bluuebunny/crossref_metadata_2025 huggingface dataset:
Metal–Chalcogenolate Complexes with Silyl Functionalities: Synthesis and Reaction Chemistry
Authors: DeGroot Marty W. , Corrigan John F.
Published: December 2005

Metal complexes with reactive [ESiR3]− (E = S, Se, Te) or [S(SiMe2)]2− ligands provide a means for the delivery of {MEn}m− units in the formation of heterometallic polynuclear complexes and clusters. These complexes can be reacted with M′ salts to promote M–E–M′ interactions via the elimination of a silane side product. This research report summarizes the recent developments in the synthesis of silylchalcogenolate complexes of the d‐block metals with emphasis directed to those for which reactivity studies for the formation of ternary clusters have been carried out. The effects of varying the groups on the silyl moiety on the stability and reactivity of these precursor molecules are also discussed.
Synthesis and Crystal Structure of Lithium Tetrametaphosphimate Tetrahydrate Li4(PO2NH)4 · 4 H2O
Authors: Römer S. Rebecca , Schnick Wolfgang
Published: December 2005

Single crystals of Li4(PO2NH)4 · 4 H2O were obtained by dissolving LiOH and H4(PO2NH)4 · 2 H2O in water and subsequent precipitation with acetone and ethanol followed by slow evaporation of the solvents. The structure of Li4(PO2NH)4 · 4 H2O was solved by single‐crystal X‐ray methods ($P{\bar 1}$ (No. 2), a = 489.2(2), b = 853.2(2), c = 880.5(2) pm, α = 101.71(3), β = 102.39(3), γ = 94.88(3)°, Z = 1). The structure is composed of LiO4 tetrahedra and (PO2NH)44− ions. The P4N4 rings of the anions exhibit a slightly distorted chair–1 conformation, which is supported by IR data and has been described by torsion angles, displacement asymmetry parameters and puckering parameters. Via Li+ ions and hydrogen bonds, the tetrametaphosphimate anions are connected forming a three‐dimensional network.
Polymorphism of [Zn(2,2′‐bipy)(H2PO4)2]2
Authors: Natarajan Srinivasan , Prots Yurii , Ewald Bastian , Niewa Rainer , Kniep Rüdiger
Published: December 2005

Two polymorphs of a zero‐dimensional (molecular) zinc phosphate with the formula [Zn(2,2′‐bipy)(H2PO4)2]2 have been synthesized by a mild hydrothermal route and their crystal structures were determined by single crystal X‐ray diffraction (triclinic, space group $P{\bar 1}$ (No. 2), Z = 2, α‐form: a = 8.664(1), b = 8.849(2), c = 10.113(2) Å, α = 97.37(2)°, β = 100.54(2)°, γ = 100.98(2)°, V = 737.5(3) Å3; β‐form: a = 7.5446(15), b = 10.450(2), c = 10.750(2) Å, α = 67.32(3)°, β = 81.67(3)°, γ = 69.29(3)°, V = 731.4(3) Å3). Both structures consist of distorted trigonal‐bipyramidal ZnO3N2 units condensed with PO2(OH)2 tetrahedra through common vertices giving rise to dimers [Zn(2,2′‐bipy)(H2PO4)2]2. The structures are stabilized by extensive inter‐ and intramolecular hydrogen bond interactions. Both modifications display subtle differences in their packing originating from the hydrogen bond interactions as well as π…π interactions between the organic ligands.
Drei Alkalimetall‐Erbium‐Thiophosphate: Von der Schichtstruktur bei KEr[P2S7] zur dreidimensionalen Vernetzung in NaEr[P2S6] und Cs3Er5[PS4]6
Authors: Komm Theresa , Schleid Thomas
Published: December 2005

Three Alkali‐Metal Erbium Thiophosphates: From the Layered Structure of KEr[P2S7] to the Three‐Dimensional Cross‐Linkage in NaEr[P2S6] and Cs3Er5[PS4]6

The three alkali‐metal erbium thiophosphates NaEr[P2S6], KEr[P2S7], and Cs3Er5[PS4] show a small selection of the broad variety of thiophosphate units: from ortho‐thiophosphate [PS4]3− and pyro‐thiophosphate [S3P–S–PS3]4− with phosphorus in the oxidation state +V to the [S3P–PS3]3− anion with a phosphorus‐phosphorus bond (d(P–P) = 221 pm) and tetravalent phosphorus. In spite of all differences, a whole string of structural communities can be shown, in particular for coordination and three‐dimensional linkage as well as for the phosphorus‐sulfur distances (d(P–S) = 200 – 213 pm). So all three compounds exhibit eightfold coordinated Er3+ cations and comparably high‐coordinated alkali‐metal cations (CN(Na+) = 8, CN(K+) = 9+1, and CN(Cs+) ≈ 10). NaEr[P2S6] crystallizes triclinically (${\rm P}{\bar 1}$; a = 685.72(5), b = 707.86(5), c = 910.98(7) pm, α = 87.423(4), β = 87.635(4), γ = 88.157(4)°; Z = 2) in the shape of rods, as well as monoclinic KEr[P2S7] (P21/c; a = 950.48(7), b = 1223.06(9), c = 894.21(6) pm, β = 90.132(4)°; Z = 4). The crystal structure of Cs3Er5[PS4] can also be described monoclinically (C2/c; a = 1597.74(11), b = 1295.03(9), c = 2065.26(15) pm, β = 103.278(4)°; Z = 4), but it emerges as irregular bricks. All crystals show the common pale pink colour typical for transparent erbium(III) compounds.
HgCl2(Caf): Co‐crystallization of Mercuric Chloride and Caffeine
Authors: Meyer Gerd , Nolte Matthias , Mudring Anja‐Verena
Published: December 2005

Colourless single crystals of the co‐crystallizate of mercuric chloride and caffeine, HgCl2(Caf), were obtained from an ethanolic solution of mercuric chloride, HgCl2, and caffeine (Caf) and recrystallized from hot water. The crystal structure (monoclinic, P21, Z = 2, a = 398.36(8), b = 1964.5(4), c = 809.6(2) pm, β = 99.24(3)°, Z = 2, R1 = 0.0584 for 1430 Fo > 4σ(Fo)) contains helical chains (parallel to the 21 screw axis) of almost unaffected HgCl2 molecules and caffeine molecules which are very weakly bound to one keto‐oxygen atom (O4) of one and N9 of a second caffeine molecule at distances of 282 and 281 pm, respectively. To the contrary, theoretical calculations show that the molecule HgCl2(Caf)2 is stable (in the gas phase at T = 0 K) with surprisingly strong bonding as indicated by the “tetrahedrization” of the molecule.
Die Reaktion von SePh2 mit N‐Chlorsuccinimid. Kristallstrukturen von [SeCl2Ph2] und [SeCl2Ph2(Succinimid)2]
Authors: Neumüller Bernhard , Dehnicke Kurt
Published: December 2005

Reaction of SePh2 with N‐Chlorosuccinimide. Crystal Structures of [SeCl2Ph2] and [SeCl2Ph2(succinimide)2]

SePh2 reacts with N‐chlorosuccinimide in acetonitrile solution to give [SeCl2Ph2] (1) and [SeCl2Ph2(succinimide)2] (2) as colourless crystals, which can be separated by fractional crystallization. According to X‐ray single crystal determinations both compounds contain [SeCl2Ph2] molecules with ψ‐trigonal‐bipyramidal coordination at the selenium atom, the chloro ligands being in apical positions. In 2 the dimeric unit (HNC4O2H4)2 is linked with its [SeCl2Ph2] unit via a weak C–H···O hydrogen bond.

1: Space group Pbcn, Z = 4, lattice dimensions at 193 K: a = 1350.6(1), b = 573.3(1), c = 1503.3(2) pm, R1 = 0.0326.

2: Space group I2/a, Z = 4, lattice dimensions at 193 K: a = 1363.9(1), b = 557.7(1), c = 2781.3(1) pm, β = 101.01(1)°, R1 = 0.0286.
‘Now and England’: Britten's Gloriana and the ‘New Elizabethans’
Authors: WIEBE HEATHER
Published: December 2005

During the Coronation of Elizabeth II in 1953, Elizabethan culture was insistently invoked as a source of solidarity and renewal. Through the trope of ‘New Elizabethanism’ members of the press and public reimagined Britain's future on the foundations of a most productive period in its past. This article traces forms of ‘New Elizabethanism’ and other complex negotiations between modernity and the past in the music presented for the Coronation. Its central focus is the debate surrounding Britten's Gloriana, an opera based on the life of Elizabeth I, commissioned for the Coronation Gala by the Arts Council. The opera and the debate it inspired reveal both the stakes placed in the Elizabethan period and a marked anxiety about the status of the past in the remaking of the present – an anxiety that arguably plagued the Coronation as a whole.
Hidden Places: Hyper-realism in Björk’s Vespertine and Dancer in the Dark
Authors: GRIMLEY DANIEL M.
Published: December 2005

Björk’s collaboration with the director Lars von Trier on the film Dancer in the Dark was marked by well-publicized personal and aesthetic differences. Their work nevertheless shares an intense preoccupation with the nature and quality of sound. Björk’s soundtrack systematically explores the boundaries between music and noise, and the title of von Trier’s film itself presupposes a heightened attention to aural detail. This paper proposes a theoretical context for understanding Björk’s music in the light of her work with von Trier. Whereas Björk’s soundtrack responds to the visual and narrative stimuli of von Trier’s film, the use of sound in her album Vespertine thematicizes more familiar Björk subjects: the relationship between music, landscape and the natural world, and Björk’s own (constructed) sense of Nordic musical identity. By placing Vespertine alongside Björk’s music for Dancer in the Dark, the sense of ‘hyperreality’ that defines both also emerges as a primary characteristic of her work.
The London Sinfonietta 1968–2004: A Perspective
Authors: WRIGHT DAVID C.H.
Published: December 2005

The London Sinfonietta’s reputation as a contemporary music ensemble comes from the continuing commitment by its players and artistic directors to its quality of performance. The ensemble also developed a sense of its musical identity by generating a repertoire of commissioned works. This article looks at some of the ways that the Sinfonietta defined its musical ideology and has functioned as a performance-centred art world in which composers are invited to collaborate but are not there by right. It examines the Sinfonietta’s strategies for audience building, the ensemble’s contribution to the development of London’s concert life since its foundation in 1968, and looks at the ways that it has sought to renew itself in response to the different funding and aesthetic environments it has encountered in its history. The Sinfonietta’s venture into Broadway repertoire is discussed in terms of social identity. The article argues, after Jürgen Habermas and T. W. C. Blanning, that one of the most significant contributions of the Sinfonietta has been its continued commitment to the concert event as a forum for critical engagement and cultural debate.
Parameter sensitivity studies for the ice flow of the Ross Ice Shelf, Antarctica
Authors: Humbert A. , Greve R. , Hutter K.
Published: December 2005

The diagnostic, dynamic/thermodynamic ice shelf model Finite Element Shallow Shelf Approximation Code (FESSACODE) is applied to the Ross Ice Shelf. We simulate the present ice flow which results from the ice thickness distribution, the inflow at the grounding line, and the surface and bottom temperatures and compare results with measured flow velocities. Our reference simulation reproduces the general flow pattern and the magnitudes of the flow velocities reasonably well. The ice flow is found to be very sensitive to the flow enhancement factor, the ice thickness, and the ice temperature but robust against inflow velocities from ice streams, glaciers, and ice rises. The ice rises (Roosevelt Island and Crary Ice Rise) stabilize the ice shelf by significantly decreasing the flow velocities for the entire ice shelf area. The ice shelf is susceptible to global warming in that a 2°C surface warming entails an increase of the flow velocities by a factor 1.25, whereas a 10°C warming leads to an increase by a factor 3.1.
A mechanism for sun‐climate connection
Authors: Hameed Sultan , Lee Jae N.
Published: December 2005

Mechanisms by which small changes in the sun's energy output during the solar cycle can cause changes in weather and climate have been a puzzle and the subject of intense research in recent decades. Here we report that differences in surface circulation conditions during solar maximum and minimum periods are caused by differences in the frequencies with which circulation perturbations in the stratosphere reach the surface. A much greater fraction of stratospheric perturbations penetrate to the surface during solar maximum conditions than during minimum conditions. This difference is more striking when the zonal wind direction in the tropics is from the west: no stratospheric signals reach the surface when equatorial 50 hPa winds are from the west under solar minimum conditions, and over 50 percent reach the surface under solar maximum conditions. It has been previously shown that stratospheric circulation perturbations reaching the surface change weather patterns by imposing atmospheric pressure anomalies characteristic of the Arctic oscillation.
Variability of sea ice cover in the Chukchi Sea (western Arctic Ocean) during the Holocene
Authors: de Vernal Anne , Hillaire‐Marcel Claude , Darby Dennis A.
Published: December 2005

Dinocysts from cores collected in the Chukchi Sea from the shelf edge to the lower slope were used to reconstruct changes in sea surface conditions and sea ice cover using modern analogue techniques. Holocene sequences have been recovered in a down‐slope core (B15: 2135 m, 75°44′N, sedimentation rate of ∼1 cm kyr−1) and in a shelf core (P1: 201 m, 73°41′N, sedimentation rate of ∼22 cm kyr−1). The shelf record spanning about 8000 years suggests high‐frequency centennial oscillations of sea surface conditions and a significant reduction of the sea ice at circa 6000 and 2500 calendar (cal) years B.P. The condensed offshore record (B15) reveals an early postglacial optimum with minimum sea ice cover prior to 12,000 cal years B.P., which corresponds to a terrestrial climate optimum in Bering Sea area. Dinocyst data indicate extensive sea ice cover (>10 months yr−1) from 12,000 to 6000 cal years B.P. followed by a general trend of decreasing sea ice and increasing sea surface salinity conditions, superimposed on large‐amplitude millennial‐scale oscillations. In contrast, δ18O data in mesopelagic foraminifers (Neogloboquadrina pachyderma) and benthic foraminifers (Cibicides wuellerstorfi) reveal maximum subsurface temperature and thus maximum inflow of the North Atlantic water around 8000 cal years B.P., followed by a trend toward cooling of the subsurface to bottom water masses. Sea‐surface to subsurface conditions estimated from dinocysts and δ18O data in foraminifers thus suggest a decoupling between the surface water layer and the intermediate North Atlantic water mass with the existence of a sharp halocline and a reverse thermocline, especially before 6000 years B.P. The overall data and sea ice reconstructions from core B15 are consistent with strong sea ice convergence in the western Arctic during the early Holocene as suggested on the basis of climate model experiments including sea ice dynamics, matching a higher inflow rate of North Atlantic Water.
Prediction of molecular-dynamics simulation results using feedforward neural networks: Reaction of a C2 dimer with an activated diamond (100) surface
Authors: Agrawal Paras M. , Samadh Abdul N. A. , Raff Lionel M. , Hagan Martin T. , Bukkapatnam Satish T. , Komanduri Ranga
Published: December 2005

A new approach involving neural networks combined with molecular dynamics has been used for the determination of reaction probabilities as a function of various input parameters for the reactions associated with the chemical-vapor deposition of carbon dimers on a diamond (100) surface. The data generated by the simulations have been used to train and test neural networks. The probabilities of chemisorption, scattering, and desorption as a function of input parameters, such as rotational energy, translational energy, and direction of the incident velocity vector of the carbon dimer, have been considered. The very good agreement obtained between the predictions of neural networks and those provided by molecular dynamics and the fact that, after training the network, the determination of the interpolated probabilities as a function of various input parameters involves only the evaluation of simple analytical expressions rather than computationally intensive algorithms show that neural networks are extremely powerful tools for interpolating the probabilities and rates of chemical reactions. We also find that a neural network fits the underlying trends in the data rather than the statistical variations present in the molecular-dynamics results. Consequently, neural networks can also provide a computationally convenient means of averaging the statistical variations inherent in molecular-dynamics calculations. In the present case the application of this method is found to reduce the statistical uncertainty in the molecular-dynamics results by about a factor of 3.5.
Solvent-free model for self-assembling fluid bilayer membranes: Stabilization of the fluid phase based on broad attractive tail potentials
Authors: Cooke Ira R. , Deserno Markus
Published: December 2005

We present a simple and highly adaptable method for simulating coarse-grained lipid membranes without explicit solvent. Lipids are represented by one head bead and two tail beads, with the interaction between tails being of key importance in stabilizing the fluid phase. Two such tail-tail potentials were tested, with the important feature in both cases being a variable range of attraction. We examined phase diagrams of this range versus temperature for both functional forms of the tail-tail attraction and found that a certain threshold attractive width was required to stabilize the fluid phase. Within the fluid-phase region we find that material properties such as area per lipid, orientational order, diffusion constant, interleaflet flip-flop rate, and bilayer stiffness all depend strongly and monotonically on the attractive width. For three particular values of the potential width we investigate the transition between gel and fluid phases via heating or cooling and find that this transition is discontinuous with considerable hysteresis. We also investigated the stretching of a bilayer to eventually form a pore and found excellent agreement with recent analytic theory.
Landau damping in space plasmas with generalized (r,q) distribution function
Authors: Qureshi M. N. S. , Shi J. K. , Ma S. Z.
Published: December 2005

Space plasmas possessing non-Maxwellian particle distribution functions with an enhanced high-energy tail and shoulder in the profile of distribution function take an important role to the wave particle interaction. In the present paper Landau damping of electron plasma (Langmuir) waves and ion-acoustic waves in a hot, isotropic, unmagnetized plasma is studied with the generalized (r,q) distribution function. The results show that for the Langmuir oscillations Landau damping becomes severe as the spectral index r or q reduces. However, for the ion-acoustic waves Landau damping is more sensitive to the ion temperature than the spectral indices.
Analysis of a cyclotron maser instability in cylindrical geometry
Authors: Vorgul I. , Cairns R. A. , Bingham R.
Published: December 2005

Cyclotron maser instability is known to be one of the main mechanisms of coherent radio emission in space and laboratory plasmas. This paper investigates a particular case of such an instability induced by a horseshoe- or crescent-shaped electron velocity distribution function, which is produced when an electron beam propagates in a convergent magnetic field, whether it is Earth’s magnetic field or one introduced in a laboratory experiment. The instability is analyzed in cylindrical geometry which is relevant to auroral kilometric radiation and to a laboratory experiment. Exact modeling of TE and TM anisotropic modes for circular electronic beam shows its high growth rate for modes with almost perpendicular propagation.
Ultracold neutral plasma expansion in two dimensions
Authors: Cummings E. A. , Daily J. E. , Durfee D. S. , Bergeson S. D.
Published: December 2005

An isothermal model of ultracold neutral plasma expansion is extended to systems without spherical symmetry. It is used to interpret new fluorescence measurements on ultracold neutral calcium plasmas. For a self-similar expansion, the fluid equations are solved both analytically and numerically. The density and velocity solutions are used to predict fluorescence signals induced by a laser beam weakly focused into the plasma. Despite the simplicity of the model, predicted fluorescence signals reproduce major features of the experimental data.
Turbulence spreading, anomalous transport, and pinch effect
Authors: Naulin V. , Nielsen A. H. , Rasmussen J. Juul
Published: December 2005

A paradigmatic model describing transport and turbulence spreading as coupled processes is proposed, trying to unify the approaches of penetrative overshoot and overshoot. As a natural consequence asymmetric radial spreading of the turbulence, up-gradient transport of the particle density, and front propagation are observed. The model accounts for the interaction between the microscale of the turbulence and the meso-, respectively, system scale on which profile modifications occur. Comparison with direct numerical simulations of two-dimensional interchange turbulence shows qualitatively good agreement with the proposed transport model. Key transport features are reproduced even in the presence of coherent bloblike structures. Features of density pulse dynamics are also investigated.
An Ab Initio Pseudopotential Study of MnPo (M = Cu, Ag, Au; n = 1, 2) Systems
Authors: Surong Qi-Mu , Zhao Yongfang , Jing Xiaogong , Liu Fengli , Li Xinying , Su Wenhui
Published: December 2005

The small coinage-metal polonium compounds MPo and M2Po, (M = Cu, Ag, Au) are studied at Hartree–Fock (HF), second-order Møller–Plesset perturbation theory (MP2), and coupled cluster method CCSD(T) levels using relativistic and non-relativistic pseudopotentials. The calculated geometries indicate that the M2Po (M = Cu, Ag, Au) systems have bent structures of ~64° angles. Electron correlation corrections to the bond length M–Po are extremely small, but to the bond angle M–Po–M are significant; in general, it was reduced from 86° to 64°. Relativistic effects on bond angle are small, but on bond length are distinct. Both electron correlation effects and relativistic effects are essential to determine the geometry and relative stability of the systems. It can be predicted that Au2Po is relatively stable compared with Ag2Po.
Synthesis of New β-Amino Acids via 5-Oxazolidinones and the Arndt - Eistert Procedure
Authors: Hughes Andrew B. , Sleebs Brad E.
Published: December 2005

N-Methyl β-amino acids are potentially useful amino acid derivatives for incorporation in lead peptide therapeutics. The syntheses of five such compounds are presented. Their synthesis via 6-oxazinanones was low yielding. Alternatively, reductive cleavage of a 5-oxazolidinone gave the N-methyl α-amino acid, which was then homologated via an Arndt–Eistert procedure in high yield to give the N-methyl β-amino acid.
Template-Directed Assembly of a Macrocyclic Porphyrin Tetramer Using Olefin Metathesis
Authors: Bakker Jacinta M. , Langford Steven J. , Latter Melissa J. , Lee Katrina A. , Woodward Clint P.
Published: December 2005

A macrocyclic porphyrin tetramer was prepared in 52% yield by olefin metathesis employing a 5,10,15,20-tetrapyridylporphyrin template.
Importance of surface charge characteristics when selecting soils for wastewater re-use
Authors: Phillips I. R. , Sheehan K. J.
Published: December 2005

Land application represents a viable option in the management of wastewater such as landfill leachate. The surface charge and ion adsorption characteristics of the receiving soil will play an important role in the success of this disposal strategy. The surface charge characteristics of 6 soils with contrasting chemical and physical properties were studied using charge balance principles. The point of zero net proton charge density, point of zero salt effect and point of zero net charge, and the concentrations of permanent and variable charge as a function of pH, were determined for each soil. The presence and magnitude of permanent negative surface charge was largely dependant on clay mineralogy. All soils displayed increasing negative surface charge density with increasing pH. The magnitude of increase for any particular soil was dependent on the type and amount of colloids exhibiting variable surface charge. The increased negative surface charge was attributed to the ionisation of functional groups on organic matter, hydrous Fe and Al oxides, and edge sites of kaolinite and smectite. The variation in surface charge with pH conformed to charge balance principles for soils containing a mixture of both permanent and variable surface charge, but not for soils containing predominantly permanent surface charge. Proton-consuming processes (e.g. adsorption on permanent charge sites, neutralisation of inherent alkalinity) influenced the overall charge balance, particularly for soils with predominantly permanent surface charge. Ammonium adsorption from landfill leachate was measured as a function of pH for each soil type. Increased negative surface charge resulted in increased ammonium adsorption, and for most soils the preference of the newly created adsorption sites for ammonium remained relatively constant. Since many soils contain a mixture of colloids with permanent and variable surface charge, these charge characteristics and their effect on individual soil properties, contaminant availability, and contaminant mobility must be taken into account when evaluating the suitability of land for wastewater re-use.
Chemical properties of two soils irrigated with thermo-mechanical pulp mill effluent
Authors: Wang Hailong , Magesan G. N. , Kimberley Mark O. , Gielen Gerty J. H. P. , Pearce Stephen H.
Published: December 2005

The effect of land application of thermo-mechanical pulp (TMP) mill effluent on soil chemical properties was examined using barrel lysimeters. Twelve lysimeters, 500 mm in diameter and 800 mm high, containing either a volcanic soil (Udivitrand) or a pallic soil (Haplustalfs), were collected from 2 plantation forest sites. A TMP mill effluent containing high concentrations of total organic C (1136 mg/L) was irrigated at 30 mm/week over a period of 16 months. Soil sample analysis indicated that build up of soil organic C was negligible despite large additions of organic C (equivalent to 19 t/ha) through irrigation with TMP mill effluent. Mass balance calculation implied that microbial degradation or mineralisation of the organic compounds might be the main mechanism involved in the high renovation rates. Irrigation with TMP mill effluent significantly increased soil pH, concentrations of soil total S, available P, and exchangeable K and Na, but it had no significant effect on concentrations of soil total N, and exchangeable Ca and Mg. The results from this study indicate that TMP mill effluent irrigated at a loading rate not greater than 30 mm/week would cause little detrimental effect on the quality of soils at these 2 plantation forest sites.
The viral polymerase mediates adaptation of an avian influenza virus to a mammalian host
Authors: Gabriel G. , Dauber B. , Wolff T. , Planz O. , Klenk H.-D. , Stech J.
Published: December 2005

Mammalian influenza viruses are descendants of avian strains that crossed the species barrier and underwent further adaptation. Since 1997 in southeast Asia, H5N1 highly pathogenic avian influenza viruses have been causing severe, even fatal disease in humans. Although no lineages of this subtype have been established until now, such repeated events may initiate a new pandemic. As a model of species transmission, we used the highly pathogenic avian influenza virus
SC35
(H7N7), which is low-pathogenic for mice, and its lethal mouse-adapted descendant
SC35M
. Specific mutations in
SC35M
polymerase considerably increase its activity in mammalian cells, correlating with high virulence in mice. Some of these mutations are prevalent in chicken and mammalian isolates, especially in the highly pathogenic H5N1 viruses from southeast Asia. These activity-enhancing mutations of the viral polymerase complex demonstrate convergent evolution in nature and, therefore, may be a prerequisite for adaptation to a new host paving the way for new pandemic viruses.
Topology of biological networks and reliability of information processing
Authors: Klemm Konstantin , Bornholdt Stefan
Published: December 2005

Survival of living cells and organisms is largely based on highly reliable function of their regulatory networks. However, the elements of biological networks, e.g., regulatory genes in genetic networks or neurons in the nervous system, are far from being reliable dynamical elements. How can networks of unreliable elements perform reliably? We here address this question in networks of autonomous noisy elements with fluctuating timing and study the conditions for an overall system behavior being reproducible in the presence of such noise. We find a clear distinction between reliable and unreliable dynamical attractors. In the reliable case, synchrony is sustained in the network, whereas in the unreliable scenario, fluctuating timing of single elements can gradually desynchronize the system, leading to nonreproducible behavior. The likelihood of reliable dynamical attractors strongly depends on the underlying topology of a network. Comparing with the observed architectures of gene regulation networks, we find that those 3-node subgraphs that allow for reliable dynamics are also those that are more abundant in nature, suggesting that specific topologies of regulatory networks may provide a selective advantage in evolution through their resistance against noise.
Social relationships, sleep quality, and interleukin-6 in aging women
Authors: Friedman Elliot M. , Hayney Mary S. , Love Gayle D. , Urry Heather L. , Rosenkranz Melissa A. , Davidson Richard J. , Singer Burton H. , Ryff Carol D.
Published: December 2005

This study examined the interplay of social engagement, sleep quality, and plasma levels of interleukin-6 (IL-6) in a sample of aging women (
n
= 74, aged 61-90,
M
age = 73.4). Social engagement was assessed by questionnaire, sleep was assessed by using the NightCap in-home sleep monitoring system and the Pittsburgh Sleep Quality Index, and blood samples were obtained for analysis of plasma levels of IL-6. Regarding subjective assessment, poorer sleep (higher scores on the Pittsburgh Sleep Quality Index) was associated with lower positive social relations scores. Multivariate regression analyses showed that lower levels of plasma IL-6 were predicted by greater sleep efficiency (
P
< 0.001), measured objectively and by more positive social relations (
P
< 0.05). A significant interaction showed that women with the highest IL-6 levels were those with both poor sleep efficiency and poor social relations (
P
< 0.05). However, those with low sleep efficiency but compensating good relationships as well as women with poor relationships but compensating high sleep efficiency had IL-6 levels comparable to those with the protective influences of both good social ties and good sleep.
Gene sequence signatures revealed by mining the UniGene affiliation network
Authors: Zhang Jiexin , Zhang Li , Coombes Kevin R.
Published: December 2005

Background: In the post-genomic era, developing tools to decode biological information from genomic sequences is important. Inspired by affiliation network theory, we investigated gene sequences of two kinds of UniGene clusters (UCs): narrowly expressed transcripts (NETs), whose expression is confined to a few tissues; and prevalently expressed transcripts (PETs) that are expressed in many tissues.

Results: We explored the human and the mouse UniGene databases to compare NETs and PETs from different perspectives. We found that NETs were associated with smaller cluster size, shorter sequence length, a lower likelihood of having LocusLink annotations, and lower and more sporadic levels of expression. Significantly, the dinucleotide frequencies of NETs are similar to those of intergenic sequences in the genome, and they differ from those of PETs. We used these differences in dinucleotide frequencies to develop a discriminant analysis model to distinguish PETs from intergenic sequences.

Conclusions: Our results show that most NETs resemble intergenic sequences, casting doubts on the quality of such UniGene clusters. However, we also noted that a fraction of NETs resemble PETs in terms of dinucleotide frequencies and other features. Such NETs may have fewer quality problems. This work may be helpful in the studies of non-coding RNAs and in the validation of gene sequence databases.

Availability:  

Contact:  kcoombes@mdanderson.org

Supplementary information:
An extensible automated protein annotation tool: standardizing input and output using validated XML
Authors: Deevi S. Vishnu V. , Martin Andrew C. R.
Published: December 2005

Motivation: There is a frequent need to apply a large range of local or remote prediction and annotation tools to one or more sequences. We have created a tool able to dispatch one or more sequences to assorted services by defining a consistent XML format for data and annotations.

Results: By analyzing annotation tools, we have determined that annotations can be described using one or more of the six forms of data: numeric or textual annotation of residues, domains (residue ranges) or whole sequences. With this in mind, XML DTDs have been designed to store the input and output of any server. Plug-in wrappers to a number of services have been written which are called from a master script. The resulting APATML is then formatted for display in HTML. Alternatively further tools may be written to perform post-analysis.

Availability: The ‘Automated Protein Annotation Tool’ (APAT) can be downloaded from . As well as source code and documentation, a demonstration web server is provided which uses APAT to perform a number of annotations of a sequence.

Contact:  andrew@bioinf.org.uk; martin@biochem.ucl.ac.uk
Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae
Authors: Guo Xiang , Tatsuoka Kay , Liu Rongxiang
Published: December 2005

Motivation: In eukaryotic genomes, histone acetylation and thereafter departure from the chromatin are essential for gene transcription initiation. Because gene transcription is tightly regulated by transcription factors, there are some speculations on the cooperation of histone acetylation and transcription factor binding. However, systematic statistical analyses of this relationship on a genomic scale have not been reported.

Results: We apply several statistical methods to explore this relationship on two recent genomic datasets: acetylation levels on 11 histone lysines and binding activities of 203 transcription factors, both in promoter regions across the yeast genome. By canonical correlation analysis, we find that a histone acetylation pattern is correlated with a certain profile of transcription factor binding in the genome. Furthermore, after clustering the genes by their acetylation levels on the 11 histone lysines, the genes within clusters show distinct transcription factor binding profiles, as discovered by principle component analysis. Even after applying fairly stringent statistical measurement, most of these clusters have transcription factors with binding activities significantly deviated from the overall genome. We conclude that in the yeast genome, there is a strong correlation between histone acetylation and transcription factor binding in the promoter regions.

Contact:  ron.2.liu@gsk.com

Supplementary information: Supplementary Data are available at Bioinformatics online.
Marginal Welfare Costs of Taxation with Human and Physical Capital
Authors: Allgood Sam , Snow Arthur
Published: December 2005

We develop a perfect foresight, overlapping generations model with intragenerational inequality and endogenous human and physical capital investment, and we calculate welfare costs for marginal reforms of taxation and public spending. Welfare costs are uniformly lower than in the equivalent static model where human and physical capital are fixed. Most of the upward bias in static estimates arises from fixed human capital because welfare cost is predominantly tax leakage from lower effective labor supply, but reallocating time between education and labor can leave effective labor supply unchanged. Hence, adjustments in human capital have an important mitigating influence on marginal welfare costs. (JEL D91, H20, H31, H41, J22, J24)
Garlic blocks quorum sensing and promotes rapid clearing of pulmonary Pseudomonas aeruginosa infections
Authors: Bjarnsholt Thomas , Jensen Peter Østrup , Rasmussen Thomas B. , Christophersen Lars , Calum Henrik , Hentzer Morten , Hougen Hans-Petter , Rygaard Jørgen , Moser Claus , Eberl Leo , Høiby Niels , Givskov Michael
Published: December 2005

The opportunistic human pathogen Pseudomonas aeruginosa is the predominant micro-organism of chronic lung infections in cystic fibrosis patients. P. aeruginosa colonizes the lungs by forming biofilm microcolonies throughout the lung. Quorum sensing (QS) renders the biofilm bacteria highly tolerant to otherwise lethal doses of antibiotics, and protects against the bactericidal activity of polymorphonuclear leukocytes (PMNs). It has been previously demonstrated that QS is inhibited by garlic extract. In this study, the synergistic effects of garlic and tobramycin, and PMNs activities have been evaluated. P. aeruginosa was grown in vitro in continuous-culture once-through flow chambers with and without garlic extract. The garlic-treated biofilms were susceptible to both tobramycin and PMN grazing. Furthermore, the PMNs showed an increase in respiratory burst activation, when incubated with the garlic-treated biofilm. Garlic extract was administered as treatment for a mouse pulmonary infection model. Mice were treated with garlic extract or placebo for 7 days, with the initial 2 days being prophylactic before P. aeruginosa was instilled in the left lung of the mice. Bacteriology, mortality, histopathology and cytokine production were used as indicators. The garlic treatment initially provoked a higher degree of inflammation, and significantly improved clearing of the infecting bacteria. The results indicate that a QS-inhibitory extract of garlic renders P. aeruginosa sensitive to tobramycin, respiratory burst and phagocytosis by PMNs, as well as leading to an improved outcome of pulmonary infections.
Biofilm-control strategies based on enzymic disruption of the extracellular polymeric substance matrix – a modelling study
Authors: Xavier Joao B. , Picioreanu Cristian , Rani Suriani Abdul , van Loosdrecht Mark C. M. , Stewart Philip S.
Published: December 2005

A kinetic model is proposed to assess the feasibility of strategies for the removal of biofilms by using substances that induce detachment by affecting the cohesiveness of the matrix of extracellular polymeric substances (EPSs). The model uses a two-state description of the EPS (natural EPS and compromised EPS) to provide a unified representation of diverse mechanisms of action of detachment-promoting agents (DPAs), which include enzymes that degrade the EPS and other agents described in the literature. A biofilm-cohesiveness factor describes local increases in detachment rates resultant from losses in cohesive strength. The kinetic model was implemented in an individual-based biofilm-modelling framework, including detachment rates dependent on local cohesiveness. The efficacy of treatments with DPAs was assessed by three-dimensional model simulations. Changes in treatment efficacy were evaluated quantitatively by using a Thiele modulus, which quantifies the relationship between diffusion of the DPA through the biofilm matrix and DPA decay rate, and a Damköhler number relating the rate of EPS reaction with a DPA and the rate of EPS production by the micro-organisms in the biofilm. This study demonstrates the feasibility and limits of implementing biofilm-control strategies based on attacking the EPS.
Overall control of nitrogen metabolism in Lactococcus lactis by CodY, and possible models for CodY regulation in Firmicutes
Authors: Guédon Eric , Sperandio Brice , Pons Nicolas , Ehrlich Stanislav Dusko , Renault Pierre
Published: December 2005

CodY, a pleiotropic transcriptional regulator conserved in low G+C species of Gram-positive bacteria, was previously described to be the central regulator of proteolysis in Lactococcus lactis. In this study, over 100 potential CodY targets were identified by DNA-microarray analysis. Complementary transcriptional analysis experiments were carried out to validate the newly defined CodY regulon. Moreover, the direct role of CodY in the regulation of several target genes was demonstrated by gel retardation experiments. Interestingly, 45 % of CodY-dependent genes encode enzymes involved in amino acid biosynthesis pathways, while most of the other genes are involved in functions related to nitrogen supply. CodY of L. lactis represents the first example of a regulator in Gram-positive bacteria that globally controls amino acid biosynthesis. This global control leads to growth inhibition in several amino-acid-limited media containing an excess of isoleucine. A conserved 15 nt palindromic sequence (AATTTTCNGAAAATT), the so-called CodY-box, located in the vicinity of the −35 box of target promoter regions was identified. Relevance of the CodY-box as an operator for CodY was demonstrated by base substitutions in gel retardation experiments. This motif is also frequently found in the promoter region of genes potentially regulated by CodY in other Gram-positive bacteria.
Probing the domain structure of FtsZ by random truncation and insertion of GFP
Authors: Osawa Masaki , Erickson Harold P.
Published: December 2005

Random transposon-mediated mutagenesis has been used to create truncations and insertions of green fluorescent protein (GFP), and Venus-yellow fluorescent protein (YFP), in Escherichia coli FtsZ. Sixteen unique insertions were obtained, and one of them, in the poorly conserved C-terminal spacer, was functional for cell division with the Venus-YFP insert. The insertion of enhanced GFP (eGFP) at this same site was not functional; Venus-YFP was found to be superior to eGFP in other respects too. Testing the constructs for dominant negative effects led to the following general conclusion. The N-terminal domain, aa 1–195, is an independently folding domain that can poison Z-ring function when expressed without a functional C-terminal domain. The effects were weak, requiring expression of the mutant at 3–5 times the level of wild-type FtsZ. The C-terminal domain, aa 195–383, was also independently folding, but had no activity in vivo. The differential activity of the N- and C-terminal domains suggests that FtsZ protofilament assembly is directional, with subunits adding primarily at the bottom of the protofilament. Directional assembly could occur by either a treadmilling or a dynamic instability mechanism.
Dimerization and DNA binding of the Salmonella enterica PhoP response regulator are phosphorylation independent
Authors: Perron-Savard Philippe , De Crescenzo Gregory , Moual Hervé Le
Published: December 2005

InSalmonella enterica, PhoP is the response regulator of the PhoP/PhoQ two-component regulatory system that controls the expression of various virulence factors in response to external Mg2+. Previous studies have shown that phosphorylation of a PhoP variant with a C-terminal His tag (PhoPHis) enhances dimerization and binding to target DNA. Here, the effect of phosphorylation on the oligomerization and DNA binding properties of both wild-type PhoP (PhoP) and PhoPHisare compared. Gel filtration chromatography showed that PhoP exists as a mixture of monomer and dimer regardless of its phosphorylation state. In contrast, unphosphorylated PhoPHiswas mostly monomeric, whereas PhoPHis∼P existed as a mixture of monomer and dimer. By monitoring the tryptophan fluorescence of the proteins and the fluorescence of the probe 1-anilinonaphthalene-8-sulfonic acid bound to them, it was found that PhoP and PhoPHisexhibited different spectral properties. The interaction between PhoP or PhoPHisand the PhoP box of themgtApromoter was monitored by surface plasmon resonance. Binding of PhoP to the PhoP box was barely influenced by phosphorylation. In contrast, phosphorylation of PhoPHisclearly increased the interaction of PhoPHiswith target DNA. Altogether, these data show that a His tag at the C-terminus of PhoP affects its biochemical properties, most likely by affecting its conformation and/or its oligomerization state. More importantly, these results show that wild-type PhoP dimerization and interaction with target DNA are independent of phosphorylation, which is in contrast to the previously proposed model.
A GntR family transcriptional regulator (PigT) controls gluconate-mediated repression and defines a new, independent pathway for regulation of the tripyrrole antibiotic, prodigiosin, in Serratia
Authors: Fineran Peter C. , Everson Lee , Slater Holly , Salmond George P. C.
Published: December 2005

Biosynthesis of the red, tripyrrole antibiotic prodigiosin (Pig) bySerratiasp. ATCC 39006 (39006) is controlled by a complex regulatory network involving anN-acyl homoserine lactone (N-AHL) quorum-sensing system, at least two separate two-component signal transduction systems and a multitude of other regulators. In this study, a new transcriptional activator, PigT, and a physiological cue (gluconate), which are involved in an independent pathway controlling Pig biosynthesis, have been characterized. PigT, a GntR homologue, activates transcription of thepigA–Obiosynthetic operon in the absence of gluconate. However, addition of gluconate to the growth medium of 39006 repressed transcription ofpigA–O, via a PigT-dependent mechanism, resulting in a decrease in Pig production. Finally, expression of thepigTtranscript was shown to be maximal in exponential phase, preceding the onset of Pig production. This work expands our understanding of both the physiological and genetic factors that impinge on the biosynthesis of the secondary metabolite Pig in 39006.
Yersiniophage ϕR1-37 is a tailed bacteriophage having a 270 kb DNA genome with thymidine replaced by deoxyuridine
Authors: Kiljunen Saija , Hakala Kristo , Pinta Elise , Huttunen Suvi , Pluta Patrycja , Gador Aneta , Lönnberg Harri , Skurnik Mikael
Published: December 2005

BacteriophageϕR1-37 was isolated based on its ability to infect strain YeO3-R1, a virulence-plasmid-cured O antigen-negative derivative ofYersinia enterocoliticaserotype O : 3. In this study, the phage receptor was found to be a structure in the outer core hexasaccharide ofY. enterocoliticaO : 3 LPS. The phage receptor was present in the outer core of strains of many otherY. enterocoliticaserotypes, but also in someYersinia intermediastrains. Surprisingly, the receptor structure resided in the O antigen ofYersinia pseudotuberculosisO : 9. Electron microscopy demonstrated thatϕR1-37 particles have an icosahedral head of 88 nm, a short neck of 10 nm, a long contractile tail of 236 nm, and tail fibres of at least 86 nm. This implies that the phage belongs to the orderCaudoviralesand the familyMyoviridaein the ICTV (International Committee for Taxonomy of Viruses) classification.ϕR1-37 was found to have a lytic life cycle, with eclipse and latent periods of 40 and 50 min, respectively, and a burst size of ∼80 p.f.u. per infected cell. Restriction digestions and PFGE showed that theϕR1-37 genome was dsDNA and ∼270 kb in size. Enzymically hydrolysed DNA was subjected to HPLC-MS/MS analysis, which demonstrated that theϕR1-37 genome is composed of DNA in which thymidine (T) is >99 % replaced by deoxyuridine (dU). The only organisms known to have similar DNA are theBacillus subtilis-specific bacteriophages PBS1 and PBS2. N-terminal amino acid sequences of four major structural proteins did not show any similarity to (viral) protein sequences in databases, indicating that close relatives ofϕR1-37 have not yet been characterized. Genes for two of the structural proteins, p24 and p46, were identified from the partially sequencedϕR1-37 genome.