bluuebunny/crossref_metadata_2025 huggingface dataset:
Intravenous Anakinra can Achieve Experimentally Effective Concentrations in the Central Nervous System within a Therapeutic Time Window: Results of a Dose-Ranging Study
Authors: Galea James , Ogungbenro Kayode , Hulme Sharon , Greenhalgh Andrew , Aarons Leon , Scarth Sylvia , Hutchinson Peter , Grainger Samantha , King Andrew , Hopkins Stephen J , Rothwell Nancy , Tyrrell Pippa
Published: July 2010

The naturally occurring antagonist of interleukin-1, IL-1RA, is highly neuroprotective experimentally, shows few adverse effects, and inhibits the systemic acute phase response to stroke. A single regime pilot study showed slow penetration into cerebrospinal fluid (CSF) at experimentally therapeutic concentrations. Twenty-five patients with subarachnoid hemorrhage (SAH) and external ventricular drains were sequentially allocated to five administration regimes, using intravenous bolus doses of 100 to 500 mg and 4 hours intravenous infusions of IL-1RA ranging from 1 to 10 mg per kg per hour. Choice of regimes and timing of plasma and CSF sampling was informed by pharmacometric analysis of pilot study data. Data were analyzed using nonlinear mixed effects modeling. Plasma and CSF concentrations of IL-1RA in all regimes were within the predicted intervals. A 500-mg bolus followed by an intravenous infusion of IL-1RA at 10 mg per kg per hour achieved experimentally therapeutic CSF concentrations of IL-1RA within 45 minutes. Experimentally, neuroprotective CSF concentrations in patients with SAH can be safely achieved within a therapeutic time window. Pharmacokinetic analysis suggests that IL-1RA transport across the blood–CSF barrier in SAH is passive. Identification of the practicality of this delivery regime allows further studies of efficacy of IL-1RA in acute cerebrovascular disease.
Desmosomes: adhesive strength and signalling in health and disease
Authors: Thomason Helen A. , Scothern Anthea , McHarg Selina , Garrod David R.
Published: July 2010

Desmosomes are intercellular junctions whose primary function is strong intercellular adhesion, known as hyperadhesion. In the present review, we discuss how their structure appears to support this function as well as how they are assembled and down-regulated. Desmosomal components also have signalling functions that are important in tissue development and remodelling. Their adhesive and signalling functions are both compromised in genetic and autoimmune diseases that affect the heart, skin and mucous membranes. We conclude that much work is required on structure–function relationships within desmosomes in vivo and on how they participate in signalling processes to enhance our knowledge of tissue homoeostasis and human disease.
The hydrophobic core region governs mutant prion protein aggregation and intracellular retention
Authors: Biasini Emiliano , Tapella Laura , Restelli Elena , Pozzoli Manuela , Massignan Tania , Chiesa Roberto
Published: July 2010

Approx. 15% of human prion diseases have a pattern of autosomal dominant inheritance, and are linked to mutations in the gene encoding PrP (prion protein), a GPI (glycosylphosphatidylinositol)-anchored protein whose function is not clear. The cellular mechanisms by which PrP mutations cause disease are also not known. Soon after synthesis in the ER (endoplasmic reticulum), several mutant PrPs misfold and become resistant to phospholipase cleavage of their GPI anchor. The biosynthetic maturation of the misfolded molecules in the ER is delayed and, during transit in the secretory pathway, they form detergent-insoluble and protease-resistant aggregates, suggesting that intracellular PrP aggregation may play a pathogenic role. We have investigated the consequence of deleting residues 114–121 within the hydrophobic core of PrP on the aggregation and cellular localization of two pathogenic mutants that accumulate in the ER and Golgi apparatus. Compared with their full-length counterparts, the deleted molecules formed smaller protease-sensitive aggregates and were more efficiently transported to the cell surface and released by phospholipase cleavage. These results indicate that mutant PrP aggregation and intracellular retention are closely related and depend critically on the integrity of the hydrophobic core. The discovery that Δ114–121 counteracts misfolding and improves the cellular trafficking of mutant PrP provides an unprecedented model for assessing the role of intracellular aggregation in the pathogenesis of prion diseases.
Bilateral hydronephrosis secondary to anticoagulant rodenticide intoxication in a dog
Authors: Hansen Naomi , Beck Cathy
Published: July 2010

Objective:To describe an unusual site of hemorrhage in a case of anticoagulant rodenticide toxicity.

Case summary:A dog treated for Brodifacoum anticoagulant rodenticide intoxication was referred for treatment of thrombocytopenia and dysuria. Sonographic examination revealed a large blood clot within the urinary bladder, extending proximally along both ureters, and a bilateral hydronephrosis. In this dog, management of the vitamin K1‐dependent coagulopathy was unusually complicated by uremia and thrombocytopenia.

New information provided:This is the first reported case of hydronephrosis secondary to anticoagulant rodenticide intoxication in a dog.
Viscoelasticity of liquid organic foam: Relaxations, temporal dependence, and bubble loading effects on flow behavior
Authors: Kropka Jamie M. , Celina Mathew
Published: July 2010

Liquid organic foams are prepared using a new blowing process based on the chemical generation of carbon dioxide. The foams are volumetrically stable for periods up to hours and can be fabricated with gas volume fractions ranging from 0.10 to 0.95. Both the “fresh” and temporal dependences of the linear viscoelastic response of these materials are evaluated. The organic foams exhibit rheological behavior characteristic of their aqueous counterparts: a weak dependence of the shear moduli over an extended frequency/time regime that is bounded by both a fast and slow relaxation. The onset of the fast mechanical response of the organic foams occurs at approximately the same frequency as in aqueous foams despite the continuous phase viscosity differing by orders of magnitude between the systems. This suggests that the viscosity does not affect the time scale of the “anomalous” viscous loss characteristic of these materials, which challenges currently proposed mechanisms for this dissipation and leaves the origin of the loss behavior unclear. The relative contribution of cell growth and bubble motion to the slow relaxation is also discerned by evaluating the relation between the transient and dynamic responses of the foam. Finally, the development of elasticity in the foam due to bubble interactions is analyzed and a bubble slip process is postulated to account for the lack of a true elastic response of the foam at intermediate time scales (between the fast and slow mechanical response) when gas fractions exceed 0.64.
Strain induced anisotropies in silica polydimethylsiloxane composites
Authors: Schneider G. J. , Göritz D.
Published: July 2010

Structural changes of silica in polydimethylsiloxane rubber induced by external forces were studied by means of small-angle X-ray scattering experiments. The silica fraction varies from 9 up to 23 vol% and the elongation ratio from 1 to 3. Within the q-range of 0.02 nm−1<q<1 nm−1 the primary particles and the clusters which consist of these basic units could be resolved. The scattering diagrams of the samples without external deformation are radially symmetric and, in particular, the mass fractal dimension does not depend on the silica fraction. Due to the deformation the contours of the two-dimensional scattering diagrams become elliptic. A model independent analysis of the intensity as a function of the q-vector perpendicular and parallel to the deformation axis revealed that the microscopic cluster size is systematically increased by the macroscopic external deformation. In particular, the deformation ratio at the microscopic and the macroscopic length scale is very similar. The mass fractal dimension, as obtained by the slope of the scattering curve, increases significantly with growing deformation ratio, but is the same in vertical and horizontal directions. A simple relation derived for the crossover from self-similar to self-affine fractals can be used to relate the cluster sizes perpendicular and parallel to the deformation and the mass fractal dimension. By that means, it is demonstrated that the mean number of particles within each aggregate is constant, although the rubber was stretched up to a factor of 3.
Classical density functional theory for the prediction of the surface tension and interfacial properties of fluids mixtures of chain molecules based on the statistical associating fluid theory for potentials of variable range
Authors: Llovell Fèlix , Galindo Amparo , Blas Felipe J. , Jackson George
Published: July 2010

The statistical associating fluid theory for attractive potentials of variable range (SAFT-VR) density functional theory (DFT) developed by [G. J. Gloor et al., J. Chem. Phys. 121, 12740 (2004)] is revisited and generalized to treat mixtures. The Helmholtz free-energy functional, which is based on the SAFT-VR approach for homogeneous fluids, is constructed by partitioning the free-energy density into a reference term (which incorporates all of the short-range interactions and is treated locally) and an attractive perturbation (which incorporates the long-range dispersion interactions). In this work, two different functionals are compared. In the first, one uses a mean-field version of the theory to treat the long-range dispersive interaction, incorporating an approximate treatment of the effect of the correlations on the attractive energy between the segments by introducing a short-range attractive contribution in the reference term. In the second, one approximates the correlation function of the molecular segments in the inhomogeneous system with that of a homogeneous system for an average density of the two positions, following the ideas proposed by Toxvaerd [S. Toxvaerd, J. Chem. Phys. 64, 2863 (1976)]. The SAFT-VR DFT formalism is then used to study interfacial properties and adsorption phenomena at the interface. A detailed analysis of the influence of the molecular parameters on the surface tension and density/composition profiles of the mixtures is undertaken for binary mixtures of molecules of different chain length, segment diameter, dispersive energy, and attractive range. The effect of the asymmetry of the molecular species on the adsorption phenomena is examined in some depth. The adequacy of the approach is demonstrated by comparing the theoretical predictions with the interfacial properties of some real mixtures. The relative merits of the two approximate free-energy functionals are assessed by examining the vapor-liquid interfacial tension of selected mixtures of n-alkanes. The theory generally provides an excellent description of the interfacial properties of the mixtures without the need for further adjustment of intermolecular parameters obtained from an examination of the bulk fluid-phase behavior alone.
Microwave and plasma interaction in a rectangular waveguide: Effect of ponderomotive force
Authors: Malik Hitendra K. , Aria Anil K.
Published: July 2010

Studies on the propagation of high power microwave and its interaction with a plasma in a metallic waveguide are carried out. For this we consider the fundamental TE10 mode that propagates in an evacuated rectangular waveguide and encounters a plasma which is filled in another waveguide of the same size. Using Maxwell’s equations we evaluate the field components of the mode in the evacuated waveguide and then obtain coupled differential equations for the field components of the mode in the plasma filled waveguide, where the plasma effect enters in terms of its dielectric constant. These equations are solved numerically using the fourth-order Runge–Kutta method for the electric field amplitude of the microwave and its wavelength under the effect of plasma density, waveguide width, and microwave frequency. All the investigations are carried out for different initial plasma density profiles, namely homogeneous density, linear density with gradient in the propagation direction and the density with Gaussian profile along the waveguide width. The structure of the perturbed density due to the ponderomotive force exerted by the mode is also investigated under the effect of microwave parameters and waveguide width. Numerical studies are conducted for the isothermal plasma in the waveguide.
Structural transitions and dipole moment of water clusters (H2O)n=4–100
Authors: Gelman-Constantin Julián , Carignano Marcelo A. , Szleifer Igal , Marceca Ernesto J. , Corti Horacio R.
Published: July 2010

The properties of water clusters (H2O)n over a broad range of sizes (n=4–100) were studied by microcanonical parallel tempering Monte Carlo and replica exchange molecular dynamics simulations at temperatures between 20 and 300 K, with special emphasis in the understanding of relation between the structural transitions and dipole behavior. The effect of the water interaction potential was analyzed using six nonpolarizable models, but more extensive calculations were performed using the TIP4P-ice water model. We find that, in general, the dipole moment of the cluster increases significantly as the cluster melts, suggesting that it could be used to discriminate between the solidlike and liquidlike phases. The effect of a moderate electric field on the cluster heat capacity and total dipole moment was found to be negligible.
Direct numerical simulations of magnetic field effects on turbulent flow in a square duct
Authors: Chaudhary R. , Vanka S. P. , Thomas B. G.
Published: July 2010

Magnetic fields are crucial in controlling flows in various physical processes of industrial significance. One such process is the continuous casting of steel, where different magnetic field configurations are used to control the turbulent flow of steel in the mold in order to minimize defects in the cast steel. The present study has been undertaken to understand the effects of a magnetic field on mean velocities and turbulence parameters in turbulent molten metal flow through a square duct. The coupled Navier–Stokes magnetohydrodynamic equations have been solved using a three-dimensional fractional-step numerical procedure. The Reynolds number was kept low in order to resolve all the scales in the flow without using a subgrid scale turbulence model. Computations were performed with three different grid resolutions, the finest grid having 8.4×106 cells. Because liquid metals have low magnetic Reynolds number, the induced magnetic field has been considered negligible and the electric potential method for magnetic field-flow coupling has been implemented. After validation of the computer code, computations of turbulent flow in a square duct with different Hartmann numbers were performed until complete laminarization of the flow. The time-dependent and time-averaged nature of the flow has been examined through distribution of mean velocities, turbulent fluctuations, vorticity, and turbulent kinetic energy budgets.
Wideband and high-gain frequency stabilization of a 100-W injection-locked Nd:YAG laser for second-generation gravitational wave detectors
Authors: Ohmae Noriaki , Moriwaki Shigenori , Mio Norikatsu
Published: July 2010

Second-generation gravitational wave detectors require a highly stable laser with an output power greater than 100 W to attain their target sensitivity. We have developed a frequency stabilization system for a 100-W injection-locked Nd:YAG (yttrium aluminum garnet) laser. By placing an external wideband electro-optic modulator used as a fast-frequency actuator in the optical path of the slave output, we can circumvent a phase delay in the frequency control loop originating from the pole of an injection-locked slave cavity. Thus, we have developed an electro-optic modulator made of a MgO-doped stoichiometric LiNbO3 crystal. Using this modulator, we achieve a frequency control bandwidth of 800 kHz and a control gain of 180 dB at 1 kHz. These values satisfy the requirement for a laser frequency control loop in second-generation gravitational wave detectors.
Surface current reduction in (211) oriented Cd0.46Zn0.04Te.50 crystals by Ar bombardment
Authors: Voss L. F. , Beck P. R. , Conway A. M. , Graff R. T. , Nikolic R. J. , Nelson A. J. , Payne S. A.
Published: July 2010

Cd 0.46 Zn 0.04 Te .50 crystals have been exposed to high density Ar plasmas in order to modify the surface chemistry and control the surface conductivity. X-ray photoelectron spectroscopy reveals that this bombardment results in a modified surface atomic ratio, with Cd being preferentially removed compared to Te. In addition, the native oxide is removed and suppressed for an extended period of time. Current-voltage data is analyzed in order to determine the effect on surface leakage current after exposure. It is found that surface leakage current can be decreased by approximately 2.5 orders of magnitude following Ar+ bombardment.
Temperature dependence of superluminescence in InGaN-based superluminescent light emitting diode structures
Authors: Holc Katarzyna , Marona Łucja , Czernecki Robert , Boćkowski Michał , Suski Tadeusz , Najda Stephen , Perlin Piotr
Published: July 2010

We have studied the temperature dependence of electroluminescence in superluminescent light emitting diode InGaN structures emitting light at 405 nm. Devices were fabricated in the “tilted ridge” geometry. We measured the superluminescence emission as a function of temperature from 263 to 295 K and observed a very pronounced power sensitivity with temperature. Simple modeling of the optical intensity reveals that the main temperature dependence is related to the spontaneous emission factor in the amplified spontaneous emission and the temperature dependence of gain is of secondary importance. This result strongly suggests the need for reducing nonradiative recombination in superluminescent devices.
Strongly enhanced incorporation of oxygen into barium titanate based multilayer ceramic capacitors using water vapor
Authors: Kessel M. , De Souza R. A. , Yoo H.-I. , Martin M.
Published: July 2010

The reoxidation of sintered BaTiO3-based multilayer ceramic capacitors (MLCCs) is currently an empirically determined, but poorly understood, procedure. In this work, the incorporation of oxygen into BaTiO3-based MLCCs has been studied by means of isotope exchange annealing (O182/O162, H12O18/H12O16 or H22O16/H12O16) and subsequent determination of the isotope profiles in the solid by secondary ion mass spectrometry. Oxygen isotope profiles in the barium titanate dielectric can be described by a bulk diffusion coefficient D∗ and a surface exchange coefficient k∗. The values obtained for k∗ indicate that oxygen incorporation from H2O is much faster than from dry O2; it thus plays the key role in the reoxidation process.
Ultrabroadband terahertz generation using 4-N,N-dimethylamino-4′-N′-methyl-stilbazolium tosylate single crystals
Authors: Katayama I. , Akai R. , Bito M. , Shimosato H. , Miyamoto K. , Ito H. , Ashida M.
Published: July 2010

Ultrabroadband terahertz generation up to 200 THz has been demonstrated using a 5 fs Ti:sapphire laser and a 4-N,N-dimethylamino-4′-N′-methyl-stilbazolium tosylate (DAST) crystal. The high-frequency components beyond 100 THz are much stronger than those generated using conventional electro-optic crystals such as GaSe. A simple simulation of the difference frequency generation in the DAST crystal by considering the refractive index dispersion can reproduce the broadband generation of the terahertz wave and its chirp dependence. Because the generated terahertz wave is coherent and has a broad bandwidth, it can serve as a suitable light source for ultrabroadband terahertz time-domain spectroscopy of a material.
A uniform source-and-sink scheme for calculating thermal conductivity by nonequilibrium molecular dynamics
Authors: Cao Bing-Yang , Li Yuan-Wei
Published: July 2010

A uniform source-and-sink (USS) scheme, which combines features of the reverse [F. Müller-Plathe, J. Chem. Phys. 106, 6082 (1997)] and improved relaxation [B. Y. Cao, J. Chem. Phys. 129, 074106 (2008)] methods, is developed to calculate the thermal conductivity by nonequilibrium molecular dynamics (NEMD). The uniform internal heat source and sink are realized by exchanging the velocity vectors of individual atoms in the right half and left half systems, and produce a periodically quadratic temperature profile throughout the system. The thermal conductivity can be easily extracted from the mean temperatures of the right and left half systems rather than by fitting the temperature profiles. In particular, this scheme greatly increases the relaxation of the exited localized phonon modes which often worsen the calculation accuracy and efficiency in most other NEMD methods. The calculation of the thermal conductivities of solid argon shows that the simple USS scheme gives accurate results with fast convergence.
Molecular χ(2) gratings via electron-beam lithography
Authors: Domínguez-Juárez Jorge Luis , Macovez Roberto , González María Ujue , Martorell Jordi
Published: July 2010

We show that the nonlinear optical activity of an organic molecule may be quenched by electron irradiation. Exploiting this effect, we inscribe periodic χ(2) patterns in the molecular films by means of a scanning electron microscope. The second harmonic diffraction efficiency of the resulting χ(2) gratings is measured. The relative intensity of the diffraction orders observed agrees with the expectations for a sheet of nonlinear dipoles with a periodic modulation. No linear diffraction is seen. The present method allows realizing any type of two-dimensional χ(2) pattern with a resolution only limited by the electron beam patterning capabilities.
Phylogenetic analysis based on nuclear DNA and morphology defines a clade of eastern Australian species of Acacia s.s. (section Juliflorae): the 'Acacia longifolia group'
Authors: Brown Gillian K. , Clowes Catherine , Murphy Daniel J. , Ladiges Pauline Y.
Published: July 2010

Seventeen Australian, phyllodinous species of Acacia s.s. (from sections Juliflorae and Phyllodineae) were analysed to test the monophyly and relationships of ‘the Acacia longifolia group’, an informal group recognised in the Flora of Australia. Analyses were based on both morphological and molecular data, with A. triptera as an outgroup. A total of 92 herbarium specimens was investigated, with 15 phyllode, inflorescence, flower, pod and seed characters scored. The ITS and ETS regions of nuclear rDNA were sequenced and combined with a larger dataset sampled from species of all major clades of Acacia, totalling 65 accessions. Cladistic analyses provided evidence of a clade that defines the A. longifolia group as follows: A. alpina, A. axillaris, A. courtii, A. dallachiana, A. derwentiana, A. floribunda, A. longifolia subsp. longifolia and A. longifolia subsp. sophorae, A. longissima, A. maidenii, A. mucronata, A. obtusifolia, A. orites, A. oxycedrus, A. phlebophylla, A. rhigiophylla and A. riceana (all sect. Juliflorae), but excluding A. verticillata (section Juliflorae) and A. genistifolia (section Phyllodineae). The A. longifolia group is recognised as including south-eastern Australian species with cylindrically spiked inflorescences and phyllodes with prominent anastomosing venation.
Phylogeny and generic taxonomy of the New Zealand Pteridaceae ferns from chloroplast rbcL DNA sequences
Authors: Bouma Whitney L. M. , Ritchie Peter , Perrie Leon R.
Published: July 2010

Previous molecular phylogenetic studies of the species-rich Pteridaceae fern family have revealed that many of its constituent genera are not monophyletic. Within this context, we generated rbcL chloroplast DNA sequences for the 17 Pteridaceae species indigenous to New Zealand to assess how they are related to the type species of their genus. Of the five genera presently recognised in New Zealand, no taxonomic change is needed for the species of Anogramma, or, probably, of Cheilanthes and Pellaea. In contrast, most species presently attributed to Pteris, including those in New Zealand, probably do not belong there. The status of Adiantum remains unclear, although the New Zealand species are not especially closely related to the type species. The Adiantum species in New Zealand belong to a wide-ranging, principally southern hemisphere, clade that appears to be pivotal to resolving the relationships of Adiantum, although it has been little sampled. The closest relatives of the New Zealand species are in Australia and South America for Cheilanthes, Australia and South-east Asia for Pellaea, and the south-western Pacific for both of the Pteris lineages in New Zealand, whereas Anogramma leptophylla (L.) Link is subcosmopolitan.
The genus Karoowia (Parmeliaceae, Ascomycota) includes unrelated clades nested within Xanthoparmelia
Authors: Amo de Paz Guillermo , Lumbsch H. Thorsten , Cubas Paloma , Elix John A. , Crespo Ana
Published: July 2010

Thallus morphology has traditionally played a major role in the classification of lichenised fungi. We have used a combined dataset of nuITS, nuLSU and mtSSU rDNA sequences to evaluate the phylogenetic relationships between the subcrustose genus Karoowia and the mostly foliose genus Xanthoparmelia. Our phylogenetic analyses using maximum parsimony, maximum likelihood and a Bayesian approach show that Karoowia species do not form a monophyletic group but cluster in different clades nested within Xanthoparmelia. The monophyly of Karoowia either as a separate clade from Xanthoparmelia, or nested within Xanthoparmelia is significantly rejected using alternative hypothesis testing. These results suggest that the usefulness of the phenotypic features used to define Karoowia has been overestimated because the subcrustose growth form has evolved independently in several clades within Xanthoparmelia. Other characters used to circumscribe Karoowia, such as the presence of cylindrical conidia, also occur in Xanthoparmelia, and the differences in rhizine morphology are minimal. Consequently, we propose to reduce Karoowia to synonymy with Xanthoparmelia. The enlarged genus is characterised by the presence of Xanthoparmelia-type lichenan in the hyphal cell walls and the presence of an arachiform vacuolar body in the ascospores. Fifteen new combinations in Xanthoparmelia and the new name Xanthoparmelia mucinae for Karoowia squamatica are made.
Sum frequency generation and solid-state NMR study of the structure, orientation, and dynamics of polystyrene-adsorbed peptides
Authors: Weidner Tobias , Breen Nicholas F. , Li Kun , Drobny Gary P. , Castner David G.
Published: July 2010

The power of combining sum frequency generation (SFG) vibrational spectroscopy and solid-state nuclear magnetic resonance (ssNMR) spectroscopy to quantify, with site specificity and atomic resolution, the orientation and dynamics of side chains in synthetic model peptides adsorbed onto polystyrene (PS) surfaces is demonstrated in this study. Although isotopic labeling has long been used in ssNMR studies to site-specifically probe the structure and dynamics of biomolecules, the potential of SFG to probe side chain orientation in isotopically labeled surface-adsorbed peptides and proteins remains largely unexplored. The 14 amino acid leucine-lysine peptide studied in this work is known to form an α-helical secondary structure at liquid-solid interfaces. Selective, individual deuteration of the isopropyl group in each leucine residue was used to probe the orientation and dynamics of each individual leucine side chain of LKα14 adsorbed onto PS. The selective isotopic labeling methods allowed SFG analysis to determine the orientations of individual side chains in adsorbed peptides. Side chain dynamics were obtained by fitting the deuterium ssNMR line shape to specific motional models. Through the combined use of SFG and ssNMR, the dynamic trends observed for individual side chains by ssNMR have been correlated with side chain orientation relative to the PS surface as determined by SFG. This combination provides a more complete and quantitative picture of the structure, orientation, and dynamics of these surface-adsorbed peptides than could be obtained if either technique were used separately.
Supramolecular insulin assembly II for a sustained treatment of type 1 diabetes mellitus
Authors: Gupta Sarika , Chattopadhyay Tandrika , Pal Singh Mahendra , Surolia Avadhesha
Published: July 2010

Diabetes is a chronic disease requiring continuous medical supervision and patient education to prevent acute secondary complications. In this study, we have harnessed the inherent property of insulin to aggregate into an oligomeric intermediate on the pathway to amyloid formation, to generate a form that exhibits controlled and sustained release for extended periods. Administration of a single dose of the insulin oligomer, defined here as the supramolecular insulin assembly II (SIA-II), to experimental animals rendered diabetic by streptozotocin or alloxan, released the hormone capable of maintaining physiologic glucose levels for > 120 days for bovine and > 140 days for recombinant human insulin without fasting hypoglycemia. Moreover, the novel SIA-II described here not only improved the glycemic control, but also reduced the extent of secondary diabetic complications.
Network architecture of the long-distance pathways in the macaque brain
Authors: Modha Dharmendra S. , Singh Raghavendra
Published: July 2010

Understanding the network structure of white matter communication pathways is essential for unraveling the mysteries of the brain's function, organization, and evolution. To this end, we derive a unique network incorporating 410 anatomical tracing studies of the macaque brain from the
Co
llation of
Co
nnectivity data on the
Mac
aque brain (CoCoMac) neuroinformatic database. Our network consists of 383 hierarchically organized regions spanning cortex, thalamus, and basal ganglia; models the presence of 6,602 directed long-distance connections; is three times larger than any previously derived brain network; and contains subnetworks corresponding to classic corticocortical, corticosubcortical, and subcortico-subcortical fiber systems. We found that the empirical degree distribution of the network is consistent with the hypothesis of the maximum entropy exponential distribution and discovered two remarkable bridges between the brain's structure and function via network-theoretical analysis. First, prefrontal cortex contains a disproportionate share of topologically central regions. Second, there exists a tightly integrated core circuit, spanning parts of premotor cortex, prefrontal cortex, temporal lobe, parietal lobe, thalamus, basal ganglia, cingulate cortex, insula, and visual cortex, that includes much of the task-positive and task-negative networks and might play a special role in higher cognition and consciousness.
Microbisporicin gene cluster reveals unusual features of lantibiotic biosynthesis in actinomycetes
Authors: Foulston Lucy C. , Bibb Mervyn J.
Published: July 2010

Lantibiotics are ribosomally synthesized, posttranslationally modified peptide antibiotics. The biosynthetic gene cluster for microbisporicin, a potent lantibiotic produced by the actinomycete
Microbispora corallina
containing chlorinated tryptophan and dihydroxyproline residues, was identified by genome scanning and isolated from an
M. corallina
cosmid library. Heterologous expression in
Nonomuraea
sp. ATCC 39727 confirmed that all of the genes required for microbisporicin biosynthesis were present in the cluster. Deletion, in
M.
corallina, of the gene (
mibA
) predicted to encode the prepropeptide abolished microbisporicin production. Further deletion analysis revealed insights into the biosynthesis of this unusual and potentially clinically useful lantibiotic, shedding light on mechanisms of regulation and self-resistance. In particular, we report an example of the involvement of a tryptophan halogenase in the modification of a ribosomally synthesized peptide and the pathway-specific regulation of an antibiotic biosynthetic gene cluster by an extracytoplasmic function σ factor–anti-σ factor complex.
Emission wavelength extension of mid-infrared InAsSb/InP nanostructures using InGaAsSb sandwich layers
Authors: Lei W , Tan H H , Jagadish C
Published: July 2010

This paper presents a study on the emission wavelength extension of InAsSb nanostructures using InGaAsSb sandwich layers. Due to the reduced lattice mismatch between InAsSb nanostructure layer and buffer/capping layer, the introduction of InGaAsSb sandwich layers leads to larger island size, reduced compressive strain and lower confinement barrier for InAsSb nanostructures, thus resulting in a longer emission wavelength. For InGaAsSb sandwich layers with nominal Sb concentration higher than 10%, type II band alignment is observed for the InAsSb/InGaAsSb heterostructure, which also contributes to the extension of emission wavelength. The InGaAsSb sandwich layers provide an effective approach to extend the emission wavelength of InAsSb nanostructures well beyond 2 µm, which is very useful for device applications in the mid-infrared region.
Numerical calculation model for spin-dependent transport of photoexcited electrons across Fe/GaAs(0 0 1) interfaces
Authors: Kurebayashi H , Trypiniotis T , Lee K , Moutafis C , Easton S , Ionescu A , Bland J A C , Barnes C H W
Published: July 2010

Spin-dependent transport of photogenerated electrons across Fe/GaAs(0 0 1) interfaces is calculated using a one-dimensional electron transport model. Creation of spin-polarized electrons by photoexcitation in this model is defined by the band structure of GaAs along the [0 0 1] direction and the optical selection rules. The tunnel probability across the interface is obtained from Chang's model and first principles calculations are employed to calculate the spin polarization of Fe for electrons propagating along the [0 0 1] direction. By combining the above ingredients, the spin-filtering current, I
SF, was calculated for different parameter values, including Schottky barrier height and photon energy. The model is used to fit with experimental results of the photoexcitation technique, yielding qualitative agreement especially for the observed sign switching of the spin-filtering current.
Spectrum of fast electrons in a subnanosecond breakdown of air-filled diodes at atmospheric pressure
Authors: Baksht E H , Burachenko A G , Kozhevnikov V Yu , Kozyrev A V , Kostyrya I D , Tarasenko V F
Published: July 2010

In this work, the spectra of electron beams produced in air-filled diodes at atmospheric pressure were studied for different cathode designs. The feasibility of correct reconstruction of the electron beam spectrum from an experimental dependence of its attenuation factor in foils of different thicknesses was demonstrated. The electron energy distributions were calculated on minimum a priori assumptions by regularization of an ill-posed problem—a Fredholm integral equation. The spectra of a subnanosecond electron beam generated in the gas gap during the voltage pulse rise time were reconstructed and analysed. A time-of-flight spectrometer study and reconstruction of the spectrum from the data on e-beam attenuation confirmed the fact that groups of electrons with two-three characteristic energies can be generated in gas-filled diodes. In experiments, electrons of energy greater than that corresponding to the nominal voltage amplitude across the gap were detected.
Facile synthesis of bioconjugated fluorescent CdS nanoparticles of tunable light emission
Authors: Kalasad M N , Rabinal M K , Mulimani B G
Published: July 2010

Bioconjugated CdS nanoparticles capped with L-cysteine molecules are prepared by an aqueous route. A new source of sulfur that is a complex of hydrazine hydrate–sulfur is used to develop the aqueous synthesis of these nanoparticles. The change in volume ratio of sulfur and cadmium ions with a fixed molarity of capping molecules, as prepared colloids exhibits different colours. These nanoparticles are characterized by optical absorption, photoluminescence, FTIR, x-ray diffraction and transmission electron microscopic measurements. It is observed that the present technique yields nanoparticles that are spherical in shape whose size ranges from 1.7 to 3.39 nm (estimated from optical absorption). The resulting colloids are highly stable (for more than a few months) and exhibit high quantum yield for fluorescence (close to 34%). This demonstrates that the present route of synthesis is simple and easily scalable to prepare highly fluorescent and biologically important nanoparticles of CdS.
Oxygen plasma effects on the electrical conductance of single-walled carbon nanotube bundles
Authors: Kim Sanghun , Kim Ho-Jong , Lee Hyeong Rag , Song Jung-Hoon , Yi Sam Nyung , Ha Dong Han
Published: July 2010

We report the electrical properties of single-walled carbon nanotube bundles aligned between two electrodes with a gap of 8 µm by the alternating current dielectrophoresis method. The resistance increased exponentially as the number of structural defects increased from the oxygen plasma treatment. However, no noticeable change was observed in the carrier concentration and tube–tube interaction. The resistance dependence on the plasma treatment time was explained on the basis of the localization of electron states at defect sites. The aspects of the defects were examined by measuring the effects of ammonia adsorption on the conductance of the device.
Thermal properties and glass transition in PMMA + SWCNT composites
Authors: Pradhan N R , Iannacchione G S
Published: July 2010

The effective thermal and dynamic properties of composites containing polymethyl-metha-acralyte (PMMA) dispersed with single-wall carbon nanotubes (SWCNTs) were studied by modulation/ac calorimetry (ACC) and modulation-differential-scanning (MDSC) calorimetric techniques. The specific heat and effective thermal conductivity were determined by ACC from 300 to 400 K as a function of SWCNT content. A large enhancement of the effective thermal conductivity is observed as the mass fraction (ϕm) of SWCNTs increases from 0.014 to 0.083. These results are in good agreement with a simple geometric model at low SWCNT content but are better described by more sophisticated models above ϕm ∼ 0.039. The dynamics of the glass transition were studied by MDSC as a function of temperature scan rate. The hysteresis of the reversible specific heat between heating and cooling scans decreases with decreasing scan rate for pure PMMA but is essentially zero in the composites, indicating that the SWCNT may be quenching slow glass dynamics. In all samples, the effective glass transition temperature, T
g, increases with increasing scan rate (though less so for higher ϕm) but the MDSC determined T
g does not fall inline with that determined by the ACC method. This discrepancy is attributed to the effect of prolonged heat treatment of the composite sample used in the ACC experiments.
Logic Forest: an ensemble classifier for discovering logical combinations of binary markers
Authors: Wolf Bethany J. , Hill Elizabeth G. , Slate Elizabeth H.
Published: July 2010

Motivation: Highly sensitive and specific screening tools may reduce disease -related mortality by enabling physicians to diagnose diseases in asymptomatic patients or at-risk individuals. Diagnostic tests based on multiple biomarkers may achieve the needed sensitivity and specificity to realize this clinical gain.

Results: Logic regression, a multivariable regression method predicting an outcome using logical combinations of binary predictors, yields interpretable models of the complex interactions in biologic systems. However, its performance degrades in noisy data. We extend logic regression for classification to an ensemble of logic trees (Logic Forest, LF). We conduct simulation studies comparing the ability of logic regression and LF to identify variable interactions predictive of disease status. Our findings indicate LF is superior to logic regression for identifying important predictors. We apply our method to single nucleotide polymorphism data to determine associations of genetic and health factors with periodontal disease.

Availability: LF code is publicly available on CRAN, http://cran.r-project.org/.

Contact:  wolfb@musc.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
PriorsEditor: a tool for the creation and use of positional priors in motif discovery
Authors: Klepper Kjetil , Drabløs Finn
Published: July 2010

Summary: Computational methods designed to discover transcription factor binding sites in DNA sequences often have a tendency to make a lot of false predictions. One way to improve accuracy in motif discovery is to rely on positional priors to focus the search to parts of a sequence that are considered more likely to contain functional binding sites. We present here a program called PriorsEditor that can be used to create such positional priors tracks based on a combination of several features, including phylogenetic conservation, nucleosome occupancy, histone modifications, physical properties of the DNA helix and many more.

Availability: PriorsEditor is available as a web start application and downloadable archive from http://tare.medisin.ntnu.no/priorseditor (requires Java 1.6). The web site also provides tutorials, screenshots and example protocol scripts.

Contact:  kjetil.klepper@ntnu.no
A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data
Authors: Wang Penghao , Yang Pengyi , Arthur Jonathan , Yang Jean Yee Hwa
Published: July 2010

Motivation: Mass spectrometry (MS)-based proteomics is one of the most commonly used research techniques for identifying and characterizing proteins in biological and medical research. The identification of a protein is the critical first step in elucidating its biological function. Successful protein identification depends on various interrelated factors, including effective analysis of MS data generated in a proteomic experiment. This analysis comprises several stages, often combined in a pipeline or workflow. The first component of the analysis is known as spectra pre-processing. In this component, the raw data generated by the mass spectrometer is processed to eliminate noise and identify the mass-to-charge ratio (m/z) and intensity for the peaks in the spectrum corresponding to the presence of certain peptides or peptide fragments. Since all downstream analyses depend on the pre-processed data, effective pre-processing is critical to protein identification and characterization. There is a critical need for more robust pre-processing algorithms that perform well on tandem mass spectra under a variety of different conditions and can be easily integrated into sophisticated data analysis pipelines for practical wet-lab applications.

Result: We have developed a new pre-processing algorithm. Based on wavelet theory, our method uses a dynamic peak model to identify peaks. It is designed to be easily integrated into a complete proteomic analysis workflow. We compared the method with other available algorithms using a reference library of raw MS and tandem MS spectra with known protein composition information. Our pre-processing algorithm results in the identification of significantly more peptides and proteins in the downstream analysis for a given false discovery rate.

Availability: Software available at: http://www.maths.usyd.edu.au/u/penghao/index.html

Contact:  penghao.wang@sydney.edu.au
Editing, validating and translating of SBGN maps
Authors: Czauderna Tobias , Klukas Christian , Schreiber Falk
Published: July 2010

Motivation: The recently proposed Systems Biology Graphical Notation (SBGN) provides a standard for the visual representation of biochemical and cellular processes. It aims to support more efficient and accurate communication of biological knowledge between different research communities in the life sciences. However, to increase the use of SBGN, tools for editing, validating and translating SBGN maps are desirable.

Results: We present SBGN-ED, a tool which allows the creation of all three types of SBGN maps from scratch or the editing of existing maps, the validation of these maps for syntactical and semantical correctness, the translation of networks from the KEGG and MetaCrop databases into SBGN and the export of SBGN maps into several file and image formats.

Availability:  SBGN-ED is freely available from http://vanted.ipk-gatersleben.de/addons/sbgn-ed. The web site contains also tutorials and example files.

Contact:  schreibe@ipk-gatersleben.de
BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks
Authors: Rialle Stéphanie , Felicori Liza , Dias-Lopes Camila , Pérès Sabine , El Atia Sanaâ , Thierry Alain R. , Amar Patrick , Molina Franck
Published: July 2010

Motivation: Synthetic biology studies how to design and construct biological systems with functions that do not exist in nature. Biochemical networks, although easier to control, have been used less frequently than genetic networks as a base to build a synthetic system. To date, no clear engineering principles exist to design such cell-free biochemical networks.

Results: We describe a methodology for the construction of synthetic biochemical networks based on three main steps: design, simulation and experimental validation. We developed BioNetCAD to help users to go through these steps. BioNetCAD allows designing abstract networks that can be implemented thanks to CompuBioTicDB, a database of parts for synthetic biology. BioNetCAD enables also simulations with the HSim software and the classical Ordinary Differential Equations (ODE). We demonstrate with a case study that BioNetCAD can rationalize and reduce further experimental validation during the construction of a biochemical network.

Availability and implementation: BioNetCAD is freely available at http://www.sysdiag.cnrs.fr/BioNetCAD. It is implemented in Java and supported on MS Windows. CompuBioTicDB is freely accessible at http://compubiotic.sysdiag.cnrs.fr/

Contact:  stephanie.rialle@sysdiag.cnrs.fr; franck.molina@sysdiag.cnrs.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Differentiating Arabidopsis Shoots from Leaves by Combined YABBY Activities
Authors: Sarojam Rajani , Sappl Pia G. , Goldshmidt Alexander , Efroni Idan , Floyd Sandra K. , Eshed Yuval , Bowman John L.
Published: July 2010

In seed plants, leaves are born on radial shoots, but unlike shoots, they are determinate dorsiventral organs made of flat lamina. YABBY genes are found only in seed plants and in all cases studied are expressed primarily in lateral organs and in a polar manner. Despite their simple expression, Arabidopsis thaliana plants lacking all YABBY gene activities have a wide range of morphological defects in all lateral organs as well as the shoot apical meristem (SAM). Here, we show that leaves lacking all YABBY activities are initiated as dorsiventral appendages but fail to properly activate lamina programs. In particular, the activation of most CINCINNATA-class TCP genes does not commence, SAM-specific programs are reactivated, and a marginal leaf domain is not established. Altered distribution of auxin signaling and the auxin efflux carrier PIN1, highly reduced venation, initiation of multiple cotyledons, and gradual loss of the SAM accompany these defects. We suggest that YABBY functions were recruited to mold modified shoot systems into flat plant appendages by translating organ polarity into lamina-specific programs that include marginal auxin flow and activation of a maturation schedule directing determinate growth.