A parallel-serial binary arbitration scheme for collision-free multi-access techniques

Multi-access techniques are widely used in computer networking and distributed multiprocessor systems. On-the-fly arbitration schemes permit one of the many contenders to access the medium without collisions. Serial arbitration is cost effective but is slow and hence unsuitable for high-speed multiprocessor environments supporting very high data transfer rates. A fully parallel arbitration scheme takes less time but is not practically realisable for large numbers of contenders. In this paper, a generalised parallel-serial scheme is proposed which significantly reduces the arbitration time and is practically realisable.

Rapid transfection assay for screening mutagens and carcinogens

Testing for mutagenicity and carcinogenicity has become an integral part of the toxicological evaluation of drugs and chemicals. Standard carcinogenicity tests in vivo require both large numbers of animals and prolonged experiments. To circumvent these problems, several rapid tests have been developed for preliminary screening of mutagens and carcinogens in vitro. Ames and his associates, the first to develop a mutation test, used mutant strains of Salmonella typhimurium [1]. Mutation tests with Escherichia coli, Bacillus subtilis, Neurospora crassa and Saccharomyces cerevisiae, and DNA-repair tests with E. coli and B. subtilis, have been developed. Cytogenetic assays, in vivo as well as in vitro, in both plant and animal systems, are also used to detect potential mutagens and carcinogens. Transfection is inhibited by base mutation, cleavage of DNA, loss of cohesive ends, interaction with histones, spermidine, nalidixic acid, etc. [3]. The efficiency of transfection is affected by temperature, DNA structure and the condition of the competence of the recipient cells [3]. Transfection assays with phages MS: RNA and ~i, x 174-DNA have been reported [15]. A fast and easy transfection assay using colitis bacteriophage DNA is reported in this communication.

Conformal invariance and scalar-tensor theories

A new generalisation of Einstein’s theory is proposed which is invariant under conformal mappings. Two scalar fields are introduced in addition to the metric tensor field, so that two special choices of gauge are available for physical interpretation, the ‘Einstein gauge’ and the ‘atomic gauge’. The theory is not unique but contains two adjustable parameters ζ anda. Witha=1 the theory viewed from the atomic gauge is Brans-Dicke theory (ω=−3/2+ζ/4). Any other choice ofa leads to a creation-field theory. In particular the theory given by the choicea=−3 possesses a cosmological solution satisfying Dirac’s ‘large numbers’ hypothesis.

Embodied energy in cement stabilised rammed earth walls

Rammed earth walls are low carbon emission and energy efficient alternatives to load bearing walls. Large numbers of rammed earth buildings have been constructed in the recent past across the globe. This paper is focused on embodied energy in cement stabilised rammed earth (CSRE) walls. Influence of soil grading, density and cement content on compaction energy input has been monitored. A comparison between energy content of cement and energy in transportation of materials, with that of the actual energy input during rammed earth compaction in the actual field conditions and the laboratory has been made. Major conclusions of the investigations are (a) compaction energy increases with increase in clay fraction of the soil mix and it is sensitive to density of the CSRE wall, (b) compaction energy varies between 0.033 MJ/m(3) and 0.36 MJ/m(3) for the range of densities and cement contents attempted, (c) energy expenditure in the compaction process is negligible when compared to energy content of the cement and (d) total embodied energy in CSRE walls increases linearly with the increase in cement content and is in the range of 0.4-0.5 GJ/m(3) for cement content in the rage of 6-8%. (C) 2009 Elsevier B.V. All rights reserved.

Characteristics of yeasts isolated from phenol- and catechol-adapted activated sludges

Phenol- and catechol-adapted sludges contained large numbers of the yeasts, Candida tropicalis and Trichosporon cutaneum. Both were able to grow on a variety of aromatic compounds and utilized phenol and catechol at a high rate. This property was inducible. The feasibility of using these yeasts for removing phenols from waste waters is suggested.

Svetlichny's inequality and genuine tripartite nonlocality in three-qubit pure states

The violation of the Svetlichny's inequality (SI) [Phys. Rev. D 35, 3066 (1987)] is sufficient but not necessary for genuine tripartite nonlocal correlations. Here we quantify the relationship between tripartite entanglement and the maximum expectation value of the Svetlichny operator (which is bounded from above by the inequality) for the two inequivalent subclasses of pure three-qubit states: the Greenberger-Horne-Zeilinger (GHZ) class and the W class. We show that the maximum for the GHZ-class states reduces to Mermin's inequality [Phys. Rev. Lett. 65, 1838 (1990)] modulo a constant factor, and although it is a function of the three tangle and the residual concurrence, large numbers of states do not violate the inequality. We further show that by design SI is more suitable as a measure of genuine tripartite nonlocality between the three qubits in the W-class states,and the maximum is a certain function of the bipartite entanglement (the concurrence) of the three reduced states, and only when their sum attains a certain threshold value do they violate the inequality.

sRNAscanner: A Computational Tool for Intergenic Small RNA Detection in Bacterial Genomes

Background:Bacterial non-coding small RNAs (sRNAs) have attracted considerable attention due to their ubiquitous nature and contribution to numerous cellular processes including survival, adaptation and pathogenesis. Existing computational approaches for identifying bacterial sRNAs demonstrate varying levels of success and there remains considerable room for improvement. Methodology/Principal Findings: Here we have proposed a transcriptional signal-based computational method to identify intergenic sRNA transcriptional units (TUs) in completely sequenced bacterial genomes. Our sRNAscanner tool uses position weight matrices derived from experimentally defined E. coli K-12 MG1655 sRNA promoter and rho-independent terminator signals to identify intergenic sRNA TUs through sliding window based genome scans. Analysis of genomes representative of twelve species suggested that sRNAscanner demonstrated equivalent sensitivity to sRNAPredict2, the best performing bioinformatics tool available presently. However, each algorithm yielded substantial numbers of known and uncharacterized hits that were unique to one or the other tool only. sRNAscanner identified 118 novel putative intergenic sRNA genes in Salmonella enterica Typhimurium LT2, none of which were flagged by sRNAPredict2. Candidate sRNA locations were compared with available deep sequencing libraries derived from Hfq-co-immunoprecipitated RNA purified from a second Typhimurium strain (Sittka et al. (2008) PLoS Genetics 4: e1000163). Sixteen potential novel sRNAs computationally predicted and detected in deep sequencing libraries were selected for experimental validation by Northern analysis using total RNA isolated from bacteria grown under eleven different growth conditions. RNA bands of expected sizes were detected in Northern blots for six of the examined candidates. Furthermore, the 5'-ends of these six Northern-supported sRNA candidates were successfully mapped using 5'-RACE analysis. Conclusions/Significance: We have developed, computationally examined and experimentally validated the sRNAscanner algorithm. Data derived from this study has successfully identified six novel S. Typhimurium sRNA genes. In addition, the computational specificity analysis we have undertaken suggests that similar to 40% of sRNAscanner hits with high cumulative sum of scores represent genuine, undiscovered sRNA genes. Collectively, these data strongly support the utility of sRNAscanner and offer a glimpse of its potential to reveal large numbers of sRNA genes that have to date defied identification. sRNAscanner is available from: http://bicmku.in:8081/sRNAscanner or http://cluster.physics.iisc.ernet.in/sRNAscanner/.

In vitro meristem cloning of Eucalyptus tereticornis Sm

Rapid multiplication of axillary meristems and direct shoot development occurred from nodal explants of mature Eucalyptus tereticornis Sm. with 5.3 mgrM NAA, 1.1 mgrM IAA and 4.4 mgrM BA in Murashige-Skoog medium. Repeated subcultures of the second generation shoot cultures into low cytokinin-auxin containing media (0.44�0.88 mgrM BA+0.1 mgrM NAA) yielded axillary microshoots in large numbers. Half-strength MS liquid medium with 4.9 mgrM IBA, 5.5 mgrM IAA and 5.3 mgrM NAA for four days, half-strength semi-solid hormonefree MS medium with charcoal, and MS liquid medium without charcoal and hormones, in sequence, induced rooting of shoots in the dark. This system is suitable for the mass propagation of this difficult-to-root eucalypt.

Strong spin-two interaction and general relativity

The concept of short range strong spin-two (f) field (mediated by massive f-mesons) and interacting directly with hadrons was introduced along with the infinite range (g) field in early seventies. In the present review of this growing area (often referred to as strong gravity) we give a general relativistic treatment in terms of Einstein-type (non-abelian gauge) field equations with a coupling constant Gf reverse similar, equals 1038 GN (GN being the Newtonian constant) and a cosmological term λf ƒ;μν (ƒ;μν is strong gravity metric and λf not, vert, similar 1028 cm− is related to the f-meson mass). The solutions of field equations linearized over de Sitter (uniformly curves) background are capable of having connections with internal symmetries of hadrons and yielding mass formulae of SU(3) or SU(6) type. The hadrons emerge as de Sitter “microuniverses” intensely curved within (radius of curvature not, vert, similar10−14 cm).The study of spinor fields in the context of strong gravity has led to Heisenberg's non-linear spinor equation with a fundamental length not, vert, similar2 × 10−14 cm. Furthermore, one finds repulsive spin-spin interaction when two identical spin-Image particles are in parallel configuration and a connection between weak interaction and strong gravity.Various other consequences of strong gravity embrace black hole (solitonic) solutions representing hadronic bags with possible quark confinement, Regge-like relations between spins and masses, connection with monopoles and dyons, quantum geons and friedmons, hadronic temperature, prevention of gravitational singularities, providing a physical basis for Dirac's two metric and large numbers hypothesis and projected unification with other basic interactions through extended supergravity.

Structure and Bonding in Stannadiphospholes and their Dianions SnC(2)P(2)R(2)(m) (R=H, tBu m=0,-2): A Comparative Study with C(5)H(5)(+) and C(5)H(5)(-) Analogues

The potential energy surfaces of both neutral and dianionic SnC(2)P(2)R(2) (R=H, tBu) ring systems have been explored at the B3PW91/LANL2DZ (Sn) and 6-311 + G* (other atoms) level. In the neutral isomers the global minimum is a nido structure in which a 1,2-diphosphocyclobutadiene ring (1,2-DPCB) is capped by the Sn. Interestingly, the structure established by Xray diffraction analysis, for R=tBu, is a 1,3-DPCB ring capped by Sn and it is 2.4 kcal mol(-1) higher in energy than the 1,2-DPCB ring isomer. This is possibly related to the kinetic stability of the 1,3-DPCB ring, which might originate from the synthetic precursor ZrCp(2)tBu(2)C(2)P(2). In the case of the dianionic isomers we observe only a 6 pi-electron aromatic structure as the global minimum, similarly to the cases of our previously reported results with other types of heterodiphospholes.([1,4,19]) The existence of large numbers of cluster-type isomers in neutral and 6 pi-planar structures in the dianions SnC(2)P(2)R(2)(2-) (R=H, tBu) is due to 3D aromaticity in neutral clusters and to 2D pi aromaticity of the dianionic rings. Relative energies of positional isomers mainly depend on: 1) the valency and coordination number of the Sn centre, 2) individual bond strengths, and 3) the steric effect of tBu groups. A comparison of neutral stannadiphospholes with other structurally related C(5)H(5)(+) analogues indicates that Sn might be a better isolobal analogue to P(+) than to BH or CH(+). The variation in global minima in these C(5)H(5)(+) analogues is due to characteristic features such as 1) the different valencies of C, B, P and Sn, 2) the electron deficiency of B, 3) weaker p pi-p pi bonding by P and Sn atoms, and 4) the tendency of electropositive elements to donate electrons to nido clusters. Unlike the C5H5+ systems, all C(5)H(5)(-) analogues have 6 pi-planar aromatic structures as global minima. The differences in the relative ordering of the positional isomers and ligating properties are significant and depend on 1) the nature of the pi orbitals involved, and 2) effective overlap of orbitals.

Plasmodium falciparum Prp16 homologue and its role in splicing

Large numbers of Plasmodium genes have been predicted to have introns. However, little information exists on the splicing mechanisms in this organism. Here, we describe the DExD/DExH-box containing Pre-mRNA processing proteins (Prps), PfPrp2p, PfPrp5p, PfPrp16p, PfPrp22p, PfPrp28p, PfPrp43p and PfBrr2p, present in the Plasmodium falciparum genome and characterized the role of one of these factors, PfPrp16p. It is a member of DEAH-box protein family with nine collinear sequence motifs, a characteristic of helicase proteins. Experiments with the recombinantly expressed and purified PfPrp16 helicase domain revealed binding to RNA, hydrolysis of ATP as well as catalytic helicase activities. Expression of helicase domain with the C-terminal helicase-associated domain (HA2) reduced these activities considerably, indicating that the helicase-associated domain may regulate the PfPrp16 function. Localization studies with the PfPrp16 GFP transgenic lines suggested a role of its N-terminal domain (1-80 amino acids) in nuclear targeting. Immunodepletion of PfPrp16p, from nuclear extracts of parasite cultures, blocked the second catalytic step of an in vitro constituted splicing reaction suggesting a role for PfPrp16p in splicing catalysis. Further we show by complementation assay in yeast that a chimeric yeast-Plasmodium Prp16 protein, not the full length PfPrp16, can rescue the yeast prp16 temperature-sensitive mutant. These results suggest that although the role of Prp16p in catalytic step II is highly conserved among Plasmodium, human and yeast, subtle differences exist with regards to its associated factors or its assembly with spliceosomes. (C) 2012 Elsevier B.V. All rights reserved.

Sea-level changes and its impact on coastal archaeological monuments: seven pagodas of Mahabalipuram, a case study

The name `Seven Pagodas' has served as a nickname for the south Indian port of Mahabalipuram since the early European explorers used it as landmark for navigation as they could see summits of seven temples from the sea. There are many theories concerning the name Seven Pagodas. The present study has compared coastline and adjacent seven monuments illustrated in a 17th century Portolan Chart (maritime map) with recent remote sensing data. This analysis throws new light on the name ``Seven Pagodas'' for the city. This study has used DEM of the site to simulate the coastline which is similar to the one depicted in the old portolan chart. Through this, the then sea level and corresponding flooding extent according to topography of the area and their effect on monuments could be analyzed. Most importantly this work has in the process identified possibly the seven monuments that constituted the name Seven Pagodas and this provides an alternative explanation to one of the mysteries of history. This work has demonstrated unique method of studying coastal archaeological sites. As large numbers of heritage sites around the world are on coastlines, this methodology has potential to be very useful for coastal heritage preservation and management.

Phenotypic characters of rice landraces reveal independent lineages of short-grain aromatic indica rice

Rice landraces are lineages developed by farmers through artificial selection during the long-term domestication process. Despite huge potential for crop improvement, they are largely understudied in India. Here, we analyse a suite of phenotypic characters from large numbers of Indian landraces comprised of both aromatic and non-aromatic varieties. Our primary aim was to investigate the major determinants of diversity, the strength of segregation among aromatic and non-aromatic landraces as well as that within aromatic landraces. Using principal component analysis, we found that grain length, width and weight, panicle weight and leaf length have the most substantial contribution. Discriminant analysis can effectively distinguish the majority of aromatic from non-aromatic landraces. More interestingly, within aromatic landraces long-grain traditional Basmati and short-grain non-Basmati aromatics remain morphologically well differentiated. The present research emphasizes the general patterns of phenotypic diversity and finds out the most important characters. It also confirms the existence of very unique short-grain aromatic landraces, perhaps carrying signatures of independent origin of an additional aroma quantitative trait locus in the indica group, unlike introgression of specific alleles of the BADH2 gene from the japonica group as in Basmati. We presume that this parallel origin and evolution of aroma in short-grain indica landraces are linked to the long history of rice domestication that involved inheritance of several traits from Oryza nivara, in addition to O. rufipogon. We conclude with a note that the insights from the phenotypic analysis essentially comprise the first part, which will likely be validated with subsequent molecular analysis.

The relationship between classification of multi-domain proteins using an alignment-free approach and their functions: a case study with immunoglobulins

Establishing functional relationships between multi-domain protein sequences is a non-trivial task. Traditionally, delineating functional assignment and relationships of proteins requires domain assignments as a prerequisite. This process is sensitive to alignment quality and domain definitions. In multi-domain proteins due to multiple reasons, the quality of alignments is poor. We report the correspondence between the classification of proteins represented as full-length gene products and their functions. Our approach differs fundamentally from traditional methods in not performing the classification at the level of domains. Our method is based on an alignment free local matching scores (LMS) computation at the amino-acid sequence level followed by hierarchical clustering. As there are no gold standards for full-length protein sequence classification, we resorted to Gene Ontology and domain-architecture based similarity measures to assess our classification. The final clusters obtained using LMS show high functional and domain architectural similarities. Comparison of the current method with alignment based approaches at both domain and full-length protein showed superiority of the LMS scores. Using this method we have recreated objective relationships among different protein kinase sub-families and also classified immunoglobulin containing proteins where sub-family definitions do not exist currently. This method can be applied to any set of protein sequences and hence will be instrumental in analysis of large numbers of full-length protein sequences.

Pure shift NMR approach for fast and accurate extraction of heteronuclear couplings

The direct and accurate determination of heteronuclear ((n)J(HX), X = F-19, P-31) couplings from the one dimensional H-1-NMR spectrum is severely hampered due to the simultaneous presence of large numbers of (n)J(HH). The present study demonstrates the utility of the pure shift NMR approach for spectral simplification, and precise and direct measurement of heteronuclear couplings. As a consequence of refocusing of homonuclear couplings ((n)J(HH)) by the pure shift NMR, only heteronuclear couplings ((n)J(HX)) appear as simple multiplets at the resonance position of each chemically non-equivalent proton, enabling their direct measurement from the 1D-H-1 spectrum. The experiment is demonstrated on a number of molecules containing either F-19 or P-31, where (n)J(HF) and (n)J(HP) could be precisely measured in a straightforward manner. The distinct advantage of the experiment is demonstrated on molecules containing more than one fluorine atom, where most of the available NMR experiments fail or have restricted utility.