bluuebunny/crossref_metadata_2025 huggingface dataset:
Determination of the class and isoform selectivity of small-molecule histone deacetylase inhibitors
Authors: Khan Nagma , Jeffers Michael , Kumar Sampath , Hackett Craig , Boldog Ferenc , Khramtsov Nicholai , Qian Xiaozhong , Mills Evan , Berghs Stanny C. , Carey Nessa , Finn Paul W. , Collins Laura S. , Tumber Anthony , Ritchie James W. , Jensen Peter Buhl , Lichenstein Henri S. , Sehested Maxwell
Published: January 2008

The human HDAC (histone deacetylase) family, a well-validated anticancer target, plays a key role in the control of gene expression through regulation of transcription. While HDACs can be subdivided into three main classes, the class I, class II and class III HDACs (sirtuins), it is presently unclear whether inhibiting multiple HDACs using pan-HDAC inhibitors, or targeting specific isoforms that show aberrant levels in tumours, will prove more effective as an anticancer strategy in the clinic. To address the above issues, we have tested a number of clinically relevant HDACis (HDAC inhibitors) against a panel of rhHDAC (recombinant human HDAC) isoforms. Eight rhHDACs were expressed using a baculoviral system, and a Fluor de Lys™ (Biomol International) HDAC assay was optimized for each purified isoform. The potency and selectivity of ten HDACs on class I isoforms (rhHDAC1, rhHDAC2, rhHDAC3 and rhHDAC8) and class II HDAC isoforms (rhHDAC4, rhHDAC6, rhHDAC7 and rhHDAC9) was determined. MS-275 was HDAC1-selective, MGCD0103 was HDAC1- and HDAC2-selective, apicidin was HDAC2- and HDAC3-selective and valproic acid was a specific inhibitor of class I HDACs. The hydroxamic acid-derived compounds (trichostatin A, NVP-LAQ824, panobinostat, ITF2357, vorinostat and belinostat) were potent pan-HDAC inhibitors. The growth-inhibitory effect of the HDACis on HeLa cells showed that both pan-HDAC and class-I-specific inhibitors inhibited cell growth. The results also showed that both pan-HDAC and class-I-specific inhibitor treatment resulted in increased acetylation of histones, but only pan-HDAC inhibitor treatment resulted in increased tubulin acetylation, which is in agreement with their activity towards the HDAC6 isoform.
Chelator-facilitated removal of iron from transferrin: relevance to combined chelation therapy
Authors: Devanur Lakshmi D. , Evans Robert W. , Evans Patricia J. , Hider Robert C.
Published: January 2008

Current iron chelation therapy consists primarily of DFO (desferrioxamine), which has to be administered via intravenous infusion, together with deferiprone and deferasirox, which are orally-active chelators. These chelators, although effective at decreasing the iron load, are associated with a number of side effects. Grady suggested that the combined administration of a smaller bidentate chelator and a larger hexadentate chelator, such as DFO, would result in greater iron removal than either chelator alone [Grady, Bardoukas and Giardina (1998) Blood 92, 16b]. This in turn could lead to a decrease in the chelator dose required. To test this hypothesis, the rate of iron transfer from a range of bidentate HPO (hydroxypyridin-4-one) chelators to DFO was monitored. Spectroscopic methods were utilized to monitor the decrease in the concentration of the Fe–HPO complex. Having established that the shuttling of iron from the bidentate chelator to DFO does occur under clinically relevant concentrations of chelator, studies were undertaken to evaluate whether this mechanism of transfer would apply to iron removal from transferrin. Again, the simultaneous presence of both a bidentate chelator and DFO was found to enhance the rate of iron chelation from transferrin at clinically relevant chelator levels. Deferiprone was found to be particularly effective at ‘shuttling’ iron from transferrin to DFO, probably as a result of its small size and relative low affinity for iron compared with other analogous HPO chelators.
Human group III secreted phospholipase A2 promotes neuronal outgrowth and survival
Authors: Masuda Seiko , Yamamoto Kei , Hirabayashi Tetsuya , Ishikawa Yukio , Ishii Toshiharu , Kudo Ichiro , Murakami Makoto
Published: January 2008

Human sPLA2-III [group III secreted PLA2 (phospholipase A2)] is an atypical sPLA2 isoenzyme that consists of a central group III sPLA2 domain flanked by unique N- and C-terminal domains. In the present study, we found that sPLA2-III is expressed in neuronal cells, such as peripheral neuronal fibres, spinal DRG (dorsal root ganglia) neurons and cerebellar Purkinje cells. Adenoviral expression of sPLA2-III in PC12 cells (pheochromocytoma cells) or DRG explants facilitated neurite outgrowth, whereas expression of a catalytically inactive sPLA2-III mutant or use of sPLA2-III-directed siRNA (small interfering RNA) reduced NGF (nerve growth factor)-induced neuritogenesis. sPLA2-III also suppressed neuronal death induced by NGF deprivation. Lipid MS revealed that sPLA2-III overexpression increased the cellular level of lysophosphatidylcholine, a PLA2 reaction product with neuritogenic and neurotropic activities, whereas siRNA knockdown reduced the level of lysophosphatidylcholine. These observations suggest the potential contribution of sPLA2-III to neuronal differentiation and its function under certain conditions.
Polyamines modulate the subcellular localization of RNA-binding protein HuR through AMP-activated protein kinase-regulated phosphorylation and acetylation of importin α1
Authors: Zou Tongtong , Liu Lan , Rao Jaladanki N. , Marasa Bernard S. , Chen Jie , Xiao Lan , Zhou Huiping , Gorospe Myriam , Wang Jian-Ying
Published: January 2008

Polyamines are required for maintenance of intestinal epithelial integrity, and a decrease in cellular polyamines increases the cytoplasmic levels of RNA-binding protein HuR stabilizing p53 and nucleophosmin mRNAs, thus inhibiting IEC (intestinal epithelial cell) proliferation. The AMPK (AMP-activated protein kinase), an enzyme involved in responding to metabolic stress, was recently found to be implicated in regulating the nuclear import of HuR. Here, we provide evidence showing that polyamines modulate subcellular localization of HuR through AMPK-regulated phosphorylation and acetylation of Impα1 (importin α1) in IECs. Decreased levels of cellular polyamines as a result of inhibiting ODC (ornithine decarboxylase) with DFMO (D,L-α-difluoromethylornithine) repressed AMPK activity and reduced Impα1 levels, whereas increased levels of polyamines as a result of ODC overexpression induced both AMPK and Impα1 levels. AMPK activation by overexpression of the AMPK gene increased Impα1 but reduced the cytoplasmic levels of HuR in control and polyamine-deficient cells. IECs overexpressing wild-type Impα1 exhibited a decrease in cytoplasmic HuR abundance, while cells overexpressing Impα1 proteins bearing K22R (lacking acetylation site), S105A (lacking phosphorylation site) or K22R/S105A (lacking both sites) mutations displayed increased levels of cytoplasmic HuR. Ectopic expression of these Impα1 mutants also prevented the increased levels of cytoplasmic HuR following polyamine depletion. These results indicate that polyamine-mediated AMPK activation triggers HuR nuclear import through phosphorylation and acetylation of Impα1 in IECs and that polyamine depletion increases cytoplasmic levels of HuR as a result of inactivation of the AMPK-driven Impα1 pathway.
Conserved substrate binding by chaperones in the bacterial periplasm and the mitochondrial intermembrane space
Authors: Alcock Felicity H. , Grossmann J. Günter , Gentle Ian E. , Likić Vladimir A. , Lithgow Trevor , Tokatlidis Kostas
Published: January 2008

Mitochondria were derived from intracellular bacteria and the mitochondrial intermembrane space is topologically equivalent to the bacterial periplasm. Both compartments contain ATP-independent chaperones involved in the transport of hydrophobic membrane proteins. The mitochondrial TIM (translocase of the mitochondrial inner membrane) 10 complex and the periplasmic chaperone SurA were examined in terms of evolutionary relation, structural similarity, substrate binding specificity and their function in transporting polypeptides for insertion into membranes. The two chaperones are evolutionarily unrelated; structurally, they are also distinct both in their characteristics, as determined by SAXS (small-angle X-ray scattering), and in pairwise structural comparison using the distance matrix alignment (DALILite server). Despite their structural differences, SurA and the TIM10 complex share a common binding specificity in Pepscan assays of substrate proteins. Comprehensive analysis of the binding on a total of 1407 immobilized 13-mer peptides revealed that the TIM10 complex, like SurA, does not bind hydrophobic peptides generally, but that both chaperones display selectivity for peptides rich in aromatic residues and with net positive charge. This common binding specificity was not sufficient for SurA to completely replace TIM10 in yeast cells in vivo. In yeast cells lacking TIM10, when SurA is targeted to the intermembrane space of mitochondria, it binds translocating substrate proteins, but fails to completely transfer the substrate to the translocase in the mitochondrial inner membrane. We suggest that SurA was incapable of presenting substrates effectively to the primitive TOM (translocase of the mitochondrial outer membrane) and TIM complexes in early mitochondria, and was replaced by the more effective small Tim chaperone.
A gain-of-function mutant of Munc18-1 stimulates secretory granule recruitment and exocytosis and reveals a direct interaction of Munc18-1 with Rab3
Authors: Graham Margaret E. , Handley Mark T. W. , Barclay Jeff W. , Ciufo Leo F. , Barrow Stephanie L. , Morgan Alan , Burgoyne Robert D.
Published: January 2008

Munc18-1 plays a crucial role in regulated exocytosis in neurons and neuroendocrine cells through modulation of vesicle docking and membrane fusion. The molecular basis for Munc18 function is still unclear, as are the links with Rabs and SNARE [SNAP (soluble N-ethylmaleimide-sensitive factor-attachment protein) receptor] proteins that are also required. Munc18-1 can bind to SNAREs through at least three modes of interaction, including binding to the closed conformation of syntaxin 1. Using a gain-of-function mutant of Munc18-1 (E466K), which is based on a mutation in the related yeast protein Sly1p, we have identified a direct interaction of Munc18-1 with Rab3A, which is increased by the mutation. Expression of Munc18-1 with the E466K mutation increased exocytosis in adrenal chromaffin cells and PC12 cells (pheochromocytoma cells) and was found to increase the density of secretory granules at the periphery of PC12 cells, suggesting a stimulatory effect on granule recruitment through docking or tethering. Both the increase in exocytosis and changes in granule distribution appear to require Munc18-1 E466K binding to the closed form of syntaxin 1, suggesting a role for this interaction in bridging Rab- and SNARE-mediated events in exocytosis.
Complementary roles of SufA and IscA in the biogenesis of iron–sulfur clusters in Escherichia coli
Authors: Lu Jianxin , Yang Juanjuan , Tan Guoqiang , Ding Huangen
Published: January 2008

Biogenesis of iron–sulfur clusters requires a concerted delivery of iron and sulfur to target proteins. It is now clear that sulfur in iron–sulfur clusters is derived from L-cysteine via cysteine desulfurases. However, the specific iron donor for the iron–sulfur cluster assembly still remains elusive. Previous studies showed that IscA, a member of the iron–sulfur cluster assembly machinery in Escherichia coli, is a novel iron-binding protein, and that the iron-bound IscA can provide iron for the iron–sulfur cluster assembly in a proposed scaffold IscU in vitro. However, genetic studies have indicated that IscA is not essential for the cell growth of E. coli. In the present paper, we report that SufA, an IscA paralogue in E. coli, may represent the redundant activity of IscA. Although deletion of IscA or SufA has only a mild effect on cell growth, deletion of both IscA and SufA in E. coli results in a severe growth phenotype in minimal medium under aerobic growth conditions. Cell growth is restored when either IscA or SufA is re-introduced into the iscA−/sufA− double mutant, demonstrating further that either IscA or SufA is sufficient for their functions in vivo. Purified SufA, like IscA, is an iron-binding protein that can provide iron for the iron–sulfur cluster assembly in IscU in the presence of a thioredoxin reductase system which emulates the intracellular redox potential. Site-directed mutagenesis studies show that the SufA/IscA variants that lose the specific iron-binding activity fail to restore the cell growth of the iscA−/sufA− double mutant. The results suggest that SufA and IscA may constitute the redundant cellular activities to recruit intracellular iron and deliver iron for the iron–sulfur cluster assembly in E. coli.
The lectin-like oxidized low-density-lipoprotein receptor: a pro-inflammatory factor in vascular disease
Authors: Dunn Sarah , Vohra Ravinder S. , Murphy Jane E. , Homer-Vanniasinkam Shervanthi , Walker John H. , Ponnambalam Sreenivasan
Published: January 2008

Scavenger receptors are membrane glycoproteins that bind diverse ligands including lipid particles, phospholipids, apoptotic cells and pathogens. LOX-1 (lectin-like oxidized low-density lipoprotein receptor-1) is increasingly linked to atherosclerotic plaque formation. Transgenic mouse models for LOX-1 overexpression or gene knockout suggests that LOX-1 contributes to atherosclerotic plaque formation and progression. LOX-1 activation by oxidized LDL (low-density lipoprotein) binding stimulates intracellular signalling, gene expression and production of superoxide radicals. A key question is the role of leucocyte LOX-1 in pro-atherogenic lipid particle trafficking, accumulation and signalling leading to differentiation into foam cells, necrosis and plaque development. LOX-1 expression is elevated within vascular lesions and a serum soluble LOX-1 fragment appears diagnostic of patients with acute coronary syndromes. LOX-1 is increasingly viewed as a vascular disease biomarker and a potential therapeutic target in heart attack and stroke prevention.
Elasticity and photoelasticity relationships for polyethylene terephthalate fiber networks by molecular simulation
Authors: Nayak Kapileswar , Das Sushanta , Nanavati Hemant
Published: January 2008

We present a framework for the development of elasticity and photoelasticity relationships for polyethylene terephthalate fiber networks, incorporating aspects of the primary molecular structure. Semicrystalline polymeric fiber networks are modeled as sequentially arranged crystalline and amorphous regions. Rotational isomeric states-Monte Carlo simulations of amorphous chains of up to 360 bonds (degree of polymerization, DP=60), confined between and bridging infinite impenetrable crystalline walls, have been characterized by Ω, the probability density of the intercrystal separation h, and Δβ, the polarizability anisotropy. lnΩ and Δβ have been modeled as functions of h, yielding the chain deformation relationships. The development has been extended to the fiber network to yield the photoelasticity relationships. We execute our framework by fitting to experimental stress-elongation data and employing the single fitted parameter to directly predict the birefringence-elongation behavior, without any further fitting. Incorporating the effect of strain-induced crystallization into the framework makes it physically more meaningful and yields accurate predictions of the birefringence-elongation behavior.
Neutron Scattering in Condensed-Matter Physics
Authors: Axe John D. , Nicklow Robert M.
Published: January 2008

Since its discovery 50 years ago, the neutron has commanded public attention and respect. As an intermediary in nuclear fission, it is woven into the political fabric of modern life and seems destined to remain so. But the neutron plays many other, less prominent and controversial roles as well. It has, for example, technological applications in fields as diverse as logging oil wells, detecting art forgeries and doping electronic semiconductor materials, as D. Allan Bromley has reviewed in these pages.
Forbidden Fivefold Symmetry May Indicate Quasicrystal Phase
Authors: Schwarzschild Bertram
Published: January 2008

You can't tile a bathroom floor with regular pentagons. The crystallographic equivalent of this mundane truth is the inviolate classical rule that no crystal structure—in two or three dimensions—can possess fivefold rotational symmetry. It was with complete surprise, therefore, that Dan Shechtman and his colleagues recently discovered a fivefold symmetric point diffraction pattern for micron-size grains of metallic alloy prepared by rapid cooling in their National Bureau of Standards laboratory.
Livermore Group Reports Soft X-Ray Laser
Authors: Levi Barbara Gos
Published: January 2008

A group at Lawrence Livermore Laboratory has operated the first soft x-ray laser. As proof, they have extensive diagnostics from more than 100 test shots showing not only that radiation emitted at two wavelengths near 20 nm were up to 700 times more intense than those from spontaneous emission, but also that these lines behaved in other ways characteristic of a laser. Group leader Dennis Matthews, together with Mordecai Rosen, presented Livermore's results at the Boston meeting of the APS Division of Plasma Physics last October. The announcement is a welcome milestone in the quest for an x-ray laser, which has been underway since the first theoretical suggestions of x-ray lasing schemes in the late sixties. Other participants in that search, now more confident of their own eventual success, can be expected to join Livermore in the drive towards greater efficiency, higher power and ever-shorter wavelengths.
Major Facilities for Physics Research
Authors: Havens William W.
Published: January 2008

The idea for a special issue of PHYSICS TODAY on major physics research facilities originated at a meeting of the APS Executive Committee in June 1984 during discussion of a report presented by L. Charles Hebel, Chairman of the APS Panel of Public Affairs, recommending what APS could do for the physics community about several proposals to the Federal government for the construction of large and expensive research facilities. The editors of PHYSICS TODAY enthusiastically reacted to the APS suggestion, and this special issue became a cooperative endeavor. Hebel's article, beginning on page 25, is based on that POPA report.
Research in Small Groups
Authors: Kleppner Daniel
Published: January 2008

In Munich's Deutsches Museum one can come upon an Italian Renaissance study, meticulously recreated and handsomely furnished save for one intrusion: A plank, one end propped on a trestle, the other resting on the floor. With such a crude apparatus and using his pulse to clock how long a brass ball takes to roll various distances, Galileo first explored the nature of uniformly accelerated motion. With the aid of these measurements he discovered the basics of dynamics; in so doing he also established a tradition for experimental research that has animated physics ever since.
Free-Electron Lasers Achieve High Microwave Power
Authors: Schwarzschild Bertram
Published: January 2008

The output wavelength of a free-electron laser varies as the inverse square of the energy of the electrons whose undulation through the FEL generates the laser light. Accelerators and storage rings of the kind one uses for highenergy physics have provided FEL researchers with electron beams of sufficient energy to yield laser output in the near infrared and even in the visible (see PHYSICS TODAY, December 1983, page 17). But such rf linacs and storage rings are typically limited to rather low electron currents, thus seriously limiting the peak output power of the freeelectron lasers that depend on them.
Investigation of thickness-dependent stress in PbTiO3 thin films
Authors: Bartasyte A. , Chaix-Pluchery O. , Kreisel J. , Jimenez C. , Weiss F. , Abrutis A. , Saltyte Z. , Boudard M.
Published: January 2008

X-ray diffraction (XRD) and Raman spectroscopy were used to investigate stress dependence on thickness in PbTiO3 (PTO) films grown by pulsed liquid injection metalorganic chemical vapor deposition on a LaAlO3 (001) substrate (LAO). Films on sapphire substrate (R plane) were used as the polycrystalline film reference. Epitaxial PTO films with a dominant c domain structure are grown on LAO substrate, whereas the films on sapphire are polycrystalline. A detailed investigation of the PTO/LAO film microstructure by XRD gives evidence of PTO twinning. Both techniques reveal that PTO films are under tensile in-plane stresses. The study of the film thickness dependence of microstrains, grain size, volume fraction of a domains, as well as surface morphology of PTO/LAO films indicates that these parameters are clearly correlated. A change in the relaxation mechanism between 65 and 125 nm of film thickness has been evidenced. A c parameter gradient occurs throughout the film depth; it originates in stress relaxation due to an increase in thickness. Raman spectra of PTO films allowed in-plane residual stress values to be estimated from the Raman shifts, and are in good agreement with those determined by XRD. Both techniques also indicate that thinner films are more stressed and residual stresses are partially relaxed with increasing thickness. Moreover, a domains are more stressed than c domains. The two components of the large A1(2TO) and A1(3TO) Raman modes have been associated with a and c domains and their intensity ratio clearly correlated with the volume fraction of a domains.
A megahertz nanomechanical resonator with room temperature quality factor over a million
Authors: Verbridge Scott S. , Craighead Harold G. , Parpia Jeevak M.
Published: January 2008

We demonstrate the fabrication and operation of high aspect ratio tensile stressed silicon nitride string resonators. We explore the parameter space of small cross sections, on the order of 100nm, and long lengths up to 325μm, demonstrating that such high aspect ratio resonators can be made with standard wet release processing using a material with internal tensile stress. Room temperature quality factors exceed one million at frequencies above 1MHz. The utility of such high quality factor flexural resonators to probe the interaction of high frequency nanoscale devices with rarefied gases is demonstrated.
Design and construction of a magnetic resonance compatible multi-injector gas jet delivery system
Authors: Megias-Alguacil David , Keller Thierry , Lutz Kai , Barlow Ashley P. , Ettlin Dominik A.
Published: January 2008

We present the design, construction, and performance of a novel multi-injector gas jet delivery capable of operating in a magnetic resonance imaging environment. This apparatus is computer controlled and built with two separate pneumatic circuits enabling gas jet applications at variable sites through four independently activated injectors. Gas jet delivery is fully controllable in terms of pressure, flow rate, gas temperature, application time, and duration of interstimulus interval. We characterized these parameters, considering effects such as pressure drop by flow transport, transient effects, and delays in activation. The system offers new possibilities for use in various biomedical contexts such as, e.g., quantitative sensory testing or dental hypersensitivity assessment.
Spectra of phase point operators in odd prime dimensions and the extended Clifford group
Authors: Appleby D. M. , Bengtsson Ingemar , Chaturvedi S.
Published: January 2008

We analyze the role of the extended Clifford group in classifying the spectra of phase point operators within the framework laid out by [Gibbons et al., Phys. Rev. A 70, 062101 (2004)] for setting up Wigner distributions on discrete phase spaces based on finite fields. To do so we regard the set of all the discrete phase spaces as a symplectic vector space over the finite field. Auxiliary results include a derivation of the conjugacy classes of ESL(2,FN).
The electronic surface barrier of boron-doped diamond by anodic oxidation
Authors: Denisenko A. , Pietzka C. , Romanyuk A. , El-Hajj H. , Kohn E.
Published: January 2008

It was shown that a strong anodic oxidation of 100-oriented diamond induces the electronic surface states, which pin the surface Fermi level at about 3.6 eV above the valence-band maximum. The characteristics of the electronic surface barrier were evaluated from the analysis of boron-doped diamond electrodes and correlated with the four-point probe measurements of an oxidized diamond resistor with a boron delta-doped channel. The same evaluation procedure applied to the case of a wet chemical oxidation yielded a surface barrier of 1.9 eV, which is consistent with the data in the literature. The characteristics of the 3.6 eV barrier by the anodic oxidation remained stable after subsequent chemical treatments even at elevated temperatures, and were also not degraded in air for a long time. The x-ray photoemission spectroscopy study showed that the anodic oxidation generates complex oxygen functionalities, like polycarbonate groups, and also C-O-C bridging bond structures with possible contribution of an additional chemisorbed layer.
X-ray excited optical luminescence detection by scanning near-field optical microscope: A new tool for nanoscience
Authors: Larcheri Silvia , Rocca Francesco , Jandard Frank , Pailharey Daniel , Graziola Roberto , Kuzmin Alexei , Purans Juris
Published: January 2008

Investigations of complex nanostructured materials used in modern technologies require special experimental techniques able to provide information on the structure and electronic properties of materials with a spatial resolution down to the nanometer scale. We tried to address these needs through the combination of x-ray absorption spectroscopy (XAS) using synchrotron radiation microbeams with scanning near-field optical microscopy (SNOM) detection of the x-ray excited optical luminescence (XEOL) signal. This new instrumentation offers the possibility to carry out a selective structural analysis of the sample surface with the subwavelength spatial resolution determined by the SNOM probe aperture. In addition, the apex of the optical fiber plays the role of a topographic probe, and chemical and topographic mappings can be simultaneously recorded. Our working XAS-SNOM prototype is based on a quartz tuning-fork head mounted on a high stability nanopositioning system; a coated optical fiber tip, operating as a probe in shear-force mode; a detection system coupled with the microscope head control system; and a dedicated software/hardware setup for synchronization of the XEOL signal detection with the synchrotron beamline acquisition system. We illustrate the possibility to obtain an element-specific contrast and to perform nano-XAS experiments by detecting the Zn K and W L3 absorption edges in luminescent ZnO and mixed ZnWO4–ZnO nanostructured thin films.
Spin-torque driven ferromagnetic resonance of Co∕Ni synthetic layers in spin valves
Authors: Chen W. , Beaujour J.-M. L. , de Loubens G. , Kent A. D. , Sun J. Z.
Published: January 2008

Spin-torque driven ferromagnetic resonance (ST-FMR) is used to study thin Co∕Ni synthetic layers with perpendicular anisotropy confined in spin valve based nanojunctions. Field swept ST-FMR measurements were conducted with a magnetic field applied perpendicular to the layer surface. The resonance lines were measured under low amplitude rf excitation, from 1to20GHz. These results are compared with those obtained using conventional rf field driven FMR on extended films with the same Co∕Ni layer structure. The layers confined in spin valves have a lower resonance field, a narrower resonance linewidth, and approximately the same linewidth vs frequency slope, implying the same damping parameter. The critical current for magnetic excitations is determined from measurements of the resonance linewidth vs dc current and is in accord with the one determined from I-V measurements.
Defect chemistry and dielectric properties of Yb3+:CaTiO3 perovskite
Authors: Bassoli M. , Buscaglia M. T. , Bottino C. , Buscaglia V. , Molinari M. , Maglia F. , Parravicini G. , Dapiaggi M.
Published: January 2008

The defect chemistry of Yb3+:CaTiO3 solid solutions has been investigated both theoretically and experimentally. Three different incorporation mechanisms with similar solution energy were predicted for Yb3+ by atomistic simulation: (i) Ca site substitution with Ca vacancy compensation; (ii) Ti site substitution with O vacancy compensation; (iii) simultaneous substitution at both Ca and Ti sites with self-compensation. X-ray diffraction and scanning electron microscopy results strongly support the possibility to realize the above defect chemistries in CaTiO3 by changing the Ca∕Ti ratio to force Yb3+ on the Ca site (Ca∕Ti<1), on Ti site (Ca∕Ti>1), or on both sites (Ca∕Ti=1) according to the calculations. The temperature dependence of the relative dielectric constant (102–105Hz) of ceramics corresponding to predominant Yb substitution either at the Ca site or the Ti site is qualitatively similar to that of undoped CaTiO3. The Curie-Weiss temperature is shifted to more negative values in comparison to CaTiO3, suggesting that the compositions Ca1−3∕2xYbxTiO3 and CaYbxTi1−xO3 are further driven away from the ferroelectric instability. In contrast, the dielectric properties (102–105Hz) of ceramics corresponding to Ca1−x∕2YbxTi1−x∕2O3 are radically different. The relative dielectric constant is increased of about one order of magnitude (2200 at 30K), is almost independent of temperature, with a maximum variation of 20% in range of 20–300K, and shows frequency dispersion above 150K. The loss tangent at 20–300K is <5% for frequencies ⩾1kHz. The possible mechanism for the observed dielectric behavior is discussed.
Characterization of nanoscale electronic structure in nonpolar GaN using scanning capacitance microscopy
Authors: Law J. J. M. , Yu E. T. , Haskell B. A. , Fini P. T. , Nakamura S. , Speck J. S. , DenBaars S. P.
Published: January 2008

Scanning capacitance microscopy is used to characterize nanoscale, local electronic structure in nonpolar n-type GaN grown in the a-plane orientation using lateral epitaxial overgrowth (LEO). Analysis of the bias dependence of the scanning capacitance image contrast observed reveals the presence of a linear, positively charged feature aligned along the [1¯100] direction, extending from an LEO window region into the adjacent wing region and terminating a few microns into the wing region. Comparison of the scanning capacitance images with cathodoluminescence and transmission electron microscopy data, revealing the presence of line defects aligned along the [1¯100] direction that emerge from the window regions, indicates that this positively charged feature likely corresponds to a partial dislocation at the edge of a stacking fault. The observation of positive dislocation charge is striking in that studies of GaN grown in the polar c-plane orientation have predominantly revealed the presence only of negatively charged or electrically neutral dislocations.
Photoinduced metallic state in VO2 proved by the terahertz pump-probe spectroscopy
Authors: Nakajima M. , Takubo N. , Hiroi Z. , Ueda Y. , Suemoto T.
Published: January 2008

We investigated the ultrafast terahertz response to the photoexcitation for vanadium dioxide single crystals and thin films using the optical-pump terahertz-probe technique at room temperature. The optical excitation induced an ultrafast decrease of the transmittance of the terahertz radiation within 0.7ps. Since we expect only the free carrier response in the terahertz range, the decrease of the transmittance is unambiguously assigned to the appearance of the high electronic conductivity due to free carriers. The conductivity increases more than ten times in the picosecond time range after photoexcitation and it is concluded that the electronic states are metallic.
Spatially resolved photocurrent mapping of operating organic photovoltaic devices using atomic force photovoltaic microscopy
Authors: Leever B. J. , Durstock M. F. , Irwin M. D. , Hains A. W. , Marks T. J. , Pingree L. S. C. , Hersam M. C.
Published: January 2008

A conductive atomic force microscopy (cAFM) technique, atomic force photovoltaic microscopy (AFPM), has been developed to characterize spatially localized inhomogeneities in organic photovoltaic (OPV) devices. In AFPM, a biased cAFM probe is raster scanned over an array of illuminated solar cells, simultaneously generating topographic and photocurrent maps. As proof of principle, AFPM is used to characterize 7.5×7.5μm2 poly(3-hexylthiophene):[6,6]-phenyl-C61-butyric acid methyl ester OPVs, revealing substantial device to device and temporal variations in the short-circuit current. The flexibility of AFPM suggests applicability to nanoscale characterization of a wide range of optoelectronically active materials and devices.
Two-dimensional eccentric elliptic electromagnetic cloaks
Authors: Kwon Do-Hoon , Werner Douglas H.
Published: January 2008

A spatial transformation technique is applied to an important class of two-dimensional electromagnetic cloaks that do not possess rotational symmetry around the longitudinal axis. These cloaks are based on an eccentric elliptic annular geometry, which represents a generalization of previously published cloaking configurations. The required material properties of the cloak are derived in terms of the geometrical parameters and the coordinates in the transformed system. The validity of the cloak parameters is verified by a full-wave finite-element simulation of plane wave scattering from uncloaked and cloaked perfectly conducting cylinders with elliptic cross section.
Amino-acid-assisted synthesis and size-dependent magnetic behaviors of hematite nanocubes
Authors: Cao Huaqiang , Wang Guozhi , Warner Jamie H. , Watt Andrew A. R.
Published: January 2008

This article reports the amino-acid-assisted synthesis and size-dependent magnetic properties of hematite nanocubes. The products were characterized using x-ray diffraction, Raman spectroscopy, transmission electron microscopy (TEM), and high-resolution TEM. The magnetic behavior of hematite nanocubes was studied using a vibrating sample magnetometer at room temperature. The sizes of hematite nanocubes were controlled by tuning the reaction parameters. The amino acid has double-hydrophilic functional groups, –NH2 and –COOH, which are utilized to control the growth and final size of hematite nanocubes. We show that utilizing biomolecules in chemical synthesis is a useful method for tailoring the physical properties of nanomaterials.
Effect of epitaxial strain on ferroelectric polarization in multiferroic BiFeO3 films
Authors: Kim Dae Ho , Lee Ho Nyung , Biegalski Michael D. , Christen Hans M.
Published: January 2008

Multiferroic BiFeO3 epitaxial films with thicknesses ranging from 40to960nm were grown by pulsed laser deposition on SrTiO3 (001) substrates with SrRuO3 bottom electrodes. X-ray characterization shows that the structure evolves from angularly distorted tetragonal with c∕a≈1.04 to more bulklike distorted rhombohedral (c∕a≈1.01) as the strain relaxes with increasing thickness. Despite this significant structural evolution, the ferroelectric polarization along the body diagonal of the distorted pseudocubic unit cells, as calculated from measurements along the normal direction, barely changes.
Flexible-foam-based capacitive sensor arrays for object detection at low cost
Authors: Metzger Christian , Fleisch Elgar , Meyer Jan , Dansachmüller Mario , Graz Ingrid , Kaltenbrunner Martin , Keplinger Christoph , Schwödiauer Reinhard , Bauer Siegfried
Published: January 2008

Polymer foams are used in the automotive and construction industries for thermal insulation, vibration attenuation, and pressure absorption, due to their lightweight structure, thermal characteristics and low manufacturing costs. These foams have higher elasticity in their cross sections than bulk polymers, which makes them the preferred mount for capacitive sensor arrays. The authors describe a flexible pressure-sensitive surface mounted on packaging foam. The elastic properties of the foam are presented along with the sensor array’s weight sensitivity. The authors illustrate an inventory management application where objects on display can be detected through their weights.
Intra-Brillouin-zone bandgaps due to periodic misalignment in one-dimensional magnetophotonic crystals
Authors: Wang Fei , Lakhtakia Akhlesh
Published: January 2008

One-dimensional (1D) magnetophotonic crystals (MPCs) can incorporate optical gyrotropy induced by a bias magnetic field, crystalline misalignment, and differential linear birefringence in a single photonic-crystal structure. A 1D MPC whose unit cell contains two layers—one magnetophotonic, the other not—displays intra-Brillouin-zone photonic bandgaps (PBGs) in the Brillouin diagram. While the optical gyrotropy makes the PBG bandwidths tunable by a bias magnetic field, the bicrystalline misalignment modifies and can even trump this magnetic tunability. Magnetic tunability is greatly affected by a proper selection of the two materials; e.g., a large birefringence ratio between the two layers can dramatically enhance the magnetic tunability of the MPC. We also expect our 1D MPCs to be useful for detecting magnetic fields.
Structural anisotropy in a Zr57Ti5Cu20Al10Ni8 bulk metallic glass deformed by high pressure torsion at room temperature
Authors: Révész Ádám , Schafler Erhard , Kovács Zsolt
Published: January 2008

Fully amorphous Zr57Ti5Cu20Al10Ni8 bulk metallic glass specimens were subjected to deformation by high pressure torsion at room temperature. Consecutive high resolution synchrotron x-ray diffraction mapping has revealed the variation of the average atomic bond length and shown no evidence of crystallization in this excellent glass former. Difference in the sign of the atomic distortion obtained in direction parallel to the sample surface and along the cross section indicates strong structural anisotropy.
Is the Moon There When Nobody Looks? Reality and the Quantum Theory
Authors: Mermin N. David
Published: January 2008

In May 1935, Albert Einstein, Boris Podolsky and Nathan Rosen published an argument that quantum mechanics fails to provide a complete description of physical reality. Today, 50 years later, the EPR paper and the theoretical and experimental work it inspired remain remarkable for the vivid illustration they provide of one of the most bizarre aspects of the world revealed to us by the quantum theory.
Space Missions to Comets
Authors: Neugebauer Marcia
Published: January 2008

Comets appear to be the most pristine remnants of the material from which the solar system formed. We wish to know more about these eccentric objects to gain insight into the conditions and processes that prevailed during the solar system's formation and early stages of evolution. Chemical, isotopic and mineralogic studies of comets will tell us about the dynamical and nucleosynthetic processes that operated prior to and during formation of the nebula, and about the original chemistry of the solar system. Studies of the physical properties of comets and of the material of which they are composed will tell us about the agglomeration and accretion of bodies in the outer solar system. The study of comets is also relevant to the evolution of life: Comets may have made substantial contributions to the present atmospheres of Venus, Earth and Mars, and it is possible that either the prebiotic molecules necessary for the evolution of life or the raw materials from which these molecules formed were brought to Earth by comet-like objects. Finally, the study of the interactions between sunlight, plasmas, gas and dust in comets should have applications to processes in a great variety of astrophysical settings throughout the universe.
Large Facilities for Condensed-Matter Science
Authors: Blume Martin , Moncton David E.
Published: January 2008

The structural perfection and the optical beauty of natural crystals have always been a source of fascination. The attempt to provide a scientific understanding of crystal structure—to understand the natural laws that underlie the aesthetic appeal—marked the beginning of condensed-matter physics. This intellectual revolution began in 1912, when Walter Friedrich, Paul Knipping and Max von Laue presented an elementary theory of xray diffraction by crystals and reported the first experimental results. Remarkably, this monumental work not only heralded the modern era of condensedmatter physics, it demonstrated conclusively the wave nature of x rays—one cornerstone in the modern development of physics. The discovery of electron and neutron diffraction—in 1926 and 1936, respectively—greatly increased the range of phenomena that could be studied in condensed matter. Today the quest for useful new probes continues; muons and positrons, for example, are being investigated. However, it is overwhelmingly clear that electrons, neutrons and photons are still the most important probes in their collective contributions to our field and their potential for future discovery. The profound impact these probes have had on the microscopic understanding of materials becomes clear when one asks questions such as: What would we know about the geometric and electronic structure of solids without photon scattering and spectroscopy? What would we know about magnetism, phase transitions and excitations in solids without neutron scattering?
Applications of Neutron Scattering to Biology
Authors: Moore Peter B.
Published: January 2008

During the past 20 years neutron scattering has developed into an important tool for the determination of the structure of biologically important compounds. Traditionally these kinds of problems have been solved by x-ray crystallography or electron microscopy, both of which require far cheaper and simpler instrumentation. The justification for the use of neutrons in biological research, which might seem at first an outrageous extravagance, is contained in a single word: “hydrogen.” The scattering of neutrons from hydrogen (and deuterium) is far larger compared to other atoms than is the comparative scattering of x rays and electrons; neutrons, therefore, are a much better probe for these light atoms.
Nuclear Mean-Field Theory
Authors: Negele John W.
Published: January 2008

One of the fundamental challenges common to all areas of physics is to understand the properties of systems having large or infinite numbers of degrees of freedom in terms of known underlying interactions. Simply knowing the Schrödinger equation and Coulomb's law, for example, is not sufficient to let us understand the chain through which atoms form molecules, which, in turn, beget macromolcules, which eventually aggregate into a biological object with a life of its own. Nor has knowledge of the Lagrangian for quantum chromodynamics yet yielded an understanding of hadrons. The physics of systems with many degrees of freedom often differs in crucial ways from what we understand for simple systems.
D-loop formation by Brh2 protein of
Ustilago maydis
Authors: Mazloum Nayef , Zhou Qingwen , Holloman William K.
Published: January 2008

Brh2, the ortholog of the BRCA2 tumor suppressor in
Ustilago maydis
, works hand in hand with Rad51 to promote repair of DNA by homologous recombination. Previous studies established that Brh2 can stimulate DNA strand exchange by enabling Rad51 nucleoprotein filament formation on replication protein A-coated ssDNA. But, more recently, it was noted that Brh2 has an inherent DNA annealing activity, raising the notion that it might have roles in recombination in addition to or beyond the mediator function. Here, we found that Brh2 can autonomously promote the formation of D-loops in reactions with plasmid DNA and homologous single-stranded oligonucleotides. The reaction differs from that catalyzed by Rad51 in having no requirement for cofactors or preloading phase on ssDNA. D-loop formation was most effective when Brh2 was mixed with plasmid DNA before addition of single-stranded oligomer. D-loop formation catalyzed by Rad51 was also enhanced when Brh2 was premixed with plasmid DNA. Brh2 rendered defective in Rad51 interaction by mutation in the BRC element was still capable of promoting D-loop formation. However, the mutant protein was unable to enhance the Rad51-catalyzed reaction. The results suggest a model in which Brh2 binding to plasmid DNA attracts and helps capture Rad51-coated ssDNA.
X-ray absorption spectroscopic characterization of a cytochrome P450 compound II derivative
Authors: Newcomb Martin , Halgrimson James A. , Horner John H. , Wasinger Erik C. , Chen Lin X. , Sligar Stephen G.
Published: January 2008

The cytochrome P450 enzyme CYP119, its compound II derivative, and its nitrosyl complex were studied by iron K-edge x-ray absorption spectroscopy. The compound II derivative was prepared by reaction of the resting enzyme with peroxynitrite and had a lifetime of ≈10 s at 23°C. The CYP119 nitrosyl complex was prepared by reaction of the enzyme with nitrogen monoxide gas or with a nitrosyl donor and was stable at 23°C for hours. Samples of CYP119 and its derivatives were studied by x-ray absorption spectroscopy at temperatures below 140 (K) at the Advanced Photon Source of Argonne National Laboratory. The x-ray absorption near-edge structure spectra displayed shifts in edge and pre-edge energies consistent with increasing effective positive charge on iron in the series native CYP119 < CYP119 nitrosyl complex < CYP119 compound II derivative. Extended x-ray absorption fine structure spectra were simulated with good fits for
k
= 12 Å
−1
for native CYP119 and
k
= 13 Å
−1
for both the nitrosyl complex and the compound II derivative. The important structural features for the compound II derivative were an iron-oxygen bond length of 1.82 Å and an iron-sulfur bond length of 2.24 Å, both of which indicate an iron-oxygen single bond in a ferryl-hydroxide, Fe
IV
OH, moiety.
The impact of Miocene atmospheric carbon dioxide fluctuations on climate and the evolution of terrestrial ecosystems
Authors: Kürschner Wolfram M. , Kvaček Zlatko , Dilcher David L.
Published: January 2008

The Miocene is characterized by a series of key climatic events that led to the founding of the late Cenozoic icehouse mode and the dawn of modern biota. The processes that caused these developments, and particularly the role of atmospheric CO
2
as a forcing factor, are poorly understood. Here we present a CO
2
record based on stomatal frequency data from multiple tree species. Our data show striking CO
2
fluctuations of ≈600–300 parts per million by volume (ppmv). Periods of low CO
2
are contemporaneous with major glaciations, whereas elevated CO
2
of 500 ppmv coincides with the climatic optimum in the Miocene. Our data point to a long-term coupling between atmospheric CO
2
and climate. Major changes in Miocene terrestrial ecosystems, such as the expansion of grasslands and radiations among terrestrial herbivores such as horses, can be linked to these marked fluctuations in CO
2
.
Dendritic glutamate release produces autocrine activation of mGluR1 in cerebellar Purkinje cells
Authors: Shin Jung Hoon , Kim Yu Shin , Linden David J.
Published: January 2008

In recent years, it has become clear that, in addition to conventional anterograde transmission, signaling in neural circuits can occur in a retrograde manner. This suggests the additional possibility that postsynaptic release of neurotransmitter might be able to act in an autocrine fashion. Here, we show that brief depolarization of a cerebellar Purkinje cell triggers a slow inward current. This depolarization-induced slow current (DISC) is attenuated by antagonists of mGluR1 or TRP channels. DISC is eliminated by a mixture of voltage-sensitive Ca
2+
channel blockers and is mimicked by a brief climbing fiber burst. DISC is attenuated by an inhibitor of vesicular glutamate transporters or of vesicular fusion. These data suggest that Ca
2+
-dependent postsynaptic fusion of glutamate-loaded vesicles evokes a slow inward current produced by activation of postsynaptic mGluR1, thereby constituting a useful form of feedback regulation.