bluuebunny/crossref_metadata_2025 huggingface dataset:
Local inflammation, endothelial dysfunction and fibrinolysis in coronary heart disease
Authors: Lowe Gordon D. O.
Published: November 2007

Prospective epidemiological studies have shown associations of circulating inflammatory markers with risk of CHD (coronary heart disease); however, these associations are modest after adjustment for confounding by established risk factors, and do not add significantly to the predictive value of current clinical risk scores. In contrast, experimental human studies of local arterial inflammation, such as the brachial artery infusion of TNF-α (tumour necrosis factor-α) model reported in this issue of Clinical Science by Robinson and co-workers, are of value in elucidating the pathophysiology of atherothrombosis.
The RANTES −403G>A promoter polymorphism in Korean men: association with serum RANTES concentration and coronary artery disease
Authors: Jang Yangsoo , Chae Jey Sook , Hyun Yae Jung , Koh Soo Jeong , Kim Ji Young , Ko Min Ji , Rim Se-Joong , Shin Hyun-Joon , Ordovas Jose M. , Lee Jong Ho
Published: November 2007

In the present study we investigated the association of the RANTES (regulated upon activation, normal T-cell expressed and secreted) −28C>G and −403G>A promoter polymorphisms with the concentration of serum RANTES and CAD (coronary artery disease) in Korean men. We included 553 male CAD patients with (n=176) or without (n=377) Type 2 diabetes, aged 40–65 years with previous myocardial infarction (∼50%) or angiographically confirmed CAD (∼50%), and 416 aged-matched healthy male controls. The main outcome measures were the OR (odds ratio) of CAD risk and the serum RANTES concentration evaluated by sandwich ELISA. Although the RANTES −28C>G genotype had no significant association with CAD risk, the presence of the minor allele of the RANTES −403G>A single nucleotide polymorphism was associated with a lower risk of CAD {OR 0.70 [95% CI (confidence interval) 0.54–0.92], P=0.011} after adjusting for age, BMI (body mass index), cigarette smoking and alcohol consumption. Serum RANTES concentrations were significantly associated with the −403G>A genotype in controls (G/G: 44.7±3.3 ng/ml, G/A: 36.5±2.0 ng/ml, A/A: 28.7±2.5 ng/ml; P<0.001), non-diabetic CAD patients (G/G: 50.9±3.0 ng/ml, G/A: 42.2±2.6 ng/ml, A/A: 41.3±4.4 ng/ml; P<0.05) and diabetic CAD patients (G/G: 58.5±3.5 ng/ml, G/A: 49.6±4.1 ng/ml, A/A: 42.2±4.3 ng/ml; P<0.05); however, such associations were not observed in the subgroup of CAD patients taking lipid-lowering medication. Moreover, serum RANTES was positively correlated with C-reactive protein (r=0.289, P<0.001) and platelet counts (r=0.253, P<0.001). The results of the present study demonstrate that the RANTES −403A allele is associated with lower serum RANTES concentrations and consequently with reduced CAD risk.
Wenn es pathologisch wird – Labordiagnostik bei Erkrankungen der Bauchspeicheldrüse
Authors: Volkmann Martin Erich Philipp
Published: November 2007

Vorgehen bei der Labordiagnostik von Pankreaserkrankungen hängt wesentlich von der klinischen Fragestellung ab. Im Anamnesegespräch müssen zunächst die Symptome des Patienten genau erfragt und differenziert werden, bevor dann die Verdachtsdiagnose gestellt wird, die schließlich über das weitere labordiagnostische Vorgehen entscheidet. Welche laborchemischen Möglichkeiten es heute zur Diagnose der Pankreatitis bzw. der exokrinen und endokrinen Pankreasinsuffizienz gibt, hat PD Dr. Martin Volkmann hier für Sie zusammengestellt.
Nuclear quantum effects on the nonadiabatic decay mechanism of an excited hydrated electron
Authors: Borgis Daniel , Rossky Peter J. , Turi László
Published: November 2007

We present a kinetic analysis of the nonadiabatic decay mechanism of an excited state hydrated electron to the ground state. The theoretical treatment is based on a quantized, gap dependent golden rule rate constant formula which describes the nonadiabatic transition rate between two quantum states. The rate formula is expressed in terms of quantum time correlation functions of the energy gap and of the nonadiabatic coupling. These gap dependent quantities are evaluated from three different sets of mixed quantum-classical molecular dynamics simulations of a hydrated electron equilibrated (a) in its ground state, (b) in its first excited state, and (c) on a hypothetical mixed potential energy surface which is the average of the ground and the first excited electronic states. The quantized, gap dependent rate results are applied in a phenomenological kinetic equation which provides the survival probability function of the excited state electron. Although the lifetime of the equilibrated excited state electron is computed to be very short (well under 100fs), the survival probability function for the nonequilibrium process in pump-probe experiments yields an effective excited state lifetime of around 300fs, a value that is consistent with the findings of several experimental groups and previous theoretical estimates.
Transient molecular dynamics simulations of viscosity for simple fluids
Authors: Thomas Jason C. , Rowley Richard L.
Published: November 2007

A transient molecular dynamics (TMD) method has been developed for simulation of fluid viscosity. In this method a sinusoidal velocity profile is instantaneously overlaid onto equilibrated molecular velocities, and the subsequent decay of that velocity profile is observed. The viscosity is obtained by matching in a least-squares sense the analytical solution of the corresponding momentum transport boundary-value problem to the simulated decay of the initial velocity profile. The method was benchmarked by comparing results obtained from the TMD method for a Lennard-Jones fluid with those previously obtained using equilibrium molecular dynamics (EMD) simulations. Two different constitutive models were used in the macroscopic equations to relate the shear rate to the stress. Results using a Newtonian fluid model agree with EMD results at moderate densities but exhibit an increasingly positive error with increasing density at high densities. With the initial velocity profiles used in this study, simulated transient velocities displayed clear viscoelastic behavior at dimensionless densities above 0.7. However, the use of a linear viscoelastic model reproduces the simulated transient velocity behavior well and removes the high-density bias observed in the results obtained under the assumption of Newtonian behavior. The viscosity values obtained using the viscoelastic model are in excellent agreement with the EMD results over virtually the entire fluid domain. For simplicity, the Newtonian fluid model can be used at lower densities and the viscoelastic model at higher densities; the two models give equivalent results at intermediate densities.
An improved thermodynamic perturbation theory for Mercedes-Benz water
Authors: Urbic T. , Vlachy V. , Kalyuzhnyi Yu. V. , Dill K. A.
Published: November 2007

We previously applied Wertheim’s thermodynamic perturbation theory for associative fluids to the simple Mercedes-Benz model of water. We found that the theory reproduced well the physical properties of hot water, but was less successful in capturing the more structured hydrogen bonding that occurs in cold water. Here, we propose an improved version of the thermodynamic perturbation theory in which the effective density of the reference system is calculated self-consistently. The new theory is a significant improvement, giving good agreement with Monte Carlo simulations of the model, and predicting key anomalies of cold water, such as minima in the molar volume and large heat capacity, in addition to giving good agreement with the isothermal compressibility and thermal expansion coefficient.
Two-dimensional Stokes flow driven by elliptical paddles
Authors: Cox Stephen M. , Finn Matthew D.
Published: November 2007

A fast and accurate numerical technique is developed for solving the biharmonic equation in a multiply connected domain, in two dimensions. We apply the technique to the computation of slow viscous flow (Stokes flow) driven by multiple stirring rods. Previously, the technique has been restricted to stirring rods of circular cross section; we show here how the prior method fails for noncircular rods and how it may be adapted to accommodate general rod cross sections, provided only that for each there exists a conformal mapping to a circle. Corresponding simulations of the flow are described, and their stirring properties and energy requirements are discussed briefly. In particular the method allows an accurate calculation of the flow when flat paddles are used to stir a fluid chaotically.
Direct measurement of fluid velocity in an electrospinning jet using particle image velocimetry
Authors: Bellan Leon M. , Craighead Harold G. , Hinestroza Juan P.
Published: November 2007

By observing the movement of small fluorescent particles in an electrospinning jet, we have directly measured the fluid velocity along the jet axis. The correlation between these direct velocity measurements and the velocity calculated from the jet radius using volume conservation indicates when evaporation is a significant factor. Measurements of the fluid properties of the solution used in the experiment allow us to construct a plot of Deborah number as a function of position along the jet. Our data also indicate transverse movement at the beginning of the fluid jet, potentially indicating the precursor to the macroscopic bending instability.
Nanopatterning of Mn12-acetate single-molecule magnet films
Authors: Kim K. , Ford A. , Meenakshi V. , Teizer W. , Zhao H. , Dunbar K. R.
Published: November 2007

We report the fabrication of the artificial nanopatterns of Mn12-acetate films using e-beam lithography. Scanning electron micrographs and atomic force micrographs of the patterns reveal the minimum lateral size (∼50nm), height, and surface morphology of the patterns. X-ray photoelectron spectroscopy data indicate the presence of Mn12-acetate in the patterned structure. The thin film material indicates magnetic properties consistent with Mn12-acetate, supporting the conclusion that the lithographic chemicals used in this study do not interfere with the core properties of Mn12-acetate. The successful fabrication of Mn12-acetate nanopatterns enables a range of possibilities for designed hybrid systems with three-dimensional positional control on the nanometer scale.
The variable stripe-length method revisited: Improved analysis
Authors: Lange C. , Schwalm M. , Chatterjee S. , Rühle W. W. , Gerhardt N. C. , Johnson S. R. , Wang J.-B. , Zhang Y.-H.
Published: November 2007

The variable stripe length method described by Shaklee and Leheny, [Appl. Phys. Lett. 18, 475 (1971)] is a straightforward way to determine the steady-state gain spectrum of laser material. Here, common sources of error are identified and several new, robust ways of calculating the gain from the data are presented. The advantages of these methods are underlined by applying them to data obtained from a Ga(AsSb)∕GaAs∕(AlGa)As heterostructure.
Patterning of an amine-terminated nanolayer by extreme ultraviolet
Authors: Moon Sangwoon , Chung Sukmin , Jeon Cheolho , Park Chong-Yun , Hwang Han-Na , Hwang Chan-Cuk , Song Hajin , Shin Hyun-Joon
Published: November 2007

The adsorption of NH3 molecules on the Si(100)2×1 surface constructs a cleaner and more well-defined amine layer than self-assembled monolayer such as aminosilylated layer, which make it possible to study photoinduced reactions between amines and monochromatic light with shorter wavelength than ultraviolet, i.e., extreme ultraviolet and soft x ray. We report that the molecular layer of amine groups reacts with extreme ultraviolet and soft x ray, which can be used to make fine patterns on the amine-terminated layer. The amine patterning with the leading postoptical lithography using extreme ultraviolet could be applied to fabricating future molecular nanodevices.
Magnetocaloric properties of (La,RE)Fe11.4Si1.6 compounds (RE=Y,Gd)
Authors: Passamani E. C. , Takeuchi A. Y. , Alves A. L. , Demuner A. S. , Favre-Nicolin E. , Larica C. , Proveti J. R. , Gomes A. M.
Published: November 2007

The mechanosynthesis process has been applied in theLaFe11.4Si1.6 compound to reduce the undesirable segregated rich-Fe phases that impair its application as a solid magnetic refrigerant. The influence of La substitution (5 at. %) by Y or Gd atoms on the magnetic and magnetocaloric properties has been also studied. Y- and Gd-substituted compounds have a magnetic ordering temperature higher than the pure La compound. While the Y-substituted compound keeps a first-order-like magnetic transition feature, the Gd-substituted one seems to suppress it. The maximum value of the magnetic entropy change of the Y compound is roughly the same as the La compound (−18 J∕kg K) but with a magnetic entropy change peak significantly broader. For the Gd-compound case a drastic reduction of the magnetic entropy change (−7 J∕kg K) is found.
Effect of bias current on the resisitivity and photoconductivity of oxygen-deficient La2∕3Sr1∕3MnO3−δ thin films
Authors: Sheng Z. G. , Sun Y. P. , Zhu X. B. , Dai J. M. , Song W. H. , Yang Z. R.
Published: November 2007

The influence of bias current on resistivity and photoconductivity in oxygen-deficient La2∕3Sr1∕3MnO3−δ thin films has been investigated. There exists a giant resistance drop induced by dc electrical currents alone especially near the temperature of resistance peak (TP). Moreover, the photoconductivity emerges only when the current exceeds a threshold and this effect is quite different from magnetoresistance induced by magnetic fields. It is found that the magnitude of photoconductivity increases with increasing of bias current and the threshold current increases with decreasing temperatures and increasing magnetic fields. The magnitude of photoconductivity achieves 10.2% at temperature of 100K with light density of 4.3mW∕cm2 and current of 1mA. The current-assisted electroresistance and photoconductivity are discussed based on the delocalization of localized state by light illumination and bias current.
Influence of the reactor wall composition on radicals' densities and total pressure in Cl2 inductively coupled plasmas: I. Without silicon etching
Authors: Cunge G. , Sadeghi N. , Ramos R.
Published: November 2007

Laser absorption at 355nm is used to monitor the time variations of the Cl2 density in high-density industrial inductively coupled plasma. This technique is combined with the measurement of the gas temperature from the Doppler width of the 811.5nm line of argon, added as a trace gas and with the measurement of the total gas pressure with a Baratron gauge. These measurements permit to estimate the mole fractions of Cl2 and Cl species in Cl2 inductively coupled plasmas in a waferless reactor. The impact of the chemical nature of the reactor wall coatings on the Cl and Cl2 mole fractions is studied systematically. We show that under otherwise identical plasma conditions, the Cl mole fraction is completely different when the plasma is operated in SiOCl, AlF, CCl, or TiOCl coated reactors, because the homogeneous recombination probability of Cl atoms is strongly surface dependant. The Cl atom mole fraction reached at 100W radiofrequency power in SiOCl coated reactor (80%) is much higher than that obtained at 900W in a “clean” AlF reactor (40%). A simple zero-dimensional model permits to provide the recombination coefficient of Cl atoms, γrec: 0.005 on SiOCl film and about 0.3 on the other three coatings. It is proposed to get benefit of this very high sensitivity of Cl2 dissociation rate to the wall coating for the control of the chamber wall status from the Cl2 density measurements in standard conditions.
Ge nanocrystals in lanthanide-based Lu2O3 high-k dielectric for nonvolatile memory applications
Authors: Chan M. Y. , Lee P. S. , Ho V. , Seng H. L.
Published: November 2007

Ge nanocrystals embedded in lanthanide-based high-k dielectric (amorphous Lu2O3 in this work) were formed using pulsed laser deposition followed by rapid thermal annealing in N2 ambient. The formation and evolution of the Ge nanocrystals have been studied using transmission electron microscopy (TEM), x-ray photoelectron spectroscopy (XPS) in conjunction with depth profiling, and secondary ion mass spectroscopy (SIMS) analysis. Plan-view TEM images indicated that the formation of nanocrystals was first initiated during the deposition process. The annealing treatment significantly enhanced the nucleation of Ge nanocrystals, resulting in a high areal density of 7×1011cm−2 Ge nanocrystals with a mean size of about 6nm in diameter in the amorphous Lu2O3 matrix. XPS depth profile analysis revealed that Ge nanocrystals were predominantly formed from the precipitation of Ge nuclei from the oxide phase. A low annealing temperature of 400°C was sufficient to dissociate the GeO2 and GeOx leading to the formation of Ge nanocrystals. An accumulation of Ge species close to the upper Ge∕Lu2O3 interface was observed from XPS and SIMS depth profile analysis. Different charge storage behaviors observed from the memory capacitor devices before and after annealing could be correlated to the changes in structure and composition of the film. The memory capacitor device fabricated from the annealed sample showed efficient charge storage effect under a low operation voltage without significant initial charge decay.
Electrolyte effects on charge, polarization, and conduction in thin anodic Al2O3 films. I. Initial charge and temperature-dependent polarization
Authors: Hickmott T. W.
Published: November 2007

A sequence of three current-voltage (I-V) curves of Al–Al2O3–Au capacitors has been used to study the effect of anodizing electrolyte on Qin, the initial charge introduced into Al2O3 during anodization and the temperature dependence of polarization of anodic Al2O3. The first I-V curve, with VA<0V, polarizes the Al2O3 film; the difference between the next two I-V curves is a measure of polarization induced by the negative voltage. Two aqueous electrolytes, 0.1M ammonium pentaborate (bor-H2O) and 0.1M ammonium citrate (citrate), and one nonaqueous electrolyte, 0.1M ammonium pentaborate per liter of ethylene glycol (bor-gly), are used for anodizing; Al2O3 thicknesses are between 12 and 54nm. The galvanostatic anodizing rate is the same for anodizing in bor-H2O and bor-gly electrolytes after initial transients. The anodizing rate in citrate electrolyte is constant but is 0.7 times the rate in the other two electrolytes. Qin for Al2O3 films formed in bor-H2O and bor-gly is proportional to Al2O3 thickness; it is distributed throughout the film. The magnitude of Qin is ∼100 times greater for Al2O3 films formed in the aqueous electrolyte. Qin for Al2O3 films formed in citrate is nearly constant with thickness. Qin anneals out when I-V curves are measured. Two quantities are measured that depend on polarization of anodic Al2O3, QPK, and Qmax. QPK is due solely to polarization produced by negative bias. Both polarization and conduction currents contribute to Qmax. Both QPK and Qmax depend exponentially on the polarizing field. Maximum values of QPK for samples anodized in bor-H2O or citrate are ∼13 times larger than for Al2O3 formed in bor-gly; maximum values of Qmax are more than 100 times larger for anodic Al2O3 formed in aqueous electrolytes. The temperature dependence of Qmax is also less for Al2O3 films formed in bor-gly than for Al2O3 formed in bor-H2O or citrate.
Hole transport in molecularly doped naphthyl diamine
Authors: Tong K. L. , Tsang S. W. , Tsung K. K. , Tse S. C. , So S. K.
Published: November 2007

The effects of dopants on the hole-transporting properties of NPB, i.e., (N,N′-diphenyl-N,N′-bis(1-naphthyl)(1,1′-biphenyl)-4,4′ diamine), were studied by time-of-flight technique and admittance spectroscopy. Three dopants were chosen in this study. They were 4-dicyanmethylene-2-methyl-6-4H-pyran (DCM1), rubrene (RB), and tris-(8-hydroxyquinoline) aluminum (Alq3). It can be shown that DCM1 behaves as hole traps whereas Alq3 behaves as hole scatterers in NPB. Generally, both trapping and scattering lower hole mobilities in NPB. The hole mobilities decrease when DCM1 and Alq3 are introduced into NPB whereas the hole mobility remains nearly unchanged when RB is doped into NPB. The effect of doping on carrier dispersion is also studied.
Time dependent plasma properties during microarcing in radio frequency plasmas
Authors: Yin Y. , Allan S. Y. , Bilek M. M. M. , McKenzie D. R.
Published: November 2007

We report experimental results for time dependent plasma properties during microarcing in a rf plasma system. A cutoff discriminator bias voltage can be defined as a parameter representing plasma potential. The cutoff voltage during the microarcing does not exactly follow the dependence of floating potential. The plasma/ion density increases significantly after microarc initiation and then reduces slowly. We propose that a significant number of electrons enter the plasma in the initial period of the microarc and gain very high energy. These high energy electrons lose their energy through a relatively slower process of collisions while generating a significantly higher plasma density.
Improving efficiency of organic photovoltaic cells with pentacene-doped CuPc layer
Authors: Chen Wei-Bing , Xiang Hai-Feng , Xu Zong-Xiang , Yan Bei-Ping , Roy V. A. L. , Che Chi-Ming , Lai Pui-To
Published: November 2007

We have fabricated efficient heterojunction organic photovoltaic (OPV) cells based on pentacene-doped copper(II) phthalocyanine (CuPc) layer as donor and fullerene (C60) layer as acceptor. The power conversion efficiency of 4% pentacene-doped CuPc∕C60 OPV cell (3.06%) is increased by 77% compared with that of the standard CuPc∕C60 OPV cell (1.73%). The efficiency improvement can be attributed to the higher carrier mobility instead of the stronger photon absorption of the pentacene-doped CuPc layer.
Effects of different plasma species (atomic N, metastable N2*, and ions) on the optical properties of dilute nitride materials grown by plasma-assisted molecular-beam epitaxy
Authors: Oye Michael M. , Mattord Terry J. , Hallock Gary A. , Bank Seth R. , Wistey Mark A. , Reifsnider Jason M. , Ptak Aaron J. , Yuen Homan B. , Harris James S. , Holmes Archie L.
Published: November 2007

This letter studies the effects of atomic N, metastable N2*, and ionic species on the optical properties of dilute nitride materials. Ga0.8In0.2N0.01As0.99 was grown using a 1% N2 in Ar gas mix from an Applied-Epi Unibulb™ rf plasma source. Isonitrogen samples with and without ions were studied using various plasma operating conditions. Optical emission spectrometry was used to characterize relative proportions of different active nitrogen plasma species (atomic N and metastable N2*). Samples grown without ions and with a higher proportion of atomic N resulted in the best overall material quality, although this improvement was observed at high annealing temperatures. At lower annealing temperatures, increased blueshifts were observed for samples grown with a higher proportion of atomic N; however, there was no noticeable influence of ions on blueshift regardless of whether atomic N or metastable N2* was the dominant species present in the plasma. The key implication of this work is that it helps to elucidate a possible reason for some of the contradictory reports in the literature. The ions are not solely responsible for the commonly reported “plasma damage.” Furthermore, we demonstrate herein that atomic N and metastable N2* each have different effects on the optical properties of dilute nitride materials grown by plasma-assisted molecular-beam epitaxy.
Charge transport and intrinsic fluorescence in amyloid-like fibrils
Authors: del Mercato Loretta Laureana , Pompa Pier Paolo , Maruccio Giuseppe , Torre Antonio Della , Sabella Stefania , Tamburro Antonio Mario , Cingolani Roberto , Rinaldi Ross
Published: November 2007

The self-assembly of polypeptides into stable, conductive, and intrinsically fluorescent biomolecular nanowires is reported. We have studied the morphology and electrical conduction of fibrils made of an elastin-related polypeptide, poly(ValGlyGlyLeuGly). These amyloid-like nanofibrils, with a diameter ranging from 20 to 250 nm, result from self-assembly in aqueous solution at neutral pH. Their morphological properties and conductivity have been investigated by atomic force microscopy, scanning tunneling microscopy, and two-terminal transport experiments at the micro- and nanoscales. We demonstrate that the nanofibrils can sustain significant electrical conduction in the solid state at ambient conditions and have remarkable stability. We also show intrinsic blue-green fluorescence of the nanofibrils by confocal microscopy analyses. These results indicate that direct (label-free) excitation can be used to investigate the aggregation state or the polymorphism of amyloid-like fibrils (and possibly of other proteinaceous material) and open up interesting perspectives for the use of peptide-based nanowire structures, with tunable physical and chemical properties, for a wide range of nanobiotechnological and bioelectronic applications.
Genetically regulated epigenetic transcriptional activation of retrotransposon insertion confers mouse dactylaplasia phenotype
Authors: Kano Hiroki , Kurahashi Hiroki , Toda Tatsushi
Published: November 2007

Dactylaplasia, characterized by missing central digital rays, is an inherited mouse limb malformation that depends on two genetic loci. The first locus,
Dac
, is an insertional mutation around the dactylin gene that is inherited as a semidominant trait. The second locus is an unlinked modifier,
mdac
/
Mdac
, that is polymorphic among inbred strains.
Mdac
dominantly suppresses the dactylaplasia phenotype in mice carrying
Dac
. However, little is known about either locus or the nature of their interaction. Here we show that
Dac
is a LTR retrotransposon insertion caused by the type D mouse endogenous provirus element (MusD). This insertion exhibits different epigenetic states and spatiotemporally expresses depending on the
mdac/Mdac
modifier background. In dactylaplasia mutants (
Dac
/+
mdac/mdac
), the LTRs of the insertion contained unmethylated CpGs and active chromatin. Furthermore, MusD elements expressed ectopically at the apical ectodermal ridge of limb buds, accompanying the dactylaplasia phenotype. On the other hand, in
Dac
mutants carrying
Mdac
(
Dac
/+
Mdac/mdac
), the 5′ LTR of the insertion was heavily methylated and enriched with inactive chromatin, correlating with inhibition of the dactylaplasia phenotype. Ectopic expression was not observed in the presence of
Mdac
, which we refined to a 9.4-Mb region on mouse chromosome 13. We report a pathogenic mutation caused by MusD. Our findings indicate that ectopic expression from the MusD insertion correlates with the dactylaplasia phenotype and that
Mdac
acts as a defensive factor to protect the host genome from pathogenic MusD insertions.
β-arrestin 2 oligomerization controls the Mdm2-dependent inhibition of p53
Authors: Boularan Cédric , Scott Mark G. H. , Bourougaa Karima , Bellal Myriam , Esteve Emmanuel , Thuret Alain , Benmerah Alexandre , Tramier Marc , Coppey-Moisan Maité , Labbé-Jullié Catherine , Fåhraeus Robin , Marullo Stefano
Published: November 2007

β-arrestins (β-arrs), two ubiquitous proteins involved in serpentine heptahelical receptor regulation and signaling, form constitutive homo- and heterooligomers stabilized by inositol 1,2,3,4,5,6-hexakisphosphate (IP6). Monomeric β-arrs are believed to interact with receptors after agonist activation, and therefore, β-arr oligomers have been proposed to represent a resting biologically inactive state. In contrast to this, we report here that the interaction with and subsequent titration out of the nucleus of the protooncogene Mdm2 specifically require β-arr2 oligomers together with the previously characterized nucleocytoplasmic shuttling of β-arr2. Mutation of the IP6-binding sites impair oligomerization, reduce interaction with Mdm2, and inhibit p53-dependent antiproliferative effects of β-arr2, whereas the competence for receptor regulation and signaling is maintained. These observations suggest that the intracellular concentration of β-arr2 oligomers might control cell survival and proliferation.
Clonal interference in large populations
Authors: Park Su-Chan , Krug Joachim
Published: November 2007

Clonal interference, the competition between lineages arising from different beneficial mutations in an asexually reproducing population, is an important factor determining the tempo and mode of microbial adaptation. The standard theory of this phenomenon neglects the occurrence of multiple mutations as well as the correlation between loss by genetic drift and clonal competition, which is questionable in large populations. Working within the Wright–Fisher model with multiplicative fitness (no epistasis), we determine the rate of adaptation asymptotically for very large population sizes and show that the standard theory fails in this regime. Our study also explains the success of the standard theory in predicting the rate of adaptation for moderately large populations. Furthermore, we show that the nature of the substitution process changes qualitatively when multiple mutations are allowed for, because several mutations can be fixed in a single fixation event. As a consequence, the index of dispersion for counts of the fixation process displays a minimum as a function of population size, whereas the origination process of fixed mutations becomes completely regular for very large populations. We find that the number of mutations fixed in a single event is geometrically distributed as in the neutral case. These conclusions are based on extensive simulations combined with analytic results for the limit of infinite population size.
Mg
2+
mediates interaction between the voltage sensor and cytosolic domain to activate BK channels
Authors: Yang Huanghe , Hu Lei , Shi Jingyi , Delaloye Kelli , Horrigan Frank T. , Cui Jianmin
Published: November 2007

The voltage-sensor domain (VSD) of voltage-dependent ion channels and enzymes is critical for cellular responses to membrane potential. The VSD can also be regulated by interaction with intracellular proteins and ligands, but how this occurs is poorly understood. Here, we show that the VSD of the BK-type K
+
channel is regulated by a state-dependent interaction with its own tethered cytosolic domain that depends on both intracellular Mg
2+
and the open state of the channel pore. Mg
2+
bound to the cytosolic RCK1 domain enhances VSD activation by electrostatic interaction with Arg-213 in transmembrane segment S4. Our results demonstrate that a cytosolic domain can come close enough to the VSD to regulate its activity electrostatically, thereby elucidating a mechanism of Mg
2+
-dependent activation in BK channels and suggesting a general pathway by which intracellular factors can modulate the function of voltage-dependent proteins.
Arousal of cerebral cortex electroencephalogram consequent to high-frequency stimulation of ventral medullary reticular formation
Authors: Wu Hui-Bing , Stavarache Mihaela , Pfaff Donald W. , Kow Lee-Ming
Published: November 2007

We have theorized that large neurons in the ventral and medial reticular formation of the medulla are critical for both autonomic and cortical arousal. To test this theory, we anesthetized rats with urethane, lowered concentric bipolar stimulating electrodes into the medullary reticular formation, and implanted electroencephalogram (EEG) and ECG recording electrodes. We stimulated in the medulla with pulse frequencies ranging from 50 to 300 Hz while recording cortical EEG and ECG. These female rats were ovariectomized, and one subgroup was administered estradiol. Electrical stimulation at either 200 or 300 Hz among the large medullary reticular neurons in nucleus paragigantocellularis (PGi) caused a significant reduction in the portion of the EEG power spectrum represented by δ-waves (0.1–4 Hz) and θ-waves (4.1–8 Hz). Correspondingly, there were increases in γ-wave power (22–50 Hz), especially when using 300 Hz. Stimulation at ≤100 Hz produced fewer changes in cortical EEG. The major features of these results were not significantly different according to estradiol treatment. In contrast, estradiol administration significantly lowered ECG. Electrical stimulation in PGi increased ECG in vehicle control animals, but decreased it in estradiol-treated animals. Regarding the EEG, we conclude that, even in anesthetized animals, stimulation of PGi reticular neurons can increase cortical arousal and that high frequencies of stimulation amplify this effect.
Conditional inactivation of Fbxw7 impairs cell-cycle exit during T cell differentiation and results in lymphomatogenesis
Authors: Onoyama Ichiro , Tsunematsu Ryosuke , Matsumoto Akinobu , Kimura Taichi , de Alborán Ignacio Moreno , Nakayama Keiko , Nakayama Keiichi I.
Published: November 2007

Cell proliferation is strictly controlled during differentiation. In T cell development, the cell cycle is normally arrested at the CD4+CD8+ stage, but the mechanism underlying such differentiation-specific exit from the cell cycle has been unclear. Fbxw7 (also known as Fbw7, Sel-10, hCdc4, or hAgo), an F-box protein subunit of an SCF-type ubiquitin ligase complex, induces the degradation of positive regulators of the cell cycle, such as c-Myc, c-Jun, cyclin E, and Notch. FBXW7 is often mutated in a subset of human cancers. We have now achieved conditional inactivation of Fbxw7 in the T cell lineage of mice and found that the cell cycle is not arrested at the CD4+CD8+ stage in the homozygous mutant animals. The mutant mice manifested thymic hyperplasia as a result of c-Myc accumulation and eventually developed thymic lymphoma. In contrast, mature T cells of the mutant mice failed to proliferate in response to mitogenic stimulation and underwent apoptosis in association with accumulation of c-Myc and p53. These latter abnormalities were corrected by deletion of p53. Our results suggest that Fbxw7 regulates the cell cycle in a differentiation-dependent manner, with its loss resulting in c-Myc accumulation that leads to hyperproliferation in immature T cells but to p53-dependent cell-cycle arrest and apoptosis in mature T cells.
An emerging cyberinfrastructure for biodefense pathogen and pathogen–host data
Authors: Zhang C. , Crasta O. , Cammer S. , Will R. , Kenyon R. , Sullivan D. , Yu Q. , Sun W. , Jha R. , Liu D. , Xue T. , Zhang Y. , Moore M. , McGarvey P. , Huang H. , Chen Y. , Zhang J. , Mazumder R. , Wu C. , Sobral B.
Published: November 2007

The NIAID-funded Biodefense Proteomics Resource Center (RC) provides storage, dissemination, visualization and analysis capabilities for the experimental data deposited by seven Proteomics Research Centers (PRCs). The data and its publication is to support researchers working to discover candidates for the next generation of vaccines, therapeutics and diagnostics against NIAID's Category A, B and C priority pathogens. The data includes transcriptional profiles, protein profiles, protein structural data and host–pathogen protein interactions, in the context of the pathogen life cycle in vivo and in vitro. The database has stored and supported host or pathogen data derived from Bacillus, Brucella, Cryptosporidium, Salmonella, SARS, Toxoplasma, Vibrio and Yersinia, human tissue libraries, and mouse macrophages. These publicly available data cover diverse data types such as mass spectrometry, yeast two-hybrid (Y2H), gene expression profiles, X-ray and NMR determined protein structures and protein expression clones. The growing database covers over 23 000 unique genes/proteins from different experiments and organisms. All of the genes/proteins are annotated and integrated across experiments using UniProt Knowledgebase (UniProtKB) accession numbers. The web-interface for the database enables searching, querying and downloading at the level of experiment, group and individual gene(s)/protein(s) via UniProtKB accession numbers or protein function keywords. The system is accessible at http://www.proteomicsresource.org/.
Dynamical systems and the transition to turbulence in linearly stable shear flows
Authors: Eckhardt Bruno , Faisst Holger , Schmiegel Armin , Schneider Tobias M
Published: November 2007

Plane Couette flow and pressure-driven pipe flow are two examples of flows where turbulence sets in while the laminar profile is still linearly stable. Experiments and numerical studies have shown that the transition has features compatible with the formation of a strange saddle rather than an attractor. In particular, the transition depends sensitively on initial conditions and the turbulent state is not persistent but has an exponential distribution of lifetimes. Embedded within the turbulent dynamics are coherent structures, which transiently show up in the temporal evolution of the turbulent flow. Here we summarize the evidence for this transition scenario in these two flows, with an emphasis on lifetime studies in the case of plane Couette flow and on the coherent structures in pipe flow.
Nonlinear vortex development in rotating flows
Authors: Hewitt R.E , Mullin T , Tavener S.J , Khan M.A.I , Treacher P.D
Published: November 2007

We present the results of a combined experimental and numerical investigation into steady secondary vortex flows confined between two concentric right circular cylinders. When the flow is driven by the symmetric rotation of both end walls and the inner cylinder, toroidal vortex structures arise through the creation of stagnation points (in the meridional plane) at the inner bounding cylinder or on the mid-plane of symmetry. A detailed description of the flow regimes is presented, suggesting that a cascade of such vortices can be created. Experimental results are reported, which visualize some of the new states and confirm the prediction that they are stable to (mid-plane) symmetry-breaking perturbations.

We also present some brief results for the flows driven by the rotation of a single end wall. Vortex structures may also be observed at low Reynolds numbers in this geometry. We show that standard flow visualization methods lead to some interesting non-axisymmetric particle paths in this case.
Comparative genome analysis across a kingdom of eukaryotic organisms: Specialization and diversification in the Fungi
Authors: Cornell Michael J. , Alam Intikhab , Soanes Darren M. , Wong Han Min , Hedeler Cornelia , Paton Norman W. , Rattray Magnus , Hubbard Simon J. , Talbot Nicholas J. , Oliver Stephen G.
Published: November 2007

The recent proliferation of genome sequencing in diverse fungal species has provided the first opportunity for comparative genome analysis across a eukaryotic kingdom. Here, we report a comparative study of 34 complete fungal genome sequences, representing a broad diversity of Ascomycete, Basidiomycete, and Zygomycete species. We have clustered all predicted protein-encoding gene sequences from these species to provide a means of investigating gene innovations, gene family expansions, protein family diversification, and the conservation of essential gene functions—empirically determined in Saccharomyces cerevisiae—among the fungi. The results are presented with reference to a phylogeny of the 34 fungal species, based on 29 universally conserved protein-encoding gene sequences. We contrast this phylogeny with one based on gene presence and absence and show that, while the two phylogenies are largely in agreement, there are differences in the positioning of some species. We have investigated levels of gene duplication and demonstrate that this varies greatly between fungal species, although there are instances of coduplication in distantly related fungi. We have also investigated the extent of orthology for protein families and demonstrate unexpectedly high levels of diversity among genes involved in lipid metabolism. These analyses have been collated in the e-Fungi data warehouse, providing an online resource for comparative genomic analysis of the fungi.
28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
Authors: Miller Webb , Rosenbloom Kate , Hardison Ross C. , Hou Minmei , Taylor James , Raney Brian , Burhans Richard , King David C. , Baertsch Robert , Blankenberg Daniel , Kosakovsky Pond Sergei L. , Nekrutenko Anton , Giardine Belinda , Harris Robert S. , Tyekucheva Svitlana , Diekhans Mark , Pringle Thomas H. , Murphy William J. , Lesk Arthur , Weinstock George M. , Lindblad-Toh Kerstin , Gibbs Richard A. , Lander Eric S. , Siepel Adam , Haussler David , Kent W. James
Published: November 2007

This article describes a set of alignments of 28 vertebrate genome sequences that is provided by the UCSC Genome Browser. The alignments can be viewed on the Human Genome Browser (March 2006 assembly) at http://genome.ucsc.edu, downloaded in bulk by anonymous FTP from http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz28way, or analyzed with the Galaxy server at http://g2.bx.psu.edu. This article illustrates the power of this resource for exploring vertebrate and mammalian evolution, using three examples. First, we present several vignettes involving insertions and deletions within protein-coding regions, including a look at some human-specific indels. Then we study the extent to which start codons and stop codons in the human sequence are conserved in other species, showing that start codons are in general more poorly conserved than stop codons. Finally, an investigation of the phylogenetic depth of conservation for several classes of functional elements in the human genome reveals striking differences in the rates and modes of decay in alignability. Each functional class has a distinctive period of stringent constraint, followed by decays that allow (for the case of regulatory regions) or reject (for coding regions and ultraconserved elements) insertions and deletions.
The mineral marrucciite: monoclinic Hg3Pb16Sb18S46
Authors: Laufek František , Sejkora Jiří , Fejfarová Karla , Dušek Michal , Ozdín Daniel
Published: November 2007

Recently, a new mineral species, monoclinic marrucciite, mercury lead antimony sulfide, Hg3Pb16Sb18S46 [Orlandi et al. (2007). Eur. J. Mineral.
19, 267–279], was discovered in the Fe—Ba deposit of Buca della Vena, Apuan Alps (Italy). In that report, the crystal structure was refined to R = 0.096. Our new discovery of crystals of this sulfosalt in the Gelnica ore district, situated in the Spišsko-gemerské rudohorie mountain range, Slovak Republic, has now allowed a substantially more precise determination of the crystal structure (R = 0.024). The monoclinic unit cell contains 19 independent cation positions (including two mixed SbIII/PbII positions) and 23 independent S positions.
(Z)-2,5-Dimethyl-3,4-diphenylhex-3-ene-2,5-diol
Authors: Li Shu-Hong , Xu Cai-Hong
Published: November 2007

The title molecule, C20H24O2, shows a Z configuration with respect to the C=C double bond. The crystal structure is stabilized by intra- and intermolecular O—H...O hydrogen bonds.
[N,N′-Bis(2,6-dimethylphenyl)pentane-2,4-diiminato-κ2
N,N′]trichlorido(tetrahydrofuran-κO)zirconium
Authors: Fortuné Rose-Verla , Verguet Emilie , Oguadinma Paul O. , Schaper Frank
Published: November 2007

The nacnac (pentane-2,4-diiminato) ligand in the title compound, [Zr(C21H25N2)Cl3(C4H8O)], displays a κ2-coordination to the Zr center. Three chlorido ligands and a coordinated tetrahydrofuran (THF) molecule complete the octahedral environment of the metal. Despite the C
2 symmetry observed in the 1H NMR spectrum, the THF molecule is found trans to one of the N atoms of the nacnac ligand. The asymmetric unit contains two molecules. In one THF ligand one C atom and four H atoms are disordered over two sites in the ratio ca 0.58:0.42.
N-(5-Chloro-3-methyl-1-phenylpyrazol-4-ylcarbonyl)-N′-(4-methylphenyl)thiourea
Authors: Du Hai-Tang , Lu Ming , Zhou Wei-Yi , Sun Li-Li
Published: November 2007

The crystal structure of the title compound, C19H17ClN4OS, has been determined in order to elucidate the molecular conformation. The pyrazole ring makes dihedral angles of 74.3 (3)° and 2.9 (3)° with the phenyl and tolyl rings, respectively; these two six-membered rings are twisted by 71.6 (3)° with respect to each other. The crystal packing of the title compound is stabilized by intramolcular N—H...O and intermolcular N—H...S hydrogen bonds.
(E)-3-(2-Chloro-3,3,3-trifluoroprop-1-enyl)-N-(9,10-dioxo-9,10-dihydroanthracen-1-yl)-2,2-dimethylcyclopropanecarboxamide
Authors: Yan Fan-Yong , Liu Dong-Qing
Published: November 2007

In the title compound, C23H17ClF3NO3, the dihedral angle between the dihydroanthracene and cyclopropane ring systems is 58.5 (4)°. The amino H atom forms an intramolecular hydrogen bond to a carbonyl O atom of the dioxodihydroanthracene moiety. The crystal packing is further stabilized by an intermolecular C—H...F contact.
Diiodidobis(thioacetamide-κS)cadmium(II)
Authors: Zamilatskov Ilia A. , Buravlev Evgeny A. , Savinkina Elena V. , Roukk Natalya S. , Albov Dmitry V.
Published: November 2007

Thioacetamide complexes are used for the synthesis of metal sulfide powders. In the title molecular complex, [CdI2(C2H5NS)2], the CdII atom is located on a twofold rotation axis and is tetrahedrally coordinated by two iodine atoms and two thioacetamide molecules. The Cd—I distance is 2.7615 (17) Å and the Cd—S distance is 2.5586 (17) Å.
4-[(1,3-Dioxoisochroman-4-ylidene)hydroxymethyl]benzonitrile
Authors: Kakou-Yao Rita , Djande Abdoulaye , Kabore Leopold , Saba Adama , Aycard Jean Pierre
Published: November 2007

The crystal structure of the title compound, C17H9NO4, shows that the exocyclic enolic tautomer exists as it has been observed in solution. The structure is stabilized by intramolecular O—H...O hydrogen bonding.
Octane-1,8-diammonium dichloride monohydrate
Authors: Blerk Charmaine van , Kruger Gert J.
Published: November 2007

The crystal structure of the title compound, C8H22N2
2+·2Cl−·H2O, exhibits layered stacking in which the organic cations are separated by inorganic layers containing the chloride anions and the water molecules. The diammonium octane chain straddles a centre of inversion and the single water of crystallization sits on a twofold rotation axis. The diammonium octane chains pack in parallel layers with every second hydrocarbon layer alternating in a staggered configuration with respect to the previous layer. The three-dimensional hydrogen-bonding network links the organic and inorganic layers together in a highly intricate and complex manner. The torsion angles of the hydrocarbon chain deviate from 180° as a result of hydrogen-bonding interactions to the water molecule and the surrounding chloride anions.
4-(Acetylaminomethyl)-1-methylpyridinium iodide
Authors: Slawin Alexandra M. Z. , Harrison William T. A.
Published: November 2007

In the title compound, C9H13N2O+·I−, the dihedral angle between the aromatic ring and the N-acetyl group is 73.93 (8)°. In the crystal structure, the cation and anion interact by way of an N—H...I hydrogen bond.
A second polymorph of 1-(carboxymethyl)-5-fluorouracil
Authors: Zhang Qiao-Chu , Shu Zhan , Shen Liang , Wang Qi , Jin Zhi-Min
Published: November 2007

The molecular structure of the title compound (systematic name: 5-fluoro-2,4,-dioxo-1,2,3,4-tetrahydropyrimidine-1-acetic acid), C6H5FN2O4, is essentially identical to that in the previously reported polymorph [Zhang et al. (2006). Z. Kristallogr. New Cryst. Struct.
221, 57–58]. The molecules are linked by O—H...O, N—H...O and weak C—H...O hydrogen bonds to form layers parallel to the (100) plane.
(11R)-13-(1-Naphthylmethylamino)-4,5-epoxy-11,13-dihydrocostunolide
Authors: Nasim Shama , Parkin Sean , Crooks Peter A.
Published: November 2007

Crystals of the title compound, C26H31NO3, were obtained by the reaction of 1-naphthylmethylamine with parthenolide. X-ray crystal structure determination reveals a stacked conformation between the cyclodecane ring of the parthenolide moiety and the pendant naphthalene ring. The configuration of the new chiral center at C11 (the point of attachment of the naphthylmethylamino side group) in the title compound is R, establishing the stereospecificity of the amination reaction.