bluuebunny/crossref_metadata_2025 huggingface dataset:
Diet‐induced Renal Changes in Zucker Rats Are Ameliorated by the Superoxide Dismutase Mimetic TEMPOL
Authors: Ebenezer Philip J. , Mariappan Nithya , Elks Carrie M. , Haque Masudul , Francis Joseph
Published: May 2009

Diabetic nephropathy is the leading cause of renal failure in the United States. The obese Zucker rat (OZR; fa/fa) is a commonly used model of type 2 diabetes and metabolic syndrome (MetS), and of the nephropathy and renal oxidative stress commonly seen in these disorders. Heterozygous lean Zucker rats (LZRs; fa/+) are susceptible to high‐fat diet (HFD)‐induced obesity and MetS. The present study was designed to investigate whether 4‐hydroxy‐2,2,6,6‐tetramethylpiperidine‐N‐oxyl (TEMPOL), a membrane‐permeable radical scavenger, could alleviate the renal effects of MetS in OZR and LZR fed a HFD, which resembles the typical “Western” diet. OZR and LZR were fed a HFD (OZR‐HFD and LZR‐HFD) or regular diet (OZR‐RD and LZR‐RD) and allowed free access to drinking water or water containing 1 mmol/l TEMPOL for 10 weeks. When compared to OZR‐RD animals, OZR‐HFD animals exhibited significantly higher levels of total renal cortical reactive oxygen species (ROS) production, plasma lipids, insulin, C‐reactive protein, blood urea nitrogen (BUN), creatinine (Cr), and urinary albumin excretion (P < 0.05); these changes were accompanied by a significant decrease in plasma high‐density lipoprotein levels (P < 0.05). The mRNA expression levels of desmin, tumor necrosis factor‐α (TNF‐α), nuclear factor κB (NFκB), and NAD(P)H oxidase‐1 (NOX‐1) were significantly higher in the renal cortical tissues of OZR‐HFD animals; NFκB p65 DNA binding activity as determined by electrophoretic mobility shift assay was also significantly higher in these animals. The same trends were noted in LZR‐HFD animals. Our data demonstrate that TEMPOL may prove beneficial in treating the early stages of the nephropathy often associated with MetS.
Pseudomonas aeruginosa MurE amide ligase: enzyme kinetics and peptide inhibitor
Authors: Paradis-Bleau Catherine , Lloyd Adrian , Sanschagrin François , Maaroufi Halim , Clarke Tom , Blewett Anne , Dowson Chris , Roper David I. , Bugg Timothy D. H. , Levesque Roger C.
Published: May 2009

The enzyme kinetics of the amide ligase MurE, a cell wall biosynthesis enzyme, from Pseudomonas aeruginosa were determined using the synthesized nucleotide substrate UDP-MurNAc-Ala-Glu (uridine 5′-diphosphoryl N-acetylmuramoyl-L-alanyl-D-glutamate). When coupled to a competitive bio-panning technique using a M13 phage display library encoding ∼2.7×109 random peptide permutations and the specific substrates meso-A2pm (meso-diaminopimelic acid) and ATP, a peptide inhibitor of MurE was identified. The MurEp1 dodecamer selected and synthesized inhibited MurE ATPase activity with an IC50 value of 500 μM. The inhibition was shown to be time-dependent and was reversed by the addition of meso-A2pm or UDP-MurNAc-Ala-Glu during the pre-incubation step. Kinetic analysis defined MurEp1 as a mixed inhibitor against both substrates with Ki values of 160 and 80 μM respectively. MurEp1 was found to interfere in meso-A2pm and UDP-MurNAc-Ala-Glu binding necessary for amide bond formation. Modelling of Ps. aeruginosa MurE and docking of MurEp1 on the Ps. aeruginosa MurE surface indicated that MurEp1 binds at the juxtaposition of both meso-A2pm- and UDP-MurNAc-Ala-Glu-binding sites in the closed conformational state of the enzyme. Identification of the MurEp1 residues involved in MurE binding and inhibition will allow the development of a novel class of inhibitors having a novel mode of action against MurE.
Functional characterization of LePGT1, a membrane-bound prenyltransferase involved in the geranylation of p-hydroxybenzoic acid
Authors: Ohara Kazuaki , Muroya Ayumu , Fukushima Nobuhiro , Yazaki Kazufumi
Published: May 2009

The AS-PT (aromatic substrate prenyltransferase) family plays a critical role in the biosynthesis of important quinone compounds such as ubiquinone and plastoquinone, although biochemical characterizations of AS-PTs have rarely been carried out because most members are membrane-bound enzymes with multiple transmembrane α-helices. PPTs [PHB (p-hydroxybenzoic acid) prenyltransferases] are a large subfamily of AS-PTs involved in ubiquinone and naphthoquinone biosynthesis. LePGT1 [Lithospermum erythrorhizon PHB geranyltransferase] is the regulatory enzyme for the biosynthesis of shikonin, a naphthoquinone pigment, and was utilized in the present study as a representative of membrane-type AS-PTs to clarify the function of this enzyme family at the molecular level. Site-directed mutagenesis of LePGT1 with a yeast expression system indicated three out of six conserved aspartate residues to be critical to the enzymatic activity. A detailed kinetic analysis of mutant enzymes revealed the amino acid residues responsible for substrate binding were also identified. Contrary to ubiquinone biosynthetic PPTs, such as UBIA in Escherichia coli which accepts many prenyl substrates of different chain lengths, LePGT1 can utilize only geranyl diphosphate as its prenyl substrate. Thus the substrate specificity was analysed using chimeric enzymes derived from LePGT1 and UBIA. In vitro and in vivo analyses of the chimeras suggested that the determinant region for this specificity was within 130 amino acids of the N-terminal. A 3D (three-dimensional) molecular model of the substrate-binding site consistent with these biochemical findings was generated.
Hsp70 is required for optimal cell proliferation in mouse A6 mesoangioblast stem cells
Authors: Turturici Giuseppina , Geraci Fabiana , Candela Maria E. , Cossu Giulio , Giudice Giovanni , Sconzo Gabriella
Published: May 2009

Mouse Hsp70 (70 kDa heat shock protein) is preferentially induced by heat or stress stimuli. We previously found that Hsp70 is constitutively expressed in A6 mouse mesoangioblast stem cells, but its possible role in these cells and the control of its basal transcription remained unexplored. Here we report that in the absence of stress, Ku factor is able to bind the HSE (heat shock element) consensus sequence in vitro, and in vivo it is bound to the proximal hsp70 promoter. In addition, we show that constitutive hsp70 transcription depends on the co-operative interaction of different factors such as Sp1 (specificity protein 1) and GAGA-binding protein with Ku factor, which binds the HSE consensus sequence. We used mRNA interference assays to select knockdown cell clones. These cells were able to respond to heat stress by producing a large amount of Hsp70, and produced the same amount of Hsp70 as that synthesized by stressed A6 cells. However, severe Hsp70 knockdown cells had a longer duplication time, suggesting that constitutive Hsp70 expression has an effect on the rate of proliferation.
Thioesterase superfamily member 2 (Them2)/acyl-CoA thioesterase 13 (Acot13): a homotetrameric hotdog fold thioesterase with selectivity for long-chain fatty acyl-CoAs
Authors: Wei Jie , Kang Hye Won , Cohen David E.
Published: May 2009

Them2 (thioesterase superfamily member 2) is a 140-amino-acid protein of unknown biological function that comprises a single hotdog fold thioesterase domain. On the basis of its putative association with mitochondria, accentuated expression in oxidative tissues and interaction with StarD2 (also known as phosphatidylcholine-transfer protein, PC-TP), a regulator of fatty acid metabolism, we explored whether Them2 functions as a physiologically relevant fatty acyl-CoA thioesterase. In solution, Them2 formed a stable homotetramer, which denatured in a single transition at 59.3 °C. Them2 exhibited thioesterase activity for medium- and long-chain acyl-CoAs, with Km values that decreased exponentially as a function of increasing acyl chain length. Steady-state kinetic parameters for Them2 were characteristic of long-chain mammalian acyl-CoA thioesterases, with minimal values of Km and maximal values of kcat/Km observed for myristoyl-CoA and palmitoyl-CoA. For these acyl-CoAs, substrate inhibition was observed when concentrations approached their critical micellar concentrations. The acyl-CoA thioesterase activity of Them2 was optimized at physiological temperature, ionic strength and pH. For both myristoyl-CoA and palmitoyl-CoA, the addition of StarD2 increased the kcat of Them2. Enzymatic activity was decreased by the addition of phosphatidic acid/phosphatidylcholine small unilamellar vesicles. Them2 expression, which was most pronounced in mouse heart, was associated with mitochondria and was induced by activation of PPARα (peroxisome-proliferator-activated receptor α). We conclude that, under biological conditions, Them2 probably functions as a homotetrameric long-chain acyl-CoA thioesterase. Accordingly, Them2 has been designated as the 13th member of the mammalian acyl-CoA thioesterase family, Acot13.
The RhoU/Wrch1 Rho GTPase gene is a common transcriptional target of both the gp130/STAT3 and Wnt-1 pathways
Authors: Schiavone Davide , Dewilde Sarah , Vallania Francesco , Turkson James , Di Cunto Ferdinando , Poli Valeria
Published: May 2009

STAT3 (signal transducer and activator of transcription 3) is a transcription factor activated by cytokines, growth factors and oncogenes, whose activity is required for cell survival/proliferation of a wide variety of primary tumours and tumour cell lines. Prominent among its multiple effects on tumour cells is the stimulation of cell migration and metastasis, whose functional mechanisms are however not completely characterized. RhoU/Wrch1 (Wnt-responsive Cdc42 homologue) is an atypical Rho GTPase thought to be constitutively bound to GTP. RhoU was first identified as a Wnt-1-inducible mRNA and subsequently shown to act on the actin cytoskeleton by stimulating filopodia formation and stress fibre dissolution. It was in addition recently shown to localize to focal adhesions and to Src-induced podosomes and enhance cell migration. RhoU overexpression in mammary epithelial cells stimulates quiescent cells to re-enter the cell cycle and morphologically phenocopies Wnt-1-dependent transformation. In the present study we show that Wnt-1-mediated RhoU induction occurs at the transcriptional level. Moreover, we demonstrate that RhoU can also be induced by gp130 cytokines via STAT3, and we identify two functional STAT3-binding sites on the mouse RhoU promoter. RhoU induction by Wnt-1 is independent of β-catenin, but does not involve STAT3. Rather, it is mediated by the Wnt/planar cell polarity pathway through the activation of JNK (c-Jun N-terminal kinase). Both the so-called non-canonical Wnt pathway and STAT3 are therefore able to induce RhoU, which in turn may be involved in mediating their effects on cell migration.
Receptor-associated protein (RAP) has two high-affinity binding sites for the low-density lipoprotein receptor-related protein (LRP): consequences for the chaperone functions of RAP
Authors: Jensen Jan K. , Dolmer Klavs , Schar Christine , Gettins Peter G. W.
Published: May 2009

RAP (receptor-associated protein) is a three domain 38 kDa ER (endoplasmic reticulum)-resident protein that is a chaperone for the LRP (low-density lipoprotein receptor-related protein). Whereas RAP is known to compete for binding of all known LRP ligands, neither the location, the number of binding sites on LRP, nor the domains of RAP involved in binding is known with certainty. We have systematically examined the binding of each of the three RAP domains (D1, D2 and D3) to tandem and triple CRs (complement-like repeats) that span the principal ligand-binding region, cluster II, of LRP. We found that D3 binds with low nanomolar affinity to all (CR)2 species examined. Addition of a third CR domain increases the affinity for D3 slightly. A pH change from 7.4 to 5.5 gave only a 6-fold increase in Kd for D3 at 37 °C, whereas temperature change from 22 °C to 37 °C has a similar small effect on affinity, raising questions about the recently proposed D3-destabilization mechanism of RAP release from LRP. Surprisingly, and in contrast to literature suggestions, D1 and D2 also bind to most (CR)2 and (CR)3 constructs with nanomolar affinity. Although this suggested that there might be three high-affinity binding sites in RAP for LRP, studies with intact RAP showed that only two binding sites are available in the intact chaperone. These findings suggest a new model for RAP to function as a folding chaperone and also for the involvement of YWTD domains in RAP release from LRP in the Golgi.
Limb-specific and cross-transfer effects of arm-crank exercise training in patients with symptomatic peripheral arterial disease
Authors: Tew Garry , Nawaz Shah , Zwierska Irena , Saxton John M.
Published: May 2009

Arm cranking is a useful alternative exercise modality for improving walking performance in patients with intermittent claudication; however, the mechanisms of such an improvement are poorly understood. The main aim of the present study was to investigate the effects of arm-crank exercise training on lower-limb O2 delivery in patients with intermittent claudication. A total of 57 patients with intermittent claudication (age, 70±8 years; mean±S.D.) were randomized to an arm-crank exercise group or a non-exercise control group. The exercise group trained twice weekly for 12 weeks. At baseline and 12 weeks, patients completed incremental tests to maximum exercise tolerance on both an arm-crank ergometer and a treadmill. Respiratory variables were measured breath-by-breath to determine peak V̇O2 (O2 uptake) and ventilatory threshold. Near-IR spectroscopy was used in the treadmill test to determine changes in calf muscle StO2 (tissue O2 saturation). Patients also completed a square-wave treadmill-walking protocol to determine V̇O2 kinetics. A total of 51 patients completed the study. In the exercise group, higher maximum walking distances (from 496±250 to 661±324 m) and peak V̇O2 values (from 17.2±2.7 to 18.2±3.4 ml·kg−1 of body mass·min−1) were recorded in the incremental treadmill test (P<0.05). After training, there was also an increase in time to minimum StO2 (from 268±305 s to 410±366 s), a speeding of V̇O2 kinetics (from 44.7±10.4 to 41.3±14.4 s) and an increase in submaximal StO2 during treadmill walking (P<0.05). There were no significant changes in the control group. The results suggest that the improvement in walking performance after arm-crank exercise training in patients with intermittent claudication is attributable, at least in part, to improved lower-limb O2 delivery.
Thermoelectric properties of quantum dot chains
Authors: Yadav A. , Pipe K. P. , Ye W. , Goldman R. S.
Published: May 2009

We have studied the thermoelectric properties of quantum dot (QD) chain nanocomposites in which the QDs are aligned to form chains. In both the InAs/GaAs and Ge/Si systems, we use a constant relaxation time approximation to calculate and compare the electrical conductivity, Seebeck coefficient, and thermoelectric power factor for QD chains, three-dimensional ordered QD arrays, random QD arrays, and bulk GaAs or Si. Our calculations suggest that the incorporation of QD chains into a matrix increases its thermoelectric power factor by a factor of 3 (1.5) for the InAs/GaAs (Ge/Si) system.
Nuclear magnetic resonance signal dynamics of liquids in the presence of distant dipolar fields, revisited
Authors: Barros Wilson , Gochberg Daniel F. , Gore John C.
Published: May 2009

The description of the nuclear magnetic resonance magnetization dynamics in the presence of long-range dipolar interactions, which is based upon approximate solutions of Bloch–Torrey equations including the effect of a distant dipolar field, has been revisited. New experiments show that approximate analytic solutions have a broader regime of validity as well as dependencies on pulse-sequence parameters that seem to have been overlooked. In order to explain these experimental results, we developed a new method consisting of calculating the magnetization via an iterative formalism where both diffusion and distant dipolar field contributions are treated as integral operators incorporated into the Bloch–Torrey equations. The solution can be organized as a perturbative series, whereby access to higher order terms allows one to set better boundaries on validity regimes for analytic first-order approximations. Finally, the method legitimizes the use of simple analytic first-order approximations under less demanding experimental conditions, it predicts new pulse-sequence parameter dependencies for the range of validity, and clarifies weak points in previous calculations.
A hard x-ray nanoprobe for scanning and projection nanotomography
Authors: Bleuet Pierre , Cloetens Peter , Gergaud Patrice , Mariolle Denis , Chevalier Nicolas , Tucoulou Rémi , Susini Jean , Chabli Amal
Published: May 2009

To fabricate and qualify nanodevices, characterization tools must be developed to provide a large panel of information over spatial scales spanning from the millimeter down to the nanometer. Synchrotron x-ray-based tomography techniques are getting increasing interest since they can provide fully three-dimensional (3D) images of morphology, elemental distribution, and crystallinity of a sample. Here we show that by combining suitable scanning schemes together with high brilliance x-ray nanobeams, such multispectral 3D volumes can be obtained during a single analysis in a very efficient and nondestructive way. We also show that, unlike other techniques, hard x-ray nanotomography allows reconstructing the elemental distribution over a wide range of atomic number and offers truly depth resolution capabilities. The sensitivity, 3D resolution, and complementarity of our approach make hard x-ray nanotomography an essential characterization tool for a large panel of scientific domains.
Molecular-dynamics simulations of stacking-fault-induced dislocation annihilation in prestrained ultrathin single-crystalline copper films
Authors: Kolluri Kedarnath , Gungor M. Rauf , Maroudas Dimitrios
Published: May 2009

We report results of large-scale molecular-dynamics simulations of dynamic deformation under biaxial tensile strain of prestrained single-crystalline nanometer-scale-thick face-centered cubic (fcc) copper films. Our results show that stacking faults, which are abundantly present in fcc metals, may play a significant role in the dissociation, cross slip, and eventual annihilation of dislocations in small-volume structures of fcc metals. The underlying mechanisms are mediated by interactions within and between extended dislocations that lead to annihilation of Shockley partial dislocations or formation of perfect dislocations. Our findings demonstrate dislocation starvation in small-volume structures with ultrathin film geometry, governed by a mechanism other than dislocation escape to free surfaces, and underline the significant role of geometry in determining the mechanical response of metallic small-volume structures.
Image formation, resolution, and height measurement in scanning ion conductance microscopy
Authors: Rheinlaender Johannes , Schäffer Tilman E.
Published: May 2009

Scanning ion conductance microscopy (SICM) is an emerging tool for the noncontact investigation of biological samples such as live cells. It uses an ion current through the opening of a tapered nanopipette filled with an electrolyte for topography measurements. Despite its successful application to numerous systems no systematic investigation of the image formation process has yet been performed. Here, we use finite element modeling to investigate how the scanning ion conductance microscope images small particles on a planar surface, providing a fundamental characterization of the imaging process. We find that a small particle appears with a height that is only a fraction of its actual height. This has significant consequences for the quantitative interpretation of SICM images. Furthermore, small and low particles are imaged as rings in certain cases. This can cause small, closely spaced particles to appear with a lateral orientation that is rotated by 90°. Considering both real space and spatial frequency space we find that a reasonable and useful definition of lateral resolution of SICM is the smallest distance at which two small particles can clearly be resolved from each other in an image. We find that this resolution is approximately equal to three times the inner radius of the pipette tip opening.
Two- and three-photon absorption of organic ionic pyrylium based materials
Authors: Jha Prakash Chandra , Luo Yi , Polyzos Ioannis , Persephonis Peter , Ågren Hans
Published: May 2009

Pyrylium dyes having the same basic chemical structure, differing only to a specific substituent, have been used as novel materials for multiphoton three-dimensional data storage. Electronic absorption spectra, two-photon and three-photon absorption properties of this class of pyrylium dyes, have been studied theoretically and compared to experimental results. The effects of the counteranion, the surrounding solvent, and electron releasing and electron withdrawing groups in specific positions of the basic structure have been explored in detail. It is argued that on grounds of the quality of experimental spectroscopic agreement, the computed two- and three-photon data may be used in pulse propagation simulations of three-dimensional recording in optical memories.
Influence of polarization induced electric fields on the wavelength and the refractive index of intersubband transitions in AlN/GaN coupled double quantum wells
Authors: Cen L. B. , Shen B. , Qin Z. X. , Zhang G. Y.
Published: May 2009

The influence of polarization induced electric fields on the wavelength and the refractive index of intersubband transitions (ISBTs) in AlN/GaN coupled double quantum wells (CDQWs) has been performed by solving Schrödinger and Poisson equations self-consistently. It is found that the intersubband refractive index change of the ISBT between the ground state and the second excited state (1odd-2odd ISBT) increases, while that of the ISBT between the ground state and the third excited state (1odd-2even ISBT) decreases with the increase of the polarization induced electric fields. The maximal intersubband refractive index change of the 1odd-2odd ISBT can be up to 0.142. The results are finally used to discuss the prospects of nitride quantum wells for electric-optical modulation via cross-phase modulation operating within optical communication wavelength range.
Constructal entransy dissipation minimization of an electromagnet
Authors: Chen Lingen , Wei Shuhuan , Sun Fengrui
Published: May 2009

How to determine the optimal distribution of high conductivity material through the given volume such that the heat generated at every point was transferred most effectively to its boundary has become the focus of attention in the current constructal theory literature. In general, the minimization of maximum temperature difference in the volume is taken as the optimization objective. A physical quantity, entransy, has been identified as a basis for optimizing heat transfer processes in terms of the analogy between heat and electrical conduction recently. Heat transfer analyses show that the entransy of an object describes its heat transfer ability, as the electrical energy in a capacitor describes its charge transfer ability. Entransy dissipation occurs during heat transfer processes, as a measure of the heat transfer irreversibility with the dissipation related thermal resistance. Based on entransy dissipation, the mean temperature difference of solenoid (electromagnet) with high thermal conductivity material inserted is deduced, which can be taken as the fundamental for heat transfer optimization using the extremum principle of entransy dissipation. Then, the electromagnet working at steady state (constant magnetic field, constant heat generating rate per unit volume) is optimized for entransy dissipation minimization (i.e., mean temperature difference minimization) with and without volume constraint. The variation of minimum mean temperature difference with volume and magnetic field and the corresponding optimal constructs are obtained. The effect of high thermal conductivity material on the magnetic field is analyzed. The optimization results show that for fixed G parameter and ϕ, the minimum mean temperature difference decreases as the number of cooling disks n increases but the decreasing magnitude of minimum mean temperature difference is relatively decreased. As n increases, the radius of the solenoid decreases, the length of the solenoid increases, and the volume decreases. The solenoid optimized based on minimization of entransy dissipation with fixed magnetic induction is considerably larger than the winding optimized solely from the electromagnetic point of view. The mean temperature difference decrease as the volume increases.
Nonadiabatic dynamics at metal surfaces: Independent-electron surface hopping
Authors: Shenvi Neil , Roy Sharani , Tully John C.
Published: May 2009

Recent experiments have shown convincing evidence for nonadiabatic energy transfer from adsorbate degrees of freedom to surface electrons during the interaction of molecules with metal surfaces. In this paper, we propose an independent-electron surface hopping algorithm for the simulation of nonadiabatic gas-surface dynamics. The transfer of energy to electron-hole pair excitations of the metal is successfully captured by hops between electronic adiabats. The algorithm is able to account for the creation of multiple electron-hole pairs in the metal due to nonadiabatic transitions. Detailed simulations of the vibrational relaxation of nitric oxide on a gold surface, employing a multistate potential energy surface fit to density functional theory calculations, confirm that our algorithm can capture the underlying physics of the inelastic scattering process.
Application of laser-accelerated protons to the demonstration of DNA double-strand breaks in human cancer cells
Authors: Yogo A. , Sato K. , Nishikino M. , Mori M. , Teshima T. , Numasaki H. , Murakami M. , Demizu Y. , Akagi S. , Nagayama S. , Ogura K. , Sagisaka A. , Orimo S. , Nishiuchi M. , Pirozhkov A. S. , Ikegami M. , Tampo M. , Sakaki H. , Suzuki M. , Daito I. , Oishi Y. , Sugiyama H. , Kiriyama H. , Okada H. , Kanazawa S. , Kondo S. , Shimomura T. , Nakai Y. , Tanoue M. , Sasao H. , Wakai D. , Bolton P. R. , Daido H.
Published: May 2009

We report the demonstrated irradiation effect of laser-accelerated protons on human cancer cells. In vitro (living) A549 cells are irradiated with quasimonoenergetic proton bunches of 0.8–2.4 MeV with a single bunch duration of 15 ns. Irradiation with the proton dose of 20 Gy results in a distinct formation of γ-H2AX foci as an indicator of DNA double-strand breaks generated in the cancer cells. This is a pioneering result that points to future investigations of the radiobiological effects of laser-driven ion beams. Unique high-current and short-bunch features make laser-driven proton bunches an excitation source for time-resolved determination of radical yields.
Nonequilibrium molecular dynamics simulations of vibrational energy relaxation of HOD in D2O
Authors: Kandratsenka Alexander , Schroeder Jörg , Schwarzer Dirk , Vikhrenko Vyacheslav S.
Published: May 2009

Vibrational energy relaxation of HOD in deuterated water is investigated performing classical nonequilibrium molecular dynamics simulations. A flexible SPC/E model is employed to describe the intermolecular interactions and the intramolecular potential of the D2O solvent. A more accurate intramolecular potential is used for HOD. Our results for the OH stretch, OD stretch, and HOD bend vibrational relaxation times are 2.7, 0.9, and 0.57 ps, respectively. Exciting the OH stretching mode the main relaxation pathway involves a transition to the bending vibration. These results are in agreement with recent semiclassical Landau–Teller calculations. Contrary to this previous work, however, we observe a strong coupling of bending and OH stretching mode to the HOD rotation. As a result almost half of the total vibrational energy is transferred through the HOD rotation to the bath. At the same time the most efficient acceptor mode is the D2O rotation indicating the importance of resonant libration-to-libration energy transfer. We also find significant vibrational excitation of the D2O bending mode of the D2O solvent by V-V energy transfer from the HOD bending mode.
Diffusion-controlled reaction on an elliptic site
Authors: Strieder William
Published: May 2009

The exact analytical solution for the concentration profile of a diffusion-controlled reaction at an elliptic site is presented. The resulting site reaction rate includes a factor of pi, the “diameter” of the major axis, the external reactant concentration, and the diffusion coefficient, divided by the complete elliptic integral of the first kind with an eccentricity squared argument. This rate reduces with zero eccentricity to the simple well-known form for diffusion control at a circular site. A comparison of these two rates for fixed site area permits a study of site shape on diffusion-controlled reaction rates. The reaction rate enhancement from the circular site case, which always occurs for noncircular site shapes, is discussed in the context of important site reactions in chemical physics and biophysics.
TIGER2: An improved algorithm for temperature intervals with global exchange of replicas
Authors: Li Xianfeng , Latour Robert A. , Stuart Steven J.
Published: May 2009

An empirical sampling method for molecular simulation based on “temperature intervals with global exchange of replicas” (TIGER2) has been developed to reduce the high demand for computational resources and the low computational efficiency of the conventional replica-exchange molecular dynamics (REMD) method. This new method overcomes the limitation of its previous version, called TIGER, which requires the assumption of constant heat capacity during quenching of replicas from elevated temperatures to the baseline temperature. The robustness of the TIGER2 method is examined by comparing it against a Metropolis Monte Carlo simulation for sampling the conformational distribution of a single butane molecule in vacuum, a REMD simulation for sampling the behavior of alanine dipeptide in explicit solvent, and REMD simulations for sampling the folding behavior of two peptides, (AAQAA)3 and chignolin, in implicit solvent. The agreement between the results from these conventional sampling methods and the TIGER2 simulations indicates that the TIGER2 algorithm is able to closely approximate a Boltzmann-weighted ensemble of states for these systems but without the limiting assumptions that were required for the original TIGER algorithm. TIGER2 is an efficient replica-exchange sampling method that enables the number of replicas that are used for a replica-exchange simulation to be substantially reduced compared to the conventional REMD method.
Development of a compact magnetic resonance imaging system for a cold room
Authors: Adachi Satoru , Ozeki Toshihiro , Shigeki Ryosuke , Handa Shinya , Kose Katsumi , Haishi Tomoyuki , Aoki Masaaki
Published: May 2009

A compact magnetic resonance imaging (MRI) system for a cold (−5 °C) room has been developed to acquire MR images below the freezing point of water. The MRI system consists of a 1.0 T permanent magnet, a higher-order shim coil set, and a gradient coil probe, installed in the cold room, and a compact MRI console installed in a room at normal temperature (20–25 °C). The most difficult problem for the installation of the MRI system in the cold room was the degradation of the field homogeneity of the permanent magnet shimmed at 25 °C. To overcome this problem, higher-order shim coils were developed and the temperature variation of the magnetic field distribution was measured using a standard phantom with and without shim coil currents. As a result, it was confirmed that the homogeneity (the difference between the minimum and maximum values) of the magnetic field in the 17×17×19 mm3 rectangular parallelepiped region was improved from 117 to 59 ppm using an appropriate combination of shim coil currents. A snowpack immersed in dodecane (C12H26) was imaged using a driven-equilibrium three-dimensional (3D) spin-echo sequence at −5 °C. The visualized 3D structure of the snowpack demonstrated the effectiveness of our approach.
Huge reduction in pressure drop of water, glycerol/water mixture, and aqueous solution of polyethylene oxide in high speed flows through micro-orifices
Authors: Hasegawa Tomiichi , Ushida Akiomi , Narumi Takatsune
Published: May 2009

Microfluid mechanics is one of the most exciting research areas in modern fluid mechanics and fluid engineering because of its many potential industrial and biological applications. In the present study, pressure drops (PDs) were measured for water, a 50/50 glycerol/water mixture, and a 0.1% aqueous solution of polyethylene oxide (PEO) 8000 flowing at high velocities through various sizes of micro-orifice. It was found that the measured PD of water and the glycerol/water mixture agrees with the prediction of the Navier–Stokes equation for orifices 100 and 400 μm in diameter, but it is lower for orifices less than 50 μm in diameter. In particular, the measured maximum PD was almost two orders of magnitude lower than the prediction for the 10 and 5 μm diameter orifices. The glycerol/water mixture, possessing a viscosity ten times higher than water, provided nearly the same PDs as water when the reduction was generated. The solution of PEO produced a lower PD than water and the glycerol/water mixture except for the 400 μm diameter orifice. Several factors, including orifice shape, deformation of orifice foil, wall slip, transition, cavitation, and elasticity were considered but the evidence suggests that the reduction in PD may be caused by wall slip or the elasticity induced in a flow of high elongational rate.
On the nature of radial transport across sheared zonal flows in electrostatic ion-temperature-gradient gyrokinetic tokamak plasma turbulence
Authors: Sánchez R. , Newman D. E. , Leboeuf J.-N. , Carreras B. A. , Decyk V. K.
Published: May 2009

It is argued that the usual understanding of the suppression of radial turbulent transport across a sheared zonal flow based on a reduction in effective transport coefficients is, by itself, incomplete. By means of toroidal gyrokinetic simulations of electrostatic, ion-temperature-gradient turbulence, it is found instead that the character of the radial transport is altered fundamentally by the presence of a sheared zonal flow, changing from diffusive to anticorrelated and subdiffusive. Furthermore, if the flows are self-consistently driven by the turbulence via the Reynolds stresses (in contrast to being induced externally), radial transport becomes non-Gaussian as well. These results warrant a reevaluation of the traditional description of radial transport across sheared flows in tokamaks via effective transport coefficients, suggesting that such description is oversimplified and poorly captures the underlying dynamics, which may in turn compromise its predictive capabilities.
Influence of global magnetic state on chemical interactions in high-pressure high-temperature synthesis of B2 Fe2Si
Authors: Ponomareva A. V. , Ruban A. V. , Dubrovinskaia N. , Dubrovinsky L. , Abrikosov I. A.
Published: May 2009

We show that effective chemical interactions in an alloy can be tuned by its global magnetic state, which opens exciting possibilities for materials synthesis. Using first-principles theory we demonstrate that at pressure of 20 GPa and at high temperatures, the effective chemical interactions in paramagnetic Fe–Si system are strongly influenced by the magnetic disorder favoring a formation of cubic Fe2Si phase with B2 structure, which is not present in the alloy phase diagram. Our experiments confirm theoretical predictions, and the B2 Fe2Si alloy is synthesized from Fe–Si mixture using multianvil press.
Synthesis and exchange bias effect of single-crystalline SrMn3O6−δ nanoribbons
Authors: Yu J. Y. , Tang S. L. , Zhang X. K. , Zhai L. , Shi Y. G. , Deng Y. , Du Y. W.
Published: May 2009

Single-crystalline SrMn3O6−δ nanoribbons (width of 30–500 nm and lengths of up to several hundred micrometers) are synthesized by a molten-salt method. In contrast with the antiferromagnetism in bulk SrMn3O6−δ, magnetization measurements show weak ferromagnetism in these nanoribbons at low temperature. In particular, a notable exchange-bias effect, which strongly depends on the cooling field, is observed in applied magnetic field H≤5 kOe. These results suggest that the exchange bias in the SrMn3O6−δ nanoribbons can be effectively tuned by the cooling field, which is of very special interests for applications.
In situ observation of stress-induced Au–Si phase transformation
Authors: Huitink D. , Peng L. , Ribeiro R. , Liang H.
Published: May 2009

Nonequilibrium AuSi3 was found due to indenting contact forces at a gold and silicon interface. An in situ transmission electron microscope was used to observe interactions at the material interface during nanoindentation and to identify crystal structures. Furthermore, sliding of a gold-coated atomic-force microscope probe over a silicon substrate forms organized nanostructures. An evaluation of the observed interfacial mechanisms concluded that the contact stress triggered the phase transformation leading to the formation of a metastable interface that mediates the adhesion of contacting materials.
Plasmon-based photosensors comprising a very thin semiconducting region
Authors: Le Perchec J. , Desieres Y. , Espiau de Lamaestre R.
Published: May 2009

We theoretically investigate an elementary subwavelength plasmonic sensor comprising a very thin active region. High quantum efficiency (QE), broad spectral band and nearly no sensitivity to the incidence angle and polarization can be achieved. We particularly discuss different examples based on HgCdTe for infrared detection: QEs of 75% are obtained for active layers λ/(8n) thin, corresponding to a tenfold absorption enhancement.
Experimental characterization of three-wave mixing in a multimode nonlinear KTiOPO4 waveguide
Authors: Karpiński Michał , Radzewicz Czesław , Banaszek Konrad
Published: May 2009

We report experimental determination of the phase-matching function for type-II three-wave mixing in a periodically poled KTiOPO4 waveguide in the 792–815 nm spectral region. The measurement was performed by sum-frequency generation of spectrally tuned fundamental components. Strong dependence of the observed signal on the excited spatial modes in the waveguide has been observed and fully interpreted. These results indicate a route to employ the waveguide for spontaneous parametric down-conversion producing photon pairs in well-defined spatial modes.
Strengthening of lateral activation in adult rat visual cortex after retinal lesions captured with voltage-sensitive dye imaging in vivo
Authors: Palagina Ganna , Eysel Ulf T. , Jancke Dirk
Published: May 2009

Sensory deprivation caused by peripheral injury can trigger functional cortical reorganization across the initially silenced cortical area. It is proposed that intracortical connectivity enables recovery of function within such a lesion projection zone (LPZ), thus substituting lost subcortical input. Here, we investigated retinal lesion-induced changes in the function of lateral connections in the primary visual cortex of the adult rat. Using voltage-sensitive dye recordings, we visualized in millisecond-time resolution spreading synaptic activity across the LPZ. Shortly after lesion, the majority of neurons within the LPZ were subthresholdly activated by delayed propagation of activity that originated from unaffected cortical regions. With longer recovery time, latencies within the LPZ gradually decreased, and activation reached suprathreshold levels. Targeted electrode recordings confirmed that receptive fields of intra-LPZ neurons were displaced to the retinal lesion border while displaying normal orientation and direction selectivity. These results corroborate the view that cortical horizontal connections have a central role in functional reorganization, as revealed here by progressive facilitation of synaptic activity and the traveling wave of excitation that propagates horizontally into the deprived cortical region.
Apoptosis is not required for mammalian neural tube closure
Authors: Massa Valentina , Savery Dawn , Ybot-Gonzalez Patricia , Ferraro Elisabetta , Rongvaux Anthony , Cecconi Francesco , Flavell Richard , Greene Nicholas D. E. , Copp Andrew J.
Published: May 2009

Apoptotic cell death occurs in many tissues during embryonic development and appears to be essential for processes including digit formation and cardiac outflow tract remodeling. Studies in the chick suggest a requirement for apoptosis during neurulation, because inhibition of caspase activity was found to prevent neural tube closure. In mice, excessive apoptosis occurs in association with failure of neural tube closure in several genetic mutants, but whether regulated apoptosis is also necessary for neural tube closure in mammals is unknown. Here we investigate the possible role of apoptotic cell death during mouse neural tube closure. We confirm the presence of apoptosis in the neural tube before and during closure, and identify a correlation with 3 main events: bending and fusion of the neural folds, postfusion remodeling of the dorsal neural tube and surface ectoderm, and emigration of neural crest cells. BothCasp3andApaf1null embryos exhibit severely reduced apoptosis, yet neurulation proceeds normally in the forebrain and spine. In contrast, the mutant embryos fail to complete neural tube closure in the midbrain and hindbrain. Application of the apoptosis inhibitors z-Vad-fmk and pifithrin-α to neurulation-stage embryos in culture suppresses apoptosis but does not prevent initiation or progression of neural tube closure along the entire neuraxis, including the midbrain and hindbrain. Remodeling of the surface ectoderm to cover the closed tube, as well as delamination and migration of neural crest cells, also appear to be normal in the apoptosis-suppressed embryos. We conclude that apoptosis is not required for neural tube closure in the mouse embryo.
Examining the relative influence of familial, genetic, and environmental covariate information in flexible risk models
Authors: Bravo Héctor Corrada , Lee Kristine E. , Klein Barbara E. K. , Klein Ronald , Iyengar Sudha K. , Wahba Grace
Published: May 2009

We present a method for examining the relative influence of familial, genetic, and environmental covariate information in flexible nonparametric risk models. Our goal is investigating the relative importance of these three sources of information as they are associated with a particular outcome. To that end, we developed a method for incorporating arbitrary pedigree information in a smoothing spline ANOVA (SS-ANOVA) model. By expressing pedigree data as a positive semidefinite kernel matrix, the SS-ANOVA model is able to estimate a log-odds ratio as a multicomponent function of several variables: one or more functional components representing information from environmental covariates and/or genetic marker data and another representing pedigree relationships. We report a case study on models for retinal pigmentary abnormalities in the Beaver Dam Eye Study. Our model verifies known facts about the epidemiology of this eye lesion—found in eyes with early age-related macular degeneration—and shows significantly increased predictive ability in models that include all three of the genetic, environmental, and familial data sources. The case study also shows that models that contain only two of these data sources, that is, pedigree-environmental covariates, or pedigree-genetic markers, or environmental covariates-genetic markers, have comparable predictive ability, but less than the model with all three. This result is consistent with the notions that genetic marker data encode—at least in part—pedigree data, and that familial correlations encode shared environment data as well.
A possible mechanism for exonuclease 1-independent eukaryotic mismatch repair
Authors: Kadyrov Farid A. , Genschel Jochen , Fang Yanan , Penland Elisabeth , Edelmann Winfried , Modrich Paul
Published: May 2009

Mismatch repair contributes to genetic stability, and inactivation of the mammalian pathway leads to tumor development. Mismatch correction occurs by an excision-repair mechanism and has been shown to depend on the 5′ to 3′ hydrolytic activity exonuclease 1 (Exo1) in eukaryotic cells. However, genetic and biochemical studies have indicated that one or more Exo1-independent modes of mismatch repair also exist. We have analyzed repair of nicked circular heteroduplex DNA in extracts of Exo1-deficient mouse embryo fibroblast cells. Exo1-independent repair under these conditions is MutLα-dependent and requires functional integrity of the MutLα endonuclease metal-binding motif. In contrast to the Exo1-dependent reaction, we have been unable to detect a gapped excision intermediate in Exo1-deficient extracts when repair DNA synthesis is blocked. A possible explanation for this finding has been provided by analysis of a purified system comprised of MutSα, MutLα, replication factor C, proliferating cell nuclear antigen, replication protein A, and DNA polymerase δ that supports Exo1-independent repair in vitro. Repair in this system depends on MutLα incision of the nicked heteroduplex strand and dNTP-dependent synthesis-driven displacement of a DNA segment spanning the mismatch. Such a mechanism may account, at least in part, for the Exo1-independent repair that occurs in eukaryotic cells, and hence the modest cancer predisposition of Exo1-deficient mammalian cells.
Gender differences in educational attainment: Influences of the family environment
Authors: Mensah Fiona K. , Kiernan Kathleen E.
Published: May 2009

There are gender differences in educational attainment amongst British children and there is evidence that these differences emerge early in life. In this study we investigate whether boys’ and girls’ early educational attainment levels are similarly related to disadvantage in the family environment. This study uses survey data from the Millennium Cohort Study linked with the teachers Foundation Stage Profile assessment for children in the primary year of school in England between 2005 and 2006. The study finds lower attainment in communication, language and literacy and mathematical development for both boys and girls in families experiencing socio‐economic disadvantage. Early motherhood, low maternal qualifications, low family income and unemployment most strongly predict lower scores. Tests for gender interaction shows boys in families where mothers are young, where they lack qualifications or if they are living in poor quality areas are more disadvantaged compared to girls in similar circumstances.
Exploring transition to postgraduate study: Shifting identities in interaction with communities, practice and participation
Authors: Tobbell Jane , O'donnell Victoria , Zammit Maria
Published: May 2009

There has been relatively little research to date that has explored the transition to postgraduate study. This paper reports findings from a project (funded by the UK's Higher Education Academy) that sought to address this gap. The research project was ethnographic and explored university practice and student participation in five UK universities. A significant emergent feature of the research was that a multiplicity of identities construct student experience and contribute to student transition. This finding provides support for learning theory that argues for inextricable links between learning and wider social identities. Moreover, the process of negotiating an academic identity in light of wider experience and university practices emerged as a key factor in understanding transition together with the imperative for independent study, which was a particularly powerful practice that necessitated complex identity negotiations in order to enable full participation in the university community of practice.