assessed by Cyclophosphamide-induced myelosuppression assay, Macrophage phagocytosis by Carbon clearance method, Humoral antibody response and Delayed type hypersensitivity reaction using SRBC as an antigen.  Oral administration of methanolic extract of Mucuna roots at 100, 200 and 400 mg/kg in mice dose dependently potentiated the delayed-type hypersensitivity reaction induced by sheep red blood cells.  It significantly enhanced the circulating antibody titre in response to SRBC and macrophage phagocytosis. Cyclophosphamide induced myelosuppression was counteracted in a dose dependent manner with increase in the levels of WBC compared to cyclophosphamide group.  The results of the present study suggests that the developed HPTLC fingerprint profiles of the major constituents in methanolic extract along with their Rf values would serve as a reference standard, methods developed for the quantification of L-dopa and  β-Sitosterol  can be used to ensure the identity and  quality of the plant and the results of the biological studies indicates that the roots of Mucuna pruriens  influenced both humoral and cell mediated immunity and offered protection against immunosuppression induced by cytotoxic agent Cyclophosphamide  holds promise as an immunomodulator.

Numerics of High Performance Computers and Benchmark Evaluation of Distributed Memory Computers

The internal representation of numerical data, their speed of manipulation to generate the desired result through efficient utilisation of central processing unit, memory, and communication links are essential steps of all high performance scientific computations. Machine parameters, in particular, reveal accuracy and error bounds of computation, required for performance tuning of codes. This paper reports diagnosis of machine parameters, measurement of computing power of several workstations, serial and parallel computers, and a component-wise test procedure for distributed memory computers. Hierarchical memory structure is illustrated by block copying and unrolling techniques. Locality of reference for cache reuse of data is amply demonstrated by fast Fourier transform codes. Cache and register-blocking technique results in their optimum utilisation with consequent gain in throughput during vector-matrix operations. Implementation of these memory management techniques reduces cache inefficiency loss, which is known to be proportional to the number of processors. Of the two Linux clusters-ANUP16, HPC22 and HPC64, it has been found from the measurement of intrinsic parameters and from application benchmark of multi-block Euler code test run that ANUP16 is suitable for problems that exhibit fine-grained parallelism. The delivered performance of ANUP16 is of immense utility for developing high-end PC clusters like HPC64 and customised parallel computers with added advantage of speed and high degree of parallelism

Accurate implementation of leaping in space: The spatial partitioned-leaping algorithm

There is a great need for accurate and efficient computational approaches that can account for both the discrete and stochastic nature of chemical interactions as well as spatial inhomogeneities and diffusion. This is particularly true in biology and nanoscale materials science, where the common assumptions of deterministic dynamics and well-mixed reaction volumes often break down. In this article, we present a spatial version of the partitioned-leaping algorithm (PLA), a multiscale accelerated-stochastic simulation approach built upon the tau-leaping framework of Gillespie. We pay special attention to the details of the implementation, particularly as it pertains to the time step calculation procedure. We point out conceptual errors that have been made in this regard in prior implementations of spatial tau-leaping and illustrate the manifestation of these errors through practical examples. Finally, we discuss the fundamental difficulties associated with incorporating efficient exact-stochastic techniques, such as the next-subvolume method, into a spatial-leaping framework and suggest possible solutions.Comment: 15 pages, 9 figures, 2 table

On the AC spectrum of one-dimensional random Schroedinger operators with matrix-valued potentials

We consider discrete one-dimensional random Schroedinger operators with decaying matrix-valued, independent potentials. We show that if the l^2-norm of this potential has finite expectation value with respect to the product measure then almost surely the Schroedinger operator has an interval of purely absolutely continuous (ac) spectrum. We apply this result to Schroedinger operators on a strip. This work provides a new proof and generalizes a result obtained by Delyon, Simon, and Souillard.Comment: (1 figure

The physiological basis for genetic variation in water use efficiency and carbon isotope composition in Arabidopsis thaliana.

Ecologists and physiologists have documented extensive variation in water use efficiency (WUE) in Arabidopsis thaliana, as well as association of WUE with climatic variation. Here, we demonstrate correlations of whole-plant transpiration efficiency and carbon isotope composition (δ(13)C) among life history classes of A. thaliana. We also use a whole-plant cuvette to examine patterns of co-variation in component traits of WUE and δ(13)C. We find that stomatal conductance (g s) explains more variation in WUE than does A. Overall, there was a strong genetic correlation between A and g s, consistent with selection acting on the ratio of these traits. At a more detailed level, genetic variation in A was due to underlying variation in both maximal rate of carboxylation (V cmax) and maximum electron transport rate (Jmax). We also found strong effects of leaf anatomy, where lines with lower WUE had higher leaf water content (LWC) and specific leaf area (SLA), suggesting a role for mesophyll conductance (g m) in variation of WUE. We hypothesize that this is due to an effect through g m, and test this hypothesis using the abi4 mutant. We show that mutants of ABI4 have higher SLA, LWC, and g m than wild-type, consistent with variation in leaf anatomy causing variation in g m and δ(13)C. These functional data also add further support to the central, integrative role of ABI4 in simultaneously altering ABA sensitivity, sugar signaling, and CO2 assimilation. Together our results highlight the need for a more holistic approach in functional studies, both for more accurate annotation of gene function and to understand co-limitations to plant growth and productivity