bluuebunny/crossref_metadata_2025 huggingface dataset:
Ion beam irradiation of embedded nanoparticles: Toward an in situ control of size and spatial distribution
Authors: Rizza G. , Cheverry H. , Gacoin T. , Lamasson A. , Henry S.
Published: January 2007

Irradiation of chemically synthesized Au nanoparticles embedded in a dielectric matrix promotes the formation of a halo of satellites around the original cluster. We show that the complete dissolution of the nanoparticles (NC) results in the formation of a narrow size distribution of small precipitates with a mean size of 2 nm and a standard deviation of 0.4 nm. By combining the chemical synthesis of the nanoparticles and the irradiation to induce their dissolution and precipitation, we give a guideline method for overcoming the difficulty of controlling the size and spatial distribution of the embedded NC associated with ion implantation technique. In particular, we showed that the irradiation can be used to tailor the size of the already formed NC. Moreover, we establish that the satellites cluster evolution under irradiation can be described by a two step process. These two steps are discussed in terms of classical and inverse Ostwald ripening mechanisms.
Feedforward control of a closed-loop piezoelectric translation stage for atomic force microscope
Authors: Li Yang , Bechhoefer John
Published: January 2007

Simple feedforward ideas are shown to lead to a nearly tenfold increase in the effective bandwidth of a closed-loop piezoelectric positioning stage used in scanning probe microscopy. If the desired control signal is known in advance, the feedforward filter can be acausal: the information about the future can be used to make the output of the stage have almost no phase lag with respect to the input. This keeps in register the images assembled from right and left scans. We discuss the design constraints imposed by the need for the feedforward filter to work robustly under a variety of circumstances. Because the feedforward needs only to modify the input signal, it can be added to any piezoelectric stage, whether closed or open loop.
Interpolation of quaternary III-V alloy parameters with surface bowing estimations
Authors: Mei T.
Published: January 2007

We present the weighted-sum expression of quaternary parameter estimations via balancing surface bowing estimation errors. Expressions have been derived for both quaternary alloys AxByCzD and AxB1−xCyD1−y and applied to the band gaps of AlGaInAs, AlGaInP, InAsPSb, GaInAsP, and GaInAsSb. Approximation can be improved by fitting known data of quaternary alloys and maximum deviations are less than 20meV with respect to the lattice-matched polynomial expressions.
Thermoelectric power factor of nanoporous semiconductors
Authors: Mingo N. , Broido D. A.
Published: January 2007

We compute the thermoelectric power factor of a nanoporous matrix material. Although the porous material is a connected, extended system, where perfect confinement cannot take place, we show that “quasi-confinement” can occur, thus increasing the matrix’s optimized power factor above bulk values. For parabolic band materials, we obtain a set of universal curves that express the power factor enhancement with respect to bulk values in terms of a single quantity relating the temperature, pore separation, and bulk effective mass. We show how results deviate from these universal curves when the bulk material’s bands are not parabolic. Reduction of the lattice thermal conductivity is also addressed. The use of a good thermoelectric material instead of a dielectric as the matrix for thermoelectric nanocomposites might thus enhance the overall nanocomposite’s power factor, and it could be advantageous for power generation applications in which the goal is to maximize the generated power.
X-ray absorption studies on cubic boron nitride thin films
Authors: Zhou X. T. , Sham T. K. , Zhang W. J. , Chan C. Y. , Bello I. , Lee S. T. , Hofsäss H.
Published: January 2007

Cubic boron nitride (c-BN) films synthesized by various energetic species assisted physical vapor deposition and chemical vapor deposition techniques on Si and diamond-coated Si substrates have been investigated by boron and nitrogen K-edge angle-resolved x-ray absorption near-edge structure in both total electron yield and fluorescence yield modes. X-ray absorption spectrum has been developed to study the film structure, the quantity and distribution of the partially ordered turbostratic (t-BN) and amorphous (a-BN) sp2-hybridized BN phases, and the t-BN∕a-BN ratios. The preferred direction of the t-BN basal planes at the interface between c-BN and substrate is found to be normal or nearly normal to the substrate. The content of the sp2-bonded BN in the c-BN films deposited on diamond-coated Si substrates reduces remarkably. The modifications of the electronic structure of the c-BN films with respect to bulk hexagonal BN and c-BN have been investigated and the crystallinity of c-BN films has also been evaluated from the x-ray absorption near edge structure results.
Tuning the effective properties of metamaterials by changing the substrate properties
Authors: Sheng Zhongyan , Varadan Vasundara V.
Published: January 2007

Tunable properties of materials are highly desirable in many applications. Metamaterials with negative properties (permittivity, permeability, or both) can have many applications if such properties can be made tunable or can be switched alternatively between positive and negative property behavior. This paper is a numerical study of the effect of substrate properties on the effective properties of a metamaterial slab. We present both simulation results and measurement data for a specific split-ring resonator structure for two different substrate thicknesses and demonstrate very good agreement. Then, using finite element simulation, varying the permittivity of the substrate from 1 to 14 while keeping its physical thickness fixed, we show that the resonance frequency drops from ∼16to∼6GHz. Alternately, when the physical thickness of the substrate is varied from 0.05to2mm, keeping its permittivity fixed, the resonance frequency decreases from ∼13.2to∼9.2GHz. In each case, the effective refractive index is retrieved from the simulated S parameters (normalized reflected and transmitted fields). Our results show that the properties of metamaterials can be effectively tuned by changing the substrate properties. If the metamaterials are negative index materials, the effective refractive index can also be agilely switched between negative and positive values. This numerical study can serve as a guide for the design of voltage tunable dielectric substrates for realizing tunable metamaterials.
Lorentzian line shape due to an inhomogeneous size distribution without relaxation
Authors: Lehmann Kevin K.
Published: January 2007

In this paper, it is demonstrated that a Lorentzian line shape is predicted for a resonance interacting with a bath of equally spaced levels, even in the sparse, low density of states limit, if one performs an inhomogeneous average over the position of the bath states relative to the bright state. The implication for the spectroscopy of molecules in helium nanodroplets and possibly other samples with a significant size distribution is that coupling of excitations to phonons can lead to Lorentzian shaped transitions entirely from inhomogeneous broadening with no population relaxation in the sample.
Mass fluctuation kinetics: Capturing stochastic effects in systems of chemical reactions through coupled mean-variance computations
Authors: Gómez-Uribe Carlos A. , Verghese George C.
Published: January 2007

The intrinsic stochastic effects in chemical reactions, and particularly in biochemical networks, may result in behaviors significantly different from those predicted by deterministic mass action kinetics (MAK). Analyzing stochastic effects, however, is often computationally taxing and complex. The authors describe here the derivation and application of what they term the mass fluctuation kinetics (MFK), a set of deterministic equations to track the means, variances, and covariances of the concentrations of the chemical species in the system. These equations are obtained by approximating the dynamics of the first and second moments of the chemical master equation. Apart from needing knowledge of the system volume, the MFK description requires only the same information used to specify the MAK model, and is not significantly harder to write down or apply. When the effects of fluctuations are negligible, the MFK description typically reduces to MAK. The MFK equations are capable of describing the average behavior of the network substantially better than MAK, because they incorporate the effects of fluctuations on the evolution of the means. They also account for the effects of the means on the evolution of the variances and covariances, to produce quite accurate uncertainty bands around the average behavior. The MFK computations, although approximate, are significantly faster than Monte Carlo methods for computing first and second moments in systems of chemical reactions. They may therefore be used, perhaps along with a few Monte Carlo simulations of sample state trajectories, to efficiently provide a detailed picture of the behavior of a chemical system.
Density functional calculations of NMR shielding tensors for paramagnetic systems with arbitrary spin multiplicity: Validation on 3d metallocenes
Authors: Hrobárik Peter , Reviakine Roman , Arbuznikov Alexei V. , Malkina Olga L. , Malkin Vladimir G. , Köhler Frank H. , Kaupp Martin
Published: January 2007

The calculation of nuclear shieldings for paramagnetic molecules has been implemented in the ReSpect program, which allows the use of modern density functional methods with accurate treatments of spin-orbit effects for all relevant terms up to order O(α4) in the fine structure constant. Compared to previous implementations, the methodology has been extended to compounds of arbitrary spin multiplicity. Effects of zero-field splittings in high-spin systems are approximately accounted for. Validation of the new implementation is carried out for the C13 and H1 NMR signal shifts of the 3d metallocenes V4Cp2, Cr3Cp2, Mn2Cp2, Mn6Cp2, Co2Cp2, and Ni3Cp2. Zero-field splitting effects on isotropic shifts tend to be small or negligible. Agreement with experimental isotropic shifts is already good with the BP86 gradient-corrected functional and is further improved by admixture of Hartree-Fock exchange in hybrid functionals. Decomposition of the shieldings confirms the dominant importance of the Fermi-contact shifts, but contributions from spin-orbit dependent terms are frequently also non-negligible. Agreement with C13 NMR shift tensors from solid-state experiments is of similar quality as for isotropic shifts.
Hydrodynamic coupling between micromechanical beams oscillating in viscous fluids
Authors: Basak Sudipta , Raman Arvind
Published: January 2007

We analyze the hydrodynamic coupling between long, slender micromechanical beams (microbeams) deployed in an array and oscillating in a viscous, incompressible fluid. The unsteady Stokes equations are solved using a boundary integral technique in a two-dimensional plane containing the microbeam cross sections. The oscillations of nearest neighbor and the next neighbor microbeams couple hydrodynamically in unanticipated ways depending on the gap, frequency, and the relative phase and amplitude of their oscillation. A rational basis is provided for choosing the gap between neighboring microbeams in an array in order to either decouple their hydrodynamics or to couple them strongly. The results clearly suggest that the dynamics of microbeams in an array can be tuned in a cooperative manner so as to minimize or maximize the hydrodynamic resistance on individual microbeams.
Zonal flow sawteeth and the time period between edge-localized transport bursts in tokamaks
Authors: Kleva Robert G. , Guzdar Parvez N.
Published: January 2007

The time period between particle and energy transport bursts in simulations of tokamak edge turbulence is determined by the magnitude of the diamagnetic drift parameter αd≡ω*∕γ0, where the diamagnetic drift frequency ω*=ρscs∕L0Ln and the characteristic ballooning mode growth rate γ0=cs∕(RLn∕2)1∕2. Here, R is the major radius of the torus, Ln is the density gradient scale length, ρs is the ion gyroradius, and cs is the ion acoustic speed. The scale length L0 is given by L0=2πqR(νeiρs∕2ωeR)1∕2(2R∕Ln)1∕4, where q is the safety factor, νei is the electron-ion collision frequency, and ωe is the electron cyclotron frequency. When the diamagnetic drift frequency becomes larger than the ballooning mode growth rate (αd>1), then the transport in the tokamak edge is characterized by regularly recurring bursts of particles and energy with a single well-defined frequency. As αd increases above unity, the time period between the bursts becomes much longer. The temporal dependence of the energy in the zonal flow generated nonlinearly has the appearance of sawteeth.
Evolution of a localized vortex in plane nonparallel viscous flows with constant velocity shear. II. Elliptic flow
Authors: Shukhman I. G.
Published: January 2007

This paper continues the studies of localized vortex evolution in nonparallel viscous plane flows with constant velocity shear started in our previous paper on the hyperbolic flow. This paper discusses the elliptic flow. For such a flow the evolution of a disturbance in the form of a monochromatic plane wave with a time-dependent wave vector was first investigated by Bayly [Phys. Rev. Lett. 57, 2160 (1986)] and also by Landman and Saffman [Phys. Fluids 30, 2339 (1987)] based on the Floquet theory. Here we address the evolution of a three-dimensionally localized vortex which is a package of such waves and includes both stable and exponentially unstable components. The effect of ellipticity on the character of vortex evolution is studied, as well as the possibility of its intensity amplification by a given instant of time. The dynamics of the geometrical shape of the vortex is calculated. The research is motivated by an attempt to interpret experiments on artificial generation of hairpin vortices in shear flows.
Mixing and spreading in stratified flow
Authors: Dentz Marco , Carrera Jesus
Published: January 2007

G. I. Taylor [Proc. R. Soc. London, Ser. A 219, 186 (1953)] quantified enhanced solute mixing in the flow through a tube at asymptotically long times by the constant Taylor dispersion coefficient, which provides a good representation of both the asymptotic dispersion dynamics and evolution of the solute concentration. At preasymptotic times, however, the use of the constant Taylor dispersion coefficient does not facilitate a faithful representation of either the actual mixing or spreading, which are controlling factors for chemical reaction rates. Transport in spatially varying flow fields often displays non-Fickian or anomalous behavior, which is reflected by the fact that effective dispersion evolves in time. Here we study and quantify the mechanisms leading to enhanced solute mixing in spatially nonhomogeneous flow fields using “local” spatial moments, i.e., moments of the transport Green function. On the basis of such a local moment formulation, we define effective dispersion coefficients to characterize effective preasymptotic solute spreading and mixing. We apply these concepts to the characterization of effective transport in general stratified flows, and illustrate them for the particular case of transport in a two-dimensional channel. We study effective mixing and spreading at preasymptotic times in terms of explicit analytical expressions for the effective dispersion coefficients as well as by numerical random walk simulations. We find that the vertically averaged concentration profiles contain little information on the physical mixing and spreading processes occurring at preasymptotic times. This leads us to define an alternative average, effective concentration, whose evolution is characterized by the effective dispersion coefficient and which reflects mainly the average effective solute mixing rather than purely advective spreading of the initial solute distribution.
Criticality of compressible rotating flows
Authors: Renac Florent , Sipp Denis , Jacquin Laurent
Published: January 2007

The effect of compressibility on the criticality of swirling subsonic flows is investigated. This study extends previous works by Rusak and Lee [J. Fluid Mech. 461, 301 (2002); 501, 25 (2004)] on the critical swirl of subsonic vortex flows in a circular straight pipe. We derive an asymptotic solution in the case of an isothermal plug-flow with solid-body rotation. In the limit of low Mach number M0⪡1, it is shown that the critical swirl increases with M0 as Sc∼Sc,0∕(1−M02)1∕2, where Sc,0 is the critical swirl of the incompressible flow. This result still holds when varying the thermodynamic properties of the flow or when considering different vortex models as the Batchelor vortex. Physically, compressibility is found to slow down phase and group velocities of axisymmetric Kelvin waves, thus decreasing the rotation contribution to flow criticality. It is shown that compressibility damps the stretching mechanism which contributes to the wave propagation in the incompressible limit.
Lift forces of screws in shear flows
Authors: Chen Peilong , Chao Chia-Hsin
Published: January 2007

We have measured the forces in the vorticity direction experienced by chiral screws in shear flows, with the Reynolds number at the order of 103. The measured force directions depend on the screw handedness, being in the positive vorticity direction for left-handed screws and opposite for right-handed ones. These directions are the reverse of those predicted in the low Reynolds number (Stokes flow) calculations [M. Makino and M. Doi, Phys. Fluids 17, 103605 (2005)]. The force magnitude scales with the cube of the shear rate and is about 100dyn (on the order of 10% of the drag force) when the shear rate ∼10s−1.
Analytical model for extracting mechanical properties of a single cell in a tapered micropipette
Authors: He J. H. , Xu W. , Zhu L.
Published: January 2007

A simple solid mechanical model has been developed to extract the mechanical properties of a single cell in a tapered micropipette. This analytical model is derived using the definition of elastic modulus and force equilibrium. Using the authors’ model, an elastic modulus of 21.80±4.91Pa, a Poisson ratio of 0.46±0.03, and a friction coefficient of 0.0274±0.0077 are extracted for a neutrophil cell. The model is verified by finite element software and shows good agreement with experiments. The biophysical basis of the model and application in microfluidic channels for cancer cell research are discussed, while a comparison is made with other models.
Optical gain in InGaN∕GaN quantum well structures with embedded AlGaN δ layer
Authors: Park Seoung-Hwan , Park Jongwoon , Yoon Euijoon
Published: January 2007

Optical gain characteristics of InGaN∕GaN double quantum well (QW) structures with embedded AlGaN δ layer are investigated using the multiband effective mass theory. These results are compared with those of single QW structure without a δ layer. The theoretical energies show very good agreement with the experimental results for both single and double QW structures. The inclusion effect of a δ layer is found to be dominant at a relatively low carrier density. A double QW structure has larger optical gain than the single QW structure, in particular, at higher carrier density.
A polarizable ion model for the structure of molten AgI
Authors: Bitrián Vicente , Trullàs Joaquim , Silbert Moises
Published: January 2007

The results are reported of the molecular dynamics simulations of the coherent static structure factor of molten AgI at 923K using a polarizable ion model. This model is based on a rigid ion potential, to which the many body interactions due to the anions induced polarization are added. The calculated structure factor is in better agreement with recent neutron diffraction data than that obtained by using simple rigid ion pair potentials. The Voronoi-Delaunay method has been applied to study the relationship between voids in the spatial distribution of cations and the prepeak of the structure factor.
ProMSED: protein multiple sequence editor for Windows 3.11/95
Authors: Frolov Anatoly S. , Pika Irina S. , Eroshkin Alexey M.
Published: January 2007

Motivation: Most protein sequence alignment algorithms give similar results on closely related proteins, while manual intervention may be needed for distantly related molecules. To correct the alignment, it is often necessary to repeat calculations on selected parts of the alignments and edit the alignment manually. Software implementing such interactive alignment procedures is of significance.

Results: This paper presents a new MS Windows application called ProMSED for both automatic and manual protein sequence alignment. The program reads main sequence formats and has a user-friendly interface. ProMSED performs automatic (ClustalV algorithm) alignments, alignment visualization and editing, and it allows sequences to be aligned interactively leaving previously aligned regions unchanged. Manual alignment and sequence analysis are facilitated by colouring schemes reflecting amino acid similarity of mutational and physicochemical properties. The interactive alignment of a diverged set of reverse transcriptases has located four out of six known conserved motifs.

Availability: ProMSED is available on request from the authors. DEMO is available from ftp://ftp.ebi.ac.uk/pub/software/dos/promsed/ or ftp://iubio.bio.indiana.edu/molbio/ibmpc/.
A preliminary crown biomass table for even-aged Picea abies stands in Switzerland
Authors: Usoltsev V. A. , Hoffmann C. W.
Published: January 2007

The assessment of biomass and biomass changes due to environmental influences requires not only stem or merchantable mass, but also branches and needles. They have been of relatively lit-tle importance to forest managers to date, but their inclusion in models can make the resulting predictions more precise. A hybrid method is described to derive regressions for site quality, needle and branch biomass for individual Picea abies trees. By using Swiss stand table data on tree density distributions, a traditional yield table for branch and needle biomass is computed, and from these, regressions are derived which use only age and site quality as independent vari-ables. Three tables for typical site qualities are given. The tabulated regressions include pseudo-probability values, coefficients of determination and estimated standard error for the overall models.

These biomass fractions comprise a varying fraction of the tree, being important at low ages and much less so at later ages.
Kinetics of Tissue Distribution and Elimination of Pyrene and 1-Hydroxypyrene Following Intravenous Administration of [14C]Pyrene in Rats
Authors: Bouchard Michéle , Krishnan Kannan , Viau Claude
Published: January 2007

The tissue distribution and elimination of pyrene and 1-hydroxy-pyrene (1-OHP) were evaluated in male Sprague-Dawley rats (210–240 g) following an intravenous injection of 50 μmol/kg of [14C]pyrene. Blood and tissues were removed and urine and feces were collected at 1, 2, 4, 8, 16, and 24 h postdosing. [14C]Pyrene equivalents were measured by liquid scintillation counting, and β-glucuronidase/arylsulfatase-treated blood, tissues, and excreta were analyzed for pyrene and 1-OHP by HPLC/fluorescence. At 1 h, the largest fraction of the dose was found in adipose tissue, essentially as pyrene, and its elimination followed first-order monophasic kinetics with a half-life (t½) of 4.9 h. In blood, liver, kidney, lung, muscle, and gastrointestinal (GI) tract, kinetics of [14C]pyrene equivalents were biphasic and average t½ values for the terminal elimination phase (8 to 24 h) ranged between 6.2 and 8.7 h. Elimination of pyrene in blood and these tissues except the GI tract followed first-order biphasic kinetics with average t½ values of the terminal phase ranging between 3.6 and 5.4 h. In the GI tract, a monophasic elimination kinetics of pyrene was observed with mean t½ value of 3.1 h. Kinetics of 1-OHP in blood and liver showed a monophasic elimination with mean t½ values of 6.7 and 6.2 h, respectively. Kinetics of 1-OHP in the other tissues were biphasic with average t½ values of the terminal elimination phase ranging between 5.2 and 6.2 h. At 24 h, on average, 81.7% of the dose was recovered in the urine (57.2%), feces (18.3%), and GI tract (6.2%) as [14C]pyrene equivalents with 2.7 and 1.9% of dose excreted as total 1-OHP in urine and feces, respectively. At all time points, 1-OHP in urine represented a constant fraction of total 14C in urine and feces. These results indicate that (i) [14C]pyrene was rapidly distributed, metabolized, and eliminated from the body, and (ii) although 1-OHP represents a small percentage of total pyrene eliminated from the body, it remains a reliable indicator of systemic exposure to, and overall elimination of the 14C associated with, this polycyclic aromatic hydrocarbon.
dnaJ gene sequence-based assay for species identification and phylogenetic grouping in the genus Staphylococcus
Authors: Shah Mohammad Monir , Iihara Hirotoshi , Noda Makiko , Song Sun Xiao , Nhung Pham Hong , Ohkusu Kiyofumi , Kawamura Yoshiaki , Ezaki Takayuki
Published: January 2007

In the last few years, many attempts have been made to use conserved gene sequences for identification and for phylogenetic studies ofStaphylococcusspecies. In an effort to identify a more reliable approach, adnaJgene sequence-based database was created. In this study, an approximately 883 bp portion of thednaJgene sequence from 45 staphylococcal type strains was compared with 16S rRNA and other conserved gene (hsp60,sodAandrpoB) sequences available in public databases. Nucleotide sequence comparisons revealed that the staphylococcaldnaJgene showed higher discrimination (mean similarity 77.6 %) than the 16S rRNA (mean similarity 97.4 %),rpoB(mean similarity 86 %),hsp60(mean similarity 82 %) andsodA(mean similarity 81.5 %) genes. Analysis of thednaJgene sequence from 20Staphylococcusisolates representing two clinically important species showed <1 % sequence divergence. Phylogenetic data obtained from thednaJgene sequence were in general agreement with those of 16S rRNA gene sequence analysis and DNA–DNA reassociation studies. In conclusion, thednaJgene sequence-based assay is an effective alternative to currently used methods, including 16S rRNA gene sequencing, for identification and taxonomical analysis ofStaphylococcusspecies.
Paenibacillus terrigena sp. nov., isolated from soil
Authors: Xie Cheng-Hui , Yokota Akira
Published: January 2007

A novel Gram-positive bacterium, strain A35T, was isolated from coastal soil at Chiba, Japan, and was identified as a member of the genus Paenibacillus on the basis of phenotypic and phylogenetic analyses. The bacterium was found to be a facultatively anaerobic and endospore-forming rod. The predominant menaquinone was MK-7, the major cellular fatty acid was anteiso-C15 : 0 and the DNA G+C content was 48.1 mol%. The levels of 16S rRNA gene sequence similarity between strain A35T and Paenibacillus species with validly published names were less than 94 %. Strain A35T was clearly distinguishable from reference species for the genus Paenibacillus. Therefore, on the basis of these data, a novel species of the genus Paenibacillus, Paenibacillus terrigena sp. nov., is proposed. The type strain is A35T (=IAM 15291T=CCTCC AB206026T).
Donghicola eburneus gen. nov., sp. nov., isolated from seawater of the East Sea in Korea
Authors: Yoon Jung-Hoon , Kang So-Jung , Oh Tae-Kwang
Published: January 2007

A Gram-negative, aerobic, slightly halophilic, non-motile and coccoid- or rod-shaped bacterial strain, SW-277T, was isolated from seawater, Korea, and subjected to a polyphasic taxonomic study. Strain SW-277T was catalase- and oxidase-positive and grew optimally at pH 7.0–8.0 and 37 °C in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SW-277T belongs to the Alphaproteobacteria as part of the clade comprising the genera Roseivivax and Salipiger with a bootstrap resampling value of 72.5 %. 16S rRNA gene sequence similarity values between strain SW-277T and members of the genera Roseivivax and Salipiger were between 93.8 and 94.7 %. Strain SW-277T contained Q-10 as the predominant ubiquinone and C18 : 1
ω7c and C16 : 0 as the major fatty acids. The DNA G+C content was 59.7 mol%. Strain SW-277T could be distinguished from members of the phylogenetically related genera Salipiger and Roseivivax by phenotypic differences and low 16S rRNA gene similarity values. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, strain SW-277T (=KCTC 12735T=JCM 13604T) should be classified as a representative of a novel species in a new genus, Donghicola eburneus gen. nov., sp. nov.
Haloarcula amylolytica sp. nov., an extremely halophilic archaeon isolated from Aibi salt lake in Xin-Jiang, China
Authors: Yang Yong , Cui Heng-Lin , Zhou Pei-Jin , Liu Shuang-Jiang
Published: January 2007

A starch-hydrolysing and extremely halophilic archaeon (strain BD-3T), isolated from Aibi salt lake in Xin-Jiang, China, was characterized phenotypically and genotypically in order to determine its taxonomic status. On the basis of its polar lipid composition, nucleotide sequences of its 16S rRNA genes, genomic DNA G+C content (62.4 mol%) and growth characteristics, the organism could be assigned to the genus Haloarcula. Phenotypic differences and low DNA–DNA hybridization values to related Haloarcula species distinguished strain BD-3T from recognized Haloarcula species. It is therefore concluded that strain BD-3T represents a novel species, for which the name Haloarcula amylolytica sp. nov. is proposed. The type strain is BD-3T (=CGMCC 1.5335T=JCM 13557T).
Protein binding of cefazolin is saturable in vivo both between and within patients
Authors: Vella‐Brincat Jane W. A. , Begg Evan J. , Kirkpatrick Carl M. J. , Zhang Mei , Chambers Stephen T. , Gallagher Kate
Published: January 2007

Aims

The aims of the study were a) to determine if there is evidence of saturable protein binding of cefazolin in plasma across the range of concentrations achieved clinically (between patient variability) and b) to investigate whether saturable protein binding is also evident from trough and peak concentrations in the same patient (within patient variability).

Methods

Unbound and total plasma concentrations were measured in patients who were treated with cefazolin intravenously by continuous infusion or intermittent injection. In study (i) single random samples were taken from one series of patients. In study (ii) paired samples (troughs and peaks) were taken from a second series of patients.

Results

Thirty‐one patients were included in study (i). Linear regression analysis of the percentage unbound vs. unbound plasma concentrations revealed a slope significantly different from zero, suggesting saturable protein binding. Mean values for percentage unbound ranged from 9% at low concentrations (8.5 mg l−1) to 51% at high concentrations (140 mg l−1). Twelve patients were investigated in study (ii). Values for protein binding ranged from 85% at low concentrations (2.7 mg l−1) to 52% at high concentrations (200.3 mg l−1). The percentage unbound was significantly higher (P < 0.0001) at high (peak) concentrations than at lower (trough) concentrations, confirming saturable protein binding.

Conclusions

The protein binding of cefazolin is saturable in vivo in humans, both between and within patients.
The haematopoietic cell transplantation comorbidity index score is predictive of early death and survival in patients over 60 years of age receiving induction therapy for acute myeloid leukaemia.
Authors: Giles Francis J. , Borthakur Gautam , Ravandi Farhad , Faderl Stefan , Verstovsek Srdan , Thomas Deborah , Wierda William , Ferrajoli Alessandra , Kornblau Steven , Pierce Sherry , Albitar Maher , Cortes Jorge , Kantarjian Hagop
Published: January 2007

The haematopoietic cell transplantation comorbidity index (HCTCI) predicts nonrelapse mortality and overall survival (OS) post‐stem cell transplantation. HCTCI scores were assessed in 177 patients over 60 years of age receiving acute myeloid leukaemia (AML) induction therapy. HCTCI score was 0 in 22% of patients, 1–2 in 30%, and ≥3 in 48%. In patients with scores of 0, 1–2, or ≥3, early death rates were 3%, 11% and 29% (P < 0·001) respectively; median OS was 45, 31 and 19 weeks (P = 0·04) respectively. The HCTCI score is predictive of early death rates and OS in older patients receiving AML induction therapy.
Reduction of high fetal loss rate by anticoagulant treatment during pregnancy in antithrombin, protein C or protein S deficient women
Authors: Folkeringa Nienke , Brouwer Jan Leendert P. , Korteweg Fleurisca J. , Veeger Nic J. G. M. , Erwich Jan Jaap H. M. , Holm Jozien P. , Van Der Meer Jan
Published: January 2007

Hereditary thrombophilia is associated with an increased risk of fetal loss. Assuming that fetal loss is due to placental thrombosis, anticoagulant treatment might improve pregnancy outcome. In an observational family cohort study, we prospectively assessed the effects of anticoagulant drugs on fetal loss rates in women with hereditary deficiencies of antithrombin, protein C or protein S. The cohort contained 376 women (50 probands and 326 deficient or non‐deficient relatives). Probands were consecutive deficient patients with venous tromboembolism. Thromboprophylaxis during pregnancy was recommended in deficient women, irrespective of prior venous thromboembolism, and in non‐deficient women with prior venous thromboembolism. Outcome of first pregnancy was analysed in 55 eligible women. Of 37 deficient women, 26 (70%) received thromboprophylaxis during pregnancy, compared with three of 18 (17%) non‐deficient women. Fetal loss rates were 0% in deficient women with thromboprophylaxis versus 45% in deficient women without (P = 0·001) and 7% in non‐deficient women without thromboprophylaxis (P = 0·37). The adjusted relative risk of fetal loss in women who received thromboprophylaxis versus women who did not was 0·07 (95% confidence interval 0·001–0·7; P = 0·02). Our data suggest that anticoagulant treatment during pregnancy reduces the high fetal loss rate in women with hereditary deficiencies of antithrombin, protein C or protein S.
Abnormalities of chromosome 1p/q are highly associated with chromosome 13/13q deletions and are an adverse prognostic factor for the outcome of high‐dose chemotherapy in patients with multiple myeloma
Authors: Wu Ka Lung , Beverloo Berna , Lokhorst Henk M. , Segeren Christine M. , Van Der Holt Bronno , Steijaert Monique M. , Westveer Petra H. , Poddighe Pino J. , Verhoef Gregor E. , Sonneveld Pieter ,   for the Dutch‐Belgian Haemato‐Oncology Cooperative Study Group (HOVON) and the Dutch Working Party on Cancer Genetics and Cytogenetics (NWCGC)
Published: January 2007

The prognostic value of chromosomal abnormalities was studied in untreated multiple myeloma patients who were registered into a prospective randomised multicentre phase 3 study for intensified treatment (HOVON24). A total of 453 patients aged less than 66 years with stage II and III A/B disease were registered in the clinical study. Cytogenetic analysis was introduced as a standard diagnostic assay in 1998. It was performed at diagnosis in 160 patients and was successful in 137/160 patients (86%). An abnormal karyotype was observed in 53/137 (39%) of the patients. Abnormalities of chromosome 1p and 1q were found in 19 (36% of patients with an abnormal karyotype) and 21 patients (40%). There was a strong association between chromosome 1p and/or 1q abnormalities and deletion of chromosome 13 or 13q (n = 27, P < 0·001). Patients with karyotypic abnormalities had a significantly shorter overall survival (OS) than patients with normal karyotypes. Complex abnormalities, hypodiploidy, chromosome 1p abnormalities, chromosome 1q abnormalities, and chromosome 13 abnormalities were associated with inferior OS on univariate analysis, as well as after adjustment for other prognostic factors. In conclusion, chromosome 13 abnormalities and chromosome 1p and/or 1q abnormalities were highly associated, and are risk factors for poor outcome after intensive therapy in multiple myeloma.
Epstein–Barr virus T‐cell immunity despite rituximab
Authors: Nehring Angela K. , Dua Ujjwal , Mollee Peter , Gill Devinder , Grimmett Karen , Khanna Rajiv , Moss Denis , Gandhi Maher K.
Published: January 2007

Immunosuppression following solid organ transplantation results in impaired T‐cell immunity and risk of Epstein–Barr virus (EBV)‐positive post‐transplant lymphoproliferative disorders (PTLD). The B‐cell targeting antibody rituximab has efficacy in PTLD. As B cells are the principle reservoir for EBV, we investigated the effect of rituximab on the persistence of EBV‐specific CD8+ T‐cell immunity. To avoid the confounding factor of concurrent immunosuppression to prevent transplant rejection, immunity was analysed in non‐transplanted lymphoma patients (i.e. a non‐PTLD setting). Cytomegalovirus‐specific T‐cell immunity was assessed as an internal control. Our data demonstrated that circulating B cells were not critical for maintaining EBV‐specific T‐cell immunity.
Cancer‐testis antigens in haematological malignancies
Authors: Meklat Farouk , Li Zhanfei , Wang Zhiqing , Zhang Yana , Zhang Jian , Jewell Andrew , Lim Seah H
Published: January 2007

Immunotherapy is an attractive therapeutic option for patients with haematological malignancies. Until recently, the progress in the development of tumour vaccines for haematological malignancies had been slow due to the lack of suitable targets. Cancer‐testis (CT) antigens are potentially suitable molecules for tumour vaccines of haematological malignancies because of their high immunogenicity in vivo and their relatively restricted normal tissue distribution. This review evaluates the properties and potential functions of CT antigens. We discuss the expression of CT antigens in patient with haematological malignancies and provide evidence in support of their immunogenicity in vivo in these patients. We also address the role of ‘epigenetic’ regulation of CT antigens in haematological malignancies and how hypomethylating agents could induce the expression of some of these antigens in tumour cells to overcome the problem of heterogeneity of expression of the antigen within individual tumour specimens. Data implicating the interaction of the promoter genes of some of these CT antigens with the MeCP2 protein also suggest the potential role of the histone deacetylase inhibitors in inducing antigen expression in tumour cells. Finally, we discuss the direction of future research in advancing the development of tumour vaccines for haematological malignancies.
Effect of myeloablative bone marrow transplantation on growth in children with sickle cell anaemia: results of the multicenter study of haematopoietic cell transplantation for sickle cell anaemia
Authors: Eggleston B. , Patience M. , Edwards S. , Adamkiewicz T. , Buchanan G. R. , Davies S. C. , Dickerhoff R. , Donfield S. , Feig S. A. , Giller R. H. , Haight A. , Horan J. , Hsu L. L. , Kamani N. , Lane P. , Levine J. E. , Margolis D. , Moore T. B. , Ohene‐Frempong K. , Redding‐Lallinger R. , Roberts I. A. G. , Rogers Z. R. , Sanders J. E. , Scott J. P. , Sleight B. , Thompson A. A. , Sullivan K. M. , Walters M. C. ,   for the Multicenter Study of HCT for SCA*
Published: January 2007

Although haematopoietic cell transplantation (HCT) is curative for sickle cell anaemia (SCA), concerns about its short‐ and long‐term toxicities limit its application. A potential toxicity is an adverse effect on growth. To identify an HCT growth effect, serial height and weight measurements from 53 children and adolescents with SCA after receiving a transplant were compared to historical controls. Hierarchical Linear Models for longitudinal data were used for analysis. In general growth was not impaired by HCT for SCA in young children; however, diminished growth may occur if HCT is carried out near or during the adolescent growth spurt.
Validation of a measure of maternal perception of the child’s health status
Authors: Monette S. , Séguin L. , Gauvin L. , Nikiéma B.
Published: January 2007

Background  The main objective of this population‐based and cross‐sectional study was to determine the validity of maternal perception as an indicator of the 17‐month‐old child’s health status.

Methods  Data from this study came from the Quebec Longitudinal Study of Child Development (QLSCD, Round 1999) which was based on a representative sample of babies born in Québec in 1997 and 1998. The analyses were based on the 2045 children aged 17 months who participated in the survey in 1999. Maternal perception of the child’s health status was examined as a function of a series of children’s health indicators, namely the presence of acute health problems (last 3 months), asthma attacks since birth, presence of chronic problem and hospitalizations during the previous 12 months. Confounding influences of both maternal and child‐related characteristics were controlled in the analyses.

Results  Sequential logistic regressions indicated that maternal perception was strongly associated with the different health indicators even after controlling for confounding variables. However, a significant interaction between the child’s gender and the presence of chronic health problems was observed. The association between maternal perception of the child’s health and the presence of chronic health problems was stronger for boys than for girls.

Conclusions  The analyses confirm that the mother’s perception of the health status of her 17‐month‐old child corresponds with the actual health status of the child as reflected by the presence or absence of selected health problems.
Philosophy of science underpinnings of prototype validation: Popper vs. Quine
Authors: Klein Esther E , Herskovitz Paul J
Published: January 2007

Abstract.  In this paper, we aim to provide prototype validation in both custom and packaged software development with a theoretical framework located within the philosophy of science. Towards that end, we consider Popperian and Quinean accounts of scientific knowledge and argue that the theoretical underpinning of prototype validation is Quine’s holistic philosophy of science, whose cornerstone principle is that all beliefs are revisable. Specifically, our thesis is that the systems developer and software consumer (user or customer) join forces – not as Popperian falsifiers, who make a decision rule to reject the prototype on account of any divergence, major or minor, from the software consumer’s mental model, but – as Quinean revisers, with the objective of fine‐tuning the prototype (or the software consumer’s mental model) so that the prototype and the software consumer’s mental model are congruent with each other. This paper suggests that prototype revisions are belief revisions, and, as such, should be guided – and are guided – by pragmatic norms, such as conservatism, simplicity and generality, and are influenced by social, or sociological, factors as well. Finally, we discuss the relevance, value and pragmatic implications of a Quinean philosophy of science framework for research and practice.
Continuity of care and general wellbeing of patients with comorbidities requiring joint replacement
Authors: Williams Allison , Dunning Trisha , Manias Elizabeth
Published: January 2007

Title. Continuity of care and general wellbeing of patients with comorbidities requiring joint replacement

Aim.  The aim of this paper is to examine the continuity of care and general wellbeing of patients with comorbidities undergoing elective total hip or knee joint replacement.

Background.  Advances in medical science and improved lifestyles have reduced mortality rates in most Western countries. As a result, there is an ageing population with a concomitant growth in the number of people who are living with multiple chronic illnesses, commonly referred to as comorbidities. These patients often require acute care services, creating a blend of acute and chronic illness needs. For example, joint replacement surgery is frequently performed to improve impaired mobility associated with osteoarthritis.

Method.  A purposive sample of twenty participants with multiple comorbidities who required joint replacement surgery was recruited to obtain survey, interview and medical record audit data. Data were collected during 2004 and 2005.

Findings.  Comorbidity care was poorly co‐ordinated prior to having surgery, during the acute care stay and following surgery and primarily entailed prescribed medicines. The main focus in acute care was patient throughput following joint replacement surgery according to a prescribed clinical pathway. General wellbeing was less than optimal: participants reported pain, fatigue, insomnia and alterations in urinary elimination as the chief sources of discomfort during the course of the study.

Conclusion.  Continuity of care of comorbidities was lacking. Comorbidities affected patient general wellbeing and delayed recovery from surgery. Acute care, clinical pathways and the specialisation of medicine and nursing subordinated the general problem of patients with comorbidities. Systems designed to integrate and co‐ordinate chronic illness care had limited application in the acute care setting. A multidisciplinary, holistic approach is required. Recommendations for further research conclude this paper.
Is susceptibility to tuberculosis acquired or inherited?
Authors: Schurr E.
Published: January 2007

Tuberculosis is an ongoing major public health problem on a global scale. One of the striking features of the disease is that only an estimated 10% of immunocompetent persons infected by the causative pathogen Mycobacterium tuberculosis will develop clinical signs of disease. This well‐established epidemiological observation has prompted an intense search for the factors that trigger advancement of infection to disease in the small proportion of susceptible individuals. Central to this search is the questions if tuberculosis patients are inherently susceptible to the disease or if disease development is promoted by specific environmental factors. It is known that genetic and non‐genetic factors of both the bacterium and the host have impact on the host response to M. tuberculosis. Yet, little is known about the interaction of these different factors and the resulting impact on disease development. Recent work suggests that in addition to common host susceptibility genes a second group of susceptibility loci exists the action of which strongly depends on the individual's clinical and exposure history. The latter genes may have a very strong effect on promoting advancement from infection to disease only in specific epidemiological settings. These findings suggest that a more detailed knowledge of gene–environment interactions in tuberculosis is necessary to understand why a small proportion of individuals are susceptible to the disease whilst the majority of humans are naturally resistant to tuberculosis.