A parallel genetic algorithm for the Steiner Problem in Networks

This paper presents a parallel genetic algorithm to the Steiner Problem in Networks. Several previous papers have proposed the adoption of GAs and others metaheuristics to solve the SPN demonstrating the validity of their approaches. This work differs from them for two main reasons: the dimension and the characteristics of the networks adopted in the experiments and the aim from which it has been originated. The reason that aimed this work was namely to build a comparison term for validating deterministic and computationally inexpensive algorithms which can be used in practical engineering applications, such as the multicast transmission in the Internet. On the other hand, the large dimensions of our sample networks require the adoption of a parallel implementation of the Steiner GA, which is able to deal with such large problem instances.

Parallel convolutional coder

A parallel convolutional coder (104) comprising: a plurality of serial convolutional coders (108) each having a register with a plurality of memory cells and a plurality of serial coder outputs,- input means (120) from which data can be transferred in parallel into the registers,- and a parallel coder output (124) comprising a plurality of output memory cells each of which is connected to one of the serial coder outputs so that data can be transferred in parallel from all of the serial coders to the parallel coder output.

An optical study of multiple NEIAL events driven by low energy electron precipitation

Optical data are compared with EISCAT radar observations of multiple Naturally Enhanced Ion-Acoustic Line (NEIAL) events in the dayside cusp. This study uses narrow field of view cameras to observe small-scale, short-lived auroral features. Using multiple-wavelength optical observations, a direct link between NEIAL occurrences and low energy (about 100 eV) optical emissions is shown. This is consistent with the Langmuir wave decay interpretation of NEIALs being driven by streams of low-energy electrons. Modelling work connected with this study shows that, for the measured ionospheric conditions and precipitation characteristics, growth of unstable Langmuir (electron plasma) waves can occur, which decay into ion-acoustic wave modes. The link with low energy optical emissions shown here, will enable future studies of the shape, extent, lifetime, grouping and motions of NEIALs.

Effects of solar wind magnetosphere coupling recorded at different geomagnetic latitudes: Separation of directly-driven and storage/release systems

The effect on geomagnetic activity of solar wind speed, compared with that of the strength of the interplanetary magnetic field, differs with geomagnetic latitude. In this study we construct a new index based on monthly standard deviations in the H-component of the geomagnetic field for all geomagnetic latitudes. We demonstrate that for this index the response at auroral regions correlates best with interplanetary coupling functions which include the solar wind speed while mid- and low-latitude regions respond to variations in the interplanetary magnetic field strength. These results are used to isolate the responsible geomagnetic current systems.

Wave-driven wind jets in the marine atmospheric boundary layer

The interaction between ocean surface waves and the overlying wind leads to a transfer of momentum across the air–sea interface. Atmospheric and oceanic models typically allow for momentum transfer to be directed only downward, from the atmosphere to the ocean. Recent observations have suggested that momentum can also be transferred upward when long wavelength waves, characteristic of remotely generated swell, propagate faster than the wind speed. The effect of upward momentum transfer on the marine atmospheric boundary layer is investigated here using idealized models that solve the momentum budget above the ocean surface. A variant of the classical Ekman model that accounts for the wave-induced stress demonstrates that, although the momentum flux due to the waves penetrates only a small fraction of the depth of the boundary layer, the wind profile is profoundly changed through its whole depth. When the upward momentum transfer from surface waves sufficiently exceeds the downward turbulent momentum flux, then the near-surface wind accelerates, resulting in a low-level wave-driven wind jet. This increases the Coriolis force in the boundary layer, and so the wind turns in the opposite direction to the classical Ekman layer. Calculations of the wave-induced stress due to a wave spectrum representative of fast-moving swell demonstrate upward momentum transfer that is dominated by contributions from waves in the vicinity of the peak in the swell spectrum. This is in contrast to wind-driven waves whose wave-induced stress is dominated by very short wavelength waves. Hence the role of swell can be characterized by the inverse wave age based on the wave phase speed corresponding to the peak in the spectrum. For a spectrum of waves, the total momentum flux is found to reverse sign and become upward, from waves to wind, when the inverse wave age drops below the range 0.15–0.2, which agrees reasonably well with previously published oceanic observations.

Variability of the North Atlantic eddy-driven jet stream

Much of the atmospheric variability in the North Atlantic sector is associated with variations in the eddy-driven component of the zonal flow. Here we present a simple method to specifically diagnose this component of the flow using the low-level wind field (925–700 hpa ). We focus on the North Atlantic winter season in the ERA-40 reanalysis. Diagnostics of the latitude and speed of the eddy-driven jet stream are compared with conventional diagnostics of the North Atlantic Oscillation (NAO) and the East Atlantic (EA) pattern. This shows that the NAO and the EA both describe combined changes in the latitude and speed of the jet stream. It is therefore necessary, but not always sufficient, to consider both the NAO and the EA in identifying changes in the jet stream. The jet stream analysis suggests that there are three preferred latitudinal positions of the North Atlantic eddy-driven jet stream in winter. This result is in very good agreement with the application of a statistical mixture model to the two-dimensional state space defined by the NAO and the EA. These results are consistent with several other studies which identify four European/Atlantic regimes, comprising three jet stream patterns plus European blocking events.

Parallel declines in pollinators and insect-pollinated plants in Britain and the Netherlands

Despite widespread concern about declines in pollination services, little is known about the patterns of change in most pollinator assemblages. By studying bee and hoverfly assemblages in Britain and the Netherlands, we found evidence of declines (pre- versus post-1980) in local bee diversity in both countries; however, divergent trends were observed in hoverflies. Depending on the assemblage and location, pollinator declines were most frequent in habitat and flower specialists, in univoltine species, and/or in nonmigrants. In conjunction with this evidence, outcrossing plant species that are reliant on the declining pollinators have themselves declined relative to other plant species. Taken together, these findings strongly suggest a causal connection between local extinctions of functionally linked plant and pollinator species.

Muscle hypertrophy driven by myostatin blockade does not require stem/precursor-cell activity

Myostatin, a member of the TGF-beta family, has been identified as a powerful inhibitor of muscle growth. Absence or blockade of myostatin induces massive skeletal muscle hypertrophy that is widely attributed to proliferation of the population of muscle fiber-associated satellite cells that have been identified as the principle source of new muscle tissue during growth and regeneration. Postnatal blockade of myostatin has been proposed as a basis for therapeutic strategies to combat muscle loss in genetic and acquired myopathies. But this approach, according to the accepted mechanism, would raise the threat of premature exhaustion of the pool of satellite cells and eventual failure of muscle regeneration. Here, we show that hypertrophy in the absence of myostatin involves little or no input from satellite cells. Hypertrophic fibers contain no more myonuclei or satellite cells and myostatin had no significant effect on satellite cell proliferation in vitro, while expression of myostatin receptors dropped to the limits of detectability in postnatal satellite cells. Moreover, hypertrophy of dystrophic muscle arising from myostatin blockade was achieved without any apparent enhancement of contribution of myonuclei from satellite cells. These findings contradict the accepted model of myostatin-based control of size of postnatal muscle and reorient fundamental investigations away from the mechanisms that control satellite cell proliferation and toward those that increase myonuclear domain, by modulating synthesis and turnover of structural muscle fiber proteins. It predicts too that any benefits of myostatin blockade in chronic myopathies are unlikely to impose any extra stress on the satellite cells.

A novel parallel approach to the likelihood-based estimation of admixture in population genetics

Inferring population admixture from genetic data and quantifying it is a difficult but crucial task in evolutionary and conservation biology. Unfortunately state-of-the-art probabilistic approaches are computationally demanding. Effectively exploiting the computational power of modern multiprocessor systems can thus have a positive impact to Monte Carlo-based simulation of admixture modeling. A novel parallel approach is briefly described and promising results on its message passing interface (MPI)-based C implementation are reported.

Mammal reproductive strategies driven by offspring mortality-size relationships

Trade-offs have long been a major theme in life-history theory, but they have been hard to document. We introduce a new method that reveals patterns of divergent trade-offs after adjusting for the pervasive variation in rate of resource allocation to offspring as a function of body size and lifestyle. Results suggest that preweaning vulnerability to predation has been the major factor determining how female placental mammals allocate production between a few large and many small offspring within a litter and between a few large litters and many small ones within a reproductive season. Artiodactyls, perissodactyls, cetaceans, and pinnipeds, which give birth in the open on land or in the sea, produce a few large offspring, at infrequent intervals, because this increases their chances of escaping predation. Insectivores, fissiped carnivores, lagomorphs, and rodents, whose offspring are protected in burrows or nests, produce large litters of small newborns. Primates, bats, sloths, and anteaters, which carry their young from birth until weaning, produce litters of one or a few offspring because of the need to transport and care for them.

Anthraquinone catalysis in the glucose-driven reduction of indigo to leuco-indigo

Anthraquinone immobilised onto the surface of indigo microcrystals enhances the reductive dissolution of indigo to leuco-indigo. Indigo reduction is driven by glucose in aqueous NaOH and a vibrating gold disc electrode is employed to monitor the increasing leuco-indigo concentration with time. Anthraquinone introduces a strong catalytic effect which is explained by invoking a molecular "wedge effect'' during co-intercalation of Na+ and anthraquinone into the layered indigo crystal structure. The glucose-driven indigo reduction, which is in effective in 0.1 M NaOH at 65 degrees C, becomes facile and goes to completion in the presence of anthraquinone catalyst. Electron microscopy of indigo crystals before and after reductive dissolution confirms a delamination mechanism initiated at the edges of the plate-like indigo crystals. Catalysis occurs when the anthraquinone-indigo mixture reaches a molar ratio of 1:400 (at 65 degrees C; corresponding to 3 mu M anthraquinone) with excess of anthraquinone having virtually no effect. A strong temperature effect ( with a composite E-A approximate to 120 kJ mol(-1)) is observed for the reductive dissolution in the presence of anthraquinone. The molar ratio and temperature effects are both consistent with the heterogeneous nature of the anthraquinone catalysis in the aqueous reaction mixture.

Amino acid pairing preferences in parallel beta-sheets in proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel beta-sheets. The main chain hydrogen bonding pattern in parallel beta-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favorability of a pair and that of its reverse pair, e.g. Asn(HB)-Thr(nHB)versus Thr(HB)-Asn(nHB). Significantly (p < or = 0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, Asn(HB)-Thr(nHB) and Arg(HB)-Thr(nHB) were favoured pairs, where the residues adopted favoured chi1 rotamer positions that allowed side-chain interactions to occur. In contrast, Thr(HB)-Asn(nHB) and Thr(HB)-Arg(nHB) were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable chi1 conformations. The favourability of hydrophobic pairs e.g. Ile(HB)-Ile(nHB), Val(HB)-Val(nHB) and Leu(HB)-Ile(nHB) was explained by the residues adopting their most preferred chi1 and chi2 conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The Arg(HB)-Asp(nHB) interaction was an exception to this trend and its favorability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available (http://www.rubic.rdg.ac.uk/betapairprefsparallel/).

Amino acid pairing preferences in parallel beta-sheets in proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel beta-sheets. The main chain hydrogen bonding pattern in parallel beta-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favourability of a pair and that of its reverse pair, e.g. Asn(HB)-Thr(nHB) versus Thr(HB)-Asn(nHB). Significantly (p <= 0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, Asn(HB)-Thr(nHB) and Arg(HB)-Thr(nHB) were favoured pairs, where the residues adopted favoured chi(1) rotamer positions that allowed side-chain interactions to occur. In contrast, Thr(HB)-Asn(nHB) and Thr(HB)-Arg(nHB) were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable chi(1) conformations. The favourability of hydrophobic pairs e.g. Ile(HB)-Ile(nHB), Val(HB)-Val(nHB) and Leu(HB)-Ile(nHB) was explained by the residues adopting their most preferred chi(1) and chi(2) conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The Arg(HB)-Asp(nHB) interaction was an exception to this trend and its favourability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available (http:// www.rubic.rdg.ac.uk/betapairprefsparallel/). (c) 2005 Elsevier Ltd. All rights reserved.

A suite of parallel vectors for baculovirus expression

The expression of proteins using recombinant baculoviruses is a mature and widely used technology. However, some aspects of the technology continue to detract from high throughput use and the basis of the final observed expression level is poorly understood. Here, we describe the design and use of a set of vectors developed around a unified cloning strategy that allow parallel expression of target proteins in the baculovirus system as N-terminal or C-terminal fusions. Using several protein kinases as tests we found that amino-terminal fusion to maltose binding protein rescued expression of the poorly expressed human kinase Cot but had only a marginal effect on expression of a well-expressed kinase IKK-2. In addition, MBP fusion proteins were found to be secreted from the expressing cell. Use of a carboxyl-terminal GFP tagging vector showed that fluorescence measurement paralleled expression level and was a convenient readout in the context of insect cell expression, an observation that was further supported with additional non-kinase targets. The expression of the target proteins using the same vectors in vitro showed that differences in expression level were wholly dependent on the environment of the expressing cell and an investigation of the time course of expression showed it could affect substantially the observed expression level for poorly but not well-expressed proteins. Our vector suite approach shows that rapid expression survey can be achieved within the baculovirus system and in addition, goes some way to identifying the underlying basis of the expression level obtained. (c) 2006 Elsevier Inc. All rights reserved.