Integrability and exact spectrum of a pairing model for nucleons

A pairing model for nucleons, introduced by Richardson in 1966, which describes proton-neutron pairing as well as proton-proton and neutron-neutron pairing, is re-examined in the context of the quantum inverse scattering method. Specifically, this shows that the model is integrable by enabling the explicit construction of the conserved operators. We determine the eigenvalues of these operators in terms of the Bethe ansatz, which in turn leads to an expression for the energy eigenvalues of the Hamiltonian.

A real-time PCR assay for the detection of Neisseria gonorrhoeae by LightCycler

The detection of Neisseria gonorrhoeae by the polymerase chain reaction (PCR) is now recognized as a sensitive and specific method of diagnosing infection by the organism. In this Study 152 urine specimens were examined for N. gonorrhoeae by a real-time PCR method using the LightCycler platform and results were compared to an in-house PCR assay using an ELISA-based detection method. N. gonorrhoeae DNA was detected in 29 (19%) specimens by LightCycler PCR (LC-PCR) and in 31 (20%) specimens by the in house PCR method. The LightCycler assay proved to be specific and 94% sensitive when compared to the in house PCR method. These features combined with the rapid turn-around time for results makes the LC-PCR particularly suitable for the detection of N. gonorrhoeae in a routine clinical laboratory. (C) 2002 Elsevier Science Inc. All rights reserved.

The modelling of froth zone recovery in batch and continuously operated laboratory flotation cells

This paper proposes an integrated methodology for modelling froth zone performance in batch and continuously operated laboratory flotation cells. The methodology is based on a semi-empirical approach which relates the overall flotation rate constant to the froth depth (FD) in the flotation cell; from this relationship, a froth zone recovery (R,) can be extracted. Froth zone recovery, in turn, may be related to the froth retention time (FRT), defined as the ratio of froth volume to the volumetric flow rate of concentrate from the cell. An expansion of this relationship to account for particles recovered both by true flotation and entrainment provides a simple model that may be used to predict the froth performance in continuous tests from the results of laboratory batch experiments. Crown Copyright (C) 2002 Published by Elsevier Science B.V. All rights reserved.

Patterns of gene expression are altered in the frontal and motor cortices of human alcoholics

Alcoholism is a major health problem in Western countries, yet relatively little is known about the mechanisms by which chronic alcohol abuse causes the pathologic changes associated with the disease. It is likely that chronic alcoholism affects a number of signaling cascades and transcription factors, which in turn result in distinct gene expression patterns. These patterns are difficult to detect by traditional experiments measuring a few mRNAs at a time, but are well suited to microarray analyses. We used cDNA microarrays to analyze expression of approximately 10 000 genes in the frontal and motor cortices of three groups of chronic alcoholic and matched control cases. A functional hierarchy was devised for classification of brain genes and the resulting groups were compared based on differential expression. Comparison of gene expression patterns in these brain regions revealed a selective reprogramming of gene expression in distinct functional groups. The most pronounced differences were found in myelin-related genes and genes involved in protein trafficking. Significant changes in the expression of known alcohol-responsive genes, and genes involved in calcium, cAMP, and thyroid signaling pathways were also identified. These results suggest that multiple pathways may be important for neuropathology and altered neuronal function observed in alcoholism.

Assessment of the ability to model proteins with leucine-rich repeats in light of the latest structural information

The three-dimensional structures of leucine-rich repeat (LRR) -containing proteins from five different families were previously predicted based on the crystal structure of the ribonuclease inhibitor. using an approach that combined homology-based modeling, structure-based sequence alignment of LRRs, and several rational assumptions. The structural models have been produced based on very limited sequence similarity, which, in general. cannot yield trustworthy predictions. Recently, the protein structures from three of these five families have been determined. In this report we estimate the quality of the modeling approach by comparing the models with the experimentally determined structures. The comparison suggests that the general architecture, curvature, interior/exterior orientations of side chains. and backbone conformation of the LRR structures can be predicted correctly. On the other hand. the analysis revealed that, in some cases. it is difficult to predict correctly the twist of the overall super-helical structure. Taking into consideration the conclusions from these comparisons, we identified a new family of bacterial LRR proteins and present its structural model. The reliability of the LRR protein modeling suggests that it would be informative to apply similar modeling approaches to other classes of solenoid proteins.

Transpecific microsatellites for hard pines M. Shepherd, M. Cross, T. Maguire, M. Dieters, C. Williams, R. Henry

Microsatellites are difficult to recover from large plant genomes so cross-specific utilisation is an important source of markers. Fifty micro satellites were tested for cross-specific amplification and polymorphism to two New World hard pine species, slash pine (Pinus elliottii var. elliottii) and Caribbean pine (R caribaea var. hondurensis). Twenty-nine (58%) markers amplified in both hard pine species, and 23 of these 29 were polymorphic. Soft pine (subgenus Strobus) microsatellite markers did amplify, but none were polymorphic. Pinus elliottii var. elliottii and R caribaea var. hondurensis showed mutational changes in the flanking regions and the repeat motif that were informative for Pinus spp. phylogenetic relationships. Most allele length variation could be attributed to variability in repeat unit number. There was no evidence for ascertainment bias.

A hedging point strategy - balancing effluent quality, economy and robustness in the control of wastewater treatment plants

An operational space map is an efficient tool to compare a large number of operational strategies to find an optimal choice of setpoints based on a multicriterion. Typically, such a multicriterion includes a weighted sum of cost of operation and effluent quality. Due to the relative high cost of aeration such a definition of optimality result in a relatively high fraction of the effluent total nitrogen in the form of ammonium. Such a strategy may however introduce a risk into operation because a low degree of ammonium removal leads to a low amount of nitrifiers. This in turn leads to a reduced ability to reject event disturbances, such as large variations in the ammonium load, drop in temperature, the presence of toxic/inhibitory compounds in the influent etc. Hedging is a risk minimisation tool, with the aim to "reduce one's risk of loss on a bet or speculation by compensating transactions on the other side" (The Concise Oxford Dictionary (1995)). In wastewater treatment plant operation hedging can be applied by choosing a higher level of ammonium removal to increase the amount of nitrifiers. This is a sensible way to introduce disturbance rejection ability into the multi criterion. In practice, this is done by deciding upon an internal effluent ammonium criterion. In some countries such as Germany, a separate criterion already applies to the level of ammonium in the effluent. However, in most countries the effluent criterion applies to total nitrogen only. In these cases, an internal effluent ammonium criterion should be selected in order to secure proper disturbance rejection ability.

Globalisation and the reconstruction of the literate child

In New Zealand, the turn from the welfare state since 1984 to a global market driven economy in the early mid 1990s has affected the way that primary curriculum documents have been developed and implemented. Those documents, together with teachers’ handbooks, have in turn affected the way that teachers teach. In particular, the construction of literacy and what constitutes literacy teaching in these documents have affected teachers’ work and have also constructed and are reconstructing childhood and the child literate. The way that teachers teach literacy depends on their constructions of children and childhood and that as their views of childhood and children change, so too do their views of the teaching of literacy. Against this background of locating childhood and children in educational and literacy discourses, other discourses of new technologies, cultural diversity, time and space of “new times” are also challenging the construction of literacy, the literate child and childhood.

Shear stress and sediment transport calculations for sheet flow under waves

A simple method is provided for calculating transport rates of not too fine (d(50) greater than or equal to 0.20 mm) sand under sheet flow conditions. The method consists of a Meyer-Peter-type transport formula operating on a time-varying Shields parameter, which accounts for both acceleration-asymmetry and boundary layer streaming. While velocity moment formulae, e.g.., = Constant x calibrated against U-tube measurements, fail spectacularly under some real waves (Ribberink, J.S., Dohmen-Janssen, C.M., Hanes, D.M., McLean, S.R., Vincent, C., 2000. Near-bed sand transport mechanisms under waves. Proc. 27th Int. Conf. Coastal Engineering, Sydney, ASCE, New York, pp. 3263-3276, Fig. 12), the new method predicts the real wave observations equally well. The reason that the velocity moment formulae fail under these waves is partly the presence of boundary layer streaming and partly the saw-tooth asymmetry, i.e., the front of the waves being steeper than the back. Waves with saw-tooth asymmetry may generate a net landward sediment transport even if = 0, because of the more abrupt acceleration under the steep front. More abrupt accelerations are associated with thinner boundary layers and greater pressure gradients for a given velocity magnitude. The two real wave effects are incorporated in a model of the form Q(s)(t) = Q(s)[theta(t)] rather than Q(S)(t) = Q(S)[u(infinity)(t)], i.e., by expressing the transport rate in terms of an instantaneous Shields parameter rather than in terms of the free stream velocity, and accounting for both streaming and accelerations in the 0(t) calculations. The instantaneous friction velocities u(*)(t) and subsequently theta(t) are calculated as follows. Firstly, a linear filter incorporating the grain roughness friction factor f(2.5) and a phase angle phi(tau) is applied to u(infinity)(t). This delivers u(*)(t) which is used to calculate an instantaneous grain roughness Shields parameter theta(2.5)(t). Secondly, a constant bed shear stress is added which corresponds to the streaming related bed shear stress -rho ($) over bar((u) over tilde(w) over tilde)(infinity) . The method can be applied to any u(infinity)(t) time series, but further experimental validation is recommended before application to conditions that differ strongly from the ones considered below. The method is not recommended for rippled beds or for sheet flow with typical prototype wave periods and d(50) < 0.20 turn. In such scenarios, time lags related to vertical sediment movement become important, and these are not considered by the present model. (C) 2002 Elsevier Science B.V. All rights reserved.

Boundary-layer transition measurements in hypervelocity flows in a shock tunnel

Experiments to investigate the transition process in hypervelocity boundary layers were performed in the T4 free-piston shock tunnel. An array of thin-film heat-transfer gauges was used to detect the location and extent of the transitional region on a 1500 mm long x 120 turn wide flat plate, which formed one of the walls of a duct. The experiments were performed in a Mach 6 flow of air with 6- and 12-MJ/kg nozzle-supply enthalpies at unit Reynolds numbers ranging from 1.6 x 10(6) to 4.9 x 10(6) m(-1). The results show that the characteristics typical of transition taking place through the initiation, growth, and merger of turbulent spots are evident in the heat-transfer signals. A 2-mm-high excrescence located 440 turn from the leading edge was found to be capable of generating a turbulent wedge within an otherwise laminar boundary layer at a unit Reynolds number of 2.6 x 10(6) m(-1) at the 6-MJ/kg condition. A tripping strip, located 100 mm from the leading edge and consisting of a line 37 teeth of 2 rum height equally spaced and spanning the test surface, was also found to be capable of advancing the transition location at the same condition and at the higher enthalpy condition.

PrrC from Rhodobacter sphaeroides, a homologue of eukaryotic Sco proteins, is a copper-binding protein and may have a thiol-disulfide oxidoreductase activity

PrrC from Rhodobacter sphaeroides provides the signal input to a two-component signal transduction system that senses changes in oxygen tension and regulates expression of genes involved in photosynthesis (Eraso, J.M. and Kaplan, S. (2000) Biochemistry, 39, 2052-2062; Oh, J.-I. and Kaplan, S. (2000) EMBO J. 19, 42374247). It is also a homologue of eukaryotic Sco proteins and each has a C-x-x-x-C-P sequence. In mitochondrial Sco proteins these cysteines appear to be essential for the biogenesis Of the Cu-A centre of respiratory cytochrome oxidase. Overexpression and purification of a water-soluble and monomeric form of PrrC has provided sufficient material for a chemical and spectroscopic study of the properties of the four cysteine residues of PrrC, and its ability to bind divalent cations, including copper. PrrC expressed in the cytoplasm of Escherichia coli binds Ni2+ tightly and the data are consistent with a mononuclear metal site. Following removal of Ni2+ and formation of renatured metal-free rPrrC (apo-PrrC), Cu2+ could be loaded into the reduced form of PrrC to generate a protein with a distinctive UV-visible spectrum, having absorbance with a lambda(max) of 360 nm. The copper:PrrC ratio is consistent with the presence of a mononuclear metal centre. The cysteines of metal-free PrrC oxidise in the presence of air to form two intramolecular disulfide bonds, with one pair being extremely reactive. The cysteine thiols with extreme O-2 sensitivity are involved in copper binding in reduced PrrC since the same copper-loaded protein could not be generated using oxidised PrrC. Thus, it appears that PrrC, and probably Sco proteins in general, could have both a thiol-disulfide oxidoreductase function and a copper-binding role. (C) 2002 Published by Elsevier Science B.V. on behalf of the Federation of European Biochemical Societies.

Phase variable restriction-modification systems in Moraxella catarrhalis

A repetitive DNA motif was used as a marker to identify novel genes in the mucosal pathogen Moraxella catarrhalis. There is a high prevalence of such repetitive motifs in virulence genes that display phase variable expression. Two repeat containing loci were identified using a digoxigenin-labelled 5'-(CAAC)(6)-3' oligonucleotide probe. The repeats are located in the methylase components of two distinct type III restriction-modification (R-M) systems. We suggest that the phase variable nature of these R-M systems indicates that they have an important role in the biology of M. catarrhalis. (C) 2002 Published by Elsevier Science B.V. on behalf of the Federation of European Microbiological Societies.

Copper transfer from the Cu(I) chaperone, CopZ, to the repressor, Zn(II)CopY: Metal coordination environments and protein interactions

Extracellular copper regulates the DNA binding activity of the CopY repressor of Enterococcus hirae and thereby controls expression of the copper homeostatic genes encoded by the cop operon. CopY has a CxCxxxxCxC metal binding motif. CopZ, a copper chaperone belonging to a family of metallochaperones characterized by a MxCxxC metal binding motif, transfers copper to CopY. The copper binding stoichiometries of CopZ and CopY were determined by in vitro metal reconstitutions. The stoichiometries were found to be one copper(l) per CopZ and two copper(l) per CopY monomer. X-ray absorption studies suggested a mixture of two- and three-coordinate copper in Cu(1)CopZ, but a purely three-coordinate copper coordination with a Cu-Cu interaction for Cu(1)(2)CopY. The latter coordination is consistent with the formation of a compact binuclear Cu(l)-thiolate core in the CxCxxxxCxC binding motif of CopY. Displacement of zinc, by copper. from CopY was monitored with 2,4-pyridylazoresorcinol. Two copper(l) ions were required to release the single zinc(II) ion bound per CopY monomer. The specificity of copper transfer between CopZ and CopY was dependent on electrostatic interactions. Relative copper binding affinities of the proteins were investigated using the chelator, diethyldithiocarbamic acid (DDC). These data suggest that CopY has a higher affinity for copper than CopZ. However, this affinity difference is not the sole factor in the copper exchange: a charge-based interaction between the two proteins is required for the transfer reaction to proceed. Gain-of-function mutation of a CopZ homologue demonstrated the necessity of four lysine residues on the chaperone for the interaction with CopY. Taken together, these results suggest a mechanism for copper exchange between CopZ and CopY.

A framework for table driven testing of Java classes

With the advent of object-oriented languages and the portability of Java, the development and use of class libraries has become widespread. Effective class reuse depends on class reliability which in turn depends on thorough testing. This paper describes a class testing approach based on modeling each test case with a tuple and then generating large numbers of tuples to thoroughly cover an input space with many interesting combinations of values. The testing approach is supported by the Roast framework for the testing of Java classes. Roast provides automated tuple generation based on boundary values, unit operations that support driver standardization, and test case templates used for code generation. Roast produces thorough, compact test drivers with low development and maintenance cost. The framework and tool support are illustrated on a number of non-trivial classes, including a graphical user interface policy manager. Quantitative results are presented to substantiate the practicality and effectiveness of the approach. Copyright (C) 2002 John Wiley Sons, Ltd.

Scale-up of mixer granulators for effective liquid distribution

There is considerable anecdotal evidence from industry that poor wetting and liquid distribution can lead to broad granule size distributions in mixer granulators. Current scale-up scenarios lead to poor liquid distribution and a wider product size distribution. There are two issues to consider when scaling up: the size and nature of the spray zone and the powder flow patterns as a function of granulator scale. Short, nucleation-only experiments in a 25L PMA Fielder mixer using lactose powder with water and HPC solutions demonstrated the existence of different nucleation regimes depending on the spray flux Psi(a)-from drop-controlled nucleation to caking. In the drop-controlled regime at low Psi(a) values. each drop forms a single nucleus and the nuclei distribution is controlled by the spray droplet size distribution. As Psi(a) increases, the distribution broadens rapidly as the droplets overlap and coalesce in the spray zone. The results are in excellent agreement with previous experiments and confirm that for drop-controlled nucleation. Psi(a) should be less than 0.1. Granulator flow studies showed that there are two powder flow regimes-bumping and roping. The powder flow goes through a transition from bumping to roping as impeller speed is increased. The roping regime gives good bed turn over and stable flow patterns. This regime is recommended for good liquid distribution and nucleation. Powder surface velocities as a function of impeller speed were measured using high-speed video equipment and MetaMorph image analysis software, Powder surface velocities were 0.2 to 1 ms(-1)-an order of magnitude lower than the impeller tip speed. Assuming geometrically similar granulators, impeller speed should be set to maintain constant Froude number during scale-up rather than constant tip speed to ensure operation in the roping regime. (C) 2002 Published by Elsevier Science B.V.